From d723eb260bfd9c707f6e282037c4e42670bdf48e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:15:27 +0000
Subject: Changed views.py to call the correlation code using the GN3 API + a
 function in show_corr_results for setting other template vars (might change
 this later)

---
 wqflask/wqflask/views.py | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b9181368..96f228af 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -65,7 +65,7 @@ from wqflask.comparison_bar_chart import comparison_bar_chart
 from wqflask.marker_regression import run_mapping
 from wqflask.marker_regression import display_mapping_results
 from wqflask.network_graph import network_graph
-from wqflask.correlation import show_corr_results
+from wqflask.correlation.show_corr_results import set_other_template_vars
 from wqflask.correlation.correlation_gn3_api import compute_correlation
 from wqflask.correlation_matrix import show_corr_matrix
 from wqflask.correlation import corr_scatter_plot
@@ -1082,15 +1082,9 @@ def network_graph_page():
 
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
-    logger.info("In corr_compute, request.form is:", pf(request.form))
-    logger.info(request.url)
-    template_vars = show_corr_results.CorrelationResults(request.form)
-    return render_template("correlation_page.html", **template_vars.__dict__)
-
-    # to test/disable the new  correlation api uncomment these lines
-
-    # correlation_results = compute_correlation(request.form)
-    # return render_template("test_correlation_page.html", correlation_results=correlation_results)
+    correlation_results = compute_correlation(request.form, compute_all=True)
+    correlation_results = set_other_template_vars(request.form, correlation_results)
+    return render_template("correlation_page.html", **correlation_results)
 
 
 @app.route("/test_corr_compute", methods=["POST"])
-- 
cgit v1.2.3


From c327905af1ef1a0c66a453127ee8f5ba4a824573 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:16:09 +0000
Subject: Changed correlation page template to account for differences in the
 output returned from the GN3 API correlation code

---
 wqflask/wqflask/templates/correlation_page.html | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 4cad2749..f66eb4bd 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -17,9 +17,9 @@
             <hr style="height: 1px; background-color: #A9A9A9;">
         </div>
         <div style="max-width: 100%;">
-          <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if dataset.accession_id != 'None' %}GN_AccessionId={{ dataset.accession_id }}{% else %}InfoPageName={{ dataset.name }}{% endif %}">{{ dataset.fullname }}</a>
+          <p>Values of record {{ this_trait.name }} in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if this_dataset.accession_id != 'None' %}GN_AccessionId={{ this_dataset.accession_id }}{% else %}InfoPageName={{ this_dataset.name }}{% endif %}">{{ this_dataset.fullname }}</a>
           dataset were compared to all records in the <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&{% if target_dataset.accession_id != 'None' %}GN_AccessionId={{ target_dataset.accession_id }}{% else %}InfoPageName={{ target_dataset.name }}{% endif %}">{{ target_dataset.fullname }}</a>
-          dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed.
+          dataset. The top {{ return_results }} correlations ranked by the {{ formatted_corr_type }} are displayed.
           You can resort this list by clicking the headers. Select the Record ID to open the trait data
           and analysis page.
           </p>
@@ -30,7 +30,7 @@
             <input type="hidden" name="form_url" value="" />
             <input type="hidden" name="trait_list" id="trait_list" value= "
             {% for this_trait in trait_list %}
-                {{ this_trait.name }}:{{ this_trait.dataset }},
+                {{ this_trait }}:{{ this_dataset.name }},
             {% endfor %}" >
             {% include 'tool_buttons.html' %}
           </form>
@@ -43,7 +43,7 @@
                 <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
                 <input type="hidden" name="database_name" id="database_name" value="None">
                 <input type="hidden" name="export_data" id="export_data" value="">
-                <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation">
+                <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ this_dataset.name }}_correlation">
                 <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ...">
                 <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
                 <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -146,7 +146,7 @@
     
 
     <script type="text/javascript" charset="utf-8">
-        var table_json = {{ json_results | safe }}
+        var table_json = {{ table_json | safe }}
     </script>
 
     <script type="text/javascript" charset="utf-8">
@@ -313,7 +313,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name == 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
@@ -441,7 +441,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name== 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
@@ -495,7 +495,7 @@
                       'orderSequence': [ "desc", "asc"],
                       'render': function(data, type, row, meta) {
                         if (data.sample_r != "N/A") {
-                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&dataset_1={% if this_dataset.name == 'Temp' %}Temp_{{ this_dataset.group }}{% else %}{{ this_dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
                         } else {
                           return data.sample_r
                         }
-- 
cgit v1.2.3


From f2e035bb4ff5a1dd5b465ae694105b1a7de956c8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:54:45 +0000
Subject: Added compute_all as parameter to compute_correlation and keyword
 arguments to docstring

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 6974dbd5..df0afba6 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -131,8 +131,14 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
     return (this_trait_data, results)
 
 
-def compute_correlation(start_vars, method="pearson"):
-    """compute correlation for to call gn3  api"""
+def compute_correlation(start_vars, method="pearson", compute_all=False):
+    """Compute correlations using GN3 API
+
+    Keyword arguments:
+    start_vars -- All input from form; includes things like the trait/dataset names
+    method -- Correlation method to be used (pearson, spearman, or bicor)
+    compute_all -- Include sample, tissue, and literature correlations (when applicable)
+    """
     # pylint: disable-msg=too-many-locals
 
     corr_type = start_vars['corr_type']
@@ -186,8 +192,6 @@ def compute_correlation(start_vars, method="pearson"):
 
     correlation_results = correlation_results[0:corr_return_results]
 
-    compute_all = True  # later to  be passed as argument
-
     if (compute_all):
 
         correlation_results = compute_corr_for_top_results(correlation_results,
-- 
cgit v1.2.3


From 6e1b4d1c53b96ed0bb6335deebd888c24b28d366 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:57:03 +0000
Subject: Rewrote show_corr_results.py to remove all code calculating
 correlations (that was moved to correlation_gn3_api.py, which will probably
 be renamed at some point) and only include the code generating the table JSON
 and some template variables

---
 wqflask/wqflask/correlation/show_corr_results.py | 588 ++++++-----------------
 1 file changed, 139 insertions(+), 449 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 2f3df67a..6c6d8f4e 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -18,474 +18,145 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-import collections
 import json
-import scipy
-import numpy
-# import rpy2.robjects as ro                    # R Objects
-import utility.logger
-import utility.webqtlUtil
 
-from base.trait import create_trait
+from base.trait import create_trait, jsonable
+from base.data_set import create_dataset
 
-from base import data_set
-from utility import helper_functions
-from utility import corr_result_helpers
 from utility import hmac
 
-from wqflask.correlation import correlation_functions
-from utility.benchmark import Bench
-
-from utility.type_checking import is_str
-from utility.type_checking import get_float
-from utility.type_checking import get_int
-from utility.type_checking import get_string
-from utility.db_tools import escape
-
-from flask import g
-
-logger = utility.logger.getLogger(__name__)
-
-METHOD_LIT = "3"
-METHOD_TISSUE_PEARSON = "4"
-METHOD_TISSUE_RANK = "5"
-
-TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
-
-TISSUE_MOUSE_DB = 1
-
-
-class CorrelationResults:
-    def __init__(self, start_vars):
-        # get trait list from db (database name)
-        # calculate correlation with Base vector and targets
-
-        # Check parameters
-        assert('corr_type' in start_vars)
-        assert(is_str(start_vars['corr_type']))
-        assert('dataset' in start_vars)
-        # assert('group' in start_vars) permitted to be empty?
-        assert('corr_sample_method' in start_vars)
-        assert('corr_samples_group' in start_vars)
-        assert('corr_dataset' in start_vars)
-        assert('corr_return_results' in start_vars)
-        if 'loc_chr' in start_vars:
-            assert('min_loc_mb' in start_vars)
-            assert('max_loc_mb' in start_vars)
-
-        with Bench("Doing correlations"):
-            if start_vars['dataset'] == "Temp":
-                self.dataset = data_set.create_dataset(
-                    dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group'])
-                self.trait_id = start_vars['trait_id']
-                self.this_trait = create_trait(dataset=self.dataset,
-                                               name=self.trait_id,
-                                               cellid=None)
-            else:
-                helper_functions.get_species_dataset_trait(self, start_vars)
-
-            corr_samples_group = start_vars['corr_samples_group']
-
-            self.sample_data = {}
-            self.corr_type = start_vars['corr_type']
-            self.corr_method = start_vars['corr_sample_method']
-            self.min_expr = get_float(start_vars, 'min_expr')
-            self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
-            self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
-
-
-            if ('loc_chr' in start_vars
-                and 'min_loc_mb' in start_vars
-                    and 'max_loc_mb' in start_vars):
-
-                self.location_type = get_string(start_vars, 'location_type')
-                self.location_chr = get_string(start_vars, 'loc_chr')
-                self.min_location_mb = get_int(start_vars, 'min_loc_mb')
-                self.max_location_mb = get_int(start_vars, 'max_loc_mb')
-            else:
-                self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None
-
-            self.get_formatted_corr_type()
-            self.return_number = int(start_vars['corr_return_results'])
-
-            # The two if statements below append samples to the sample list based upon whether the user
-            # rselected Primary Samples Only, Other Samples Only, or All Samples
-
-            primary_samples = self.dataset.group.samplelist
-            if self.dataset.group.parlist != None:
-                primary_samples += self.dataset.group.parlist
-            if self.dataset.group.f1list != None:
-                primary_samples += self.dataset.group.f1list
-
-            # If either BXD/whatever Only or All Samples, append all of that group's samplelist
-            if corr_samples_group != 'samples_other':
-                self.process_samples(start_vars, primary_samples)
-
-            # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
-            # exclude the primary samples (because they would have been added in the previous
-            # if statement if the user selected All Samples)
-            if corr_samples_group != 'samples_primary':
-                if corr_samples_group == 'samples_other':
-                    primary_samples = [x for x in primary_samples if x not in (
-                        self.dataset.group.parlist + self.dataset.group.f1list)]
-                self.process_samples(start_vars, list(
-                    self.this_trait.data.keys()), primary_samples)
-
-            self.target_dataset = data_set.create_dataset(
-                start_vars['corr_dataset'])
-            self.target_dataset.get_trait_data(list(self.sample_data.keys()))
-
-            self.header_fields = get_header_fields(
-                self.target_dataset.type, self.corr_method)
-
-            if self.target_dataset.type == "ProbeSet":
-                self.filter_cols = [7, 6]
-            elif self.target_dataset.type == "Publish":
-                self.filter_cols = [6, 0]
-            else:
-                self.filter_cols = [4, 0]
-
-            self.correlation_results = []
+def set_template_vars(start_vars, correlation_data):
+    corr_type = start_vars['corr_type']
+    corr_method = start_vars['corr_sample_method']
 
-            self.correlation_data = {}
+    this_dataset_ob = create_dataset(dataset_name=start_vars['dataset'])
+    this_trait = create_trait(dataset=this_dataset_ob,
+                              name=start_vars['trait_id'])
 
-            if self.corr_type == "tissue":
-                self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol")
+    correlation_data['this_trait'] = jsonable(this_trait, this_dataset_ob)
+    correlation_data['this_dataset'] = this_dataset_ob.as_dict()
 
-                tissue_corr_data = self.do_tissue_correlation_for_all_traits()
-                if tissue_corr_data != None:
-                    for trait in list(tissue_corr_data.keys())[:self.return_number]:
-                        self.get_sample_r_and_p_values(
-                            trait, self.target_dataset.trait_data[trait])
-                else:
-                    for trait, values in list(self.target_dataset.trait_data.items()):
-                        self.get_sample_r_and_p_values(trait, values)
-
-            elif self.corr_type == "lit":
-                self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
-                lit_corr_data = self.do_lit_correlation_for_all_traits()
-
-                for trait in list(lit_corr_data.keys())[:self.return_number]:
-                    self.get_sample_r_and_p_values(
-                        trait, self.target_dataset.trait_data[trait])
-
-            elif self.corr_type == "sample":
-                for trait, values in list(self.target_dataset.trait_data.items()):
-                    self.get_sample_r_and_p_values(trait, values)
-
-            self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
-                                                                   key=lambda t: -abs(t[1][0])))
-
-            # ZS: Convert min/max chromosome to an int for the location range option
-            range_chr_as_int = None
-            for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
-                if 'loc_chr' in start_vars:
-                    if chr_info.name == self.location_chr:
-                        range_chr_as_int = order_id
-
-            for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
-                trait_object = create_trait(
-                    dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
-                if not trait_object:
-                    continue
-
-                chr_as_int = 0
-                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
-                    if self.location_type == "highest_lod":
-                        if chr_info.name == trait_object.locus_chr:
-                            chr_as_int = order_id
-                    else:
-                        if chr_info.name == trait_object.chr:
-                            chr_as_int = order_id
-
-
-                if (float(self.correlation_data[trait][0]) >= self.p_range_lower
-                        and float(self.correlation_data[trait][0]) <= self.p_range_upper):
-
-                    if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
-                        if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
-                            continue
-
-                    if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
-                        continue
-                    if self.location_type == "highest_lod":
-                        if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)):
-                            continue
-                        if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)):
-                            continue
-                    else:
-                        if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
-                            continue
-                        if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
-                            continue
-
-                    (trait_object.sample_r,
-                     trait_object.sample_p,
-                     trait_object.num_overlap) = self.correlation_data[trait]
-
-                    # Set some sane defaults
-                    trait_object.tissue_corr = 0
-                    trait_object.tissue_pvalue = 0
-                    trait_object.lit_corr = 0
-                    if self.corr_type == "tissue" and tissue_corr_data != None:
-                        trait_object.tissue_corr = tissue_corr_data[trait][1]
-                        trait_object.tissue_pvalue = tissue_corr_data[trait][2]
-                    elif self.corr_type == "lit":
-                        trait_object.lit_corr = lit_corr_data[trait][1]
-
-                    self.correlation_results.append(trait_object)
-
-            if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
-                self.do_lit_correlation_for_trait_list()
-
-            if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
-                self.do_tissue_correlation_for_trait_list()
-
-        self.json_results = generate_corr_json(
-            self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
-
-############################################################################################################################################
-
-    def get_formatted_corr_type(self):
-        self.formatted_corr_type = ""
-        if self.corr_type == "lit":
-            self.formatted_corr_type += "Literature Correlation "
-        elif self.corr_type == "tissue":
-            self.formatted_corr_type += "Tissue Correlation "
-        elif self.corr_type == "sample":
-            self.formatted_corr_type += "Genetic Correlation "
-
-        if self.corr_method == "pearson":
-            self.formatted_corr_type += "(Pearson's r)"
-        elif self.corr_method == "spearman":
-            self.formatted_corr_type += "(Spearman's rho)"
-        elif self.corr_method == "bicor":
-            self.formatted_corr_type += "(Biweight r)"
-
-    def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1):
-        """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
-
-        # Gets tissue expression values for the primary trait
-        primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
-            symbol_list=[self.this_trait.symbol])
-
-        if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
-            primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower(
-            )]
-            gene_symbol_list = [
-                trait.symbol for trait in self.correlation_results if trait.symbol]
-
-            corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
-                symbol_list=gene_symbol_list)
-
-            for trait in self.correlation_results:
-                if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
-                    this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower(
-                    )]
-
-                    result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
-                                                                                this_trait_tissue_values,
-                                                                                self.corr_method)
-
-                    trait.tissue_corr = result[0]
-                    trait.tissue_pvalue = result[2]
-
-    def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
-        # Gets tissue expression values for the primary trait
-        primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
-            symbol_list=[self.this_trait.symbol])
-
-        if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
-            primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower(
-            )]
-
-            #print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
-            corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
-                symbol_list=list(self.trait_symbol_dict.values()))
-
-            #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
-
-            #print("trait_gene_symbols: ", pf(trait_gene_symbols))
-
-            tissue_corr_data = {}
-            for trait, symbol in list(self.trait_symbol_dict.items()):
-                if symbol and symbol.lower() in corr_result_tissue_vals_dict:
-                    this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
-                    )]
+    target_dataset_ob = create_dataset(correlation_data['target_dataset'])
+    correlation_data['target_dataset'] = target_dataset_ob.as_dict()
 
-                    result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
-                                                                                this_trait_tissue_values,
-                                                                                self.corr_method)
+    table_json = correlation_json_for_table(correlation_data,
+                                            correlation_data['this_trait'],
+                                            correlation_data['this_dataset'],
+                                            target_dataset_ob)
 
-                    tissue_corr_data[trait] = [symbol, result[0], result[2]]
+    correlation_data['table_json'] = table_json
 
-            tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()),
-                                                              key=lambda t: -abs(t[1][1])))
+    if target_dataset_ob.type == "ProbeSet":
+        filter_cols = [7, 6]
+    elif target_dataset_ob.type == "Publish":
+        filter_cols = [6, 0]
+    else:
+        filter_cols = [4, 0]
 
-            return tissue_corr_data
+    correlation_data['corr_method'] = corr_method
+    correlation_data['filter_cols'] = filter_cols
+    correlation_data['header_fields'] = get_header_fields(target_dataset_ob.type, correlation_data['corr_method'])
+    correlation_data['formatted_corr_type'] = get_formatted_corr_type(corr_type, corr_method)
 
-    def do_lit_correlation_for_trait_list(self):
+    return correlation_data
 
-        input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(
-            self.dataset.group.species.lower(), self.this_trait.geneid)
+def correlation_json_for_table(correlation_data, this_trait, this_dataset, target_dataset_ob):
+    """Return JSON data for use with the DataTable in the correlation result page
 
-        for trait in self.correlation_results:
+    Keyword arguments:
+    correlation_data -- Correlation results
+    this_trait -- Trait being correlated against a dataset, as a dict
+    this_dataset -- Dataset of this_trait, as a dict
+    target_dataset_ob - Target dataset, as a Dataset ob
+    """
+    this_trait = correlation_data['this_trait']
+    this_dataset = correlation_data['this_dataset']
+    target_dataset = target_dataset_ob.as_dict()
 
-            if trait.geneid:
-                trait.mouse_gene_id = self.convert_to_mouse_gene_id(
-                    self.dataset.group.species.lower(), trait.geneid)
-            else:
-                trait.mouse_gene_id = None
-
-            if trait.mouse_gene_id and str(trait.mouse_gene_id).find(";") == -1:
-                result = g.db.execute(
-                    """SELECT value
-                       FROM LCorrRamin3
-                       WHERE GeneId1='%s' and
-                             GeneId2='%s'
-                    """ % (escape(str(trait.mouse_gene_id)), escape(str(input_trait_mouse_gene_id)))
-                ).fetchone()
-                if not result:
-                    result = g.db.execute("""SELECT value
-                       FROM LCorrRamin3
-                       WHERE GeneId2='%s' and
-                             GeneId1='%s'
-                    """ % (escape(str(trait.mouse_gene_id)), escape(str(input_trait_mouse_gene_id)))
-                    ).fetchone()
-
-                if result:
-                    lit_corr = result.value
-                    trait.lit_corr = lit_corr
-                else:
-                    trait.lit_corr = 0
-            else:
-                trait.lit_corr = 0
-
-    def do_lit_correlation_for_all_traits(self):
-        input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(
-            self.dataset.group.species.lower(), self.this_trait.geneid)
-
-        lit_corr_data = {}
-        for trait, gene_id in list(self.trait_geneid_dict.items()):
-            mouse_gene_id = self.convert_to_mouse_gene_id(
-                self.dataset.group.species.lower(), gene_id)
-
-            if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
-                #print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id)
-                result = g.db.execute(
-                    """SELECT value
-                       FROM LCorrRamin3
-                       WHERE GeneId1='%s' and
-                             GeneId2='%s'
-                    """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
-                ).fetchone()
-                if not result:
-                    result = g.db.execute("""SELECT value
-                       FROM LCorrRamin3
-                       WHERE GeneId2='%s' and
-                             GeneId1='%s'
-                    """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
-                    ).fetchone()
-                if result:
-                    #print("result:", result)
-                    lit_corr = result.value
-                    lit_corr_data[trait] = [gene_id, lit_corr]
+    corr_results = correlation_data['correlation_results']
+    results_list = []
+    for i, trait_dict in enumerate(corr_results):
+        trait_name = list(trait_dict.keys())[0]
+        trait = trait_dict[trait_name]
+        target_trait_ob = create_trait(dataset=target_dataset_ob,
+                                       name=trait_name,
+                                       get_qtl_info=True)
+        target_trait = jsonable(target_trait_ob, target_dataset_ob)
+        if target_trait['view'] == False:
+            continue
+        results_dict = {}
+        results_dict['index'] = i + 1
+        results_dict['trait_id'] = target_trait['name']
+        results_dict['dataset'] = target_dataset['name']
+        results_dict['hmac'] = hmac.data_hmac(
+            '{}:{}'.format(target_trait['name'], target_dataset['name']))
+        results_dict['sample_r'] = f"{float(trait['corr_coeffient']):.3f}"
+        results_dict['num_overlap'] = trait['num_overlap']
+        results_dict['sample_p'] = f"{float(trait['p_value']):.3e}"
+        if target_dataset['type'] == "ProbeSet":
+            results_dict['symbol'] = target_trait['symbol']
+            results_dict['description'] = "N/A"
+            results_dict['location'] = target_trait['location']
+            results_dict['mean'] = "N/A"
+            results_dict['additive'] = "N/A"
+            if bool(target_trait['description']):
+                results_dict['description'] = target_trait['description']
+            if bool(target_trait['mean']):
+                results_dict['mean'] = f"{float(target_trait['mean']):.3f}"
+            try:
+                results_dict['lod_score'] = f"{float(target_trait['lrs_score']) / 4.61:.1f}"
+            except:
+                results_dict['lod_score'] = "N/A"
+            results_dict['lrs_location'] = target_trait['lrs_location']
+            if bool(target_trait['additive']):
+                results_dict['additive'] = f"{float(target_trait['additive']):.3f}"
+            results_dict['lit_corr'] = "--"
+            results_dict['tissue_corr'] = "--"
+            results_dict['tissue_pvalue'] = "--"
+            if this_dataset['type'] == "ProbeSet":
+                if 'lit_corr' in trait:
+                    results_dict['lit_corr'] = f"{float(trait['lit_corr']):.3f}"
+                if 'tissue_corr' in trait:
+                    results_dict['tissue_corr'] = f"{float(trait['tissue_corr']):.3f}"
+                    results_dict['tissue_pvalue'] = f"{float(trait['tissue_p_val']):.3e}"
+        elif target_dataset['type'] == "Publish":
+            results_dict['abbreviation_display'] = "N/A"
+            results_dict['description'] = "N/A"
+            results_dict['mean'] = "N/A"
+            results_dict['authors_display'] = "N/A"
+            results_dict['additive'] = "N/A"
+            results_dict['pubmed_link'] = "N/A"
+            results_dict['pubmed_text'] = "N/A"
+
+            if bool(target_trait['abbreviation']):
+                results_dict['abbreviation_display'] = target_trait['abbreviation']
+            if bool(target_trait['description']):
+                results_dict['description'] = target_trait['description']
+            if bool(target_trait['mean']):
+                results_dict['mean'] = f"{float(target_trait['mean']):.3f}"
+            if bool(target_trait['authors']):
+                authors_list = target_trait['authors'].split(',')
+                if len(authors_list) > 6:
+                    results_dict['authors_display'] = ", ".join(
+                        authors_list[:6]) + ", et al."
                 else:
-                    lit_corr_data[trait] = [gene_id, 0]
-            else:
-                lit_corr_data[trait] = [gene_id, 0]
-
-        lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()),
-                                                       key=lambda t: -abs(t[1][1])))
-
-        return lit_corr_data
-
-    def convert_to_mouse_gene_id(self, species=None, gene_id=None):
-        """If the species is rat or human, translate the gene_id to the mouse geneid
-
-        If there is no input gene_id or there's no corresponding mouse gene_id, return None
-
-        """
-        if not gene_id:
-            return None
-
-        mouse_gene_id = None
-
-        if species == 'mouse':
-            mouse_gene_id = gene_id
-
-        elif species == 'rat':
-
-            query = """SELECT mouse
-                   FROM GeneIDXRef
-                   WHERE rat='%s'""" % escape(gene_id)
-
-            result = g.db.execute(query).fetchone()
-            if result != None:
-                mouse_gene_id = result.mouse
-
-        elif species == 'human':
-
-            query = """SELECT mouse
-                   FROM GeneIDXRef
-                   WHERE human='%s'""" % escape(gene_id)
-
-            result = g.db.execute(query).fetchone()
-            if result != None:
-                mouse_gene_id = result.mouse
-
-        return mouse_gene_id
-
-    def get_sample_r_and_p_values(self, trait, target_samples):
-        """Calculates the sample r (or rho) and p-value
-
-        Given a primary trait and a target trait's sample values,
-        calculates either the pearson r or spearman rho and the p-value
-        using the corresponding scipy functions.
-
-        """
-
-        self.this_trait_vals = []
-        target_vals = []
-        for index, sample in enumerate(self.target_dataset.samplelist):
-            if sample in self.sample_data:
-                sample_value = self.sample_data[sample]
-                target_sample_value = target_samples[index]
-                self.this_trait_vals.append(sample_value)
-                target_vals.append(target_sample_value)
-
-        self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
-            self.this_trait_vals, target_vals)
-
-        if num_overlap > 5:
-            # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
-            # if self.corr_method == 'bicor':
-            #     sample_r, sample_p = do_bicor(
-            #         self.this_trait_vals, target_vals)
-            if self.corr_method == 'pearson':
-                sample_r, sample_p = scipy.stats.pearsonr(
-                    self.this_trait_vals, target_vals)
-            else:
-                sample_r, sample_p = scipy.stats.spearmanr(
-                    self.this_trait_vals, target_vals)
-
-            if numpy.isnan(sample_r):
-                pass
-            else:
-                self.correlation_data[trait] = [
-                    sample_r, sample_p, num_overlap]
-
-    def process_samples(self, start_vars, sample_names, excluded_samples=None):
-        if not excluded_samples:
-            excluded_samples = ()
+                    results_dict['authors_display'] = target_trait['authors']
+            if 'pubmed_id' in target_trait:
+                results_dict['pubmed_link'] = target_trait['pubmed_link']
+                results_dict['pubmed_text'] = target_trait['pubmed_text']
+            try:
+                results_dict['lod_score'] = f"{float(target_trait['lrs_score']) / 4.61:.1f}"
+            except:
+                results_dict['lod_score'] = "N/A"
+            results_dict['lrs_location'] = target_trait['lrs_location']
+            if bool(target_trait['additive']):
+                results_dict['additive'] = f"{float(target_trait['additive']):.3f}"
+        else:
+            results_dict['location'] = target_trait['lrs_location']
 
-        sample_val_dict = json.loads(start_vars['sample_vals'])
-        for sample in sample_names:
-            if sample not in excluded_samples:
-                value = sample_val_dict[sample]
-                if not value.strip().lower() == 'x':
-                    self.sample_data[str(sample)] = float(value)
+        results_list.append(results_dict)
 
+    return json.dumps(results_list)
 
 # def do_bicor(this_trait_vals, target_trait_vals):
 #     r_library = ro.r["library"]             # Map the library function
@@ -598,6 +269,25 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
     return json.dumps(results_list)
 
 
+def get_formatted_corr_type(corr_type, corr_method):
+    formatted_corr_type = ""
+    if corr_type == "lit":
+        formatted_corr_type += "Literature Correlation "
+    elif corr_type == "tissue":
+        formatted_corr_type += "Tissue Correlation "
+    elif corr_type == "sample":
+        formatted_corr_type += "Genetic Correlation "
+
+    if corr_method == "pearson":
+        formatted_corr_type += "(Pearson's r)"
+    elif corr_method == "spearman":
+        formatted_corr_type += "(Spearman's rho)"
+    elif corr_method == "bicor":
+        formatted_corr_type += "(Biweight r)"
+
+    return formatted_corr_type
+
+
 def get_header_fields(data_type, corr_method):
     if data_type == "ProbeSet":
         if corr_method == "spearman":
-- 
cgit v1.2.3


From f5a7a54741cef7285e8862ceb2493fe3f451fb84 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:57:23 +0000
Subject: Changed set_other_template_vars to set_template_vars

---
 wqflask/wqflask/views.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 96f228af..da427bfe 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -65,7 +65,7 @@ from wqflask.comparison_bar_chart import comparison_bar_chart
 from wqflask.marker_regression import run_mapping
 from wqflask.marker_regression import display_mapping_results
 from wqflask.network_graph import network_graph
-from wqflask.correlation.show_corr_results import set_other_template_vars
+from wqflask.correlation.show_corr_results import set_template_vars
 from wqflask.correlation.correlation_gn3_api import compute_correlation
 from wqflask.correlation_matrix import show_corr_matrix
 from wqflask.correlation import corr_scatter_plot
@@ -1083,7 +1083,7 @@ def network_graph_page():
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     correlation_results = compute_correlation(request.form, compute_all=True)
-    correlation_results = set_other_template_vars(request.form, correlation_results)
+    correlation_results = set_template_vars(request.form, correlation_results)
     return render_template("correlation_page.html", **correlation_results)
 
 
-- 
cgit v1.2.3


From 4f06f22071898171cb7bbc12f5dfd42b05dc3208 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:58:00 +0000
Subject: Added function as_dict to data_set.py for situations where we don't
 want to pass around the whole dataset object

---
 wqflask/base/data_set.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 75ddf278..dc338971 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -559,6 +559,7 @@ class DataSet:
         self.fullname = None
         self.type = None
         self.data_scale = None  # ZS: For example log2
+        self.accession_id = None
 
         self.setup()
 
@@ -575,6 +576,17 @@ class DataSet:
             self.group.get_samplelist()
         self.species = species.TheSpecies(self)
 
+    def as_dict(self):
+        return {
+            'name': self.name,
+            'shortname': self.shortname,
+            'fullname': self.fullname,
+            'type': self.type,
+            'data_scale': self.data_scale,
+            'group': self.group.name,
+            'accession_id': self.accession_id
+        }
+
     def get_accession_id(self):
         if self.type == "Publish":
             results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
-- 
cgit v1.2.3


From 73195c1af57cbcf0fa38f1e73e8878c02938ef4b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:58:43 +0000
Subject: Changed the function jsonable in trait.py to return a couple extra
 fields + take dataset as an optional argument (to avoid having to pointlessly
 create it)

---
 wqflask/base/trait.py | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index d09cfd40..10851e00 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -284,17 +284,19 @@ def get_sample_data():
         return None
 
 
-def jsonable(trait):
+def jsonable(trait, dataset=None):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name=trait.dataset.name,
-                             dataset_type=trait.dataset.type,
-                             group_name=trait.dataset.group.name)
+    if not dataset:
+        dataset = create_dataset(dataset_name=trait.dataset.name,
+                                dataset_type=trait.dataset.type,
+                                group_name=trait.dataset.group.name)
 
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
+                    view=trait.view,
                     symbol=trait.symbol,
                     dataset=dataset.name,
                     dataset_name=dataset.shortname,
@@ -308,37 +310,44 @@ def jsonable(trait):
     elif dataset.type == "Publish":
         if trait.pubmed_id:
             return dict(name=trait.name,
+                        view=trait.view,
                         dataset=dataset.name,
                         dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
+                        pubmed_id=trait.pubmed_id,
                         pubmed_text=trait.pubmed_text,
                         pubmed_link=trait.pubmed_link,
+                        mean=trait.mean,
                         lrs_score=trait.LRS_score_repr,
                         lrs_location=trait.LRS_location_repr,
                         additive=trait.additive
                         )
         else:
             return dict(name=trait.name,
+                        view=trait.view,
                         dataset=dataset.name,
                         dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
                         pubmed_text=trait.pubmed_text,
+                        mean=trait.mean,
                         lrs_score=trait.LRS_score_repr,
                         lrs_location=trait.LRS_location_repr,
                         additive=trait.additive
                         )
     elif dataset.type == "Geno":
         return dict(name=trait.name,
+                    view=trait.view,
                     dataset=dataset.name,
                     dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
     elif dataset.name == "Temp":
         return dict(name=trait.name,
+                    view=trait.view,
                     dataset="Temp",
                     dataset_name="Temp")
     else:
-- 
cgit v1.2.3


From 55bccdd5cf8cdac52a625228b31732b5529810b5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 22:04:41 +0000
Subject: Fixed reference to target_trait['lrs_location'] that should have been
 target_trait['location'] for correlations against genotypes

---
 wqflask/wqflask/correlation/show_corr_results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6c6d8f4e..91716a6a 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -152,7 +152,7 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
             if bool(target_trait['additive']):
                 results_dict['additive'] = f"{float(target_trait['additive']):.3f}"
         else:
-            results_dict['location'] = target_trait['lrs_location']
+            results_dict['location'] = target_trait['location']
 
         results_list.append(results_dict)
 
-- 
cgit v1.2.3


From db9b0a9df8879921217bac353eaa2c3440e8337a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:35:11 +0300
Subject: add query for fetching probeset data

---
 wqflask/base/data_set.py                           | 258 +++++++++++++--------
 wqflask/wqflask/correlation/correlation_gn3_api.py | 144 +++++++++++-
 2 files changed, 303 insertions(+), 99 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index dc338971..7531ac81 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -166,7 +166,6 @@ class DatasetType:
         if t in ['pheno', 'other_pheno']:
             group_name = name.replace("Publish", "")
 
-
         results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
         if results:
             self.datasets[name] = dataset_name_mapping[t]
@@ -278,7 +277,7 @@ class Markers:
             filtered_markers = []
             for marker in self.markers:
                 if marker['name'] in p_values:
-                    #logger.debug("marker {} IS in p_values".format(i))
+                    # logger.debug("marker {} IS in p_values".format(i))
                     marker['p_value'] = p_values[marker['name']]
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
@@ -299,7 +298,7 @@ class HumanMarkers(Markers):
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
-            #logger.debug("splat:", splat)
+            # logger.debug("splat:", splat)
             if len(specified_markers) > 0:
                 if splat[1] in specified_markers:
                     marker = {}
@@ -441,7 +440,7 @@ class DatasetGroup:
         # genotype_1 is Dataset Object without parents and f1
         # genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
-        #genotype_1 = reaper.Dataset()
+        # genotype_1 = reaper.Dataset()
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         if self.genofile:
@@ -662,9 +661,39 @@ class DataSet:
 
 
 
-    def get_trait_data(self, sample_list=None):
+
+    def chunk_dataset(self, dataset, n):
+
+
+        results = {}
+
+        query = """
+                SELECT ProbeSetXRef.DataId,ProbeSet.Name
+                FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
+                WHERE ProbeSetFreeze.Name = '{}' AND
+                      ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                      ProbeSetXRef.ProbeSetId = ProbeSet.Id
+        """.format(self.name)
+
+        # should cache this
+
+        traits_name_dict= dict(g.db.execute(query).fetchall())
+
+
+
+
+        for i in range(0, len(dataset), n):
+            matrix = list(dataset[i:i + n])
+            trait_name = traits_name_dict[matrix[0][0]]
+
+            my_values = [value for (trait_name, strain, value) in matrix]
+            results[trait_name] = my_values
+        return results
+
+    def get_probeset_data(self, sample_list=None, trait_ids=None):
         if sample_list:
             self.samplelist = sample_list
+
         else:
             self.samplelist = self.group.samplelist
 
@@ -678,27 +707,59 @@ class DataSet:
             and Strain.SpeciesId=Species.Id
             and Species.name = '{}'
             """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
-        logger.sql(query)
         results = dict(g.db.execute(query).fetchall())
         sample_ids = [results[item] for item in self.samplelist]
 
+        query = """SELECT * from ProbeSetData
+                where StrainID in {}
+                and id in (SELECT ProbeSetXRef.DataId
+                FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+                WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+                and ProbeSetFreeze.Name = '{}'
+                and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids),self.name)
+
+        query_results=list(g.db.execute(query).fetchall())
+
+        data_results=self.chunk_dataset(query_results, len(sample_ids))
+        self.trait_data=data_results
+
+    def get_trait_data(self, sample_list=None):
+        if sample_list:
+            self.samplelist=sample_list
+        else:
+            self.samplelist=self.group.samplelist
+
+        if self.group.parlist != None and self.group.f1list != None:
+            if (self.group.parlist + self.group.f1list) in self.samplelist:
+                self.samplelist += self.group.parlist + self.group.f1list
+
+        query="""
+            SELECT Strain.Name, Strain.Id FROM Strain, Species
+            WHERE Strain.Name IN {}
+            and Strain.SpeciesId=Species.Id
+            and Species.name = '{}'
+            """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
+        logger.sql(query)
+        results=dict(g.db.execute(query).fetchall())
+        sample_ids=[results[item] for item in self.samplelist]
+
         # MySQL limits the number of tables that can be used in a join to 61,
         # so we break the sample ids into smaller chunks
         # Postgres doesn't have that limit, so we can get rid of this after we transition
-        chunk_size = 50
-        number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-        trait_sample_data = []
+        chunk_size=50
+        number_chunks=int(math.ceil(len(sample_ids) / chunk_size))
+        trait_sample_data=[]
         for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
             if self.type == "Publish":
-                dataset_type = "Phenotype"
+                dataset_type="Phenotype"
             else:
-                dataset_type = self.type
-            temp = ['T%s.value' % item for item in sample_ids_step]
+                dataset_type=self.type
+            temp=['T%s.value' % item for item in sample_ids_step]
             if self.type == "Publish":
-                query = "SELECT {}XRef.Id,".format(escape(self.type))
+                query="SELECT {}XRef.Id,".format(escape(self.type))
             else:
-                query = "SELECT {}.Name,".format(escape(dataset_type))
-            data_start_pos = 1
+                query="SELECT {}.Name,".format(escape(dataset_type))
+            data_start_pos=1
             query += ', '.join(temp)
             query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
                                                                      self.type,
@@ -727,27 +788,27 @@ class DataSet:
                         """.format(*mescape(self.type, self.type, self.type, self.type,
                                             self.name, dataset_type, self.type, self.type, dataset_type))
 
-            results = g.db.execute(query).fetchall()
+            results=g.db.execute(query).fetchall()
             trait_sample_data.append(results)
 
-        trait_count = len(trait_sample_data[0])
-        self.trait_data = collections.defaultdict(list)
+        trait_count=len(trait_sample_data[0])
+        self.trait_data=collections.defaultdict(list)
 
         # put all of the separate data together into a dictionary where the keys are
         # trait names and values are lists of sample values
         for trait_counter in range(trait_count):
-            trait_name = trait_sample_data[0][trait_counter][0]
+            trait_name=trait_sample_data[0][trait_counter][0]
             for chunk_counter in range(int(number_chunks)):
                 self.trait_data[trait_name] += (
                     trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
 
 
 class PhenotypeDataSet(DataSet):
-    DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
+    DS_NAME_MAP['Publish']='PhenotypeDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields = ['Phenotype.Post_publication_description',
+        self.search_fields=['Phenotype.Post_publication_description',
                               'Phenotype.Pre_publication_description',
                               'Phenotype.Pre_publication_abbreviation',
                               'Phenotype.Post_publication_abbreviation',
@@ -760,7 +821,7 @@ class PhenotypeDataSet(DataSet):
                               'PublishXRef.Id']
 
         # Figure out what display_fields is
-        self.display_fields = ['name', 'group_code',
+        self.display_fields=['name', 'group_code',
                                'pubmed_id',
                                'pre_publication_description',
                                'post_publication_description',
@@ -778,7 +839,7 @@ class PhenotypeDataSet(DataSet):
                                'sequence', 'units', 'comments']
 
         # Fields displayed in the search results table header
-        self.header_fields = ['Index',
+        self.header_fields=['Index',
                               'Record',
                               'Description',
                               'Authors',
@@ -787,9 +848,9 @@ class PhenotypeDataSet(DataSet):
                               'Max LRS Location',
                               'Additive Effect']
 
-        self.type = 'Publish'
+        self.type='Publish'
 
-        self.query_for_group = '''
+        self.query_for_group='''
                             SELECT
                                     InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                             FROM
@@ -809,13 +870,13 @@ class PhenotypeDataSet(DataSet):
             if not this_trait.haveinfo:
                 this_trait.retrieve_info(get_qtl_info=True)
 
-            description = this_trait.post_publication_description
+            description=this_trait.post_publication_description
 
             # If the dataset is confidential and the user has access to confidential
             # phenotype traits, then display the pre-publication description instead
             # of the post-publication description
             if this_trait.confidential:
-                this_trait.description_display = ""
+                this_trait.description_display=""
                 continue   # for now, because no authorization features
 
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -823,46 +884,46 @@ class PhenotypeDataSet(DataSet):
                         userName=self.userName,
                         authorized_users=this_trait.authorized_users):
 
-                    description = this_trait.pre_publication_description
+                    description=this_trait.pre_publication_description
 
             if len(description) > 0:
-                this_trait.description_display = description.strip()
+                this_trait.description_display=description.strip()
             else:
-                this_trait.description_display = ""
+                this_trait.description_display=""
 
             if not this_trait.year.isdigit():
-                this_trait.pubmed_text = "N/A"
+                this_trait.pubmed_text="N/A"
             else:
-                this_trait.pubmed_text = this_trait.year
+                this_trait.pubmed_text=this_trait.year
 
             if this_trait.pubmed_id:
-                this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
+                this_trait.pubmed_link=webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
 
             # LRS and its location
-            this_trait.LRS_score_repr = "N/A"
-            this_trait.LRS_location_repr = "N/A"
+            this_trait.LRS_score_repr="N/A"
+            this_trait.LRS_location_repr="N/A"
 
             if this_trait.lrs:
-                query = """
+                query="""
                     select Geno.Chr, Geno.Mb from Geno, Species
                     where Species.Name = '%s' and
                         Geno.Name = '%s' and
                         Geno.SpeciesId = Species.Id
                 """ % (species, this_trait.locus)
                 logger.sql(query)
-                result = g.db.execute(query).fetchone()
+                result=g.db.execute(query).fetchone()
 
                 if result:
                     if result[0] and result[1]:
-                        LRS_Chr = result[0]
-                        LRS_Mb = result[1]
+                        LRS_Chr=result[0]
+                        LRS_Mb=result[1]
 
-                        this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
-                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+                        this_trait.LRS_score_repr=LRS_score_repr='%3.1f' % this_trait.lrs
+                        this_trait.LRS_location_repr=LRS_location_repr='Chr%s: %.6f' % (
                             LRS_Chr, float(LRS_Mb))
 
     def retrieve_sample_data(self, trait):
-        query = """
+        query="""
                     SELECT
                             Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
                     FROM
@@ -880,34 +941,34 @@ class PhenotypeDataSet(DataSet):
                             Strain.Name
                     """
         logger.sql(query)
-        results = g.db.execute(query, (trait, self.id)).fetchall()
+        results=g.db.execute(query, (trait, self.id)).fetchall()
         return results
 
 
 class GenotypeDataSet(DataSet):
-    DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
+    DS_NAME_MAP['Geno']='GenotypeDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields = ['Name',
+        self.search_fields=['Name',
                               'Chr']
 
         # Find out what display_fields is
-        self.display_fields = ['name',
+        self.display_fields=['name',
                                'chr',
                                'mb',
                                'source2',
                                'sequence']
 
         # Fields displayed in the search results table header
-        self.header_fields = ['Index',
+        self.header_fields=['Index',
                               'ID',
                               'Location']
 
         # Todo: Obsolete or rename this field
-        self.type = 'Geno'
+        self.type='Geno'
 
-        self.query_for_group = '''
+        self.query_for_group='''
                 SELECT
                         InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                 FROM
@@ -926,11 +987,11 @@ class GenotypeDataSet(DataSet):
                 this_trait.retrieveInfo()
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (
+                this_trait.location_repr='Chr%s: %.6f' % (
                     this_trait.chr, float(this_trait.mb))
 
     def retrieve_sample_data(self, trait):
-        query = """
+        query="""
                     SELECT
                             Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
                     FROM
@@ -947,7 +1008,7 @@ class GenotypeDataSet(DataSet):
                             Strain.Name
                     """
         logger.sql(query)
-        results = g.db.execute(query,
+        results=g.db.execute(query,
                                (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
                                 trait, self.name)).fetchall()
         return results
@@ -961,11 +1022,11 @@ class MrnaAssayDataSet(DataSet):
     platform and is far too specific.
 
     '''
-    DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
+    DS_NAME_MAP['ProbeSet']='MrnaAssayDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields = ['Name',
+        self.search_fields=['Name',
                               'Description',
                               'Probe_Target_Description',
                               'Symbol',
@@ -975,7 +1036,7 @@ class MrnaAssayDataSet(DataSet):
                               'RefSeq_TranscriptId']
 
         # Find out what display_fields is
-        self.display_fields = ['name', 'symbol',
+        self.display_fields=['name', 'symbol',
                                'description', 'probe_target_description',
                                'chr', 'mb',
                                'alias', 'geneid',
@@ -995,7 +1056,7 @@ class MrnaAssayDataSet(DataSet):
                                'flag']
 
         # Fields displayed in the search results table header
-        self.header_fields = ['Index',
+        self.header_fields=['Index',
                               'Record',
                               'Symbol',
                               'Description',
@@ -1006,9 +1067,9 @@ class MrnaAssayDataSet(DataSet):
                               'Additive Effect']
 
         # Todo: Obsolete or rename this field
-        self.type = 'ProbeSet'
+        self.type='ProbeSet'
 
-        self.query_for_group = '''
+        self.query_for_group='''
                         SELECT
                                 InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                         FROM
@@ -1026,7 +1087,7 @@ class MrnaAssayDataSet(DataSet):
 
         #  Note: setting trait_list to [] is probably not a great idea.
         if not trait_list:
-            trait_list = []
+            trait_list=[]
 
         for this_trait in trait_list:
 
@@ -1034,33 +1095,33 @@ class MrnaAssayDataSet(DataSet):
                 this_trait.retrieveInfo(QTL=1)
 
             if not this_trait.symbol:
-                this_trait.symbol = "N/A"
+                this_trait.symbol="N/A"
 
             # XZ, 12/08/2008: description
             # XZ, 06/05/2009: Rob asked to add probe target description
-            description_string = str(
+            description_string=str(
                 str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = str(
+            target_string=str(
                 str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
             if len(description_string) > 1 and description_string != 'None':
-                description_display = description_string
+                description_display=description_string
             else:
-                description_display = this_trait.symbol
+                description_display=this_trait.symbol
 
             if (len(description_display) > 1 and description_display != 'N/A'
                     and len(target_string) > 1 and target_string != 'None'):
-                description_display = description_display + '; ' + target_string.strip()
+                description_display=description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
-            this_trait.description_display = description_display
+            this_trait.description_display=description_display
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (
+                this_trait.location_repr='Chr%s: %.6f' % (
                     this_trait.chr, float(this_trait.mb))
 
             # Get mean expression value
-            query = (
+            query=(
                 """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
                 where ProbeSetXRef.ProbeSetFreezeId = %s and
                 ProbeSet.Id = ProbeSetXRef.ProbeSetId and
@@ -1068,44 +1129,45 @@ class MrnaAssayDataSet(DataSet):
             """ % (escape(str(this_trait.dataset.id)),
                    escape(this_trait.name)))
 
-            #logger.debug("query is:", pf(query))
+            # logger.debug("query is:", pf(query))
             logger.sql(query)
-            result = g.db.execute(query).fetchone()
+            result=g.db.execute(query).fetchone()
 
-            mean = result[0] if result else 0
+            mean=result[0] if result else 0
 
             if mean:
-                this_trait.mean = "%2.3f" % mean
+                this_trait.mean="%2.3f" % mean
 
             # LRS and its location
-            this_trait.LRS_score_repr = 'N/A'
-            this_trait.LRS_location_repr = 'N/A'
+            this_trait.LRS_score_repr='N/A'
+            this_trait.LRS_location_repr='N/A'
 
             # Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
-                query = """
+                query="""
                     select Geno.Chr, Geno.Mb from Geno, Species
                     where Species.Name = '{}' and
                         Geno.Name = '{}' and
                         Geno.SpeciesId = Species.Id
                 """.format(species, this_trait.locus)
                 logger.sql(query)
-                result = g.db.execute(query).fetchone()
+                result=g.db.execute(query).fetchone()
 
                 if result:
-                    lrs_chr, lrs_mb = result
-                    this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
-                    this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
+                    lrs_chr, lrs_mb=result
+                    this_trait.LRS_score_repr='%3.1f' % this_trait.lrs
+                    this_trait.LRS_location_repr='Chr%s: %.6f' % (
                         lrs_chr, float(lrs_mb))
 
         return trait_list
 
     def retrieve_sample_data(self, trait):
-        query = """
+        query="""
                     SELECT
                             Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
                     FROM
-                            (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
+                            (ProbeSetData, ProbeSetFreeze,
+                             Strain, ProbeSet, ProbeSetXRef)
                     left join ProbeSetSE on
                             (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
                     left join NStrain on
@@ -1121,19 +1183,19 @@ class MrnaAssayDataSet(DataSet):
                             Strain.Name
                     """ % (escape(trait), escape(self.name))
         logger.sql(query)
-        results = g.db.execute(query).fetchall()
-        #logger.debug("RETRIEVED RESULTS HERE:", results)
+        results=g.db.execute(query).fetchall()
+        # logger.debug("RETRIEVED RESULTS HERE:", results)
         return results
 
     def retrieve_genes(self, column_name):
-        query = """
+        query="""
                     select ProbeSet.Name, ProbeSet.%s
                     from ProbeSet,ProbeSetXRef
                     where ProbeSetXRef.ProbeSetFreezeId = %s and
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
                 """ % (column_name, escape(str(self.id)))
         logger.sql(query)
-        results = g.db.execute(query).fetchall()
+        results=g.db.execute(query).fetchall()
 
         return dict(results)
 
@@ -1141,40 +1203,40 @@ class MrnaAssayDataSet(DataSet):
 class TempDataSet(DataSet):
     '''Temporary user-generated data set'''
 
-    DS_NAME_MAP['Temp'] = 'TempDataSet'
+    DS_NAME_MAP['Temp']='TempDataSet'
 
     def setup(self):
-        self.search_fields = ['name',
+        self.search_fields=['name',
                               'description']
 
-        self.display_fields = ['name',
+        self.display_fields=['name',
                                'description']
 
-        self.header_fields = ['Name',
+        self.header_fields=['Name',
                               'Description']
 
-        self.type = 'Temp'
+        self.type='Temp'
 
         # Need to double check later how these are used
-        self.id = 1
-        self.fullname = 'Temporary Storage'
-        self.shortname = 'Temp'
+        self.id=1
+        self.fullname='Temporary Storage'
+        self.shortname='Temp'
 
 
 def geno_mrna_confidentiality(ob):
-    dataset_table = ob.type + "Freeze"
-    #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
+    dataset_table=ob.type + "Freeze"
+    # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
 
-    query = '''SELECT Id, Name, FullName, confidentiality,
+    query='''SELECT Id, Name, FullName, confidentiality,
                         AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
     logger.sql(query)
-    result = g.db.execute(query)
+    result=g.db.execute(query)
 
     (dataset_id,
      name,
      full_name,
      confidential,
-     authorized_users) = result.fetchall()[0]
+     authorized_users)=result.fetchall()[0]
 
     if confidential:
         return True
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index df0afba6..9fbfee48 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -27,6 +27,34 @@ def create_target_this_trait(start_vars):
     return (this_dataset, this_trait, target_dataset, sample_data)
 
 
+
+def test_process_data(this_trait,dataset,start_vars):
+    """test function for bxd,all and other sample data"""
+
+    corr_samples_group = start_vars["corr_samples_group"]
+
+
+    primary_samples = dataset.group.samplelist
+    if dataset.group.parlist != None:
+        primary_samples += dataset.group.parlist
+    if dataset.group.f1list != None:
+        primary_samples += dataset.group.f1list
+
+    # If either BXD/whatever Only or All Samples, append all of that group's samplelist
+    if corr_samples_group != 'samples_other':
+        sample_data = process_samples(start_vars, primary_samples)
+
+    # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
+    # exclude the primary samples (because they would have been added in the previous
+    # if statement if the user selected All Samples)
+    if corr_samples_group != 'samples_primary':
+        if corr_samples_group == 'samples_other':
+            primary_samples = [x for x in primary_samples if x not in (
+                dataset.group.parlist + dataset.group.f1list)]
+        sample_data = process_samples(start_vars, list(this_trait.data.keys()), primary_samples)
+
+    return sample_data
+
 def process_samples(start_vars, sample_names, excluded_samples=None):
     """process samples"""
     sample_data = {}
@@ -118,13 +146,22 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     sample_data = process_samples(
         start_vars, this_dataset.group.samplelist)
-    target_dataset.get_trait_data(list(sample_data.keys()))
+
+    # sample_data = test_process_data(this_trait,this_dataset,start_vars)
+
+    if target_dataset.type =="ProbeSet":
+        # pass
+        target_dataset.get_probeset_data(list(sample_data.keys()))
+    else:
+        target_dataset.get_trait_data(list(sample_data.keys()))
     this_trait = retrieve_sample_data(this_trait, this_dataset)
     this_trait_data = {
         "trait_sample_data": sample_data,
         "trait_id": start_vars["trait_id"]
     }
 
+    # should remove this  len(samplelist) == len(strain_values)
+
     results = map_shared_keys_to_values(
         target_dataset.samplelist, target_dataset.trait_data)
 
@@ -205,6 +242,7 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
                         "target_dataset": start_vars['corr_dataset'],
                         "return_results": corr_return_results}
 
+
     return correlation_data
 
 
@@ -265,3 +303,107 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
         }
         return (primary_tissue_data, target_tissue_data)
     return None
+
+
+def generate_corr_data(corr_results, target_dataset):
+    counter = 0
+    results_list = []
+    for (index, trait_corr) in enumerate(corr_results):
+        trait_name = list(trait_corr.keys())[0]
+        trait = create_trait(dataset=target_dataset,
+                             name=trait_name)
+
+        trait_corr_data =  trait_corr[trait_name]
+
+        if trait.view == False:
+            continue
+        results_dict = {}
+        results_dict['index'] = index + 1
+        results_dict['trait_id'] = trait.name
+        results_dict['dataset'] = trait.dataset.name
+        # results_dict['hmac'] = hmac.data_hmac(
+        #     '{}:{}'.format(trait.name, trait.dataset.name))
+        if target_dataset.type == "ProbeSet":
+            results_dict['symbol'] = trait.symbol
+            results_dict['description'] = "N/A"
+            results_dict['location'] = trait.location_repr
+            results_dict['mean'] = "N/A"
+            results_dict['additive'] = "N/A"
+            if bool(trait.description_display):
+                results_dict['description'] = trait.description_display
+            if bool(trait.mean):
+                results_dict['mean'] = f"{float(trait.mean):.3f}"
+            try:
+                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
+            except:
+                results_dict['lod_score'] = "N/A"
+            results_dict['lrs_location'] = trait.LRS_location_repr
+            if bool(trait.additive):
+                results_dict['additive'] = f"{float(trait.additive):.3f}"
+            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+            results_dict['lit_corr'] = "--"
+            results_dict['tissue_corr'] = "--"
+            results_dict['tissue_pvalue'] = "--"
+            tissue_corr = trait_corr_data.get('tissue_corr',0)
+            lit_corr = trait_corr_data.get('lit_corr',0)
+            if bool(lit_corr):
+                results_dict['lit_corr'] = f"{float(trait_corr_data.get('lit_corr',0)):.3f}"
+            if bool(tissue_corr):
+                results_dict['tissue_corr'] = f"{float(trait_corr_data.get('tissue_corr',0)):.3f}"
+                results_dict['tissue_pvalue'] = f"{float(trait_corr_data.get('tissue_pvalue',0)):.3e}"
+        elif target_dataset.type == "Publish":
+            results_dict['abbreviation_display'] = "N/A"
+            results_dict['description'] = "N/A"
+            results_dict['mean'] = "N/A"
+            results_dict['authors_display'] = "N/A"
+            results_dict['additive'] = "N/A"
+            if for_api:
+                results_dict['pubmed_id'] = "N/A"
+                results_dict['year'] = "N/A"
+            else:
+                results_dict['pubmed_link'] = "N/A"
+                results_dict['pubmed_text'] = "N/A"
+
+            if bool(trait.abbreviation):
+                results_dict['abbreviation_display'] = trait.abbreviation
+            if bool(trait.description_display):
+                results_dict['description'] = trait.description_display
+            if bool(trait.mean):
+                results_dict['mean'] = f"{float(trait.mean):.3f}"
+            if bool(trait.authors):
+                authors_list = trait.authors.split(',')
+                if len(authors_list) > 6:
+                    results_dict['authors_display'] = ", ".join(
+                        authors_list[:6]) + ", et al."
+                else:
+                    results_dict['authors_display'] = trait.authors
+            if bool(trait.pubmed_id):
+                if for_api:
+                    results_dict['pubmed_id'] = trait.pubmed_id
+                    results_dict['year'] = trait.pubmed_text
+                else:
+                    results_dict['pubmed_link'] = trait.pubmed_link
+                    results_dict['pubmed_text'] = trait.pubmed_text
+            try:
+                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
+            except:
+                results_dict['lod_score'] = "N/A"
+            results_dict['lrs_location'] = trait.LRS_location_repr
+            if bool(trait.additive):
+                results_dict['additive'] = f"{float(trait.additive):.3f}"
+            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+        else:
+            results_dict['location'] = trait.location_repr
+            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+
+        results_list.append(results_dict)
+
+    return results_list
+
+
-- 
cgit v1.2.3


From c9a133e75d32e0bb9c8e63443b0f43f084363996 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:37:36 +0300
Subject: pep8 formatting

---
 wqflask/base/data_set.py | 214 ++++++++++++++++++++++++-----------------------
 1 file changed, 109 insertions(+), 105 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 7531ac81..39296f6a 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -659,12 +659,8 @@ class DataSet:
                 "Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
 
-
-
-
     def chunk_dataset(self, dataset, n):
 
-
         results = {}
 
         query = """
@@ -677,10 +673,7 @@ class DataSet:
 
         # should cache this
 
-        traits_name_dict= dict(g.db.execute(query).fetchall())
-
-
-
+        traits_name_dict = dict(g.db.execute(query).fetchall())
 
         for i in range(0, len(dataset), n):
             matrix = list(dataset[i:i + n])
@@ -716,50 +709,50 @@ class DataSet:
                 FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
                 WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
                 and ProbeSetFreeze.Name = '{}'
-                and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids),self.name)
+                and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
 
-        query_results=list(g.db.execute(query).fetchall())
+        query_results = list(g.db.execute(query).fetchall())
 
-        data_results=self.chunk_dataset(query_results, len(sample_ids))
-        self.trait_data=data_results
+        data_results = self.chunk_dataset(query_results, len(sample_ids))
+        self.trait_data = data_results
 
     def get_trait_data(self, sample_list=None):
         if sample_list:
-            self.samplelist=sample_list
+            self.samplelist = sample_list
         else:
-            self.samplelist=self.group.samplelist
+            self.samplelist = self.group.samplelist
 
         if self.group.parlist != None and self.group.f1list != None:
             if (self.group.parlist + self.group.f1list) in self.samplelist:
                 self.samplelist += self.group.parlist + self.group.f1list
 
-        query="""
+        query = """
             SELECT Strain.Name, Strain.Id FROM Strain, Species
             WHERE Strain.Name IN {}
             and Strain.SpeciesId=Species.Id
             and Species.name = '{}'
             """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
         logger.sql(query)
-        results=dict(g.db.execute(query).fetchall())
-        sample_ids=[results[item] for item in self.samplelist]
+        results = dict(g.db.execute(query).fetchall())
+        sample_ids = [results[item] for item in self.samplelist]
 
         # MySQL limits the number of tables that can be used in a join to 61,
         # so we break the sample ids into smaller chunks
         # Postgres doesn't have that limit, so we can get rid of this after we transition
-        chunk_size=50
-        number_chunks=int(math.ceil(len(sample_ids) / chunk_size))
-        trait_sample_data=[]
+        chunk_size = 50
+        number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
+        trait_sample_data = []
         for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
             if self.type == "Publish":
-                dataset_type="Phenotype"
+                dataset_type = "Phenotype"
             else:
-                dataset_type=self.type
-            temp=['T%s.value' % item for item in sample_ids_step]
+                dataset_type = self.type
+            temp = ['T%s.value' % item for item in sample_ids_step]
             if self.type == "Publish":
-                query="SELECT {}XRef.Id,".format(escape(self.type))
+                query = "SELECT {}XRef.Id,".format(escape(self.type))
             else:
-                query="SELECT {}.Name,".format(escape(dataset_type))
-            data_start_pos=1
+                query = "SELECT {}.Name,".format(escape(dataset_type))
+            data_start_pos = 1
             query += ', '.join(temp)
             query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
                                                                      self.type,
@@ -788,27 +781,27 @@ class DataSet:
                         """.format(*mescape(self.type, self.type, self.type, self.type,
                                             self.name, dataset_type, self.type, self.type, dataset_type))
 
-            results=g.db.execute(query).fetchall()
+            results = g.db.execute(query).fetchall()
             trait_sample_data.append(results)
 
-        trait_count=len(trait_sample_data[0])
-        self.trait_data=collections.defaultdict(list)
+        trait_count = len(trait_sample_data[0])
+        self.trait_data = collections.defaultdict(list)
 
         # put all of the separate data together into a dictionary where the keys are
         # trait names and values are lists of sample values
         for trait_counter in range(trait_count):
-            trait_name=trait_sample_data[0][trait_counter][0]
+            trait_name = trait_sample_data[0][trait_counter][0]
             for chunk_counter in range(int(number_chunks)):
                 self.trait_data[trait_name] += (
                     trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
 
 
 class PhenotypeDataSet(DataSet):
-    DS_NAME_MAP['Publish']='PhenotypeDataSet'
+    DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields=['Phenotype.Post_publication_description',
+        self.search_fields = ['Phenotype.Post_publication_description',
                               'Phenotype.Pre_publication_description',
                               'Phenotype.Pre_publication_abbreviation',
                               'Phenotype.Post_publication_abbreviation',
@@ -821,7 +814,7 @@ class PhenotypeDataSet(DataSet):
                               'PublishXRef.Id']
 
         # Figure out what display_fields is
-        self.display_fields=['name', 'group_code',
+        self.display_fields = ['name', 'group_code',
                                'pubmed_id',
                                'pre_publication_description',
                                'post_publication_description',
@@ -839,7 +832,7 @@ class PhenotypeDataSet(DataSet):
                                'sequence', 'units', 'comments']
 
         # Fields displayed in the search results table header
-        self.header_fields=['Index',
+        self.header_fields = ['Index',
                               'Record',
                               'Description',
                               'Authors',
@@ -848,9 +841,9 @@ class PhenotypeDataSet(DataSet):
                               'Max LRS Location',
                               'Additive Effect']
 
-        self.type='Publish'
+        self.type = 'Publish'
 
-        self.query_for_group='''
+        self.query_for_group = '''
                             SELECT
                                     InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                             FROM
@@ -870,13 +863,13 @@ class PhenotypeDataSet(DataSet):
             if not this_trait.haveinfo:
                 this_trait.retrieve_info(get_qtl_info=True)
 
-            description=this_trait.post_publication_description
+            description = this_trait.post_publication_description
 
             # If the dataset is confidential and the user has access to confidential
             # phenotype traits, then display the pre-publication description instead
             # of the post-publication description
             if this_trait.confidential:
-                this_trait.description_display=""
+                this_trait.description_display = ""
                 continue   # for now, because no authorization features
 
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -884,46 +877,46 @@ class PhenotypeDataSet(DataSet):
                         userName=self.userName,
                         authorized_users=this_trait.authorized_users):
 
-                    description=this_trait.pre_publication_description
+                    description = this_trait.pre_publication_description
 
             if len(description) > 0:
-                this_trait.description_display=description.strip()
+                this_trait.description_display = description.strip()
             else:
-                this_trait.description_display=""
+                this_trait.description_display = ""
 
             if not this_trait.year.isdigit():
-                this_trait.pubmed_text="N/A"
+                this_trait.pubmed_text = "N/A"
             else:
-                this_trait.pubmed_text=this_trait.year
+                this_trait.pubmed_text = this_trait.year
 
             if this_trait.pubmed_id:
-                this_trait.pubmed_link=webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
+                this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
 
             # LRS and its location
-            this_trait.LRS_score_repr="N/A"
-            this_trait.LRS_location_repr="N/A"
+            this_trait.LRS_score_repr = "N/A"
+            this_trait.LRS_location_repr = "N/A"
 
             if this_trait.lrs:
-                query="""
+                query = """
                     select Geno.Chr, Geno.Mb from Geno, Species
                     where Species.Name = '%s' and
                         Geno.Name = '%s' and
                         Geno.SpeciesId = Species.Id
                 """ % (species, this_trait.locus)
                 logger.sql(query)
-                result=g.db.execute(query).fetchone()
+                result = g.db.execute(query).fetchone()
 
                 if result:
                     if result[0] and result[1]:
-                        LRS_Chr=result[0]
-                        LRS_Mb=result[1]
+                        LRS_Chr = result[0]
+                        LRS_Mb = result[1]
 
-                        this_trait.LRS_score_repr=LRS_score_repr='%3.1f' % this_trait.lrs
-                        this_trait.LRS_location_repr=LRS_location_repr='Chr%s: %.6f' % (
+                        this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
+                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
                             LRS_Chr, float(LRS_Mb))
 
     def retrieve_sample_data(self, trait):
-        query="""
+        query = """
                     SELECT
                             Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
                     FROM
@@ -941,34 +934,34 @@ class PhenotypeDataSet(DataSet):
                             Strain.Name
                     """
         logger.sql(query)
-        results=g.db.execute(query, (trait, self.id)).fetchall()
+        results = g.db.execute(query, (trait, self.id)).fetchall()
         return results
 
 
 class GenotypeDataSet(DataSet):
-    DS_NAME_MAP['Geno']='GenotypeDataSet'
+    DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields=['Name',
+        self.search_fields = ['Name',
                               'Chr']
 
         # Find out what display_fields is
-        self.display_fields=['name',
+        self.display_fields = ['name',
                                'chr',
                                'mb',
                                'source2',
                                'sequence']
 
         # Fields displayed in the search results table header
-        self.header_fields=['Index',
+        self.header_fields = ['Index',
                               'ID',
                               'Location']
 
         # Todo: Obsolete or rename this field
-        self.type='Geno'
+        self.type = 'Geno'
 
-        self.query_for_group='''
+        self.query_for_group = '''
                 SELECT
                         InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                 FROM
@@ -987,11 +980,11 @@ class GenotypeDataSet(DataSet):
                 this_trait.retrieveInfo()
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr='Chr%s: %.6f' % (
+                this_trait.location_repr = 'Chr%s: %.6f' % (
                     this_trait.chr, float(this_trait.mb))
 
     def retrieve_sample_data(self, trait):
-        query="""
+        query = """
                     SELECT
                             Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
                     FROM
@@ -1008,7 +1001,7 @@ class GenotypeDataSet(DataSet):
                             Strain.Name
                     """
         logger.sql(query)
-        results=g.db.execute(query,
+        results = g.db.execute(query,
                                (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
                                 trait, self.name)).fetchall()
         return results
@@ -1022,11 +1015,11 @@ class MrnaAssayDataSet(DataSet):
     platform and is far too specific.
 
     '''
-    DS_NAME_MAP['ProbeSet']='MrnaAssayDataSet'
+    DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
 
     def setup(self):
         # Fields in the database table
-        self.search_fields=['Name',
+        self.search_fields = ['Name',
                               'Description',
                               'Probe_Target_Description',
                               'Symbol',
@@ -1036,7 +1029,7 @@ class MrnaAssayDataSet(DataSet):
                               'RefSeq_TranscriptId']
 
         # Find out what display_fields is
-        self.display_fields=['name', 'symbol',
+        self.display_fields = ['name', 'symbol',
                                'description', 'probe_target_description',
                                'chr', 'mb',
                                'alias', 'geneid',
@@ -1056,7 +1049,7 @@ class MrnaAssayDataSet(DataSet):
                                'flag']
 
         # Fields displayed in the search results table header
-        self.header_fields=['Index',
+        self.header_fields = ['Index',
                               'Record',
                               'Symbol',
                               'Description',
@@ -1067,9 +1060,9 @@ class MrnaAssayDataSet(DataSet):
                               'Additive Effect']
 
         # Todo: Obsolete or rename this field
-        self.type='ProbeSet'
+        self.type = 'ProbeSet'
 
-        self.query_for_group='''
+        self.query_for_group = '''
                         SELECT
                                 InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
                         FROM
@@ -1087,7 +1080,7 @@ class MrnaAssayDataSet(DataSet):
 
         #  Note: setting trait_list to [] is probably not a great idea.
         if not trait_list:
-            trait_list=[]
+            trait_list = []
 
         for this_trait in trait_list:
 
@@ -1095,33 +1088,33 @@ class MrnaAssayDataSet(DataSet):
                 this_trait.retrieveInfo(QTL=1)
 
             if not this_trait.symbol:
-                this_trait.symbol="N/A"
+                this_trait.symbol = "N/A"
 
             # XZ, 12/08/2008: description
             # XZ, 06/05/2009: Rob asked to add probe target description
-            description_string=str(
+            description_string = str(
                 str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string=str(
+            target_string = str(
                 str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
             if len(description_string) > 1 and description_string != 'None':
-                description_display=description_string
+                description_display = description_string
             else:
-                description_display=this_trait.symbol
+                description_display = this_trait.symbol
 
             if (len(description_display) > 1 and description_display != 'N/A'
                     and len(target_string) > 1 and target_string != 'None'):
-                description_display=description_display + '; ' + target_string.strip()
+                description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
-            this_trait.description_display=description_display
+            this_trait.description_display = description_display
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr='Chr%s: %.6f' % (
+                this_trait.location_repr = 'Chr%s: %.6f' % (
                     this_trait.chr, float(this_trait.mb))
 
             # Get mean expression value
-            query=(
+            query = (
                 """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
                 where ProbeSetXRef.ProbeSetFreezeId = %s and
                 ProbeSet.Id = ProbeSetXRef.ProbeSetId and
@@ -1131,38 +1124,38 @@ class MrnaAssayDataSet(DataSet):
 
             # logger.debug("query is:", pf(query))
             logger.sql(query)
-            result=g.db.execute(query).fetchone()
+            result = g.db.execute(query).fetchone()
 
-            mean=result[0] if result else 0
+            mean = result[0] if result else 0
 
             if mean:
-                this_trait.mean="%2.3f" % mean
+                this_trait.mean = "%2.3f" % mean
 
             # LRS and its location
-            this_trait.LRS_score_repr='N/A'
-            this_trait.LRS_location_repr='N/A'
+            this_trait.LRS_score_repr = 'N/A'
+            this_trait.LRS_location_repr = 'N/A'
 
             # Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
-                query="""
+                query = """
                     select Geno.Chr, Geno.Mb from Geno, Species
                     where Species.Name = '{}' and
                         Geno.Name = '{}' and
                         Geno.SpeciesId = Species.Id
                 """.format(species, this_trait.locus)
                 logger.sql(query)
-                result=g.db.execute(query).fetchone()
+                result = g.db.execute(query).fetchone()
 
                 if result:
-                    lrs_chr, lrs_mb=result
-                    this_trait.LRS_score_repr='%3.1f' % this_trait.lrs
-                    this_trait.LRS_location_repr='Chr%s: %.6f' % (
+                    lrs_chr, lrs_mb = result
+                    this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
+                    this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
                         lrs_chr, float(lrs_mb))
 
         return trait_list
 
     def retrieve_sample_data(self, trait):
-        query="""
+        query = """
                     SELECT
                             Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
                     FROM
@@ -1183,19 +1176,19 @@ class MrnaAssayDataSet(DataSet):
                             Strain.Name
                     """ % (escape(trait), escape(self.name))
         logger.sql(query)
-        results=g.db.execute(query).fetchall()
+        results = g.db.execute(query).fetchall()
         # logger.debug("RETRIEVED RESULTS HERE:", results)
         return results
 
     def retrieve_genes(self, column_name):
-        query="""
+        query = """
                     select ProbeSet.Name, ProbeSet.%s
                     from ProbeSet,ProbeSetXRef
                     where ProbeSetXRef.ProbeSetFreezeId = %s and
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
                 """ % (column_name, escape(str(self.id)))
         logger.sql(query)
-        results=g.db.execute(query).fetchall()
+        results = g.db.execute(query).fetchall()
 
         return dict(results)
 
@@ -1203,40 +1196,51 @@ class MrnaAssayDataSet(DataSet):
 class TempDataSet(DataSet):
     '''Temporary user-generated data set'''
 
-    DS_NAME_MAP['Temp']='TempDataSet'
+    DS_NAME_MAP['Temp'] = 'TempDataSet'
 
     def setup(self):
-        self.search_fields=['name',
+        self.search_fields = ['name',
                               'description']
 
-        self.display_fields=['name',
+        self.display_fields = ['name',
                                'description']
 
-        self.header_fields=['Name',
+        self.header_fields = ['Name',
                               'Description']
 
-        self.type='Temp'
+        self.type = 'Temp'
 
         # Need to double check later how these are used
-        self.id=1
-        self.fullname='Temporary Storage'
-        self.shortname='Temp'
+        self.id = 1
+        self.fullname = 'Temporary Storage'
+        self.shortname = 'Temp'
 
 
 def geno_mrna_confidentiality(ob):
-    dataset_table=ob.type + "Freeze"
+    dataset_table = ob.type + "Freeze"
     # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
 
-    query='''SELECT Id, Name, FullName, confidentiality,
+    query = '''SELECT Id, Name, FullName, confidentiality,
                         AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
     logger.sql(query)
-    result=g.db.execute(query)
+    result = g.db.execute(query)
+
+    (dataset_id,
+     name,
+     full_name,
+     confidential,
+     authorized_users) = result.fetchall()[0]
+
+    if confidential:
+        return True
+uery)
+    result = g.db.execute(query)
 
     (dataset_id,
      name,
      full_name,
      confidential,
-     authorized_users)=result.fetchall()[0]
+     authorized_users) = result.fetchall()[0]
 
     if confidential:
         return True
-- 
cgit v1.2.3


From d8d3a8311106ea97c1fba4ef4606929eb9b0fdcb Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:43:45 +0300
Subject: minor fix

---
 wqflask/base/data_set.py | 1 -
 1 file changed, 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 39296f6a..4a150e86 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1233,7 +1233,6 @@ def geno_mrna_confidentiality(ob):
 
     if confidential:
         return True
-uery)
     result = g.db.execute(query)
 
     (dataset_id,
-- 
cgit v1.2.3


From aaacfe3a0abc7ca4fe5bdb486651e018cdc7aba0 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 9 Jun 2021 07:25:03 +0300
Subject: remove unused functions + minor fixes

---
 wqflask/base/data_set.py                           |   2 +
 wqflask/wqflask/correlation/correlation_gn3_api.py | 115 +--------------------
 2 files changed, 7 insertions(+), 110 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4a150e86..4d54cfae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -684,6 +684,8 @@ class DataSet:
         return results
 
     def get_probeset_data(self, sample_list=None, trait_ids=None):
+
+        # improvement of get trait data--->>>
         if sample_list:
             self.samplelist = sample_list
 
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 9fbfee48..5fa33027 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -27,13 +27,11 @@ def create_target_this_trait(start_vars):
     return (this_dataset, this_trait, target_dataset, sample_data)
 
 
-
-def test_process_data(this_trait,dataset,start_vars):
+def test_process_data(this_trait, dataset, start_vars):
     """test function for bxd,all and other sample data"""
 
     corr_samples_group = start_vars["corr_samples_group"]
 
-
     primary_samples = dataset.group.samplelist
     if dataset.group.parlist != None:
         primary_samples += dataset.group.parlist
@@ -51,10 +49,12 @@ def test_process_data(this_trait,dataset,start_vars):
         if corr_samples_group == 'samples_other':
             primary_samples = [x for x in primary_samples if x not in (
                 dataset.group.parlist + dataset.group.f1list)]
-        sample_data = process_samples(start_vars, list(this_trait.data.keys()), primary_samples)
+        sample_data = process_samples(start_vars, list(
+            this_trait.data.keys()), primary_samples)
 
     return sample_data
 
+
 def process_samples(start_vars, sample_names, excluded_samples=None):
     """process samples"""
     sample_data = {}
@@ -149,7 +149,7 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     # sample_data = test_process_data(this_trait,this_dataset,start_vars)
 
-    if target_dataset.type =="ProbeSet":
+    if target_dataset.type == "ProbeSet":
         # pass
         target_dataset.get_probeset_data(list(sample_data.keys()))
     else:
@@ -242,7 +242,6 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
                         "target_dataset": start_vars['corr_dataset'],
                         "return_results": corr_return_results}
 
-
     return correlation_data
 
 
@@ -303,107 +302,3 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
         }
         return (primary_tissue_data, target_tissue_data)
     return None
-
-
-def generate_corr_data(corr_results, target_dataset):
-    counter = 0
-    results_list = []
-    for (index, trait_corr) in enumerate(corr_results):
-        trait_name = list(trait_corr.keys())[0]
-        trait = create_trait(dataset=target_dataset,
-                             name=trait_name)
-
-        trait_corr_data =  trait_corr[trait_name]
-
-        if trait.view == False:
-            continue
-        results_dict = {}
-        results_dict['index'] = index + 1
-        results_dict['trait_id'] = trait.name
-        results_dict['dataset'] = trait.dataset.name
-        # results_dict['hmac'] = hmac.data_hmac(
-        #     '{}:{}'.format(trait.name, trait.dataset.name))
-        if target_dataset.type == "ProbeSet":
-            results_dict['symbol'] = trait.symbol
-            results_dict['description'] = "N/A"
-            results_dict['location'] = trait.location_repr
-            results_dict['mean'] = "N/A"
-            results_dict['additive'] = "N/A"
-            if bool(trait.description_display):
-                results_dict['description'] = trait.description_display
-            if bool(trait.mean):
-                results_dict['mean'] = f"{float(trait.mean):.3f}"
-            try:
-                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
-            except:
-                results_dict['lod_score'] = "N/A"
-            results_dict['lrs_location'] = trait.LRS_location_repr
-            if bool(trait.additive):
-                results_dict['additive'] = f"{float(trait.additive):.3f}"
-            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
-            results_dict['num_overlap'] = trait.num_overlap
-            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
-            results_dict['lit_corr'] = "--"
-            results_dict['tissue_corr'] = "--"
-            results_dict['tissue_pvalue'] = "--"
-            tissue_corr = trait_corr_data.get('tissue_corr',0)
-            lit_corr = trait_corr_data.get('lit_corr',0)
-            if bool(lit_corr):
-                results_dict['lit_corr'] = f"{float(trait_corr_data.get('lit_corr',0)):.3f}"
-            if bool(tissue_corr):
-                results_dict['tissue_corr'] = f"{float(trait_corr_data.get('tissue_corr',0)):.3f}"
-                results_dict['tissue_pvalue'] = f"{float(trait_corr_data.get('tissue_pvalue',0)):.3e}"
-        elif target_dataset.type == "Publish":
-            results_dict['abbreviation_display'] = "N/A"
-            results_dict['description'] = "N/A"
-            results_dict['mean'] = "N/A"
-            results_dict['authors_display'] = "N/A"
-            results_dict['additive'] = "N/A"
-            if for_api:
-                results_dict['pubmed_id'] = "N/A"
-                results_dict['year'] = "N/A"
-            else:
-                results_dict['pubmed_link'] = "N/A"
-                results_dict['pubmed_text'] = "N/A"
-
-            if bool(trait.abbreviation):
-                results_dict['abbreviation_display'] = trait.abbreviation
-            if bool(trait.description_display):
-                results_dict['description'] = trait.description_display
-            if bool(trait.mean):
-                results_dict['mean'] = f"{float(trait.mean):.3f}"
-            if bool(trait.authors):
-                authors_list = trait.authors.split(',')
-                if len(authors_list) > 6:
-                    results_dict['authors_display'] = ", ".join(
-                        authors_list[:6]) + ", et al."
-                else:
-                    results_dict['authors_display'] = trait.authors
-            if bool(trait.pubmed_id):
-                if for_api:
-                    results_dict['pubmed_id'] = trait.pubmed_id
-                    results_dict['year'] = trait.pubmed_text
-                else:
-                    results_dict['pubmed_link'] = trait.pubmed_link
-                    results_dict['pubmed_text'] = trait.pubmed_text
-            try:
-                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
-            except:
-                results_dict['lod_score'] = "N/A"
-            results_dict['lrs_location'] = trait.LRS_location_repr
-            if bool(trait.additive):
-                results_dict['additive'] = f"{float(trait.additive):.3f}"
-            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
-            results_dict['num_overlap'] = trait.num_overlap
-            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
-        else:
-            results_dict['location'] = trait.location_repr
-            results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
-            results_dict['num_overlap'] = trait.num_overlap
-            results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
-
-        results_list.append(results_dict)
-
-    return results_list
-
-
-- 
cgit v1.2.3


From 481b1fede3c815d5b9afbb07f0f69dcb7363143e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 00:52:10 +0300
Subject: remove print statements

---
 wqflask/utility/helper_functions.py | 4 ----
 1 file changed, 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 50e00421..27dd0729 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -21,15 +21,11 @@ def get_species_dataset_trait(self, start_vars):
             self.dataset = data_set.create_dataset(start_vars['dataset'])
     else:
         self.dataset = data_set.create_dataset(start_vars['dataset'])
-    logger.debug("After creating dataset")
     self.species = TheSpecies(dataset=self.dataset)
-    logger.debug("After creating species")
     self.this_trait = create_trait(dataset=self.dataset,
                                    name=start_vars['trait_id'],
                                    cellid=None,
                                    get_qtl_info=True)
-    logger.debug("After creating trait")
-
 
 def get_trait_db_obs(self, trait_db_list):
     if isinstance(trait_db_list, str):
-- 
cgit v1.2.3


From 48e66dc230292a9c0b66da946106d8c9f611074f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 00:54:02 +0300
Subject: sort sample name by sample_ids

---
 wqflask/base/data_set.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4d54cfae..991c9fee 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -705,6 +705,9 @@ class DataSet:
         results = dict(g.db.execute(query).fetchall())
         sample_ids = [results[item] for item in self.samplelist]
 
+        sorted_samplelist = [strain_name for strain_name, strain_id in sorted(
+            results.items(), key=lambda item: item[1])]
+
         query = """SELECT * from ProbeSetData
                 where StrainID in {}
                 and id in (SELECT ProbeSetXRef.DataId
@@ -714,9 +717,10 @@ class DataSet:
                 and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
 
         query_results = list(g.db.execute(query).fetchall())
-
         data_results = self.chunk_dataset(query_results, len(sample_ids))
+        self.samplelist = sorted_samplelist
         self.trait_data = data_results
+        
 
     def get_trait_data(self, sample_list=None):
         if sample_list:
-- 
cgit v1.2.3


From beea9ac15e531c32b2368e04261e521d8a03c8c8 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 00:54:55 +0300
Subject: minor refactoring

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 7 -------
 1 file changed, 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 5fa33027..d0ee7a8b 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -146,11 +146,7 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     sample_data = process_samples(
         start_vars, this_dataset.group.samplelist)
-
-    # sample_data = test_process_data(this_trait,this_dataset,start_vars)
-
     if target_dataset.type == "ProbeSet":
-        # pass
         target_dataset.get_probeset_data(list(sample_data.keys()))
     else:
         target_dataset.get_trait_data(list(sample_data.keys()))
@@ -159,9 +155,6 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
         "trait_sample_data": sample_data,
         "trait_id": start_vars["trait_id"]
     }
-
-    # should remove this  len(samplelist) == len(strain_values)
-
     results = map_shared_keys_to_values(
         target_dataset.samplelist, target_dataset.trait_data)
 
-- 
cgit v1.2.3


From c499f3418efe0a8bdb8e4800426ed6a06f9bb579 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 01:15:11 +0300
Subject: add f1list and parlist to primary_samples

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 4 ++++
 1 file changed, 4 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index d0ee7a8b..86531fa2 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -146,6 +146,10 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     sample_data = process_samples(
         start_vars, this_dataset.group.samplelist)
+
+    sample_data = test_process_data(this_trait, this_dataset, start_vars)
+
+
     if target_dataset.type == "ProbeSet":
         target_dataset.get_probeset_data(list(sample_data.keys()))
     else:
-- 
cgit v1.2.3


From 8521ba973ccf14b6918948a93cfde07d6cf1e27a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 09:28:46 +0300
Subject: delete loggers and comments

---
 wqflask/base/data_set.py | 4 ----
 1 file changed, 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 991c9fee..4cb82665 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -440,7 +440,6 @@ class DatasetGroup:
         # genotype_1 is Dataset Object without parents and f1
         # genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
-        # genotype_1 = reaper.Dataset()
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         if self.genofile:
@@ -1128,7 +1127,6 @@ class MrnaAssayDataSet(DataSet):
             """ % (escape(str(this_trait.dataset.id)),
                    escape(this_trait.name)))
 
-            # logger.debug("query is:", pf(query))
             logger.sql(query)
             result = g.db.execute(query).fetchone()
 
@@ -1183,7 +1181,6 @@ class MrnaAssayDataSet(DataSet):
                     """ % (escape(trait), escape(self.name))
         logger.sql(query)
         results = g.db.execute(query).fetchall()
-        # logger.debug("RETRIEVED RESULTS HERE:", results)
         return results
 
     def retrieve_genes(self, column_name):
@@ -1224,7 +1221,6 @@ class TempDataSet(DataSet):
 
 def geno_mrna_confidentiality(ob):
     dataset_table = ob.type + "Freeze"
-    # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
 
     query = '''SELECT Id, Name, FullName, confidentiality,
                         AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
-- 
cgit v1.2.3


From fafce2f44087edf51756f0118054d1e3aa654273 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 19:21:11 +0000
Subject: Re-enable bicor for correlations and fix issue where ro.Vector needed
 to be changed to ro.FloatVector

---
 wqflask/wqflask/correlation/show_corr_results.py | 30 ++++++++++++------------
 1 file changed, 15 insertions(+), 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 2f3df67a..f1cf3733 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -22,7 +22,7 @@ import collections
 import json
 import scipy
 import numpy
-# import rpy2.robjects as ro                    # R Objects
+import rpy2.robjects as ro                    # R Objects
 import utility.logger
 import utility.webqtlUtil
 
@@ -459,9 +459,9 @@ class CorrelationResults:
 
         if num_overlap > 5:
             # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
-            # if self.corr_method == 'bicor':
-            #     sample_r, sample_p = do_bicor(
-            #         self.this_trait_vals, target_vals)
+            if self.corr_method == 'bicor':
+                sample_r, sample_p = do_bicor(
+                    self.this_trait_vals, target_vals)
             if self.corr_method == 'pearson':
                 sample_r, sample_p = scipy.stats.pearsonr(
                     self.this_trait_vals, target_vals)
@@ -487,22 +487,22 @@ class CorrelationResults:
                     self.sample_data[str(sample)] = float(value)
 
 
-# def do_bicor(this_trait_vals, target_trait_vals):
-#     r_library = ro.r["library"]             # Map the library function
-#     r_options = ro.r["options"]             # Map the options function
+def do_bicor(this_trait_vals, target_trait_vals):
+    r_library = ro.r["library"]             # Map the library function
+    r_options = ro.r["options"]             # Map the options function
 
-#     r_library("WGCNA")
-#     r_bicor = ro.r["bicorAndPvalue"]        # Map the bicorAndPvalue function
+    r_library("WGCNA")
+    r_bicor = ro.r["bicorAndPvalue"]        # Map the bicorAndPvalue function
 
-#     r_options(stringsAsFactors=False)
+    r_options(stringsAsFactors=False)
 
-#     this_vals = ro.Vector(this_trait_vals)
-#     target_vals = ro.Vector(target_trait_vals)
+    this_vals = ro.FloatVector(this_trait_vals)
+    target_vals = ro.FloatVector(target_trait_vals)
 
-#     the_r, the_p, _fisher_transform, _the_t, _n_obs = [
-#         numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
+    the_r, the_p, _fisher_transform, _the_t, _n_obs = [
+        numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
 
-#     return the_r, the_p
+    return the_r, the_p
 
 
 def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
-- 
cgit v1.2.3


From df8476115e580fa5dfbf0e2e9a8f6e5e39ae7b99 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 19:21:30 +0000
Subject: Reenable PCA for correlation matrix

---
 .../wqflask/correlation_matrix/show_corr_matrix.py | 124 +++++++++++----------
 1 file changed, 63 insertions(+), 61 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 9ac02ac5..e7b16e77 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -23,6 +23,9 @@ import math
 import random
 import string
 
+import rpy2.robjects as ro
+from rpy2.robjects.packages import importr
+
 import numpy as np
 import scipy
 
@@ -160,23 +163,22 @@ class CorrelationMatrix:
         for sample in self.all_sample_list:
             groups.append(1)
 
-        # Not doing PCA until rpy2 is excised
         self.pca_works = "False"
-        # try:
-        #     corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results))
-        #     corr_eigen_value, corr_eigen_vectors = sortEigenVectors(
-        #         corr_result_eigen)
-
-        #     if self.do_PCA == True:
-        #         self.pca_works = "True"
-        #         self.pca_trait_ids = []
-        #         pca = self.calculate_pca(
-        #             list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors)
-        #         self.loadings_array = self.process_loadings()
-        #     else:
-        #         self.pca_works = "False"
-        # except:
-        #     self.pca_works = "False"
+        try:
+            corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results))
+            corr_eigen_value, corr_eigen_vectors = sortEigenVectors(
+                corr_result_eigen)
+
+            if self.do_PCA == True:
+                self.pca_works = "True"
+                self.pca_trait_ids = []
+                pca = self.calculate_pca(
+                    list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors)
+                self.loadings_array = self.process_loadings()
+            else:
+                self.pca_works = "False"
+        except:
+            self.pca_works = "False"
 
         self.js_data = dict(traits=[trait.name for trait in self.traits],
                             groups=groups,
@@ -185,51 +187,51 @@ class CorrelationMatrix:
                             samples=self.all_sample_list,
                             sample_data=self.sample_data,)
 
-    # def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
-    #     base = importr('base')
-    #     stats = importr('stats')
-
-    #     corr_results_to_list = robjects.FloatVector(
-    #         [item for sublist in self.pca_corr_results for item in sublist])
-
-    #     m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
-    #     eigen = base.eigen(m)
-    #     pca = stats.princomp(m, cor="TRUE")
-    #     self.loadings = pca.rx('loadings')
-    #     self.scores = pca.rx('scores')
-    #     self.scale = pca.rx('scale')
-
-    #     trait_array = zScore(self.trait_data_array)
-    #     trait_array_vectors = np.dot(corr_eigen_vectors, trait_array)
-
-    #     pca_traits = []
-    #     for i, vector in enumerate(trait_array_vectors):
-    #         # ZS: Check if below check is necessary
-    #         # if corr_eigen_value[i-1] > 100.0/len(self.trait_list):
-    #         pca_traits.append((vector * -1.0).tolist())
-
-    #     this_group_name = self.trait_list[0][1].group.name
-    #     temp_dataset = data_set.create_dataset(
-    #         dataset_name="Temp", dataset_type="Temp", group_name=this_group_name)
-    #     temp_dataset.group.get_samplelist()
-    #     for i, pca_trait in enumerate(pca_traits):
-    #         trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
-    #             this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
-    #         this_vals_string = ""
-    #         position = 0
-    #         for sample in temp_dataset.group.all_samples_ordered():
-    #             if sample in self.shared_samples_list:
-    #                 this_vals_string += str(pca_trait[position])
-    #                 this_vals_string += " "
-    #                 position += 1
-    #             else:
-    #                 this_vals_string += "x "
-    #         this_vals_string = this_vals_string[:-1]
-
-    #         Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS)
-    #         self.pca_trait_ids.append(trait_id)
-
-    #     return pca
+    def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
+        base = importr('base')
+        stats = importr('stats')
+
+        corr_results_to_list = ro.FloatVector(
+            [item for sublist in self.pca_corr_results for item in sublist])
+
+        m = ro.r.matrix(corr_results_to_list, nrow=len(cols))
+        eigen = base.eigen(m)
+        pca = stats.princomp(m, cor="TRUE")
+        self.loadings = pca.rx('loadings')
+        self.scores = pca.rx('scores')
+        self.scale = pca.rx('scale')
+
+        trait_array = zScore(self.trait_data_array)
+        trait_array_vectors = np.dot(corr_eigen_vectors, trait_array)
+
+        pca_traits = []
+        for i, vector in enumerate(trait_array_vectors):
+            # ZS: Check if below check is necessary
+            # if corr_eigen_value[i-1] > 100.0/len(self.trait_list):
+            pca_traits.append((vector * -1.0).tolist())
+
+        this_group_name = self.trait_list[0][1].group.name
+        temp_dataset = data_set.create_dataset(
+            dataset_name="Temp", dataset_type="Temp", group_name=this_group_name)
+        temp_dataset.group.get_samplelist()
+        for i, pca_trait in enumerate(pca_traits):
+            trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
+                this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
+            this_vals_string = ""
+            position = 0
+            for sample in temp_dataset.group.all_samples_ordered():
+                if sample in self.shared_samples_list:
+                    this_vals_string += str(pca_trait[position])
+                    this_vals_string += " "
+                    position += 1
+                else:
+                    this_vals_string += "x "
+            this_vals_string = this_vals_string[:-1]
+
+            Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS)
+            self.pca_trait_ids.append(trait_id)
+
+        return pca
 
     def process_loadings(self):
         loadings_array = []
-- 
cgit v1.2.3


From f314728334fde0677ea515b5910db86086fdd5ef Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 19:21:54 +0000
Subject: Re-enable bicor as an option in the trait page templatee

---
 wqflask/wqflask/templates/show_trait_calculate_correlations.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index e623a968..59f9b47c 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -70,7 +70,7 @@
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
-                    <!-- <option value="bicor">Biweight Midcorrelation</option> -->
+                    <option value="bicor">Biweight Midcorrelation</option>
                 </select>
             </div>
         </div>
-- 
cgit v1.2.3


From 31ad8698fe69da8d13c7a67cbf7e7ddeda67a734 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 5 Jan 2021 16:10:25 -0600
Subject: Added Scroller to mapping results table

---
 wqflask/wqflask/templates/mapping_results.html | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index d6fc6e37..35d8a157 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -357,7 +357,9 @@
     {% endif %}
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
-   <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script>
@@ -409,13 +411,12 @@
                   "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records",
                 },
                 "order": [[1, "asc" ]],
-                "sDom": "iRZtir",
-                "iDisplayLength": -1,
-                "autoWidth": false,
-                "deferRender": true,
+                "sDom": "itir",
+                "autoWidth": true,
                 "bSortClasses": false,
-                "scrollCollapse": false,
-                "paging": false
+                "scrollY": "100vh",
+                "scroller":  true,
+                "scrollCollapse": true
             } );
             {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
             $('#trait_table').dataTable( {
-- 
cgit v1.2.3


From 116f911561dc81565dc0f77c12e901c0d53de4e5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 5 Jan 2021 16:10:45 -0600
Subject: Changed limit from 2000 markers to 10000 markers for the number to
 show in mapping results table

---
 wqflask/wqflask/marker_regression/run_mapping.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c5b980a7..f601201b 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -673,9 +673,9 @@ def trim_markers_for_table(markers):
         sorted_markers = sorted(
             markers, key=lambda k: k['lrs_value'], reverse=True)
 
-    # ZS: So we end up with a list of just 2000 markers
-    if len(sorted_markers) >= 2000:
-        trimmed_sorted_markers = sorted_markers[:2000]
+    #ZS: So we end up with a list of just 2000 markers
+    if len(sorted_markers) >= 10000:
+        trimmed_sorted_markers = sorted_markers[:10000]
         return trimmed_sorted_markers
     else:
         return sorted_markers
-- 
cgit v1.2.3


From bab4e72f657eef01934dc7a1645dce6d3035c3fd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 1 Jul 2021 18:41:45 +0000
Subject: Fixed bug where there'd be an error if the max boot count is 0 for a
 chromosome

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index ec17d3b0..2d74ea52 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -861,6 +861,9 @@ class DisplayMappingResults:
                             (item[1], yZero - item[2] * bootHeightThresh / maxBootCount)),
                         fill=self.BOOTSTRAP_BOX_COLOR, outline=BLACK)
 
+        if maxBootCount == 0:
+            return
+
         # draw boot scale
         highestPercent = (maxBootCount * 100.0) / nboot
         bootScale = Plot.detScale(0, highestPercent)
-- 
cgit v1.2.3


From 323c52ff746dab78a2edc343958a81e0ac1b22a5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 1 Jul 2021 20:59:47 +0000
Subject: Fixed issue where zooming into chromosome 1 was causing the Y axis
 scaling to be bad

---
 .../marker_regression/display_mapping_results.py        | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 2d74ea52..dfae4065 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2289,20 +2289,9 @@ class DisplayMappingResults:
             font=VERDANA_FILE, size=int(18 * zoom * 1.5))
 
         yZero = yTopOffset + plotHeight
-        # LRSHeightThresh = drawAreaHeight
-        # AdditiveHeightThresh = drawAreaHeight/2
-        # DominanceHeightThresh = drawAreaHeight/2
-        if self.selectedChr == 1:
-            LRSHeightThresh = drawAreaHeight - yTopOffset + 30 * (zoom - 1)
-            AdditiveHeightThresh = LRSHeightThresh / 2
-            DominanceHeightThresh = LRSHeightThresh / 2
-        else:
-            LRSHeightThresh = drawAreaHeight
-            AdditiveHeightThresh = drawAreaHeight / 2
-            DominanceHeightThresh = drawAreaHeight / 2
-        # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1))
-        # AdditiveHeightThresh = LRSHeightThresh/2
-        # DominanceHeightThresh = LRSHeightThresh/2
+        LRSHeightThresh = drawAreaHeight
+        AdditiveHeightThresh = drawAreaHeight / 2
+        DominanceHeightThresh = drawAreaHeight / 2
 
         if LRS_LOD_Max > 100:
             LRSScale = 20.0
-- 
cgit v1.2.3


From d4c990beaf72dd885d6baa7dc1035a7044c79cdd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 1 Jul 2021 21:28:10 +0000
Subject: Fixed issue where the interval map QTL line might extend beyond the
 graph edge when zoomed into a Mb range + removed some commented out code

---
 .../marker_regression/display_mapping_results.py     | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index dfae4065..1fcc2832 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2561,7 +2561,10 @@ class DisplayMappingResults:
                                 Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (
                                     ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale))
                 else:
-                    Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale
+                    if qtlresult['Mb'] > endMb:
+                        Xc = startPosX + endMb * plotXScale
+                    else:
+                        Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale
 
                 # updated by NL 06-18-2011:
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
@@ -2572,36 +2575,29 @@ class DisplayMappingResults:
                 if 'lrs_value' in qtlresult:
                     if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
                         if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
-                            #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
                             Yc = yZero - webqtlConfig.MAXLRS * \
                                 LRSHeightThresh / \
                                 (LRS_LOD_Max * self.LODFACTOR)
                         else:
-                            #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
                             Yc = yZero - \
                                 qtlresult['lrs_value'] * LRSHeightThresh / \
                                 (LRS_LOD_Max * self.LODFACTOR)
                     else:
                         if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
-                            #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
                             Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max
                         else:
-                            #Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1]
                             Yc = yZero - \
                                 qtlresult['lrs_value'] * \
                                 LRSHeightThresh / LRS_LOD_Max
                 else:
                     if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf':
-                        #Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
                         Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max
                     else:
                         if self.LRS_LOD == "LRS":
-                            #Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1]
                             Yc = yZero - \
                                 qtlresult['lod_score'] * self.LODFACTOR * \
                                 LRSHeightThresh / LRS_LOD_Max
                         else:
-                            #Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1]
                             Yc = yZero - \
                                 qtlresult['lod_score'] * \
                                 LRSHeightThresh / LRS_LOD_Max
@@ -2634,14 +2630,12 @@ class DisplayMappingResults:
                         AdditiveHeightThresh / additiveMax
                     AdditiveCoordXY.append((Xc, Yc))
 
+                if qtlresult['Mb'] > endMb:
+                    break
+
                 m += 1
 
         if self.manhattan_plot != True:
-            # im_drawer.polygon(
-            #     xy=LRSCoordXY,
-            #     outline=thisLRSColor
-            #     #, closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth)
-            # )
             draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor,
                               width=lrsEdgeWidth)
 
-- 
cgit v1.2.3


From 74c1d6a6ef070271adaf486fc9a494662855d96f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 1 Jul 2021 21:40:24 +0000
Subject: Fixed issue with suggestive/significant lines extending beyond figure
 edge + fixed a couple issues with the last commit

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 1fcc2832..f941267e 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2372,8 +2372,7 @@ class DisplayMappingResults:
 
             # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
             def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
-                rightEdge = int(start_pos_x + chr_length_dist * \
-                                plotXScale - self.SUGGESTIVE_WIDTH / 1.5)
+                rightEdge = xLeftOffset + plotWidth
                 im_drawer.line(
                     xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY),
                         (rightEdge, suggestiveY)),
@@ -2561,7 +2560,7 @@ class DisplayMappingResults:
                                 Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (
                                     ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale))
                 else:
-                    if qtlresult['Mb'] > endMb:
+                    if self.selectedChr != -1 and qtlresult['Mb'] > endMb:
                         Xc = startPosX + endMb * plotXScale
                     else:
                         Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale
@@ -2630,7 +2629,7 @@ class DisplayMappingResults:
                         AdditiveHeightThresh / additiveMax
                     AdditiveCoordXY.append((Xc, Yc))
 
-                if qtlresult['Mb'] > endMb:
+                if self.selectedChr != -1 and qtlresult['Mb'] > endMb:
                     break
 
                 m += 1
-- 
cgit v1.2.3


From bc2869179f2483d9ad5995d3abb0c9dbc1024acd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 3 Jul 2021 20:44:41 +0000
Subject: Increased width of mapping options div and covariates window

---
 wqflask/wqflask/static/new/css/show_trait.css | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 27404801..782dabc2 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -159,10 +159,10 @@ div.normalize-div {
 }
 
 div.mapping-main {
-  min-width: 1200px;
+  min-width: 1400px;
 }
 div.mapping-options {
-  min-width: 500px;
+  min-width: 700px;
 }
 
 div.covar-options {
@@ -194,7 +194,7 @@ div.select-covar-div {
 .selected-covariates {
   overflow-y: scroll;
   resize: none;
-  width: 200px;
+  width: 400px;
 }
 
 .cofactor-input {
@@ -259,4 +259,4 @@ input.trait-value-input {
 
 div.inline-div {
   display: inline;
-}
\ No newline at end of file
+}
-- 
cgit v1.2.3


From 4d96be02f3127564ee64b0783b518ccd2c234563 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 6 Jul 2021 21:09:11 +0300
Subject: fix gn2 links

---
 wqflask/wqflask/templates/base.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 12dddf89..049ebe6d 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -208,7 +208,7 @@
                     <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a>
             </p>
             <p>
-            Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <span class="broken_link" href="https://webchat.freenode.net/">IRC</span> (#genenetwork channel).
+            Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <span class="broken_link" href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</span> and find us on <a href="https://webchat.freenode.net#genenetwork">IRC</a> (#genenetwork channel).
             {% if version: %}
             <p><small>GeneNetwork {{ version }}</small></p>
             {% endif %}
-- 
cgit v1.2.3


From 3a9ef933faec1f14560b1f6ced9fcd4413089770 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 6 Jul 2021 21:10:20 +0300
Subject: replace rpy2 for tissue corr

---
 .../correlation/test_correlation_functions.py      | 20 +++++++++++
 .../wqflask/correlation/correlation_functions.py   | 39 +++++-----------------
 wqflask/wqflask/correlation/show_corr_results.py   |  3 +-
 3 files changed, 30 insertions(+), 32 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 2bbeab1f..a8cf6006 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -1,10 +1,30 @@
+"""module contains tests for correlation functions"""
+
 import unittest
 from unittest import mock
+
 from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
 from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
 
 
 class TestCorrelationFunctions(unittest.TestCase):
+    """test for correlation helper functions"""
+
+    @mock.patch("wqflask.correlation.correlation_functions.compute_corr_coeff_p_value")
+    def test_tissue_corr_computation(self, mock_tiss_corr_computation):
+        """test for cal_zero_order_corr_for_tiss"""
+
+        primary_values = [9.288, 9.313, 8.988, 9.660, 8.21]
+        target_values = [9.586, 8.498, 9.362, 8.820, 8.786]
+
+        mock_tiss_corr_computation.return_value = (0.51, 0.7)
+
+        results = cal_zero_order_corr_for_tiss(primary_values, target_values)
+        mock_tiss_corr_computation.assert_called_once_with(
+            primary_values=primary_values, target_values=target_values,
+            corr_method="pearson")
+
+        self.assertEqual(len(results), 3)
 
     @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
     def test_get_trait_symbol_and_tissue_values(self, mock_class):
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index c8b9da0e..85b25d60 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -21,15 +21,10 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 #
 # Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by NL 2011/03/23
 
-import math
-import string
 
 from base.mrna_assay_tissue_data import MrnaAssayTissueData
-
-from flask import Flask, g
+from gn3.computations.correlations import compute_corr_coeff_p_value
 
 
 #####################################################################################
@@ -45,31 +40,14 @@ from flask import Flask, g
 # the same tissue order
 #####################################################################################
 
-def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearson'):
-
-    N = len(primaryValue)
-    # R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue))))
-    # for i in range(len(primaryValue)):
-    #     R_primary[i] = primaryValue[i]
 
-    # R_target = rpy2.robjects.FloatVector(list(range(len(targetValue))))
-    # for i in range(len(targetValue)):
-    #     R_target[i] = targetValue[i]
+def cal_zero_order_corr_for_tiss(primary_values, target_values, method="pearson"):
+    """function use calls gn3 to compute corr,p_val"""
 
-    # R_corr_test = rpy2.robjects.r['cor.test']
-    # if method == 'spearman':
-    #     R_result = R_corr_test(R_primary, R_target, method='spearman')
-    # else:
-    #     R_result = R_corr_test(R_primary, R_target)
-
-    # corr_result = []
-    # corr_result.append(R_result[3][0])
-    # corr_result.append(N)
-    # corr_result.append(R_result[2][0])
-
-    return [None, N, None]
-    # return corr_result
+    (corr_coeff, p_val) = compute_corr_coeff_p_value(
+        primary_values=primary_values, target_values=target_values, corr_method=method)
 
+    return (corr_coeff, len(primary_values), p_val)
 
 ########################################################################################################
 # input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
@@ -80,8 +58,9 @@ def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearso
 #          then call getSymbolValuePairDict function and merge the results.
 ########################################################################################################
 
+
 def get_trait_symbol_and_tissue_values(symbol_list=None):
     tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
-    if len(tissue_data.gene_symbols) >0:
+    if len(tissue_data.gene_symbols) > 0:
         results = tissue_data.get_symbol_values_pairs()
-        return results 
+        return results
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index f1cf3733..b0496bfe 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -34,6 +34,7 @@ from utility import corr_result_helpers
 from utility import hmac
 
 from wqflask.correlation import correlation_functions
+
 from utility.benchmark import Bench
 
 from utility.type_checking import is_str
@@ -93,7 +94,6 @@ class CorrelationResults:
             self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
             self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
-
             if ('loc_chr' in start_vars
                 and 'min_loc_mb' in start_vars
                     and 'max_loc_mb' in start_vars):
@@ -198,7 +198,6 @@ class CorrelationResults:
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
-
                 if (float(self.correlation_data[trait][0]) >= self.p_range_lower
                         and float(self.correlation_data[trait][0]) <= self.p_range_upper):
 
-- 
cgit v1.2.3


From 9080fa91f072956fb0137e36b9ef1b45e7e03e34 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 9 Jul 2021 21:32:38 +0000
Subject: Changed compute_corr_for_top_results to also do sample correlation
 when literature or tissue correlation are selected

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 86531fa2..aea91220 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -227,8 +227,8 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
     correlation_results = correlation_results[0:corr_return_results]
 
     if (compute_all):
-
-        correlation_results = compute_corr_for_top_results(correlation_results,
+        correlation_results = compute_corr_for_top_results(start_vars,
+                                                           correlation_results,
                                                            this_trait,
                                                            this_dataset,
                                                            target_dataset,
@@ -242,7 +242,8 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
     return correlation_data
 
 
-def compute_corr_for_top_results(correlation_results,
+def compute_corr_for_top_results(start_vars,
+                                 correlation_results,
                                  this_trait,
                                  this_dataset,
                                  target_dataset,
@@ -265,8 +266,12 @@ def compute_corr_for_top_results(correlation_results,
             correlation_results = merge_correlation_results(
                 correlation_results, lit_result)
 
-    if corr_type != "sample":
-        pass
+    if corr_type != "sample" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet":
+        sample_result = sample_for_trait_lists(
+            correlation_results, target_dataset, this_trait, this_dataset, start_vars)
+        if sample_result:
+            correlation_results = merge_correlation_results(
+                correlation_results, sample_result)
 
     return correlation_results
 
-- 
cgit v1.2.3


From fd726da54c9e65c0721de6f8181c2dde93831a7a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 9 Jul 2021 21:35:13 +0000
Subject: Only show literature and tissue correlation options if the trait's
 dataset is type ProbeSet

---
 wqflask/wqflask/templates/show_trait_calculate_correlations.html | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index e623a968..ffbe313c 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -7,8 +7,10 @@
             <div class="col-xs-3 controls">
                 <select name="corr_type" class="form-control">
                     <option value="sample">Sample r</option>
+                    {% if dataset.type == 'ProbeSet' %}
                     <option value="lit">Literature r</option>
                     <option value="tissue">Tissue r</option>
+                    {% endif %}
                 </select>
             </div>
         </div>
-- 
cgit v1.2.3


From 8dcb6972e4be972a37defdf96415fda7ffaac3db Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 9 Jul 2021 21:41:11 +0000
Subject: Remove commented out function do_bicor

---
 wqflask/wqflask/correlation/show_corr_results.py | 17 -----------------
 1 file changed, 17 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 91716a6a..bebef9e7 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -158,23 +158,6 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
 
     return json.dumps(results_list)
 
-# def do_bicor(this_trait_vals, target_trait_vals):
-#     r_library = ro.r["library"]             # Map the library function
-#     r_options = ro.r["options"]             # Map the options function
-
-#     r_library("WGCNA")
-#     r_bicor = ro.r["bicorAndPvalue"]        # Map the bicorAndPvalue function
-
-#     r_options(stringsAsFactors=False)
-
-#     this_vals = ro.Vector(this_trait_vals)
-#     target_vals = ro.Vector(target_trait_vals)
-
-#     the_r, the_p, _fisher_transform, _the_t, _n_obs = [
-#         numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
-
-#     return the_r, the_p
-
 
 def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
     results_list = []
-- 
cgit v1.2.3


From af6b141ac37dbc38f990a871e61127d1efde10ce Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 6 Jul 2021 14:13:43 +0300
Subject: wqflask: views: Rename endpoint for editing a trait

* wqflask/wqflask/views.py (edit_trait): Rename to
edit_phenotype. Also rename the endpoint to
"/trait/<name>/edit/inbredset-id/<inbred_set_id>" to indicate that and
inbredset-id is required. This endpoint will be only used for
phenotypes. Finally, render the "edit_phenotype.html" template
(update_trait): Rename to update_phenotype. Also, remove hard-coded
redirect, and replace it with the correct values.

* wqflask/wqflask/templates/edit_trait.html: Rename to
edit_phenotype.html
---
 wqflask/wqflask/templates/edit_phenotype.html | 234 ++++++++++++++++++++++++++
 wqflask/wqflask/templates/edit_trait.html     | 234 --------------------------
 wqflask/wqflask/views.py                      |  11 +-
 3 files changed, 240 insertions(+), 239 deletions(-)
 create mode 100644 wqflask/wqflask/templates/edit_phenotype.html
 delete mode 100644 wqflask/wqflask/templates/edit_trait.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
new file mode 100644
index 00000000..7d4c65f8
--- /dev/null
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -0,0 +1,234 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+Edit Trait for Published Database
+Submit Trait | Reset
+
+{% if diff %}
+
+<div class="container">
+    <details class="col-sm-12 col-md-10 col-lg-12">
+    <summary>
+        <h2>Update History</h2>
+    </summary>
+    <table class="table">
+    <tbody>
+        <tr>
+            <th>Timestamp</th>
+            <th>Editor</th>
+            <th>Field</th>
+            <th>Diff</th>
+        </tr>
+        {% set ns = namespace(display_cell=True) %}
+
+        {% for timestamp, group in diff %}
+        {% set ns.display_cell = True %}
+        {% for i in group %}
+        <tr>
+            {% if ns.display_cell and i.timestamp == timestamp %}
+            
+            {% set author = i.author %}
+            {% set timestamp_ = i.timestamp %}
+
+            {% else %}
+
+            {% set author = "" %}
+            {% set timestamp_ = "" %}
+
+            {% endif %}
+            <td>{{ timestamp_ }}</td>
+	    <td>{{ author }}</td>
+	    <td>{{ i.diff.field }}</td>
+            <td><pre>{{ i.diff.diff }}</pre></td>                
+            {% set ns.display_cell = False %}
+	</tr>
+        {% endfor %}
+        {% endfor %}
+    </tbody>
+    </table>
+    </details>
+
+</div>
+
+{% endif %}
+
+<form id="edit-form" class="form-horizontal" method="post" action="/trait/update">
+    <h2 class="text-center">Trait Information:</h2>
+    <div class="form-group">
+        <label for="pubmed-id" class="col-sm-2 control-label">Pubmed ID:</label>
+        <!-- Do not enter PubMed_ID if this trait has not been Published.
+             If the PubMed_ID you entered is alreday stored in our
+             database, all the following fields except Post Publication
+             Description will be ignored.  Do not enter any non-digit
+             character in this field. -->
+        <div class="col-sm-8">
+            <textarea name="pubmed-id" class="form-control" rows="1">{{ publish_xref.publication_id |default('', true) }}</textarea>
+            <input name="old_id_" class="changed" type="hidden" value="{{ publish_xref.publication_id |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="pre-pub-desc" class="col-sm-2 control-label">Pre Publication Description:</label>
+        <div class="col-sm-8">
+            <textarea name="pre-pub-desc" class="form-control" rows="4">{{ phenotype.pre_pub_description |default('', true) }}</textarea>
+            <input name="old_pre_pub_description" class="changed" type="hidden" value="{{ phenotype.pre_pub_description |default('', true) }}"/>
+        </div>
+        <!-- If the PubMed ID is entered, the Post Publication Description
+             will be shown to all users. If there is no PubMed ID, and the
+             Pre Publication Description is entered, only you and
+             authorized users can see the Post Publication Description -->
+    </div>
+    <div class="form-group">
+        <label for="post-pub-desc" class="col-sm-2 control-label">Post Publication Description:</label>
+        <div class="col-sm-8">
+            <textarea name="post-pub-desc" class="form-control" rows="4">{{ phenotype.post_pub_description |default('', true) }}</textarea>
+            <input name="old_post_pub_description" class="changed" type="hidden" value="{{ phenotype.post_pub_description |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="orig-desc" class="col-sm-2 control-label">Original Description:</label>
+        <div class="col-sm-8">
+            <textarea name="orig-desc" class="form-control" rows="4">{{ phenotype.original_description |default('', true) }}</textarea>
+            <input name="old_original_description" class="changed" type="hidden" value="{{ phenotype.original_description |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="units" class="col-sm-2 control-label">Units:</label>
+        <div class="col-sm-8">
+            <textarea name="units" class="form-control" rows="1">{{ phenotype.units |default('', true) }}</textarea>
+            <input name="old_units" class="changed" type="hidden" value="{{ phenotype.units |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="pre-pub-abbrev" class="col-sm-2 control-label">
+            Pre Publication Abbreviation:
+        </label>
+        <div class="col-sm-8">
+            <textarea name="pre-pub-abbrev" class="form-control" rows="1">{{ phenotype.pre_pub_abbreviation |default('', true) }}</textarea>
+            <input name="old_pre_pub_abbreviation" class="changed" type="hidden" value="{{ phenotype.pre_pub_abbreviation |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="post-pub-abbrev" class="col-sm-2 control-label">
+            Post Publication Abbreviation:
+        </label>
+        <div class="col-sm-8">
+            <textarea name="post-pub-abbrev" class="form-control" rows="1">{{ phenotype.post_pub_abbreviation |default('', true) }}</textarea>
+            <input name="old_post_pub_abbreviation" class="changed" type="hidden" value="{{ phenotype.post_pub_abbreviation |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="labcode" class="col-sm-2 control-label">
+            Lab Code:
+        </label>
+        <div class="col-sm-8">
+            <textarea name="labcode" class="form-control" rows="1">{{ phenotype.lab_code |default('', true) }}</textarea>
+            <input name="old_lab_code" class="changed" type="hidden" value="{{ phenotype.lab_code |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="submitter" class="col-sm-2 control-label">
+            Submitter:
+        </label>
+        <div class="col-sm-8">
+            <textarea name="submitter" class="form-control" rows="1">{{ phenotype.submitter |default('', true) }}</textarea>
+            <input name="old_submitter" class="changed" type="hidden" value="{{ phenotype.submitter |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="owner" class="col-sm-2 control-label">Owner:</label>
+        <div class="col-sm-8">
+            <textarea name="owner" class="form-control" rows="1">{{ phenotype.owner |default('', true) }}</textarea>
+            <input name="old_owner" class="changed" type="hidden" value="{{ phenotype.owner |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="authorized-users" class="col-sm-2 control-label">
+            Authorized Users:
+        </label>
+        <div class="col-sm-8">
+            <textarea name="authorized-users" class="form-control" rows="1">{{ phenotype.authorized_users |default('', true) }}</textarea>
+            <input name="old_authorized_users" class="changed" type="hidden" value="{{ phenotype.authorized_users |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="authors" class="col-sm-2 control-label">Authors:</label>
+        <div class="col-sm-8">
+            <textarea name="authors" class="form-control" rows="2">{{ publication.authors |default('', true) }}</textarea>
+            <input name="old_authors" class="changed" type="hidden" value="{{ publication.authors |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="title" class="col-sm-2 control-label">Title:</label>
+        <div class="col-sm-8">
+            <textarea name="title" class="form-control" rows="2">{{ publication.title |default('', true) }}</textarea>
+            <input name="old_title" class="changed" type="hidden" value="{{ publication.title |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="abstract" class="col-sm-2 control-label">Abstract:</label>
+        <div class="col-sm-8">
+            <textarea name="abstract" class="form-control" rows="6">{{ publication.abstract |default('', true) }}</textarea>
+            <input name="old_abstract" class="changed" type="hidden" value="{{ publication.abstract |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="journal" class="col-sm-2 control-label">Journal:</label>
+        <div class="col-sm-8">
+            <textarea name="journal" class="form-control" rows="1">{{ publication.journal |default('', true) }}</textarea>
+            <input name="old_journal" class="changed" type="hidden" value="{{ publication.journal_ |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="pages" class="col-sm-2 control-label">Pages:</label>
+        <div class="col-sm-8">
+            <textarea name="pages" class="form-control" rows="1">{{ publication.pages |default('', true) }}</textarea>
+            <input name="old_pages" class="changed" type="hidden" value="{{ publication.pages |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="month" class="col-sm-2 control-label">Month:</label>
+        <div class="col-sm-8">
+            <textarea name="month" class="form-control" rows="1">{{ publication.month |default('', true) }}</textarea>
+            <input name="old_month" class="changed" type="hidden" value="{{ publication.month |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="year" class="col-sm-2 control-label">Year:</label>
+        <div class="col-sm-8">
+            <textarea name="year" class="form-control" rows="1">{{ publication.year |default('', true) }}</textarea>
+            <input name="old_year" class="changed" type="hidden" value="{{ publication.year |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="sequence" class="col-sm-2 control-label">Sequence:</label>
+        <div class="col-sm-8">
+            <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
+            <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+        <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/>
+        <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/>
+        <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/>
+        <input name="comments" class="changed" type="hidden" value="{{ publish_xref.comments }}"/>
+        <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
+        <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
+    </div>
+</form>
+
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+ function MarkAsChanged(){
+     $(this).addClass("changed");
+ }
+ $(":input").blur(MarkAsChanged).change(MarkAsChanged);
+
+ $("input[type=submit]").click(function(){
+     $(":input:not(.changed)").attr("disabled", "disabled");
+ });
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/edit_trait.html b/wqflask/wqflask/templates/edit_trait.html
deleted file mode 100644
index 7d4c65f8..00000000
--- a/wqflask/wqflask/templates/edit_trait.html
+++ /dev/null
@@ -1,234 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Trait Submission{% endblock %}
-{% block content %}
-<!-- Start of body -->
-Edit Trait for Published Database
-Submit Trait | Reset
-
-{% if diff %}
-
-<div class="container">
-    <details class="col-sm-12 col-md-10 col-lg-12">
-    <summary>
-        <h2>Update History</h2>
-    </summary>
-    <table class="table">
-    <tbody>
-        <tr>
-            <th>Timestamp</th>
-            <th>Editor</th>
-            <th>Field</th>
-            <th>Diff</th>
-        </tr>
-        {% set ns = namespace(display_cell=True) %}
-
-        {% for timestamp, group in diff %}
-        {% set ns.display_cell = True %}
-        {% for i in group %}
-        <tr>
-            {% if ns.display_cell and i.timestamp == timestamp %}
-            
-            {% set author = i.author %}
-            {% set timestamp_ = i.timestamp %}
-
-            {% else %}
-
-            {% set author = "" %}
-            {% set timestamp_ = "" %}
-
-            {% endif %}
-            <td>{{ timestamp_ }}</td>
-	    <td>{{ author }}</td>
-	    <td>{{ i.diff.field }}</td>
-            <td><pre>{{ i.diff.diff }}</pre></td>                
-            {% set ns.display_cell = False %}
-	</tr>
-        {% endfor %}
-        {% endfor %}
-    </tbody>
-    </table>
-    </details>
-
-</div>
-
-{% endif %}
-
-<form id="edit-form" class="form-horizontal" method="post" action="/trait/update">
-    <h2 class="text-center">Trait Information:</h2>
-    <div class="form-group">
-        <label for="pubmed-id" class="col-sm-2 control-label">Pubmed ID:</label>
-        <!-- Do not enter PubMed_ID if this trait has not been Published.
-             If the PubMed_ID you entered is alreday stored in our
-             database, all the following fields except Post Publication
-             Description will be ignored.  Do not enter any non-digit
-             character in this field. -->
-        <div class="col-sm-8">
-            <textarea name="pubmed-id" class="form-control" rows="1">{{ publish_xref.publication_id |default('', true) }}</textarea>
-            <input name="old_id_" class="changed" type="hidden" value="{{ publish_xref.publication_id |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="pre-pub-desc" class="col-sm-2 control-label">Pre Publication Description:</label>
-        <div class="col-sm-8">
-            <textarea name="pre-pub-desc" class="form-control" rows="4">{{ phenotype.pre_pub_description |default('', true) }}</textarea>
-            <input name="old_pre_pub_description" class="changed" type="hidden" value="{{ phenotype.pre_pub_description |default('', true) }}"/>
-        </div>
-        <!-- If the PubMed ID is entered, the Post Publication Description
-             will be shown to all users. If there is no PubMed ID, and the
-             Pre Publication Description is entered, only you and
-             authorized users can see the Post Publication Description -->
-    </div>
-    <div class="form-group">
-        <label for="post-pub-desc" class="col-sm-2 control-label">Post Publication Description:</label>
-        <div class="col-sm-8">
-            <textarea name="post-pub-desc" class="form-control" rows="4">{{ phenotype.post_pub_description |default('', true) }}</textarea>
-            <input name="old_post_pub_description" class="changed" type="hidden" value="{{ phenotype.post_pub_description |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="orig-desc" class="col-sm-2 control-label">Original Description:</label>
-        <div class="col-sm-8">
-            <textarea name="orig-desc" class="form-control" rows="4">{{ phenotype.original_description |default('', true) }}</textarea>
-            <input name="old_original_description" class="changed" type="hidden" value="{{ phenotype.original_description |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="units" class="col-sm-2 control-label">Units:</label>
-        <div class="col-sm-8">
-            <textarea name="units" class="form-control" rows="1">{{ phenotype.units |default('', true) }}</textarea>
-            <input name="old_units" class="changed" type="hidden" value="{{ phenotype.units |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="pre-pub-abbrev" class="col-sm-2 control-label">
-            Pre Publication Abbreviation:
-        </label>
-        <div class="col-sm-8">
-            <textarea name="pre-pub-abbrev" class="form-control" rows="1">{{ phenotype.pre_pub_abbreviation |default('', true) }}</textarea>
-            <input name="old_pre_pub_abbreviation" class="changed" type="hidden" value="{{ phenotype.pre_pub_abbreviation |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="post-pub-abbrev" class="col-sm-2 control-label">
-            Post Publication Abbreviation:
-        </label>
-        <div class="col-sm-8">
-            <textarea name="post-pub-abbrev" class="form-control" rows="1">{{ phenotype.post_pub_abbreviation |default('', true) }}</textarea>
-            <input name="old_post_pub_abbreviation" class="changed" type="hidden" value="{{ phenotype.post_pub_abbreviation |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="labcode" class="col-sm-2 control-label">
-            Lab Code:
-        </label>
-        <div class="col-sm-8">
-            <textarea name="labcode" class="form-control" rows="1">{{ phenotype.lab_code |default('', true) }}</textarea>
-            <input name="old_lab_code" class="changed" type="hidden" value="{{ phenotype.lab_code |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="submitter" class="col-sm-2 control-label">
-            Submitter:
-        </label>
-        <div class="col-sm-8">
-            <textarea name="submitter" class="form-control" rows="1">{{ phenotype.submitter |default('', true) }}</textarea>
-            <input name="old_submitter" class="changed" type="hidden" value="{{ phenotype.submitter |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="owner" class="col-sm-2 control-label">Owner:</label>
-        <div class="col-sm-8">
-            <textarea name="owner" class="form-control" rows="1">{{ phenotype.owner |default('', true) }}</textarea>
-            <input name="old_owner" class="changed" type="hidden" value="{{ phenotype.owner |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="authorized-users" class="col-sm-2 control-label">
-            Authorized Users:
-        </label>
-        <div class="col-sm-8">
-            <textarea name="authorized-users" class="form-control" rows="1">{{ phenotype.authorized_users |default('', true) }}</textarea>
-            <input name="old_authorized_users" class="changed" type="hidden" value="{{ phenotype.authorized_users |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="authors" class="col-sm-2 control-label">Authors:</label>
-        <div class="col-sm-8">
-            <textarea name="authors" class="form-control" rows="2">{{ publication.authors |default('', true) }}</textarea>
-            <input name="old_authors" class="changed" type="hidden" value="{{ publication.authors |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="title" class="col-sm-2 control-label">Title:</label>
-        <div class="col-sm-8">
-            <textarea name="title" class="form-control" rows="2">{{ publication.title |default('', true) }}</textarea>
-            <input name="old_title" class="changed" type="hidden" value="{{ publication.title |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="abstract" class="col-sm-2 control-label">Abstract:</label>
-        <div class="col-sm-8">
-            <textarea name="abstract" class="form-control" rows="6">{{ publication.abstract |default('', true) }}</textarea>
-            <input name="old_abstract" class="changed" type="hidden" value="{{ publication.abstract |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="journal" class="col-sm-2 control-label">Journal:</label>
-        <div class="col-sm-8">
-            <textarea name="journal" class="form-control" rows="1">{{ publication.journal |default('', true) }}</textarea>
-            <input name="old_journal" class="changed" type="hidden" value="{{ publication.journal_ |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="pages" class="col-sm-2 control-label">Pages:</label>
-        <div class="col-sm-8">
-            <textarea name="pages" class="form-control" rows="1">{{ publication.pages |default('', true) }}</textarea>
-            <input name="old_pages" class="changed" type="hidden" value="{{ publication.pages |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="month" class="col-sm-2 control-label">Month:</label>
-        <div class="col-sm-8">
-            <textarea name="month" class="form-control" rows="1">{{ publication.month |default('', true) }}</textarea>
-            <input name="old_month" class="changed" type="hidden" value="{{ publication.month |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="year" class="col-sm-2 control-label">Year:</label>
-        <div class="col-sm-8">
-            <textarea name="year" class="form-control" rows="1">{{ publication.year |default('', true) }}</textarea>
-            <input name="old_year" class="changed" type="hidden" value="{{ publication.year |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="form-group">
-        <label for="sequence" class="col-sm-2 control-label">Sequence:</label>
-        <div class="col-sm-8">
-            <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
-            <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
-        </div>
-    </div>
-    <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
-        <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/>
-        <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/>
-        <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/>
-        <input name="comments" class="changed" type="hidden" value="{{ publish_xref.comments }}"/>
-        <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
-        <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
-    </div>
-</form>
-
-{%endblock%}
-
-{% block js %}
-<script>
- gn_server_url = "{{ gn_server_url }}";
- function MarkAsChanged(){
-     $(this).addClass("changed");
- }
- $(":input").blur(MarkAsChanged).change(MarkAsChanged);
-
- $("input[type=submit]").click(function(){
-     $(":input:not(.changed)").attr("disabled", "disabled");
- });
-</script>
-{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index da427bfe..595a0de7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -428,9 +428,9 @@ def submit_trait_form():
         version=GN_VERSION)
 
 
-@app.route("/trait/<name>/edit/<inbred_set_id>")
+@app.route("/trait/<name>/edit/inbredset-id/<inbred_set_id>")
 @admin_login_required
-def edit_trait(name, inbred_set_id):
+def edit_phenotype(name, inbred_set_id):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
@@ -476,7 +476,7 @@ def edit_trait(name, inbred_set_id):
     if len(diff_data) > 0:
         diff_data_ = groupby(diff_data, lambda x: x.timestamp)
     return render_template(
-        "edit_trait.html",
+        "edit_phenotype.html",
         diff=diff_data_,
         publish_xref=publish_xref,
         phenotype=phenotype_,
@@ -486,7 +486,7 @@ def edit_trait(name, inbred_set_id):
 
 
 @app.route("/trait/update", methods=["POST"])
-def update_trait():
+def update_phenotype():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
@@ -544,7 +544,8 @@ def update_trait():
                data=MetadataAudit(dataset_id=data_.get("dataset-name"),
                                   editor=author.decode("utf-8"),
                                   json_data=json.dumps(diff_data)))
-    return redirect("/trait/10007/edit/1")
+    return redirect(f"/trait/{data_.get('dataset-name')}"
+                    f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
 
 
 @app.route("/create_temp_trait", methods=('POST',))
-- 
cgit v1.2.3


From ffa34cc70ad70ab39682e8bdda6b6eb0d46a577d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 9 Jul 2021 13:42:22 +0300
Subject: wqflask: views: Add extra route showing probeset editing form

* wqflask/wqflask/views.py (edit_probeset): New function/ route.
---
 wqflask/wqflask/views.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 595a0de7..e1f6dd71 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -34,8 +34,10 @@ from gn3.db import insert
 from gn3.db import update
 from gn3.db.metadata_audit import MetadataAudit
 from gn3.db.phenotypes import Phenotype
+from gn3.db.phenotypes import Probeset
 from gn3.db.phenotypes import Publication
 from gn3.db.phenotypes import PublishXRef
+from gn3.db.phenotypes import probeset_mapping
 
 
 from flask import current_app
@@ -485,6 +487,23 @@ def edit_phenotype(name, inbred_set_id):
     )
 
 
+@app.route("/trait/edit/probeset-name/<dataset_name>")
+@admin_login_required
+def edit_probeset(dataset_name):
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    probeset_ = fetchone(conn=conn,
+                         table="ProbeSet",
+                         columns=list(probeset_mapping.values()),
+                         where=Probeset(name=dataset_name))
+    return render_template(
+        "edit_probeset.html",
+        probeset=probeset_
+    )
+
+
 @app.route("/trait/update", methods=["POST"])
 def update_phenotype():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
-- 
cgit v1.2.3


From 503ff72502d7bc440450c1c91ac2d5051ca446b9 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 9 Jul 2021 15:23:10 +0300
Subject: templates: edit_probeset: Add template for editing probeset data

* wqflask/wqflask/templates/edit_probeset.html: New file(template).
---
 wqflask/wqflask/templates/edit_probeset.html | 239 +++++++++++++++++++++++++++
 wqflask/wqflask/views.py                     |  31 +++-
 2 files changed, 268 insertions(+), 2 deletions(-)
 create mode 100644 wqflask/wqflask/templates/edit_probeset.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html
new file mode 100644
index 00000000..85d49561
--- /dev/null
+++ b/wqflask/wqflask/templates/edit_probeset.html
@@ -0,0 +1,239 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+Edit Trait for Probeset
+Submit Trait | Reset
+
+{% if diff %}
+
+<div class="container">
+    <details class="col-sm-12 col-md-10 col-lg-12">
+    <summary>
+        <h2>Update History</h2>
+    </summary>
+    <table class="table">
+    <tbody>
+        <tr>
+            <th>Timestamp</th>
+            <th>Editor</th>
+            <th>Field</th>
+            <th>Diff</th>
+        </tr>
+        {% set ns = namespace(display_cell=True) %}
+
+        {% for timestamp, group in diff %}
+        {% set ns.display_cell = True %}
+        {% for i in group %}
+        <tr>
+            {% if ns.display_cell and i.timestamp == timestamp %}
+
+            {% set author = i.author %}
+            {% set timestamp_ = i.timestamp %}
+
+            {% else %}
+
+            {% set author = "" %}
+            {% set timestamp_ = "" %}
+
+            {% endif %}
+            <td>{{ timestamp_ }}</td>
+	    <td>{{ author }}</td>
+	    <td>{{ i.diff.field }}</td>
+            <td><pre>{{ i.diff.diff }}</pre></td>
+            {% set ns.display_cell = False %}
+	</tr>
+        {% endfor %}
+        {% endfor %}
+    </tbody>
+    </table>
+    </details>
+
+</div>
+
+{% endif %}
+
+<form id="edit-form" class="form-horizontal" method="post" action="/probeset/update">
+    <h2 class="text-center">Probeset Information:</h2>
+    <div class="form-group">
+        <label for="symbol" class="col-sm-2 control-label">Symbol:</label>
+        <div class="col-sm-4">
+            <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea>
+            <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="description" class="col-sm-2 control-label">Description:</label>
+        <div class="col-sm-5">
+            <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea>
+            <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_target_description" class="col-sm-2 control-label">Probe Target Description:</label>
+        <div class="col-sm-4">
+            <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea>
+            <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="chr" class="col-sm-2 control-label">Chr:</label>
+        <div class="col-sm-4">
+            <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea>
+            <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="mb" class="col-sm-2 control-label">Mb:</label>
+        <div class="col-sm-4">
+            <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea>
+            <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="alias" class="col-sm-2 control-label">
+            Alias:
+        </label>
+        <div class="col-sm-4">
+            <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea>
+            <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="geneid" class="col-sm-2 control-label">
+            Gene Id:
+        </label>
+        <div class="col-sm-4">
+            <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea>
+            <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="homologeneid" class="col-sm-2 control-label">
+            Homolegene Id:
+        </label>
+        <div class="col-sm-4">
+            <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea>
+            <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="unigeneid" class="col-sm-2 control-label">
+            Unigene Id:
+        </label>
+        <div class="col-sm-4">
+            <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea>
+            <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="omim" class="col-sm-2 control-label">OMIM:</label>
+        <div class="col-sm-4">
+            <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea>
+            <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="refseq_transcriptid" class="col-sm-2 control-label">
+            Refseq TranscriptId:
+        </label>
+        <div class="col-sm-4">
+            <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea>
+            <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="blatseq" class="col-sm-2 control-label">BlatSeq:</label>
+        <div class="col-sm-8">
+            <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea>
+            <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="targetseq" class="col-sm-2 control-label">TargetSeq:</label>
+        <div class="col-sm-8">
+            <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea>
+            <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="strand_probe" class="col-sm-2 control-label">Strand Probe:</label>
+        <div class="col-sm-2">
+            <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea>
+            <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_target_region" class="col-sm-2 control-label">Probe Set Target Region:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea>
+            <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_specificity" class="col-sm-2 control-label">Probeset Specificity:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea>
+            <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_blat_score" class="col-sm-2 control-label">Probeset Blat Score:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea>
+            <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_blat_mb_start" class="col-sm-2 control-label">
+            Probeset Blat Mb Start:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea>
+            <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_blat_mb_end" class="col-sm-2 control-label">Probeset Blat Mb End:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea>
+            <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_strand" class="col-sm-2 control-label">Probeset Strand:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea>
+            <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="form-group">
+        <label for="probe_set_note_by_rw" class="col-sm-2 control-label">Probeset Strand:</label>
+        <div class="col-sm-8">
+            <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea>
+            <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/>
+        </div>
+    </div>
+    <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+        <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+        <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/>
+        <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/>
+        <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
+        <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
+    </div>
+</form>
+
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+ function MarkAsChanged(){
+     $(this).addClass("changed");
+ }
+ $(":input").blur(MarkAsChanged).change(MarkAsChanged);
+
+ $("input[type=submit]").click(function(){
+     $(":input:not(.changed)").attr("disabled", "disabled");
+ });
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index e1f6dd71..741861e6 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -498,13 +498,40 @@ def edit_probeset(dataset_name):
                          table="ProbeSet",
                          columns=list(probeset_mapping.values()),
                          where=Probeset(name=dataset_name))
+    json_data = fetchall(
+        conn,
+        "metadata_audit",
+        where=MetadataAudit(dataset_id=probeset_.id_))
+    Edit = namedtuple("Edit", ["field", "old", "new", "diff"])
+    Diff = namedtuple("Diff", ["author", "diff", "timestamp"])
+    diff_data = []
+    for data in json_data:
+        json_ = json.loads(data.json_data)
+        timestamp = json_.get("timestamp")
+        author = json_.get("author")
+        for key, value in json_.items():
+            if isinstance(value, dict):
+                for field, data_ in value.items():
+                    diff_data.append(
+                        Diff(author=author,
+                             diff=Edit(field,
+                                       data_.get("old"),
+                                       data_.get("new"),
+                                       "\n".join(difflib.ndiff(
+                                           [data_.get("old")],
+                                           [data_.get("new")]))),
+                             timestamp=timestamp))
+    diff_data_ = None
+    if len(diff_data) > 0:
+        diff_data_ = groupby(diff_data, lambda x: x.timestamp)
     return render_template(
         "edit_probeset.html",
-        probeset=probeset_
-    )
+        diff=diff_data_,
+        probeset=probeset_)
 
 
 @app.route("/trait/update", methods=["POST"])
+@admin_login_required
 def update_phenotype():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
-- 
cgit v1.2.3


From 76b4cb3cfa945c0016fa083bb672e42816707572 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 9 Jul 2021 15:27:24 +0300
Subject: wqflask: views: Add route for updating the probeset

---
 wqflask/wqflask/views.py | 59 +++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 58 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 741861e6..731ca291 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -488,7 +488,7 @@ def edit_phenotype(name, inbred_set_id):
 
 
 @app.route("/trait/edit/probeset-name/<dataset_name>")
-@admin_login_required
+# @admin_login_required
 def edit_probeset(dataset_name):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -594,6 +594,63 @@ def update_phenotype():
                     f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
 
 
+@app.route("/probeset/update", methods=["POST"])
+@admin_login_required
+def update_probeset():
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    data_ = request.form.to_dict()
+    probeset_ = {
+        "id_": data_.get("id"),
+        "symbol": data_.get("symbol"),
+        "description": data_.get("description"),
+        "probe_target_description": data_.get("probe_target_description"),
+        "chr_": data_.get("chr"),
+        "mb": data_.get("mb"),
+        "alias": data_.get("alias"),
+        "geneid": data_.get("geneid"),
+        "homologeneid": data_.get("homologeneid"),
+        "unigeneid": data_.get("unigeneid"),
+        "omim": data_.get("OMIM"),
+        "refseq_transcriptid": data_.get("refseq_transcriptid"),
+        "blatseq": data_.get("blatseq"),
+        "targetseq": data_.get("targetseq"),
+        "strand_probe": data_.get("Strand_Probe"),
+        "probe_set_target_region": data_.get("probe_set_target_region"),
+        "probe_set_specificity": data_.get("probe_set_specificity"),
+        "probe_set_blat_score": data_.get("probe_set_blat_score"),
+        "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"),
+        "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"),
+        "probe_set_strand": data_.get("probe_set_strand"),
+        "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"),
+        "flag": data_.get("flag")
+    }
+    updated_probeset = update(
+        conn, "ProbeSet",
+        data=Probeset(**probeset_),
+        where=Probeset(id_=data_.get("id")))
+
+    diff_data = {}
+    author = g.user_session.record.get(b'user_name')
+    if updated_probeset:
+        diff_data.update({"Probeset": diff_from_dict(old={
+            k: data_.get(f"old_{k}") for k, v in probeset_.items()
+            if v is not None}, new=probeset_)})
+    if diff_data:
+        diff_data.update({"probeset_name": data_.get("probeset_name")})
+        diff_data.update({"author": author.decode('utf-8')})
+        diff_data.update({"timestamp": datetime.datetime.now().strftime(
+            "%Y-%m-%d %H:%M:%S")})
+        insert(conn,
+               table="metadata_audit",
+               data=MetadataAudit(dataset_id=data_.get("id"),
+                                  editor=author.decode("utf-8"),
+                                  json_data=json.dumps(diff_data)))
+    return redirect(f"/trait/edit/probeset-name/{data_.get('probeset_name')}")
+
+
 @app.route("/create_temp_trait", methods=('POST',))
 def create_temp_trait():
     logger.info(request.url)
-- 
cgit v1.2.3


From d01b1aadcd3604e4f592f64ce7d9eb010d4c7230 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Sat, 10 Jul 2021 09:55:12 +0300
Subject: templates: show_trait_details: Show edit buttons conditionally

* wqflask/wqflask/templates/show_trait_details.html: Check the data
type, and load different edit buttons.
---
 wqflask/wqflask/templates/show_trait_details.html | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 83f7b0ac..bb30c54c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -235,8 +235,14 @@
         {% endif %}
         <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+        {% if this_trait.dataset.type == 'Publish' %}
         <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
         {% endif %}
+
+        {% if this_trait.dataset.type == 'ProbeSet' %}
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/edit/probeset-name/{{ this_trait.name }}', '_blank')">Edit</button>
+        {% endif %}
+        {% endif %}
     </div>
 </div>
 
-- 
cgit v1.2.3


From 344d6a86d2e468249ec7b583e8c0751f99cd6a5b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 12 Jul 2021 11:40:40 +0300
Subject: tests: test_markdown_routes: Remove stubbed out tests

---
 wqflask/tests/integration/test_markdown_routes.py | 21 ---------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 wqflask/tests/integration/test_markdown_routes.py

(limited to 'wqflask')

diff --git a/wqflask/tests/integration/test_markdown_routes.py b/wqflask/tests/integration/test_markdown_routes.py
deleted file mode 100644
index 5e3e5045..00000000
--- a/wqflask/tests/integration/test_markdown_routes.py
+++ /dev/null
@@ -1,21 +0,0 @@
-"Integration tests for markdown routes"
-import unittest
-
-from bs4 import BeautifulSoup
-
-from wqflask import app
-
-
-class TestGenMenu(unittest.TestCase):
-    """Tests for glossary"""
-
-    def setUp(self):
-        self.app = app.test_client()
-
-    def tearDown(self):
-        pass
-
-    def test_glossary_page(self):
-        """Test that the glossary page is rendered properly"""
-        response = self.app.get('/glossary', follow_redirects=True)
-        pass
-- 
cgit v1.2.3


From 48ac21fda375b8255bec86e83496d730bb57ffff Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 12 Jul 2021 17:49:09 +0000
Subject: Encode user_id as bytestring if not already bytestring to account for
 some user_ids being stored as different encoding

---
 wqflask/utility/authentication_tools.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 57dbf8ba..6802d689 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,7 +11,6 @@ from utility.redis_tools import (get_redis_conn,
                                  add_resource)
 Redis = get_redis_conn()
 
-
 def check_resource_availability(dataset, trait_id=None):
     # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
@@ -133,12 +132,17 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             resource_id = get_resource_id(dataset, trait_id)
 
-    if g.user_session.user_id in Redis.smembers("super_users"):
+    try:
+        user_id = g.user_session.user_id.encode('utf-8')
+    except:
+        user_id = g.user_session.user_id
+
+    if user_id in Redis.smembers("super_users"):
         return "owner"
 
     resource_info = get_resource_info(resource_id)
     if resource_info:
-        if g.user_session.user_id == resource_info['owner_id']:
+        if user_id == resource_info['owner_id']:
             return "owner"
         else:
             return check_admin(resource_id)
-- 
cgit v1.2.3


From 427071fc797d6208f9833401833f17d929f11343 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 13 Jul 2021 17:08:53 +0000
Subject: Fixed corr_coeffient to corr_coefficient

---
 wqflask/wqflask/correlation/show_corr_results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e936f28c..e2daa991 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -94,7 +94,7 @@ def correlation_json_for_table(correlation_data, this_trait, this_dataset, targe
         results_dict['dataset'] = target_dataset['name']
         results_dict['hmac'] = hmac.data_hmac(
             '{}:{}'.format(target_trait['name'], target_dataset['name']))
-        results_dict['sample_r'] = f"{float(trait['corr_coeffient']):.3f}"
+        results_dict['sample_r'] = f"{float(trait['corr_coefficient']):.3f}"
         results_dict['num_overlap'] = trait['num_overlap']
         results_dict['sample_p'] = f"{float(trait['p_value']):.3e}"
         if target_dataset['type'] == "ProbeSet":
-- 
cgit v1.2.3


From 2fbfdc0e57ad9d2b27b99b32f3d48af4fae96dd9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 16 Jul 2021 22:47:21 +0300
Subject: handle missing tissue input data

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 31 ++++++++++++----------
 1 file changed, 17 insertions(+), 14 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index aea91220..c96da8ee 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -149,7 +149,6 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     sample_data = test_process_data(this_trait, this_dataset, start_vars)
 
-
     if target_dataset.type == "ProbeSet":
         target_dataset.get_probeset_data(list(sample_data.keys()))
     else:
@@ -202,17 +201,22 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
         if tissue_input is not None:
             (primary_tissue_data, target_tissue_data) = tissue_input
 
-        corr_input_data = {
-            "primary_tissue": primary_tissue_data,
-            "target_tissues_dict": target_tissue_data
-        }
-        correlation_results = compute_tissue_correlation(
-            primary_tissue_dict=corr_input_data["primary_tissue"],
-            target_tissues_data=corr_input_data[
-                "target_tissues_dict"],
-            corr_method=method
-
-        )
+            corr_input_data = {
+                "primary_tissue": primary_tissue_data,
+                "target_tissues_dict": target_tissue_data
+            }
+            correlation_results = compute_tissue_correlation(
+                primary_tissue_dict=corr_input_data["primary_tissue"],
+                target_tissues_data=corr_input_data[
+                    "target_tissues_dict"],
+                corr_method=method
+
+            )
+        else:
+            return {"correlation_results": [],
+                    "this_trait": this_trait.name,
+                    "target_dataset": start_vars['corr_dataset'],
+                    "return_results": corr_return_results}
 
     elif corr_type == "lit":
         (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
@@ -302,5 +306,4 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
             "trait_symbol_dict": trait_symbol_dict,
             "symbol_tissue_vals_dict": corr_result_tissue_vals_dict
         }
-        return (primary_tissue_data, target_tissue_data)
-    return None
+        return (primary_tissue_data, target_tissue_data)
\ No newline at end of file
-- 
cgit v1.2.3


From be3dbbf8d7349a076be28c9eba8dc33e18adb477 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 16 Jul 2021 23:17:34 +0300
Subject: set compute_all for test_compute  to True

---
 wqflask/wqflask/views.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 731ca291..1bd11c4e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -302,6 +302,7 @@ def gsearchact():
     elif type == "phenotype":
         return render_template("gsearch_pheno.html", **result)
 
+
 @app.route("/gsearch_table", methods=('GET',))
 def gsearchtable():
     logger.info(request.url)
@@ -316,6 +317,7 @@ def gsearchtable():
 
     return flask.jsonify(current_page)
 
+
 @app.route("/gsearch_updating", methods=('POST',))
 def gsearch_updating():
     logger.info("REQUEST ARGS:", request.values)
@@ -1193,9 +1195,10 @@ def corr_compute_page():
 
 @app.route("/test_corr_compute", methods=["POST"])
 def test_corr_compute_page():
-    correlation_data = compute_correlation(request.form)
+    correlation_data = compute_correlation(request.form, compute_all=True)
     return render_template("test_correlation_page.html", **correlation_data)
-    
+
+
 @app.route("/corr_matrix", methods=('POST',))
 def corr_matrix_page():
     logger.info("In corr_matrix, request.form is:", pf(request.form))
-- 
cgit v1.2.3


From 78f0e216c165eb7879ab07755a2d74deec3a11d5 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 16 Jul 2021 23:20:14 +0300
Subject: minor fixes for test_correlation_page table columns

---
 wqflask/wqflask/templates/test_correlation_page.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html
index 0809b65e..991773a2 100644
--- a/wqflask/wqflask/templates/test_correlation_page.html
+++ b/wqflask/wqflask/templates/test_correlation_page.html
@@ -113,7 +113,7 @@ console.log(correlationResults)
             {"data":corr_type=="sample"?null:"fd","width":"25px"},
             { "data": "index","width":"120px","title":"Index" },
             { "data": "trait_name","title":"TraitName"},
-            { "data": "corr_coeffient","defaultContent": "--"},
+            { "data": "corr_coefficient","defaultContent": "--"},
             { "data": "p_value","defaultContent":"--"},
             { "data": "num_overlap","defaultContent":"--"},
             {"data":"tissue_corr","defaultContent":"--","title":"Tissue r"},
-- 
cgit v1.2.3


From b0514de0f73a9a6d756d7d5daa2a0641c5456ff2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 16 Jul 2021 13:56:10 +0300
Subject: wqflask: views: Add endpoint for getting the csv data

---
 wqflask/wqflask/views.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1bd11c4e..b97f15a4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -38,6 +38,7 @@ from gn3.db.phenotypes import Probeset
 from gn3.db.phenotypes import Publication
 from gn3.db.phenotypes import PublishXRef
 from gn3.db.phenotypes import probeset_mapping
+from gn3.db.traits import get_trait_csv_sample_data
 
 
 from flask import current_app
@@ -1313,3 +1314,19 @@ def json_default_handler(obj):
     else:
         raise TypeError('Object of type %s with value of %s is not JSON serializable' % (
             type(obj), repr(obj)))
+
+
+@app.route("/trait/<trait_name>/sampledata/<phenotype_id>")
+def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    csv_data = get_trait_csv_sample_data(conn, str(trait_name),
+                                         str(phenotype_id))
+    return Response(
+        csv_data,
+        mimetype="text/csv",
+        headers={"Content-disposition":
+                 "attachment; filename=myplot.csv"}
+    )
-- 
cgit v1.2.3


From 47f6f23c976cd72f3181d003f64740902341f51d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 22 Jul 2021 22:07:21 +0300
Subject: wqflask: views: Edit end-point to use the phenotype-id

squash! wqflask: views: Edit end-point to use the phenotype-id
---
 wqflask/wqflask/views.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b97f15a4..7fd52ac9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -433,9 +433,9 @@ def submit_trait_form():
         version=GN_VERSION)
 
 
-@app.route("/trait/<name>/edit/inbredset-id/<inbred_set_id>")
+@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>")
 @admin_login_required
-def edit_phenotype(name, inbred_set_id):
+def edit_phenotype(name, phenotype_id):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
@@ -444,7 +444,7 @@ def edit_phenotype(name, inbred_set_id):
         conn=conn,
         table="PublishXRef",
         where=PublishXRef(id_=name,
-                          inbred_set_id=inbred_set_id))
+                          phenotype_id=phenotype_id))
     phenotype_ = fetchone(
         conn=conn,
         table="Phenotype",
@@ -594,7 +594,7 @@ def update_phenotype():
                                   editor=author.decode("utf-8"),
                                   json_data=json.dumps(diff_data)))
     return redirect(f"/trait/{data_.get('dataset-name')}"
-                    f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
+                    f"/edit/phenotype-id/{data_.get('phenotype-id')}")
 
 
 @app.route("/probeset/update", methods=["POST"])
-- 
cgit v1.2.3


From 81f491e0be1ebd23bfc44bc8766b7f1aee998abb Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 12:50:02 +0300
Subject: wqflask: views: Remove un-necessary comment "#" sequence

---
 wqflask/wqflask/views.py | 2 --
 1 file changed, 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7fd52ac9..6e8d1e78 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1297,8 +1297,6 @@ def browser_inputs():
 
     return flask.jsonify(file_contents)
 
-##########################################################################
-
 
 def json_default_handler(obj):
     """Based on http://stackoverflow.com/a/2680060/1175849"""
-- 
cgit v1.2.3


From 749807d0bd676ad76e427a8151339bba2780a659 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 12:52:10 +0300
Subject: wqflask: views: Process file_csv if provided and get the diff

* wqflask/wqflask/views.py (update_phenotype): If a file is provided
in the request, get the diff and store it in a data escrow.
---
 wqflask/wqflask/views.py | 55 ++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 51 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 6e8d1e78..73829bb2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -27,6 +27,7 @@ from zipfile import ZIP_DEFLATED
 
 from wqflask import app
 
+from gn3.commands import run_cmd
 from gn3.db import diff_from_dict
 from gn3.db import fetchall
 from gn3.db import fetchone
@@ -43,6 +44,7 @@ from gn3.db.traits import get_trait_csv_sample_data
 
 from flask import current_app
 from flask import g
+from flask import flash
 from flask import Response
 from flask import request
 from flask import make_response
@@ -541,6 +543,52 @@ def update_phenotype():
                            passwd=current_app.config.get("DB_PASS"),
                            host=current_app.config.get("DB_HOST"))
     data_ = request.form.to_dict()
+    author = g.user_session.record.get(b'user_name')
+    if 'file' not in request.files:
+        flash("No sample data has been uploaded")
+    else:
+        file_ = request.files['file']
+        trait_name = str(data_.get('dataset-name'))
+        phenotype_id = str(data_.get('phenotype-id', 35))
+        SAMPLE_DATADIR = "/tmp/sample-data/"
+        if not os.path.exists(SAMPLE_DATADIR):
+            os.makedirs(SAMPLE_DATADIR)
+        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
+                                           "diffs")):
+            os.makedirs(os.path.join(SAMPLE_DATADIR,
+                                     "diffs"))
+        if not os.path.exists(os.path.join(SAMPLE_DATADIR,
+                                           "updated")):
+            os.makedirs(os.path.join(SAMPLE_DATADIR,
+                                     "updated"))
+        current_time = str(datetime.datetime.now().isoformat())
+        new_file_name = ("/tmp/sample-data/updated/"
+                         f"{author.decode('utf-8')}."
+                         f"{trait_name}.{phenotype_id}."
+                         f"{current_time}.csv")
+        uploaded_file_name = ("/tmp/sample-data/updated/"
+                              f"updated.{author.decode('utf-8')}."
+                              f"{trait_name}.{phenotype_id}."
+                              f"{current_time}.csv")
+        file_.save(new_file_name)
+        csv_ = get_trait_csv_sample_data(conn=conn,
+                                         trait_name=str(trait_name),
+                                         phenotype_id=str(phenotype_id))
+        with open(uploaded_file_name, "w") as f_:
+            f_.write(csv_)
+        r = run_cmd(cmd=("/home/bonface/opt/genenetwork3/bin/csvdiff "
+                         f"'{uploaded_file_name}' '{new_file_name}' "
+                         "--format json"))
+        diff_output = ("/tmp/sample-data/diffs/"
+                       f"{trait_name}."
+                       f"{phenotype_id}.{current_time}.json")
+        with open(diff_output, "w") as f:
+            print(r.get("output"))
+            dict_ = json.loads(r.get("output"))
+            dict_.update({"author": author.decode('utf-8')})
+            dict_.update({"timestamp": datetime.datetime.now().strftime(
+                "%Y-%m-%d %H:%M:%S")})
+            f.write(json.dumps(dict_))
     # Run updates:
     phenotype_ = {
         "pre_pub_description": data_.get("pre-pub-desc"),
@@ -582,7 +630,6 @@ def update_phenotype():
         diff_data.update({"Publication": diff_from_dict(old={
             k: data_.get(f"old_{k}") for k, v in publication_.items()
             if v is not None}, new=publication_)})
-    author = g.user_session.record.get(b'user_name')
     if diff_data:
         diff_data.update({"dataset_id": data_.get("dataset-name")})
         diff_data.update({"author": author.decode('utf-8')})
@@ -1320,10 +1367,10 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
                            host=current_app.config.get("DB_HOST"))
-    csv_data = get_trait_csv_sample_data(conn, str(trait_name),
-                                         str(phenotype_id))
+    csv_ = get_trait_csv_sample_data(conn, str(trait_name),
+                                     str(phenotype_id))
     return Response(
-        csv_data,
+        csv_,
         mimetype="text/csv",
         headers={"Content-disposition":
                  "attachment; filename=myplot.csv"}
-- 
cgit v1.2.3


From b355b91f67305c4cb3ebbad994cc0ff2906eb701 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 13:17:14 +0300
Subject: wqflask: views: Show diff files for the admin

* wqflask/wqflask/views.py (display_diffs_admin): New function.
* wqflask/wqflask/templates/display_files.html: New template to show
the diffs.
---
 wqflask/wqflask/templates/display_files.html | 21 +++++++++++++++++++++
 wqflask/wqflask/views.py                     | 12 ++++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 wqflask/wqflask/templates/display_files.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
new file mode 100644
index 00000000..e7210c1b
--- /dev/null
+++ b/wqflask/wqflask/templates/display_files.html
@@ -0,0 +1,21 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+Show files for approval
+
+<div>
+    <ul>
+        {% for file in files %}
+        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/> <button>Approve</button> <button>Reject</button></li>
+        {% endfor %}
+    </ul>
+</div>
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 73829bb2..cf7b5552 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1375,3 +1375,15 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
         headers={"Content-disposition":
                  "attachment; filename=myplot.csv"}
     )
+
+
+@app.route("/data/approve/")
+def display_diffs_admin():
+    DIFF_DIR = "/tmp/sample-data/diffs"
+    files = []
+    if os.path.exists(DIFF_DIR):
+        files = filter(lambda x: not(x.endswith((".approved", ".rejected"))),
+                       os.listdir(DIFF_DIR))
+    return render_template("display_files.html",
+                           files=files)
+
-- 
cgit v1.2.3


From 5e61c115a2c2be351c16fd9d1a764faecd8591fa Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 13:21:38 +0300
Subject: wqflask: views: Approve data when the "approve" button is clicked

* wqflask/wqflask/views.py (approve_data): New function.
---
 wqflask/wqflask/views.py | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index cf7b5552..1d50bdff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -33,6 +33,7 @@ from gn3.db import fetchall
 from gn3.db import fetchone
 from gn3.db import insert
 from gn3.db import update
+from gn3.db import update_raw
 from gn3.db.metadata_audit import MetadataAudit
 from gn3.db.phenotypes import Phenotype
 from gn3.db.phenotypes import Probeset
@@ -1387,3 +1388,41 @@ def display_diffs_admin():
     return render_template("display_files.html",
                            files=files)
 
+
+@app.route("/data-samples/approve/<name>")
+def approve_data(name):
+    sample_data = {}
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
+        sample_data = json.load(myfile)
+    modifications = [d for d in sample_data.get("Modifications")]
+    for modification in modifications:
+        if modifications.get("current"):
+            (strain_id, publish_id,
+             strain_name,
+             value, se, count) = modification.get("Current").split(",")
+            row_counts = update_sample_data(
+                conn=conn,
+                strain_name=strain_name,
+                strain_id=int(strain_id),
+                publish_data_id=int(PUBLISH_ID),
+                value=value,
+                error=se,
+                count=int(count)
+            )
+            insert(conn,
+                   table="metadata_audit",
+                   data=MetadataAudit(
+                       dataset_id=sample_data.get("publishdata_id"),
+                       editor=sample_data.get("author"),
+                       json_data=json.dumps(sample_data)))
+            
+    # Once data is approved, rename it!
+    os.rename(os.path.join("/tmp/sample-data/diffs", name),
+              os.path.join("/tmp/sample-data/diffs",
+                           f"{name}.approved"))
+    return redirect("/data/approve/")
+
-- 
cgit v1.2.3


From f5b0a59a41b1cf3b29557aa918b217b0749879b8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 13:22:38 +0300
Subject: wqflask: views: Return the json data for viewing

* wqflask/wqflask/views.py (display_file): New function.
---
 wqflask/wqflask/views.py | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1d50bdff..12b47ce9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1426,3 +1426,9 @@ def approve_data(name):
                            f"{name}.approved"))
     return redirect("/data/approve/")
 
+
+@app.route("/display-file/<name>")
+def display_file(name):
+    with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
+        content = myfile.read()
+    return Response(content, mimetype='text/json')
-- 
cgit v1.2.3


From 9b68883041b581fbd01e5568d36d82581dec7772 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 14:20:44 +0300
Subject: templates: edit_phenotype: Add enctype to form cause of file uploads

---
 wqflask/wqflask/templates/edit_phenotype.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 7d4c65f8..5edddada 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -53,7 +53,7 @@ Submit Trait | Reset
 
 {% endif %}
 
-<form id="edit-form" class="form-horizontal" method="post" action="/trait/update">
+<form id="edit-form" class="form-horizontal" method="post" action="/trait/update" enctype=multipart/form-data>
     <h2 class="text-center">Trait Information:</h2>
     <div class="form-group">
         <label for="pubmed-id" class="col-sm-2 control-label">Pubmed ID:</label>
-- 
cgit v1.2.3


From 6eab9f07e5eaf75eaa4f406b1ed3a3cfec9575f8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 26 Jul 2021 14:22:32 +0300
Subject: templates: edit_phenotype: Add file upload and "approval" buttons

---
 wqflask/wqflask/templates/edit_phenotype.html | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 5edddada..691ad27b 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -206,11 +206,31 @@ Submit Trait | Reset
             <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
             <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
         </div>
+                </div>
+    <div class="form-group">
+        <label for="sequence" class="col-sm-2 control-label">Sequence:</label>
+        <div class="col-sm-8">
+            <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
+            <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
+        </div>
+        <input type = "file" class="form-control" name = "file" />
+    </div>
+
+    <div class="form-group">
+        <a href="/data/approve/">
+            Data Approval
+        </a>
+    </div>
+
+    <div class="form-group">
+        <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}">
+            Download csv of sample data for editing
+        </a>
     </div>
     <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
         <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/>
-        <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/>
         <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/>
+        <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/>
         <input name="comments" class="changed" type="hidden" value="{{ publish_xref.comments }}"/>
         <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change">
         <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset">
-- 
cgit v1.2.3


From 4482a1c5dc61dc4813911f1439721d0407286e44 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 22:43:16 +0300
Subject: edit_phenotype: Remove duplicate html

---
 wqflask/wqflask/templates/edit_phenotype.html | 5 -----
 1 file changed, 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 691ad27b..9530fad0 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -208,11 +208,6 @@ Submit Trait | Reset
         </div>
                 </div>
     <div class="form-group">
-        <label for="sequence" class="col-sm-2 control-label">Sequence:</label>
-        <div class="col-sm-8">
-            <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
-            <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
-        </div>
         <input type = "file" class="form-control" name = "file" />
     </div>
 
-- 
cgit v1.2.3


From 097f4168901741d7913e79da09c1f3907c3d1312 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 22:47:29 +0300
Subject: templates: edit_phenotype: add some form of padding upload button

---
 wqflask/wqflask/templates/edit_phenotype.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 9530fad0..7961c188 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -208,7 +208,7 @@ Submit Trait | Reset
         </div>
                 </div>
     <div class="form-group">
-        <input type = "file" class="form-control" name = "file" />
+        <input type = "file" class="col-sm-4 control-label" name = "file" />
     </div>
 
     <div class="form-group">
-- 
cgit v1.2.3


From 0793a41cc8534b5084bbf35b437d956681a8c19d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:08:50 +0300
Subject: templates: edit_phenotype: Use proper page header for this page

---
 wqflask/wqflask/templates/edit_phenotype.html | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 7961c188..0e7c4f63 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -2,8 +2,9 @@
 {% block title %}Trait Submission{% endblock %}
 {% block content %}
 <!-- Start of body -->
-Edit Trait for Published Database
-Submit Trait | Reset
+<div class="page-header text-center">
+    <h1>Edit Trait for Published Database</h1>
+</div>
 
 {% if diff %}
 
-- 
cgit v1.2.3


From 399d388b6704d39d778617cedebec31341428b75 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:09:34 +0300
Subject: templates: edit_phenotype: Properly centre form controls

---
 wqflask/wqflask/templates/edit_phenotype.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 0e7c4f63..9810b7ab 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -223,7 +223,7 @@
             Download csv of sample data for editing
         </a>
     </div>
-    <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;">
+    <div class="controls center-block" style="width: max-content;">
         <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/>
         <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/>
         <input name="phenotype-id" class="changed" type="hidden" value="{{ publish_xref.phenotype_id }}"/>
-- 
cgit v1.2.3


From f5677ef162fec18603fce6d903fcdfd31b3541cc Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:10:07 +0300
Subject: templates: edit_phenotype: Add some margin to links for csv download

---
 wqflask/wqflask/templates/edit_phenotype.html | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 9810b7ab..83daba58 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -212,15 +212,12 @@
         <input type = "file" class="col-sm-4 control-label" name = "file" />
     </div>
 
-    <div class="form-group">
-        <a href="/data/approve/">
+    <div style="margin-left: 13%;">
+        <a href="/data/approve/" class="btn btn-link btn-sm">
             Data Approval
         </a>
-    </div>
-
-    <div class="form-group">
-        <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}">
-            Download csv of sample data for editing
+        <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}" class="btn btn-link btn-sm">
+            Sample Data(CSV Download)
         </a>
     </div>
     <div class="controls center-block" style="width: max-content;">
-- 
cgit v1.2.3


From cf278e6c119871d08f68c13e07b190b8c14e0414 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:12:14 +0300
Subject: wqflask: views: Replace `update_raw` with `update_sample_data`

---
 wqflask/wqflask/views.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 12b47ce9..4746fcc2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -33,7 +33,6 @@ from gn3.db import fetchall
 from gn3.db import fetchone
 from gn3.db import insert
 from gn3.db import update
-from gn3.db import update_raw
 from gn3.db.metadata_audit import MetadataAudit
 from gn3.db.phenotypes import Phenotype
 from gn3.db.phenotypes import Probeset
@@ -41,6 +40,7 @@ from gn3.db.phenotypes import Publication
 from gn3.db.phenotypes import PublishXRef
 from gn3.db.phenotypes import probeset_mapping
 from gn3.db.traits import get_trait_csv_sample_data
+from gn3.db.traits import update_sample_data
 
 
 from flask import current_app
@@ -1398,10 +1398,11 @@ def approve_data(name):
                            host=current_app.config.get("DB_HOST"))
     with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
         sample_data = json.load(myfile)
+    PUBLISH_ID = sample_data.get("publishdata_id")
     modifications = [d for d in sample_data.get("Modifications")]
     for modification in modifications:
-        if modifications.get("current"):
-            (strain_id, publish_id,
+        if modification.get("Current"):
+            (strain_id,
              strain_name,
              value, se, count) = modification.get("Current").split(",")
             row_counts = update_sample_data(
@@ -1419,11 +1420,10 @@ def approve_data(name):
                        dataset_id=sample_data.get("publishdata_id"),
                        editor=sample_data.get("author"),
                        json_data=json.dumps(sample_data)))
-            
-    # Once data is approved, rename it!
-    os.rename(os.path.join("/tmp/sample-data/diffs", name),
-              os.path.join("/tmp/sample-data/diffs",
-                           f"{name}.approved"))
+            # Once data is approved, rename it!
+            os.rename(os.path.join("/tmp/sample-data/diffs", name),
+                      os.path.join("/tmp/sample-data/diffs",
+                                   f"{name}.approved"))
     return redirect("/data/approve/")
 
 
-- 
cgit v1.2.3


From 52d53eb90aa0a4fbaab713704f4894e652cb91f3 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:12:51 +0300
Subject: wqflask: views: Filter out approved/ rejected files during display

* wqflask/wqflask/views.py (approve_data): Only show files that have
not been approved/ rejected.
---
 wqflask/wqflask/views.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 4746fcc2..9a961f26 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1383,8 +1383,9 @@ def display_diffs_admin():
     DIFF_DIR = "/tmp/sample-data/diffs"
     files = []
     if os.path.exists(DIFF_DIR):
+        files = os.listdir(DIFF_DIR)
         files = filter(lambda x: not(x.endswith((".approved", ".rejected"))),
-                       os.listdir(DIFF_DIR))
+                       files)
     return render_template("display_files.html",
                            files=files)
 
-- 
cgit v1.2.3


From 3804d64d6eed6c9b5fbb95758a84014ff026705d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Jul 2021 23:14:44 +0300
Subject: wqflask: views: Get the publishdata_id from the file

---
 wqflask/wqflask/views.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9a961f26..0f1df123 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -572,11 +572,19 @@ def update_phenotype():
                               f"{trait_name}.{phenotype_id}."
                               f"{current_time}.csv")
         file_.save(new_file_name)
+        publishdata_id = ""
+        lines = []
+        with open(new_file_name, "r") as f:
+            lines = f.read()
+            first_line = lines.split('\n', 1)[0]
+            publishdata_id = first_line.split("Id:")[-1].strip()
+        with open(new_file_name, "w") as f:
+            f.write(lines.split("\n\n")[-1])
         csv_ = get_trait_csv_sample_data(conn=conn,
                                          trait_name=str(trait_name),
                                          phenotype_id=str(phenotype_id))
         with open(uploaded_file_name, "w") as f_:
-            f_.write(csv_)
+            f_.write(csv_.split("\n\n")[-1])
         r = run_cmd(cmd=("/home/bonface/opt/genenetwork3/bin/csvdiff "
                          f"'{uploaded_file_name}' '{new_file_name}' "
                          "--format json"))
@@ -584,9 +592,9 @@ def update_phenotype():
                        f"{trait_name}."
                        f"{phenotype_id}.{current_time}.json")
         with open(diff_output, "w") as f:
-            print(r.get("output"))
             dict_ = json.loads(r.get("output"))
             dict_.update({"author": author.decode('utf-8')})
+            dict_.update({"publishdata_id": publishdata_id})
             dict_.update({"timestamp": datetime.datetime.now().strftime(
                 "%Y-%m-%d %H:%M:%S")})
             f.write(json.dumps(dict_))
-- 
cgit v1.2.3


From 305a2fc37bc233c9842bb12346c7e476c1d81be7 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Jul 2021 16:38:43 +0300
Subject: wqflask: views: Flash messages during edits

---
 wqflask/wqflask/templates/edit_phenotype.html | 9 +++++++++
 wqflask/wqflask/views.py                      | 4 +++-
 2 files changed, 12 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 83daba58..0d7071f7 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -2,6 +2,15 @@
 {% block title %}Trait Submission{% endblock %}
 {% block content %}
 <!-- Start of body -->
+{% with messages = get_flashed_messages(with_categories=true) %}
+{% if messages %}
+{% for category, message in messages %}
+<div class="container-fluid bg-{{ category }}">
+    <p>{{ message }}</p>
+</div>
+{% endfor %}
+{% endif %}
+{% endwith %}
 <div class="page-header text-center">
     <h1>Edit Trait for Published Database</h1>
 </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 0f1df123..18d3e99f 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -546,7 +546,7 @@ def update_phenotype():
     data_ = request.form.to_dict()
     author = g.user_session.record.get(b'user_name')
     if 'file' not in request.files:
-        flash("No sample data has been uploaded")
+        flash("No sample-data has been uploaded", "warning")
     else:
         file_ = request.files['file']
         trait_name = str(data_.get('dataset-name'))
@@ -598,6 +598,7 @@ def update_phenotype():
             dict_.update({"timestamp": datetime.datetime.now().strftime(
                 "%Y-%m-%d %H:%M:%S")})
             f.write(json.dumps(dict_))
+        flash("Sample-data has been successfully uploaded", "success")
     # Run updates:
     phenotype_ = {
         "pre_pub_description": data_.get("pre-pub-desc"),
@@ -649,6 +650,7 @@ def update_phenotype():
                data=MetadataAudit(dataset_id=data_.get("dataset-name"),
                                   editor=author.decode("utf-8"),
                                   json_data=json.dumps(diff_data)))
+        flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
     return redirect(f"/trait/{data_.get('dataset-name')}"
                     f"/edit/phenotype-id/{data_.get('phenotype-id')}")
 
-- 
cgit v1.2.3


From d9e6c4d67aa5cb18cf199f5e27fbc1ac73906c89 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 17:49:44 +0300
Subject: templates: edit_phenotype: Remove link to the approve page

---
 wqflask/wqflask/templates/edit_phenotype.html | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index 0d7071f7..a7d6f1b0 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -222,9 +222,6 @@
     </div>
 
     <div style="margin-left: 13%;">
-        <a href="/data/approve/" class="btn btn-link btn-sm">
-            Data Approval
-        </a>
         <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}" class="btn btn-link btn-sm">
             Sample Data(CSV Download)
         </a>
-- 
cgit v1.2.3


From b5fc6068a1dbe493a3d7b240df236ada36984570 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 17:51:35 +0300
Subject: templates: edit_phenotype: Put csv "oownload" button above "Browse"

---
 wqflask/wqflask/templates/edit_phenotype.html | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/edit_phenotype.html b/wqflask/wqflask/templates/edit_phenotype.html
index a7d6f1b0..7a841793 100644
--- a/wqflask/wqflask/templates/edit_phenotype.html
+++ b/wqflask/wqflask/templates/edit_phenotype.html
@@ -216,16 +216,15 @@
             <textarea name="sequence" class="form-control" rows="6">{{ publish_xref.sequence |default('', true) }}</textarea>
             <input name="old_sequence" class="changed" type="hidden" value="{{ publication.sequence |default('', true) }}"/>
         </div>
-                </div>
-    <div class="form-group">
-        <input type = "file" class="col-sm-4 control-label" name = "file" />
     </div>
-
     <div style="margin-left: 13%;">
         <a href="/trait/{{ publish_xref.id_ }}/sampledata/{{ publish_xref.phenotype_id }}" class="btn btn-link btn-sm">
             Sample Data(CSV Download)
         </a>
     </div>
+    <div class="form-group">
+        <input type = "file" class="col-sm-4 control-label" name = "file" />
+    </div>
     <div class="controls center-block" style="width: max-content;">
         <input name="dataset-name" class="changed" type="hidden" value="{{ publish_xref.id_ }}"/>
         <input name="inbred-set-id" class="changed" type="hidden" value="{{ publish_xref.inbred_set_id }}"/>
-- 
cgit v1.2.3


From 299847f03a84c5a74c51d8cb6bea6763431773c2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:08:31 +0300
Subject: templates: display_files: Add a a reject button

---
 wqflask/wqflask/templates/display_files.html | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
index e7210c1b..30974300 100644
--- a/wqflask/wqflask/templates/display_files.html
+++ b/wqflask/wqflask/templates/display_files.html
@@ -7,7 +7,8 @@ Show files for approval
 <div>
     <ul>
         {% for file in files %}
-        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/> <button>Approve</button> <button>Reject</button></li>
+        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/>
+            <button><a href="/data-samples/approve/{{ file }}">Approve</a></button> <button>Reject</button></li>
         {% endfor %}
     </ul>
 </div>
-- 
cgit v1.2.3


From f175c8806b4fbf372cbe65790ce7816b98e32695 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:24:10 +0300
Subject: wqflask: views: Add author name to generated diff's filename

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 18d3e99f..ed5398a2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -589,7 +589,7 @@ def update_phenotype():
                          f"'{uploaded_file_name}' '{new_file_name}' "
                          "--format json"))
         diff_output = ("/tmp/sample-data/diffs/"
-                       f"{trait_name}."
+                       f"{trait_name}.{author.decode('utf-8')}."
                        f"{phenotype_id}.{current_time}.json")
         with open(diff_output, "w") as f:
             dict_ = json.loads(r.get("output"))
-- 
cgit v1.2.3


From 79d6dc5ac4610ea50e61bca80598b87d42911490 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:24:39 +0300
Subject: wqflask: views: Add dataset_id to diff json that'll be stored

---
 wqflask/wqflask/views.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ed5398a2..11e1bfaa 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -593,10 +593,13 @@ def update_phenotype():
                        f"{phenotype_id}.{current_time}.json")
         with open(diff_output, "w") as f:
             dict_ = json.loads(r.get("output"))
-            dict_.update({"author": author.decode('utf-8')})
-            dict_.update({"publishdata_id": publishdata_id})
-            dict_.update({"timestamp": datetime.datetime.now().strftime(
-                "%Y-%m-%d %H:%M:%S")})
+            dict_.update({
+                "author": author.decode('utf-8'),
+                "publishdata_id": publishdata_id,
+                "dataset_id": data_.get("dataset-name"),
+                "timestamp": datetime.datetime.now().strftime(
+                    "%Y-%m-%d %H:%M:%S")
+            })
             f.write(json.dumps(dict_))
         flash("Sample-data has been successfully uploaded", "success")
     # Run updates:
-- 
cgit v1.2.3


From 2c0b0d7132ff67709de13d986a92293b68e275e2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:25:30 +0300
Subject: wqflask: views: use dataset_id when inserting into metadata_audit

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 11e1bfaa..760d5947 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1431,7 +1431,7 @@ def approve_data(name):
             insert(conn,
                    table="metadata_audit",
                    data=MetadataAudit(
-                       dataset_id=sample_data.get("publishdata_id"),
+                       dataset_id=name.split(".")[0],  # use the dataset name
                        editor=sample_data.get("author"),
                        json_data=json.dumps(sample_data)))
             # Once data is approved, rename it!
-- 
cgit v1.2.3


From e200245b2a1666b7a16f4484891c7c2b143fefe9 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:44:30 +0300
Subject: wqflask: views: Rename endpoint to "/admin/data-sample/diffs/"

---
 wqflask/wqflask/views.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 760d5947..1a8536ac 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1391,7 +1391,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
     )
 
 
-@app.route("/data/approve/")
+@app.route("/admin/data-sample/diffs/")
 def display_diffs_admin():
     DIFF_DIR = "/tmp/sample-data/diffs"
     files = []
@@ -1438,7 +1438,7 @@ def approve_data(name):
             os.rename(os.path.join("/tmp/sample-data/diffs", name),
                       os.path.join("/tmp/sample-data/diffs",
                                    f"{name}.approved"))
-    return redirect("/data/approve/")
+    return redirect("/admin/data-sample/diffs/")
 
 
 @app.route("/display-file/<name>")
-- 
cgit v1.2.3


From 4594743baf6e6fd4b50f68665d009084f605bc78 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:45:17 +0300
Subject: wqflask: views: After approval, rename the file at the right point

---
 wqflask/wqflask/views.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1a8536ac..c7582782 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1434,10 +1434,11 @@ def approve_data(name):
                        dataset_id=name.split(".")[0],  # use the dataset name
                        editor=sample_data.get("author"),
                        json_data=json.dumps(sample_data)))
-            # Once data is approved, rename it!
-            os.rename(os.path.join("/tmp/sample-data/diffs", name),
-                      os.path.join("/tmp/sample-data/diffs",
-                                   f"{name}.approved"))
+    if modifications:
+        # Once data is approved, rename it!
+        os.rename(os.path.join("/tmp/sample-data/diffs", name),
+                  os.path.join("/tmp/sample-data/diffs",
+                               f"{name}.approved"))
     return redirect("/admin/data-sample/diffs/")
 
 
-- 
cgit v1.2.3


From 366c9c433a0b18db25f5cb28d7c7dc1ed17b3c67 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:46:07 +0300
Subject: Display a flash message after a file(and data) approval

squash! Display a flash message after a file(and data) approval
---
 wqflask/wqflask/templates/display_files.html | 9 +++++++++
 wqflask/wqflask/views.py                     | 6 +++++-
 2 files changed, 14 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
index 30974300..f8bc188f 100644
--- a/wqflask/wqflask/templates/display_files.html
+++ b/wqflask/wqflask/templates/display_files.html
@@ -2,6 +2,15 @@
 {% block title %}Trait Submission{% endblock %}
 {% block content %}
 <!-- Start of body -->
+{% with messages = get_flashed_messages(with_categories=true) %}
+{% if messages %}
+{% for category, message in messages %}
+<div class="container-fluid bg-{{ category }}">
+    <p>{{ message }}</p>
+</div>
+{% endfor %}
+{% endif %}
+{% endwith %}
 Show files for approval
 
 <div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index c7582782..11c8b347 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1414,12 +1414,13 @@ def approve_data(name):
         sample_data = json.load(myfile)
     PUBLISH_ID = sample_data.get("publishdata_id")
     modifications = [d for d in sample_data.get("Modifications")]
+    row_counts = len(modifications)
     for modification in modifications:
         if modification.get("Current"):
             (strain_id,
              strain_name,
              value, se, count) = modification.get("Current").split(",")
-            row_counts = update_sample_data(
+            update_sample_data(
                 conn=conn,
                 strain_name=strain_name,
                 strain_id=int(strain_id),
@@ -1439,6 +1440,9 @@ def approve_data(name):
         os.rename(os.path.join("/tmp/sample-data/diffs", name),
                   os.path.join("/tmp/sample-data/diffs",
                                f"{name}.approved"))
+        flash((f"Just updated data from: {name}; {row_counts} "
+               "row(s) modified!"),
+              "success")
     return redirect("/admin/data-sample/diffs/")
 
 
-- 
cgit v1.2.3


From 3241306917277278a218270a6691d103df6fee4e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 21:57:41 +0300
Subject: Reject diff data on click

---
 wqflask/wqflask/templates/display_files.html | 3 ++-
 wqflask/wqflask/views.py                     | 9 +++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
index f8bc188f..4b4babc4 100644
--- a/wqflask/wqflask/templates/display_files.html
+++ b/wqflask/wqflask/templates/display_files.html
@@ -17,7 +17,8 @@ Show files for approval
     <ul>
         {% for file in files %}
         <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/>
-            <button><a href="/data-samples/approve/{{ file }}">Approve</a></button> <button>Reject</button></li>
+            <button><a href="/data-samples/approve/{{ file }}">Approve</a></button>
+            <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li>
         {% endfor %}
     </ul>
 </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 11c8b347..69b432f5 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1446,6 +1446,15 @@ def approve_data(name):
     return redirect("/admin/data-sample/diffs/")
 
 
+@app.route("/data-samples/reject/<name>")
+def reject_data(name):
+    os.rename(os.path.join("/tmp/sample-data/diffs", name),
+              os.path.join("/tmp/sample-data/diffs",
+                           f"{name}.rejected"))
+    flash(f"{name} has been rejected!", "success")
+    return redirect("/admin/data-sample/diffs/")
+
+
 @app.route("/display-file/<name>")
 def display_file(name):
     with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
-- 
cgit v1.2.3


From fbe52a11f4471d928e398f09edc2e243bbbab58a Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 22:07:06 +0300
Subject: Rename display_files.html -> display_files_admin.html

---
 wqflask/wqflask/templates/display_files.html       | 32 ----------------------
 wqflask/wqflask/templates/display_files_admin.html | 32 ++++++++++++++++++++++
 wqflask/wqflask/views.py                           |  3 +-
 3 files changed, 34 insertions(+), 33 deletions(-)
 delete mode 100644 wqflask/wqflask/templates/display_files.html
 create mode 100644 wqflask/wqflask/templates/display_files_admin.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files.html b/wqflask/wqflask/templates/display_files.html
deleted file mode 100644
index 4b4babc4..00000000
--- a/wqflask/wqflask/templates/display_files.html
+++ /dev/null
@@ -1,32 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Trait Submission{% endblock %}
-{% block content %}
-<!-- Start of body -->
-{% with messages = get_flashed_messages(with_categories=true) %}
-{% if messages %}
-{% for category, message in messages %}
-<div class="container-fluid bg-{{ category }}">
-    <p>{{ message }}</p>
-</div>
-{% endfor %}
-{% endif %}
-{% endwith %}
-Show files for approval
-
-<div>
-    <ul>
-        {% for file in files %}
-        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/>
-            <button><a href="/data-samples/approve/{{ file }}">Approve</a></button>
-            <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li>
-        {% endfor %}
-    </ul>
-</div>
-{%endblock%}
-
-{% block js %}
-<script>
- gn_server_url = "{{ gn_server_url }}";
-
-</script>
-{% endblock %}
diff --git a/wqflask/wqflask/templates/display_files_admin.html b/wqflask/wqflask/templates/display_files_admin.html
new file mode 100644
index 00000000..4b4babc4
--- /dev/null
+++ b/wqflask/wqflask/templates/display_files_admin.html
@@ -0,0 +1,32 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+{% with messages = get_flashed_messages(with_categories=true) %}
+{% if messages %}
+{% for category, message in messages %}
+<div class="container-fluid bg-{{ category }}">
+    <p>{{ message }}</p>
+</div>
+{% endfor %}
+{% endif %}
+{% endwith %}
+Show files for approval
+
+<div>
+    <ul>
+        {% for file in files %}
+        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/>
+            <button><a href="/data-samples/approve/{{ file }}">Approve</a></button>
+            <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li>
+        {% endfor %}
+    </ul>
+</div>
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 69b432f5..56f9a5eb 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1399,7 +1399,8 @@ def display_diffs_admin():
         files = os.listdir(DIFF_DIR)
         files = filter(lambda x: not(x.endswith((".approved", ".rejected"))),
                        files)
-    return render_template("display_files.html",
+    return render_template("display_files_admin.html",
+                           files=files)
                            files=files)
 
 
-- 
cgit v1.2.3


From 72bdbc512ee250ffaa1fa0c1ba91b2a065a485d0 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 22:08:25 +0300
Subject: wqflask: views: Only show user's diff

---
 wqflask/wqflask/templates/display_files_user.html | 31 +++++++++++++++++++++++
 wqflask/wqflask/views.py                          | 14 ++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 wqflask/wqflask/templates/display_files_user.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/display_files_user.html b/wqflask/wqflask/templates/display_files_user.html
new file mode 100644
index 00000000..b6bab709
--- /dev/null
+++ b/wqflask/wqflask/templates/display_files_user.html
@@ -0,0 +1,31 @@
+{% extends "base.html" %}
+{% block title %}Trait Submission{% endblock %}
+{% block content %}
+<!-- Start of body -->
+{% with messages = get_flashed_messages(with_categories=true) %}
+{% if messages %}
+{% for category, message in messages %}
+<div class="container-fluid bg-{{ category }}">
+    <p>{{ message }}</p>
+</div>
+{% endfor %}
+{% endif %}
+{% endwith %}
+Show files for approval
+
+<div>
+    <ul>
+        {% for file in files %}
+        <li><a href="/display-file/{{ file }}" target="_blank">{{ file }}</a><br/>
+            <button><a href="/data-samples/reject/{{ file }}">Reject</a></button></li>
+        {% endfor %}
+    </ul>
+</div>
+{%endblock%}
+
+{% block js %}
+<script>
+ gn_server_url = "{{ gn_server_url }}";
+
+</script>
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 56f9a5eb..78da024f 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1392,6 +1392,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
 
 
 @app.route("/admin/data-sample/diffs/")
+@admin_login_required
 def display_diffs_admin():
     DIFF_DIR = "/tmp/sample-data/diffs"
     files = []
@@ -1401,6 +1402,19 @@ def display_diffs_admin():
                        files)
     return render_template("display_files_admin.html",
                            files=files)
+
+
+@app.route("/user/data-sample/diffs/")
+def display_diffs_users():
+    DIFF_DIR = "/tmp/sample-data/diffs"
+    files = []
+    author = g.user_session.record.get(b'user_name').decode("utf-8")
+    if os.path.exists(DIFF_DIR):
+        files = os.listdir(DIFF_DIR)
+        files = filter(lambda x: not(x.endswith((".approved", ".rejected"))) \
+                       and author in x,
+                       files)
+    return render_template("display_files_user.html",
                            files=files)
 
 
-- 
cgit v1.2.3


From cbe5d6edacafe7f1afba49e20c644a34fa9aaf7d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 22:19:57 +0300
Subject: Replace TMPDIR hard-coded val with one set from flask

---
 wqflask/wqflask/views.py | 39 ++++++++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 78da024f..2f704ac9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -544,6 +544,7 @@ def update_phenotype():
                            passwd=current_app.config.get("DB_PASS"),
                            host=current_app.config.get("DB_HOST"))
     data_ = request.form.to_dict()
+    TMPDIR = current_app.config.get("TMPDIR")
     author = g.user_session.record.get(b'user_name')
     if 'file' not in request.files:
         flash("No sample-data has been uploaded", "warning")
@@ -551,7 +552,7 @@ def update_phenotype():
         file_ = request.files['file']
         trait_name = str(data_.get('dataset-name'))
         phenotype_id = str(data_.get('phenotype-id', 35))
-        SAMPLE_DATADIR = "/tmp/sample-data/"
+        SAMPLE_DATADIR = os.path.join(TMPDIR, "sample-data")
         if not os.path.exists(SAMPLE_DATADIR):
             os.makedirs(SAMPLE_DATADIR)
         if not os.path.exists(os.path.join(SAMPLE_DATADIR,
@@ -563,14 +564,17 @@ def update_phenotype():
             os.makedirs(os.path.join(SAMPLE_DATADIR,
                                      "updated"))
         current_time = str(datetime.datetime.now().isoformat())
-        new_file_name = ("/tmp/sample-data/updated/"
-                         f"{author.decode('utf-8')}."
-                         f"{trait_name}.{phenotype_id}."
-                         f"{current_time}.csv")
-        uploaded_file_name = ("/tmp/sample-data/updated/"
-                              f"updated.{author.decode('utf-8')}."
-                              f"{trait_name}.{phenotype_id}."
-                              f"{current_time}.csv")
+        new_file_name = (os.path.join(TMPDIR,
+                                      "sample-data/updated/",
+                                      (f"{author.decode('utf-8')}."
+                                       f"{trait_name}.{phenotype_id}."
+                                       f"{current_time}.csv")))
+        uploaded_file_name = (os.path.join(
+            TMPDIR,
+            "sample-data/updated/",
+            (f"updated.{author.decode('utf-8')}."
+             f"{trait_name}.{phenotype_id}."
+             f"{current_time}.csv")))
         file_.save(new_file_name)
         publishdata_id = ""
         lines = []
@@ -1425,7 +1429,9 @@ def approve_data(name):
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
                            host=current_app.config.get("DB_HOST"))
-    with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
+    TMPDIR = current_app.config.get("TMPDIR")
+    with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
+                           name), 'r') as myfile:
         sample_data = json.load(myfile)
     PUBLISH_ID = sample_data.get("publishdata_id")
     modifications = [d for d in sample_data.get("Modifications")]
@@ -1452,8 +1458,8 @@ def approve_data(name):
                        json_data=json.dumps(sample_data)))
     if modifications:
         # Once data is approved, rename it!
-        os.rename(os.path.join("/tmp/sample-data/diffs", name),
-                  os.path.join("/tmp/sample-data/diffs",
+        os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name),
+                  os.path.join(f"{TMPDIR}/sample-data/diffs",
                                f"{name}.approved"))
         flash((f"Just updated data from: {name}; {row_counts} "
                "row(s) modified!"),
@@ -1463,8 +1469,9 @@ def approve_data(name):
 
 @app.route("/data-samples/reject/<name>")
 def reject_data(name):
-    os.rename(os.path.join("/tmp/sample-data/diffs", name),
-              os.path.join("/tmp/sample-data/diffs",
+    TMPDIR = current_app.config.get("TMPDIR")
+    os.rename(os.path.join(f"{TMPDIR}/sample-data/diffs", name),
+              os.path.join(f"{TMPDIR}/sample-data/diffs",
                            f"{name}.rejected"))
     flash(f"{name} has been rejected!", "success")
     return redirect("/admin/data-sample/diffs/")
@@ -1472,6 +1479,8 @@ def reject_data(name):
 
 @app.route("/display-file/<name>")
 def display_file(name):
-    with open(os.path.join("/tmp/sample-data/diffs", name), 'r') as myfile:
+    TMPDIR = current_app.config.get("TMPDIR")
+    with open(os.path.join(f"{TMPDIR}/sample-data/diffs",
+                           name), 'r') as myfile:
         content = myfile.read()
     return Response(content, mimetype='text/json')
-- 
cgit v1.2.3


From 759b04823818cd09f5e8e78299f270b3f7b73042 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 2 Aug 2021 22:28:00 +0300
Subject: Remove hard coded PATH for csvdiff binary

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2f704ac9..a40e0d44 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -589,7 +589,7 @@ def update_phenotype():
                                          phenotype_id=str(phenotype_id))
         with open(uploaded_file_name, "w") as f_:
             f_.write(csv_.split("\n\n")[-1])
-        r = run_cmd(cmd=("/home/bonface/opt/genenetwork3/bin/csvdiff "
+        r = run_cmd(cmd=("csvdiff "
                          f"'{uploaded_file_name}' '{new_file_name}' "
                          "--format json"))
         diff_output = ("/tmp/sample-data/diffs/"
-- 
cgit v1.2.3


From a24ea03594d6879adf92cd4db2b52108ddb352bd Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 4 Aug 2021 14:51:20 +0300
Subject: wqflask: views: Replace hard-coded "/tmp" dir

---
 wqflask/wqflask/views.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a40e0d44..fe81bb6c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -592,7 +592,7 @@ def update_phenotype():
         r = run_cmd(cmd=("csvdiff "
                          f"'{uploaded_file_name}' '{new_file_name}' "
                          "--format json"))
-        diff_output = ("/tmp/sample-data/diffs/"
+        diff_output = (f"{TMPDIR}/sample-data/diffs/"
                        f"{trait_name}.{author.decode('utf-8')}."
                        f"{phenotype_id}.{current_time}.json")
         with open(diff_output, "w") as f:
@@ -1398,7 +1398,8 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
 @app.route("/admin/data-sample/diffs/")
 @admin_login_required
 def display_diffs_admin():
-    DIFF_DIR = "/tmp/sample-data/diffs"
+    TMPDIR = current_app.config.get("TMPDIR")
+    DIFF_DIR = f"{TMPDIR}/sample-data/diffs"
     files = []
     if os.path.exists(DIFF_DIR):
         files = os.listdir(DIFF_DIR)
@@ -1410,7 +1411,8 @@ def display_diffs_admin():
 
 @app.route("/user/data-sample/diffs/")
 def display_diffs_users():
-    DIFF_DIR = "/tmp/sample-data/diffs"
+    TMPDIR = current_app.config.get("TMPDIR")
+    DIFF_DIR = f"{TMPDIR}/sample-data/diffs"
     files = []
     author = g.user_session.record.get(b'user_name').decode("utf-8")
     if os.path.exists(DIFF_DIR):
-- 
cgit v1.2.3


From 457296f004e576a632d2e77c656d41d9ceed0c47 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 4 Aug 2021 16:28:34 +0300
Subject: wqflask: views: Remove unnecessary casting for "count"

Sometimes, the "count" value can be an "x", as opposed to an
int. With the cast, an un-handled error could be thrown.
---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fe81bb6c..76fe029f 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1450,7 +1450,7 @@ def approve_data(name):
                 publish_data_id=int(PUBLISH_ID),
                 value=value,
                 error=se,
-                count=int(count)
+                count=count
             )
             insert(conn,
                    table="metadata_audit",
-- 
cgit v1.2.3


From b8c88668dbf1bc96c2faf14c483e3af35babc3e5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 5 Aug 2021 20:51:46 +0000
Subject: Generate phenotype and covariate filenames for GEMMA from a hash of
 values and dataset name - previously the covariate filename was static and
 the phenotype filename was just random

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 35 ++++++++++++----------
 1 file changed, 20 insertions(+), 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index f88c5ac8..efd8bba8 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -11,6 +11,7 @@ from utility.tools import flat_files
 from utility.tools import GEMMA_WRAPPER_COMMAND
 from utility.tools import TEMPDIR
 from utility.tools import WEBSERVER_MODE
+from gn3.computations.gemma import generate_hash_of_string
 
 import utility.logger
 logger = utility.logger.getLogger(__name__)
@@ -34,10 +35,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
         genofile_name = this_dataset.group.name
 
     if first_run:
-        trait_filename = (f"{str(this_dataset.group.name)}_"
-                          f"{str(this_trait.name)}_"
-                          f"{generate_random_n_string(6)}")
-        gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename)
+        pheno_filename = gen_pheno_txt_file(this_dataset, genofile_name, vals)
 
         if not os.path.isfile(f"{webqtlConfig.GENERATED_IMAGE_DIR}"
                               f"{genofile_name}_output.assoc.txt"):
@@ -56,13 +54,13 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
 
         chr_list_string = ",".join(this_chromosomes_name)
         if covariates != "":
-            gen_covariates_file(this_dataset, covariates, samples)
+            covar_filename = gen_covariates_file(this_dataset, covariates, samples)
         if use_loco == "True":
             generate_k_command = (f"{GEMMA_WRAPPER_COMMAND} --json --loco "
                                   f"{chr_list_string} -- {GEMMAOPTS} "
                                   f"-g {flat_files('genotype/bimbam')}/"
                                   f"{genofile_name}_geno.txt -p "
-                                  f"{TEMPDIR}/gn2/{trait_filename}.txt -a "
+                                  f"{TEMPDIR}/gn2/{pheno_filename}.txt -a "
                                   f"{flat_files('genotype/bimbam')}/"
                                   f"{genofile_name}_snps.txt -gk > "
                                   f"{TEMPDIR}/gn2/{k_output_filename}.json")
@@ -73,10 +71,10 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
                              f"-- {GEMMAOPTS} "
                              f"-g {flat_files('genotype/bimbam')}/"
                              f"{genofile_name}_geno.txt "
-                             f"-p {TEMPDIR}/gn2/{trait_filename}.txt ")
+                             f"-p {TEMPDIR}/gn2/{pheno_filename}.txt ")
             if covariates != "":
                 gemma_command += (f"-c {flat_files('mapping')}/"
-                                  f"{this_dataset.group.name}_covariates.txt "
+                                  f"{covar_filename}.txt "
                                   f"-a {flat_files('genotype/bimbam')}/"
                                   f"{genofile_name}_snps.txt "
                                   f"-lmm 9 -maf {maf} > {TEMPDIR}/gn2/"
@@ -92,7 +90,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
                                   f"{GEMMAOPTS} "
                                   f" -g {flat_files('genotype/bimbam')}/"
                                   f"{genofile_name}_geno.txt -p "
-                                  f"{TEMPDIR}/gn2/{trait_filename}.txt -a "
+                                  f"{TEMPDIR}/gn2/{pheno_filename}.txt -a "
                                   f"{flat_files('genotype/bimbam')}/"
                                   f"{genofile_name}_snps.txt -gk > "
                                   f"{TEMPDIR}/gn2/{k_output_filename}.json")
@@ -106,12 +104,11 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
                              f"{genofile_name}_snps.txt "
                              f"-lmm 9 -g {flat_files('genotype/bimbam')}/"
                              f"{genofile_name}_geno.txt -p "
-                             f"{TEMPDIR}/gn2/{trait_filename}.txt ")
+                             f"{TEMPDIR}/gn2/{pheno_filename}.txt ")
 
             if covariates != "":
                 gemma_command += (f" -c {flat_files('mapping')}/"
-                                  f"{this_dataset.group.name}"
-                                  f"_covariates.txt > "
+                                  f"{covar_filename}.txt > "
                                   f"{TEMPDIR}/gn2/{gwa_output_filename}.json")
             else:
                 gemma_command += f" > {TEMPDIR}/gn2/{gwa_output_filename}.json"
@@ -129,16 +126,20 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
         return marker_obs, gwa_output_filename
 
 
-def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
+def gen_pheno_txt_file(this_dataset, genofile_name, vals):
     """Generates phenotype file for GEMMA"""
 
-    with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile:
+    filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals))
+
+    with open(f"{TEMPDIR}/gn2/{filename}.txt", "w") as outfile:
         for value in vals:
             if value == "x":
                 outfile.write("NA\n")
             else:
                 outfile.write(value + "\n")
 
+    return filename
+
 
 def gen_covariates_file(this_dataset, covariates, samples):
     covariate_list = covariates.split(",")
@@ -168,14 +169,18 @@ def gen_covariates_file(this_dataset, covariates, samples):
                     this_covariate_data.append("-9")
         covariate_data_object.append(this_covariate_data)
 
+    filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object))
+
     with open((f"{flat_files('mapping')}/"
-               f"{this_dataset.group.name}_covariates.txt"),
+               f"{filename}.txt"),
               "w") as outfile:
         for i in range(len(covariate_data_object[0])):
             for this_covariate in covariate_data_object:
                 outfile.write(str(this_covariate[i]) + "\t")
             outfile.write("\n")
 
+    return filename
+
 
 def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
 
-- 
cgit v1.2.3


From db0bdf52156b4f75402a7a92584d162aa5d9b151 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Aug 2021 18:34:31 +0000
Subject: Removed some paths that have been throwing errors in the logs
 constantly

---
 wqflask/wqflask/static/new/css/bootstrap-custom.css | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/css/bootstrap-custom.css b/wqflask/wqflask/static/new/css/bootstrap-custom.css
index 7c8549e1..a0d3ff6a 100644
--- a/wqflask/wqflask/static/new/css/bootstrap-custom.css
+++ b/wqflask/wqflask/static/new/css/bootstrap-custom.css
@@ -327,7 +327,7 @@ th {
     font-family: 'Glyphicons Halflings';
 
     src: url('../fonts/glyphicons-halflings-regular.eot');
-    src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.woff') format('woff'), url('../fonts/glyphicons-halflings-regular.ttf') format('truetype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg');
+    src: url('../fonts/glyphicons-halflings-regular.eot?#iefix') format('embedded-opentype'), url('../fonts/glyphicons-halflings-regular.svg#glyphicons_halflingsregular') format('svg');
 }
 
 .glyphicon {
@@ -7554,5 +7554,3 @@ button.close {
         display: none !important;
     }
 }
-
-/*# sourceMappingURL=bootstrap.css.map */
\ No newline at end of file
-- 
cgit v1.2.3


From 162851e8f92ed6d01c25d4f6034bcac4986e8094 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 10 Aug 2021 19:01:47 +0000
Subject: Replaced forward slashes with underscores in the hashed filenames
 used by GEMMA, since the forward slashes make the paths not work properly

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index efd8bba8..623ab87f 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -129,7 +129,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco,
 def gen_pheno_txt_file(this_dataset, genofile_name, vals):
     """Generates phenotype file for GEMMA"""
 
-    filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals))
+    filename = "PHENO_" + generate_hash_of_string(this_dataset.name + str(vals)).replace("/", "_")
 
     with open(f"{TEMPDIR}/gn2/{filename}.txt", "w") as outfile:
         for value in vals:
@@ -169,7 +169,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
                     this_covariate_data.append("-9")
         covariate_data_object.append(this_covariate_data)
 
-    filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object))
+    filename = "COVAR_" + generate_hash_of_string(this_dataset.name + str(covariate_data_object)).replace("/", "_")
 
     with open((f"{flat_files('mapping')}/"
                f"{filename}.txt"),
-- 
cgit v1.2.3


From 10ef0e532324e838c7be5a0f7f451dcaec9c2ce8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 10 Aug 2021 20:19:27 +0000
Subject: Fixed issue that caused correlations to not work with temp traits
 after switching to using the GN3 code

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 7 +++++--
 wqflask/wqflask/correlation/show_corr_results.py   | 5 ++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index c96da8ee..f7c06a46 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -18,7 +18,10 @@ from gn3.db_utils import database_connector
 def create_target_this_trait(start_vars):
     """this function creates the required trait and target dataset for correlation"""
 
-    this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset'])
+    if start_vars['dataset'] == "Temp":
+        this_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group'])
+    else:
+        this_dataset = data_set.create_dataset(dataset_name=start_vars['dataset'])
     target_dataset = data_set.create_dataset(
         dataset_name=start_vars['corr_dataset'])
     this_trait = create_trait(dataset=this_dataset,
@@ -306,4 +309,4 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
             "trait_symbol_dict": trait_symbol_dict,
             "symbol_tissue_vals_dict": corr_result_tissue_vals_dict
         }
-        return (primary_tissue_data, target_tissue_data)
\ No newline at end of file
+        return (primary_tissue_data, target_tissue_data)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e2daa991..d73965da 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -30,7 +30,10 @@ def set_template_vars(start_vars, correlation_data):
     corr_type = start_vars['corr_type']
     corr_method = start_vars['corr_sample_method']
 
-    this_dataset_ob = create_dataset(dataset_name=start_vars['dataset'])
+    if start_vars['dataset'] == "Temp":
+        this_dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group'])
+    else:
+        this_dataset_ob = create_dataset(dataset_name=start_vars['dataset'])
     this_trait = create_trait(dataset=this_dataset_ob,
                               name=start_vars['trait_id'])
 
-- 
cgit v1.2.3


From 2dce5e20b5dcfa032a32a486bb4e4a4390c5f2b7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 10 Aug 2021 20:44:13 +0000
Subject: Fixed the way n_samples is calculated for the loading page and
 mapping figure; previously it would includes parents/f1s

---
 wqflask/wqflask/views.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 76fe029f..44560427 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1033,7 +1033,7 @@ def loading_page():
                     start_vars['dataset'], group_name=start_vars['group'])
             else:
                 dataset = create_dataset(start_vars['dataset'])
-            samples = start_vars['primary_samples'].split(",")
+            samples = dataset.group.samplelist
             if 'genofile' in start_vars:
                 if start_vars['genofile'] != "":
                     genofile_string = start_vars['genofile']
@@ -1178,9 +1178,8 @@ def mapping_results_page():
                 gn1_template_vars = display_mapping_results.DisplayMappingResults(
                     result).__dict__
 
-                with Bench("Rendering template"):
-                    rendered_template = render_template(
-                        "mapping_results.html", **gn1_template_vars)
+                rendered_template = render_template(
+                    "mapping_results.html", **gn1_template_vars)
 
     return rendered_template
 
-- 
cgit v1.2.3


From 9a1e7270bc9c2130a4cb9405f2de24053dea6582 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 11 Aug 2021 20:26:45 +0000
Subject: Sort by attribute ID instead of name in
 initialize_show_trait_tables.js when defining attribute columns

---
 wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 6ca92fb6..49311f87 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -93,7 +93,7 @@ build_columns = function() {
     );
   }
 
-  attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1)
+  attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1)
   for (i = 0; i < attr_keys.length; i++){
     column_list.push(
       {
@@ -101,7 +101,7 @@ build_columns = function() {
         'type': "natural",
         'data': null,
         'render': function(data, type, row, meta) {
-          attr_name = Object.keys(data.extra_attributes).sort()[meta.col - data.first_attr_col]
+          attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col]
 
           if (attr_name != null && attr_name != undefined){
             if (Array.isArray(data.extra_attributes[attr_name])){
-- 
cgit v1.2.3


From 67bab7f9cd12ceb7ea0b0ac4b0b98c24935f3ab5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 11 Aug 2021 20:28:35 +0000
Subject: Fixed issue that caused case attribute columns to become unaligned if
 some strains didn't have values for all case attributes + changed ordering to
 use attribute ID instead of name

---
 wqflask/wqflask/show_trait/SampleList.py | 44 ++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 19 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 92cea550..e4bbe5b9 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -32,7 +32,7 @@ class SampleList:
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            # ZS: self.this_trait will be a list if it is a Temp trait
+            # self.this_trait will be a list if it is a Temp trait
             if isinstance(self.this_trait, list):
                 sample = webqtlCaseData.webqtlCaseData(name=sample_name)
                 if counter <= len(self.this_trait):
@@ -47,7 +47,7 @@ class SampleList:
                                 name=sample_name,
                                 value=float(self.this_trait[counter - 1]))
             else:
-                # ZS - If there's no value for the sample/strain,
+                # If there's no value for the sample/strain,
                 # create the sample object (so samples with no value
                 # are still displayed in the table)
                 try:
@@ -63,29 +63,29 @@ class SampleList:
 
             sample.this_id = str(counter)
 
-            # ZS: For extra attribute columns; currently only used by
+            # For extra attribute columns; currently only used by
             # several datasets
             if self.sample_attribute_values:
                 sample.extra_attributes = self.sample_attribute_values.get(
                     sample_name, {})
 
-                # ZS: Add a url so RRID case attributes can be displayed as links
-                if 'rrid' in sample.extra_attributes:
+                # Add a url so RRID case attributes can be displayed as links
+                if '36' in sample.extra_attributes:
                     if self.dataset.group.species == "mouse":
-                        if len(sample.extra_attributes['rrid'].split(":")) > 1:
-                            the_rrid = sample.extra_attributes['rrid'].split(":")[
+                        if len(sample.extra_attributes['36'].split(":")) > 1:
+                            the_rrid = sample.extra_attributes['36'].split(":")[
                                 1]
-                            sample.extra_attributes['rrid'] = [
-                                sample.extra_attributes['rrid']]
-                            sample.extra_attributes['rrid'].append(
+                            sample.extra_attributes['36'] = [
+                                sample.extra_attributes['36']]
+                            sample.extra_attributes['36'].append(
                                 webqtlConfig.RRID_MOUSE_URL % the_rrid)
                     elif self.dataset.group.species == "rat":
-                        if len(str(sample.extra_attributes['rrid'])):
-                            the_rrid = sample.extra_attributes['rrid'].split("_")[
+                        if len(str(sample.extra_attributes['36'])):
+                            the_rrid = sample.extra_attributes['36'].split("_")[
                                 1]
-                            sample.extra_attributes['rrid'] = [
-                                sample.extra_attributes['rrid']]
-                            sample.extra_attributes['rrid'].append(
+                            sample.extra_attributes['36'] = [
+                                sample.extra_attributes['36']]
+                            sample.extra_attributes['36'].append(
                                 webqtlConfig.RRID_RAT_URL % the_rrid)
 
             self.sample_list.append(sample)
@@ -128,12 +128,13 @@ class SampleList:
                         FROM CaseAttribute, CaseAttributeXRefNew
                         WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
                         AND CaseAttributeXRefNew.InbredSetId = %s
-                        ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
+                        ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),))
 
         self.attributes = {}
         for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
             key, name = attr
             self.attributes[key] = Bunch()
+            self.attributes[key].id = key
             self.attributes[key].name = name
             self.attributes[key].distinct_values = [
                 item.Value for item in values]
@@ -168,10 +169,13 @@ class SampleList:
 
             for sample_name, items in itertools.groupby(results.fetchall(), lambda row: row.SampleName):
                 attribute_values = {}
+                # Make a list of attr IDs without values (that have values for other samples)
+                valueless_attr_ids = [self.attributes[key].id for key in self.attributes.keys()]
                 for item in items:
+                    valueless_attr_ids.remove(item.Id)
                     attribute_value = item.Value
 
-                    # ZS: If it's an int, turn it into one for sorting
+                    # If it's an int, turn it into one for sorting
                     # (for example, 101 would be lower than 80 if
                     # they're strings instead of ints)
                     try:
@@ -179,8 +183,10 @@ class SampleList:
                     except ValueError:
                         pass
 
-                    attribute_values[self.attributes[item.Id].name.lower(
-                    )] = attribute_value
+                    attribute_values[str(item.Id)] = attribute_value
+                for attr_id in valueless_attr_ids:
+                    attribute_values[str(attr_id)] = ""
+
                 self.sample_attribute_values[sample_name] = attribute_values
 
     def get_first_attr_col(self):
-- 
cgit v1.2.3


From eecaad2dac6efa885540287a7ef5a273c6d18be2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 21:55:26 +0000
Subject: Get case attribute descriptions from DB and display them as mouseover
 titles in the sample table headers for the trait page

---
 wqflask/wqflask/show_trait/SampleList.py                           | 7 ++++---
 .../wqflask/static/new/javascript/initialize_show_trait_tables.js  | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index e4bbe5b9..ae30aa59 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -124,18 +124,19 @@ class SampleList:
 
         # Get attribute names and distinct values for each attribute
         results = g.db.execute('''
-                        SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttributeXRefNew.Value
+                        SELECT DISTINCT CaseAttribute.Id, CaseAttribute.Name, CaseAttribute.Description, CaseAttributeXRefNew.Value
                         FROM CaseAttribute, CaseAttributeXRefNew
                         WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
                         AND CaseAttributeXRefNew.InbredSetId = %s
                         ORDER BY CaseAttribute.Id''', (str(self.dataset.group.id),))
 
         self.attributes = {}
-        for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
-            key, name = attr
+        for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name, row.Description)):
+            key, name, description = attr
             self.attributes[key] = Bunch()
             self.attributes[key].id = key
             self.attributes[key].name = name
+            self.attributes[key].description = description
             self.attributes[key].distinct_values = [
                 item.Value for item in values]
             self.attributes[key].distinct_values = natural_sort(
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 49311f87..4de1b0ac 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -97,7 +97,7 @@ build_columns = function() {
   for (i = 0; i < attr_keys.length; i++){
     column_list.push(
       {
-        'title': "<div style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
+        'title': "<div title='" + js_data.attributes[attr_keys[i]].description + "' style='text-align: " + js_data.attributes[attr_keys[i]].alignment + "'>" + js_data.attributes[attr_keys[i]].name + "</div>",
         'type': "natural",
         'data': null,
         'render': function(data, type, row, meta) {
-- 
cgit v1.2.3


From f4fbb6d53419a19c6ee67977d18605cdcbb09c0e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 22:35:53 +0000
Subject: add function for reading in JSON file that lists sample lists unique
 to each study within a group (in this case only BXD Longevity for now)

---
 wqflask/base/data_set.py                 | 9 +++++++++
 wqflask/wqflask/show_trait/show_trait.py | 1 +
 2 files changed, 10 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..b8f2f9fb 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -398,6 +398,15 @@ class DatasetGroup:
         if maternal and paternal:
             self.parlist = [maternal, paternal]
 
+    def get_study_samplelists(self):
+        study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name)
+        try:
+            f = open(study_sample_file)
+        except:
+            return None
+        study_samples = json.load(f)
+        return study_samples
+
     def get_genofiles(self):
         jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
         try:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c07430dd..d3356bc3 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -192,6 +192,7 @@ class ShowTrait:
                 [self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
 
         self.genofiles = self.dataset.group.get_genofiles()
+        self.study_samplelists = self.dataset.group.get_study_samplelists()
 
         # ZS: No need to grab scales from .geno file unless it's using
         # a mapping method that reads .geno files
-- 
cgit v1.2.3


From 308860f05b87e5fc3899230b7312be9543e6c299 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:16:02 +0000
Subject: Add option to filter samples by study to template

---
 .../templates/show_trait_transform_and_filter.html    | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 20f78b48..56c3c30e 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -45,6 +45,25 @@
         <input type="button" id="exclude_by_attr" class="btn btn-danger" value="Block">
     </div>
     {% endif %}
+    {% if study_samplelists|length > 0 %}
+    <div id="filterMenuSpan" class="input-append block-div-2">
+      <label for="filter_study_select">Filter samples by study: </label>
+      <select id="filter_study">
+        {% for study in study_samplelists %}
+        <option value="{{ loop.index + 1 }}">{{ study }}</option>
+        {% endfor %}
+      </select>
+      <select id="filter_study_group" size="1">
+        <option value="primary">
+          {{ sample_group_types['samples_primary'] }}
+        </option>
+        <option value="other">
+          {{ sample_group_types['samples_other'] }}
+        </option>
+      </select>
+      <input type="button" id="filter_by_study" class="btn btn-danger" value="Filter">
+    </div>
+    {% endif %}
     <div id="filterMenuSpan" class="input-append block-div-2">
       <label for="filter_samples_field">Filter samples by {% if (numerical_var_list|length == 0) and (not js_data.se_exists) %}value{% endif %} </label>
       {% if (numerical_var_list|length > 0) or js_data.se_exists %}
-- 
cgit v1.2.3


From 98683bd5cc809aa03e0bd58a67733498b4f56a9d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:17:04 +0000
Subject: Fix the way the study_sample_lists path is set and checked

---
 wqflask/base/data_set.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b8f2f9fb..1042e1bd 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -399,7 +399,7 @@ class DatasetGroup:
             self.parlist = [maternal, paternal]
 
     def get_study_samplelists(self):
-        study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name)
+        study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists')
         try:
             f = open(study_sample_file)
         except:
-- 
cgit v1.2.3


From 810b2ace0a9cb2511cf0ef6f0c01f70a0ce11915 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:19:38 +0000
Subject: Return empty list instead of None in get_study_samplelists

---
 wqflask/base/data_set.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1042e1bd..0ea61faa 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -403,7 +403,7 @@ class DatasetGroup:
         try:
             f = open(study_sample_file)
         except:
-            return None
+            return []
         study_samples = json.load(f)
         return study_samples
 
-- 
cgit v1.2.3


From 11d5e9ffbf48c6a2fa7a59f10a9d7fe44cee0c23 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:20:28 +0000
Subject: Get list of study titles to use for the dropdown menu and store the
 full list of study samplelists as a hddn input (don't like this, but no easy
 alternative right now)

---
 wqflask/wqflask/show_trait/show_trait.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d3356bc3..bc97d417 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -192,7 +192,8 @@ class ShowTrait:
                 [self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
 
         self.genofiles = self.dataset.group.get_genofiles()
-        self.study_samplelists = self.dataset.group.get_study_samplelists()
+        study_samplelist_json = self.dataset.group.get_study_samplelists()
+        self.study_samplelists = [study["title"] for study in study_samplelist_json]
 
         # ZS: No need to grab scales from .geno file unless it's using
         # a mapping method that reads .geno files
@@ -281,6 +282,7 @@ class ShowTrait:
         hddn['selected_chr'] = -1
         hddn['mapping_display_all'] = True
         hddn['suggestive'] = 0
+        hddn['study_samplelists'] = json.dumps(study_samplelist_json)
         hddn['num_perm'] = 0
         hddn['categorical_vars'] = ""
         if categorical_var_list:
-- 
cgit v1.2.3


From 88c9f4f9bd2adca23052fc3f5c5b965accf6722d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:20:52 +0000
Subject: Add JS for filtering sample table rows by study samplelist

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 77ef1720..3957175b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -713,10 +713,24 @@ block_by_index = function() {
   for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
     index = index_list[_k];
     val_nodes[index - 1].childNodes[0].value = "x";
-
   }
 };
 
+filter_by_study = function() {
+  let this_study = $('#filter_study').val();
+  let block_group = $('#filter_study_group').val();
+  let study_sample_data = JSON.parse($('input[name=study_samplelists]').val())
+  let filter_samples = study_sample_data[parseInt(this_study)]['samples']
+  let sample_nodes = table_api.column(2).nodes().to$();
+  let val_nodes = table_api.column(3).nodes().to$();
+  for (i = 0; i < sample_nodes.length; i++) {
+    this_sample = sample_nodes[i].childNodes[0].innerText;
+    if (!filter_samples.includes(this_sample)){
+      val_nodes[i].childNodes[0].value = "x";
+    }
+  }
+}
+
 filter_by_value = function() {
   let filter_logic = $('#filter_logic').val();
   let filter_column = $('#filter_column').val();
@@ -1690,6 +1704,11 @@ $('#block_by_index').click(function(){
   edit_data_change();
 });
 
+$('#filter_by_study').click(function(){
+  filter_by_study();
+  edit_data_change();
+})
+
 $('#filter_by_value').click(function(){
   filter_by_value();
   edit_data_change();
-- 
cgit v1.2.3


From 9ae4c8d0370137c3a698d57566305d815929d4ce Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:28:08 +0000
Subject: Fixed issue where 1 was added to the loop.index instead of subtracted
 + only show the sample group selection if there are more than one sample
 groups

---
 wqflask/wqflask/templates/show_trait_transform_and_filter.html | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 56c3c30e..064fd3e5 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -50,9 +50,10 @@
       <label for="filter_study_select">Filter samples by study: </label>
       <select id="filter_study">
         {% for study in study_samplelists %}
-        <option value="{{ loop.index + 1 }}">{{ study }}</option>
+        <option value="{{ loop.index - 1 }}">{{ study }}</option>
         {% endfor %}
       </select>
+      {% if sample_groups|length != 1 %}
       <select id="filter_study_group" size="1">
         <option value="primary">
           {{ sample_group_types['samples_primary'] }}
@@ -61,6 +62,7 @@
           {{ sample_group_types['samples_other'] }}
         </option>
       </select>
+      {% endif %}
       <input type="button" id="filter_by_study" class="btn btn-danger" value="Filter">
     </div>
     {% endif %}
-- 
cgit v1.2.3


From 6acafff1b22089916b8323afb872e2ebed37943a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:28:49 +0000
Subject: Account for user selecting one of the two sample groups if more than
 one exist

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 3957175b..845ed907 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -718,9 +718,19 @@ block_by_index = function() {
 
 filter_by_study = function() {
   let this_study = $('#filter_study').val();
-  let block_group = $('#filter_study_group').val();
+
   let study_sample_data = JSON.parse($('input[name=study_samplelists]').val())
   let filter_samples = study_sample_data[parseInt(this_study)]['samples']
+
+  if ($('#filter_study_group').length){
+    let block_group = $('#filter_study_group').val();
+    if (block_group === "other") {
+      table_api = $('#samples_other').DataTable();
+    } else {
+      table_api = $('#samples_primary').DataTable();
+    }
+  }
+
   let sample_nodes = table_api.column(2).nodes().to$();
   let val_nodes = table_api.column(3).nodes().to$();
   for (i = 0; i < sample_nodes.length; i++) {
-- 
cgit v1.2.3


From e2ee1c489f0eb59c3efbf81d42f43a1f74cd1adb Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 6 Aug 2021 15:31:30 +0300
Subject: wqflask: show_trait:: Remove debug comment

---
 wqflask/wqflask/show_trait/show_trait.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c07430dd..b640ec27 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -520,6 +520,9 @@ class ShowTrait:
                                          sample_group_type='primary',
                                          header="%s Only" % (self.dataset.group.name))
             self.sample_groups = (primary_samples,)
+            print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
+            print(self.sample_groups)
+            print("\nttttttttttttttttttttttttttttttttttttttttttttt\n")
 
         self.primary_sample_names = primary_sample_names
         self.dataset.group.allsamples = all_samples_ordered
-- 
cgit v1.2.3


From 579ae94b08f0b1cef00350b54dadc12869ad70de Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 6 Aug 2021 16:15:17 +0300
Subject: base: data_set: Remove unnecessary comments and logging statements

---
 wqflask/base/data_set.py | 12 ------------
 1 file changed, 12 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..edc22540 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class Markers:
             filtered_markers = []
             for marker in self.markers:
                 if marker['name'] in p_values:
-                    # logger.debug("marker {} IS in p_values".format(i))
                     marker['p_value'] = p_values[marker['name']]
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
@@ -298,7 +297,6 @@ class HumanMarkers(Markers):
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
-            # logger.debug("splat:", splat)
             if len(specified_markers) > 0:
                 if splat[1] in specified_markers:
                     marker = {}
@@ -737,7 +735,6 @@ class DataSet:
             and Strain.SpeciesId=Species.Id
             and Species.name = '{}'
             """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
-        logger.sql(query)
         results = dict(g.db.execute(query).fetchall())
         sample_ids = [results[item] for item in self.samplelist]
 
@@ -908,7 +905,6 @@ class PhenotypeDataSet(DataSet):
                         Geno.Name = '%s' and
                         Geno.SpeciesId = Species.Id
                 """ % (species, this_trait.locus)
-                logger.sql(query)
                 result = g.db.execute(query).fetchone()
 
                 if result:
@@ -938,7 +934,6 @@ class PhenotypeDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """
-        logger.sql(query)
         results = g.db.execute(query, (trait, self.id)).fetchall()
         return results
 
@@ -1005,7 +1000,6 @@ class GenotypeDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """
-        logger.sql(query)
         results = g.db.execute(query,
                                (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
                                 trait, self.name)).fetchall()
@@ -1126,8 +1120,6 @@ class MrnaAssayDataSet(DataSet):
                 ProbeSet.Name = '%s'
             """ % (escape(str(this_trait.dataset.id)),
                    escape(this_trait.name)))
-
-            logger.sql(query)
             result = g.db.execute(query).fetchone()
 
             mean = result[0] if result else 0
@@ -1147,7 +1139,6 @@ class MrnaAssayDataSet(DataSet):
                         Geno.Name = '{}' and
                         Geno.SpeciesId = Species.Id
                 """.format(species, this_trait.locus)
-                logger.sql(query)
                 result = g.db.execute(query).fetchone()
 
                 if result:
@@ -1179,7 +1170,6 @@ class MrnaAssayDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """ % (escape(trait), escape(self.name))
-        logger.sql(query)
         results = g.db.execute(query).fetchall()
         return results
 
@@ -1190,7 +1180,6 @@ class MrnaAssayDataSet(DataSet):
                     where ProbeSetXRef.ProbeSetFreezeId = %s and
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
                 """ % (column_name, escape(str(self.id)))
-        logger.sql(query)
         results = g.db.execute(query).fetchall()
 
         return dict(results)
@@ -1224,7 +1213,6 @@ def geno_mrna_confidentiality(ob):
 
     query = '''SELECT Id, Name, FullName, confidentiality,
                         AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
-    logger.sql(query)
     result = g.db.execute(query)
 
     (dataset_id,
-- 
cgit v1.2.3


From 2071107566d89a12fe27fdcc94dd16b7b8680f83 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 16 Aug 2021 11:38:05 +0300
Subject: wqflask: views: Remove commented out code blocks

---
 wqflask/wqflask/views.py | 28 ----------------------------
 1 file changed, 28 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 44560427..08e895cb 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -365,20 +365,6 @@ def wcgna_setup():
     return render_template("wgcna_setup.html", **request.form)
 
 
-# @app.route("/wgcna_results", methods=('POST',))
-# def wcgna_results():
-#     logger.info("In wgcna, request.form is:", request.form)
-#     logger.info(request.url)
-#     # Start R, load the package and pointers and create the analysis
-#     wgcna = wgcna_analysis.WGCNA()
-#     # Start the analysis, a wgcnaA object should be a separate long running thread
-#     wgcnaA = wgcna.run_analysis(request.form)
-#     # After the analysis is finished store the result
-#     result = wgcna.process_results(wgcnaA)
-#     # Display them using the template
-#     return render_template("wgcna_results.html", **result)
-
-
 @app.route("/ctl_setup", methods=('POST',))
 def ctl_setup():
     # We are going to get additional user input for the analysis
@@ -388,20 +374,6 @@ def ctl_setup():
     return render_template("ctl_setup.html", **request.form)
 
 
-# @app.route("/ctl_results", methods=('POST',))
-# def ctl_results():
-#     logger.info("In ctl, request.form is:", request.form)
-#     logger.info(request.url)
-#     # Start R, load the package and pointers and create the analysis
-#     ctl = ctl_analysis.CTL()
-#     # Start the analysis, a ctlA object should be a separate long running thread
-#     ctlA = ctl.run_analysis(request.form)
-#     # After the analysis is finished store the result
-#     result = ctl.process_results(ctlA)
-#     # Display them using the template
-#     return render_template("ctl_results.html", **result)
-
-
 @app.route("/intro")
 def intro():
     doc = Docs("intro", request.args)
-- 
cgit v1.2.3


From 923d849d640e3048422e3cdfa6ce24716cfa7904 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 16 Aug 2021 18:54:16 +0300
Subject: wqflask: views: Use "inbredset_id" in the "Edit Trait" URL

---
 wqflask/wqflask/views.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 08e895cb..3f0ab93f 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -408,9 +408,9 @@ def submit_trait_form():
         version=GN_VERSION)
 
 
-@app.route("/trait/<name>/edit/phenotype-id/<phenotype_id>")
+@app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
 @admin_login_required
-def edit_phenotype(name, phenotype_id):
+def edit_phenotype(name, inbredset_id):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
                            passwd=current_app.config.get("DB_PASS"),
@@ -419,7 +419,7 @@ def edit_phenotype(name, phenotype_id):
         conn=conn,
         table="PublishXRef",
         where=PublishXRef(id_=name,
-                          phenotype_id=phenotype_id))
+                          inbred_set_id=inbredset_id))
     phenotype_ = fetchone(
         conn=conn,
         table="Phenotype",
-- 
cgit v1.2.3


From 82a7ccf6d2e5e18dcbd83f8070fd88ddc34ad419 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 16 Aug 2021 19:00:34 +0300
Subject: Update URL for editing published trait

---
 wqflask/wqflask/templates/show_trait_details.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index bb30c54c..53e16aa0 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -236,7 +236,7 @@
         <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
         {% if this_trait.dataset.type == 'Publish' %}
-        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
         {% endif %}
 
         {% if this_trait.dataset.type == 'ProbeSet' %}
-- 
cgit v1.2.3


From 83af88a4bbf9d8a67f4d11c3546ba64f09efb6d2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 17 Aug 2021 09:15:04 +0300
Subject: wqflask: wsgi: Remove it

* wqflask/wsgi.py: Delete file. Not used anywhere.
---
 wqflask/wsgi.py | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 wqflask/wsgi.py

(limited to 'wqflask')

diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
deleted file mode 100644
index 755da333..00000000
--- a/wqflask/wsgi.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from run_gunicorn import app as application  # expect application as a name
-
-if __name__ == "__main__":
-    application.run()
-- 
cgit v1.2.3


From b0610024e7cb5dec73742fd461cd662881869214 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 17 Aug 2021 09:15:47 +0300
Subject: wqflask: views: Re-enable admin access in edit probeset

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3f0ab93f..7095c392 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -466,7 +466,7 @@ def edit_phenotype(name, inbredset_id):
 
 
 @app.route("/trait/edit/probeset-name/<dataset_name>")
-# @admin_login_required
+@admin_login_required
 def edit_probeset(dataset_name):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
-- 
cgit v1.2.3


From d89a13ef9f3f4da47432eb3555df3ada7bbfbb8b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 17 Aug 2021 12:41:24 +0300
Subject: wqflask: runserver: Add DebugToolbar when running in DEBUG mode

---
 wqflask/runserver.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index df957bd9..8198b921 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -23,6 +23,9 @@ app_config()
 werkzeug_logger = logging.getLogger('werkzeug')
 
 if WEBSERVER_MODE == 'DEBUG':
+    from flask_debugtoolbar import DebugToolbarExtension
+    app.debug = True
+    toolbar = DebugToolbarExtension(app)
     app.run(host='0.0.0.0',
             port=SERVER_PORT,
             debug=True,
-- 
cgit v1.2.3


From b70bf1250bc93a47c3e3e32d4d2f4a116121d11f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 17 Aug 2021 12:43:50 +0300
Subject: wqflask:.DS_Store: Delete it

---
 wqflask/.DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 wqflask/.DS_Store

(limited to 'wqflask')

diff --git a/wqflask/.DS_Store b/wqflask/.DS_Store
deleted file mode 100644
index d992942f..00000000
Binary files a/wqflask/.DS_Store and /dev/null differ
-- 
cgit v1.2.3


From 94f278b68817fb22d363fdfd1b416f9c674c3226 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 18 Aug 2021 09:42:48 +0300
Subject: Revert "wqflask: wsgi: Remove it"

This reverts commit 83af88a4bbf9d8a67f4d11c3546ba64f09efb6d2.
---
 wqflask/wsgi.py | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 wqflask/wsgi.py

(limited to 'wqflask')

diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
new file mode 100644
index 00000000..755da333
--- /dev/null
+++ b/wqflask/wsgi.py
@@ -0,0 +1,4 @@
+from run_gunicorn import app as application  # expect application as a name
+
+if __name__ == "__main__":
+    application.run()
-- 
cgit v1.2.3


From f5f1b3e64db18dbdde39860f1f86a4bf408e3dd6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Aug 2021 19:50:24 +0000
Subject: Replace textarea with multiple select element for displaying mapping
 covariates

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3dd44c85..3f0557aa 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -77,7 +77,9 @@
                                 <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
                                 <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                               </div>
-                              <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+                              <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple>
+                                  <option value="">No covariates selected</option>
+                              </select>
                               {% endif %}
                             </div>
                         </div>
@@ -320,7 +322,9 @@
                               <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
                               <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                             </div>
-                            <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+                            <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple>
+                                <option value="">No covariates selected</option>
+                            </select>
                             {% endif %}
                           </div>
                         </div>
-- 
cgit v1.2.3


From eb7863b540bda56f3e0a769440ebc16c675d4adb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Aug 2021 19:51:07 +0000
Subject: Update get_covariates_from_collection.js to properly interact with
 the select element instead of the previous textarea

---
 .../javascript/get_covariates_from_collection.js   | 55 +++++++++++++++-------
 1 file changed, 39 insertions(+), 16 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 3e414034..62590aaf 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -65,10 +65,8 @@ if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) {
 
 collection_click = function() {
   var this_collection_url;
-  console.log("Clicking on:", $(this));
   this_collection_url = $(this).find('.collection_name').prop("href");
   this_collection_url += "&json";
-  console.log("this_collection_url", this_collection_url);
   collection_list = $("#collections_holder").html();
   return $.ajax({
     dataType: "json",
@@ -79,32 +77,57 @@ collection_click = function() {
 
 submit_click = function() {
   var covariates_string = "";
-  var covariates_display_string = "";
+  var covariates_as_set = new Set();
+  $(".selected-covariates:first option").each(function() {
+    if ($(this).val() != ""){
+      covariates_as_set.add($(this).val() + "," + $(this).text());
+    }
+  });
   $('#collections_holder').find('input[type=checkbox]:checked').each(function() {
     var this_dataset, this_trait;
     this_trait = $(this).parents('tr').find('.trait').text();
     this_trait_display = $(this).parents('tr').find('.trait').data("display_name");
     this_description = $(this).parents('tr').find('.description').text();
-    console.log("this_trait is:", this_trait_display);
     this_dataset = $(this).parents('tr').find('.dataset').data("dataset");
-    console.log("this_dataset is:", this_dataset);
-    covariates_string += this_trait + ":" + this_dataset + ","
-    //this_covariate_display_string = this_trait + ": " + this_description
     this_covariate_display_string = this_trait_display
     if (this_covariate_display_string.length > 50) {
       this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..."
     }
-    covariates_display_string += this_covariate_display_string + "\n"
+    covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string)
+  });
+
+  covariates_as_list = Array.from(covariates_as_set)
+
+  // Removed the starting "No covariates selected" option before adding options for each covariate
+  if (covariates_as_list.length > 0){
+    $(".selected-covariates option[value='']").each(function() {
+      $(this).remove();
+    });
+  }
+
+  $(".selected-covariates option").each(function() {
+    $(this).remove();
   });
-  // Trim the last newline from display_string
-  covariates_display_string = covariates_display_string.replace(/\n$/, "")
 
-  // Trim the last comma
-  covariates_string = covariates_string.substring(0, covariates_string.length - 1)
-  //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
+  covariate_list_for_form = []
+  $.each(covariates_as_list, function (index, value) {
+    option_value = value.split(",")[0]
+    option_text = value.split(",")[1]
+    $(".selected-covariates").append($("<option/>", {
+      value: option_value,
+      text: option_text
+    }))
+    covariate_list_for_form.push(option_value)
+  });
 
-  $("input[name=covariates]").val(covariates_string)
-  $(".selected-covariates").val(covariates_display_string)
+  $("input[name=covariates]").val(covariate_list_for_form.join(","));
+
+  cofactor_count = $(".selected-covariates:first option").length;
+  if (cofactor_count > 10){
+    $(".selected-covariates").attr("size", 10);
+  } else {
+    $(".selected-covariates").attr("size", cofactor_count);
+  }
 
   return $.colorbox.close();
 };
@@ -223,4 +246,4 @@ back_to_collections = function() {
 $(".collection_line").on("click", collection_click);
 $("#submit").on("click", submit_click);
 $(".trait").on("click", trait_click);
-$("#back_to_collections").on("click", back_to_collections);
\ No newline at end of file
+$("#back_to_collections").on("click", back_to_collections);
-- 
cgit v1.2.3


From 0b6da486c0480dfe15486de34260ea462b168e39 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Aug 2021 19:51:53 +0000
Subject: Update show_trait.js to make removing covariates work with the new
 select element; individual covariates can now be removed

---
 .../wqflask/static/new/javascript/show_trait.js    | 39 ++++++++++++++++++++--
 1 file changed, 37 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 845ed907..bacafca6 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -98,9 +98,44 @@ sample_group_types = js_data.sample_group_types;
 $(".select_covariates").click(function () {
   open_covariate_selection();
 });
+
 $(".remove_covariates").click(function () {
-  $("input[name=covariates]").val("")
-  $(".selected-covariates").val("")
+  $(".selected-covariates option:selected").each(function() {
+    this_val = $(this).val();
+    $(".selected-covariates option").each(function(){
+      if ($(this).val() == this_val){
+        $(this).remove();
+      }
+    })
+    cofactor_count = $(".selected-covariates:first option").length
+    if (cofactor_count > 2 && cofactor_count < 11){
+      $(".selected-covariates").each(function() {
+        $(this).attr("size", $(".selected-covariates:first option").length)
+      });
+    } else if (cofactor_count > 10) {
+      $(".selected-covariates").each(function() {
+        $(this).attr("size", 10)
+      });
+    } else {
+      $(".selected-covariates").each(function() {
+        $(this).attr("size", 2)
+      });
+    }
+    if (cofactor_count == 0){
+      $(".selected-covariates").each(function() {
+        $(this).append($("<option/>", {
+          value: "",
+          text: "No covariates selected"
+        }))
+      })
+    }
+  });
+
+  covariates_list = [];
+  $(".selected-covariates:first option").each(function() {
+    covariates_list.push($(this).val());
+  })
+  $("input[name=covariates]").val(covariates_list.join(","))
 });
 
 open_trait_selection = function() {
-- 
cgit v1.2.3


From caf2c395f3aa2dc62236128a0db9f3243170db94 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 03:06:01 +0000
Subject: Add Removal All button that removes all currently added covariates

---
 wqflask/wqflask/static/new/javascript/show_trait.js     | 7 +++++++
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 2 ++
 2 files changed, 9 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index bacafca6..81c52ff6 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -138,6 +138,13 @@ $(".remove_covariates").click(function () {
   $("input[name=covariates]").val(covariates_list.join(","))
 });
 
+$(".remove_all_covariates").click(function() {
+  $(".selected-covariates option").each(function() {
+    $(this).remove();
+  });
+  $("input[name=covariates]").val("");
+})
+
 open_trait_selection = function() {
   return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
     return function() {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3f0557aa..cc472914 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -76,6 +76,7 @@
                               <div class="select-covar-div">
                                 <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
                                 <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
+                                <button type="button" class="btn btn-default select-covar-button remove_all_covariates" style="width: 95px;">Remove All</button>
                               </div>
                               <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple>
                                   <option value="">No covariates selected</option>
@@ -321,6 +322,7 @@
                             <div class="select-covar-div">
                               <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
                               <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
+                              <button type="button" class="btn btn-default select-covar-button remove_all_covariates" style="width: 100px;">Remove All</button>
                             </div>
                             <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple>
                                 <option value="">No covariates selected</option>
-- 
cgit v1.2.3


From e98ef60db6d0986360e6c8aa920241bbb268af8e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 03:07:18 +0000
Subject: Add some CSS changing the way the colorbox pop-up for adding
 covariates looks on the trait page

---
 wqflask/wqflask/static/new/css/show_trait.css | 30 +++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 782dabc2..b0514e01 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -260,3 +260,33 @@ input.trait-value-input {
 div.inline-div {
   display: inline;
 }
+
+/* div.colorbox_border {
+  border: 1px solid grey;
+} */
+div#cboxContent {
+  /* box-shadow:
+  0 2.8px 2.2px rgba(0, 0, 0, 0.034),
+  0 6.7px 5.3px rgba(0, 0, 0, 0.048),
+  0 12.5px 10px rgba(0, 0, 0, 0.06),
+  0 22.3px 17.9px rgba(0, 0, 0, 0.072),
+  0 41.8px 33.4px rgba(0, 0, 0, 0.086),
+  0 100px 80px rgba(0, 0, 0, 0.12) */
+
+  padding: 10px 10px 5px 10px;
+
+  -moz-box-shadow: 3px 3px 5px #535353;
+  -webkit-box-shadow: 3px 3px 5px #535353;
+  box-shadow: 3px 3px 5px #535353;
+
+  -moz-border-radius: 6px 6px 6px 6px;
+  -webkit-border-radius: 6px;
+  border-radius: 6px 6px 6px 6px;
+
+  /* border: 2px solid grey; */
+}
+
+#cboxClose {
+  margin-right: 5px;
+  margin-bottom: 2px;
+}
-- 
cgit v1.2.3


From 5c879337593366005d07f390b8e0da901ec23881 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 18:34:50 +0000
Subject: Changed Remove All button to Clear and changed Select and Clear
 button colors

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index cc472914..e63d0195 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -74,9 +74,9 @@
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% else %}
                               <div class="select-covar-div">
-                                <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+                                <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
                                 <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
-                                <button type="button" class="btn btn-default select-covar-button remove_all_covariates" style="width: 95px;">Remove All</button>
+                                <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
                               </div>
                               <select size="2" name="selected_covariates_gemma" class="form-control selected-covariates" multiple>
                                   <option value="">No covariates selected</option>
-- 
cgit v1.2.3


From 9f3baccf902caff4338c72c508bfab52b472bc3a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 18:35:29 +0000
Subject: After removing all cofactors, return the size of the select element
 to 2

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 1 +
 1 file changed, 1 insertion(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 81c52ff6..99397c8e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -142,6 +142,7 @@ $(".remove_all_covariates").click(function() {
   $(".selected-covariates option").each(function() {
     $(this).remove();
   });
+  $(".selected-covariates").attr("size", 2)
   $("input[name=covariates]").val("");
 })
 
-- 
cgit v1.2.3


From 367e6c2d49284942e1ddfc3da192cffaee2a78f3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:20:15 +0000
Subject: Removed ID of 'submit' from the button in the cofactor select table,
 since it was causing trait page forms to not submit after opening it

---
 .../wqflask/static/new/javascript/get_covariates_from_collection.js   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 62590aaf..9aa9553c 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -211,7 +211,7 @@ process_traits = function(trait_data, textStatus, jqXHR) {
   console.log('in process_traits with trait_data:', trait_data);
   the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
   the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
-  the_html += "    <button id='submit' class='btn btn-primary btn-small'> Submit </button>";
+  the_html += "    <button class='btn btn-primary btn-small submit'> Submit </button>";
   the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>";
   the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>";
   the_html += "<tbody>";
@@ -244,6 +244,6 @@ back_to_collections = function() {
 };
 
 $(".collection_line").on("click", collection_click);
-$("#submit").on("click", submit_click);
+$(".submit").on("click", submit_click);
 $(".trait").on("click", trait_click);
 $("#back_to_collections").on("click", back_to_collections);
-- 
cgit v1.2.3


From 3d903b5e79ef6db71c4a650f920222ca3dc9201c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:22:45 +0000
Subject: Shorten 'Add to existing collection' button to 'Add'

---
 wqflask/wqflask/templates/collections/add.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 0398c6e4..cb4172ac 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -27,7 +27,7 @@
                 {% endfor %}
                 </select>
                 <br />
-                <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button>
+                <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button>
               </div>
             </fieldset>
             {% endif %}
-- 
cgit v1.2.3


From fc15b67ca15a8f08833a8b1e479c152bc4a2b723 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:35:50 +0000
Subject: Added option to make collection default in the colorbox pop-up

---
 wqflask/wqflask/templates/collections/add.html | 29 +++++++++++++++++++-------
 1 file changed, 21 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index cb4172ac..8640fdb8 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
         or add to an existing collection.</p>
     </div>
     <div class="modal-body" style="margin-left: 20px;">
-        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
+        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form" class="form-inline">
             {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
             {% else %}
@@ -14,10 +14,8 @@
             {% if collections|length > 0 %}
             <fieldset>
               <legend>1. Add to an existing collection</legend>
-              <div style="margin-left: 20px;">  
-                <!--<label>Existing collection name:</label>-->
-                <select name="existing_collection" class="form-control">
-                    <!--<option selected disabled>Select Collection</option>-->
+              <div style="margin-left: 20px;">
+                <select name="existing_collection" class="form-control" style="width: 80%;">
                 {% for col in collections %}
                     {% if loop.index == 1 %}
                     <option value="{{ col.id }}:{{ col.name }}" selected>{{ col.name }}</option>
@@ -26,8 +24,9 @@
                     {% endif %}
                 {% endfor %}
                 </select>
-                <br />
-                <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button>
+                <input type="button" style="display: inline;" id="make_default" value="Make Default">
+              <br><br>
+              <button type="submit" name="add_to_existing" class="btn btn-primary">Add</button>
               </div>
             </fieldset>
             {% endif %}
@@ -35,7 +34,6 @@
             <fieldset>
               <legend>{% if collections|length > 0 %}2. {% else %}{% endif %}Create a new collection</legend>
               <div style="margin-left: 20px;">
-                <!--<label>Collection name:</label>-->
                 <input type="text" name="new_collection" placeholder=" Name of new collection..."
                     data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
                 <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
@@ -54,6 +52,21 @@
     parent.jQuery.colorbox.close();
   });
 
+  make_default = function() {
+    alert("The current collection is now your default collection.")
+    let uc_id = $('[name=existing_collection] option:selected').val().split(":")[0]
+    $.cookie('default_collection', uc_id, {
+        expires: 365,
+        path: '/'
+    });
+
+    let default_collection_id = $.cookie('default_collection');
+  };
+
+  $("#make_default").on("click", function(){
+    make_default();
+  });
+
   apply_default = function() {
     let default_collection_id = $.cookie('default_collection');
     if (default_collection_id) {
-- 
cgit v1.2.3


From 1393d777bd0fee4a25ba4b1f6af6ccb9ae24c0f8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:49:16 +0000
Subject: Added hash of sample values and table of changed values to the
 loading page

---
 wqflask/wqflask/templates/loading.html | 36 ++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 6d6136ac..b02605ee 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -25,6 +25,8 @@
           <br>
           transformation = <b><i>{{ start_vars.transform }}</i></b>
           {% endif %}
+          <br>
+          hash of sample values = <b><i>{{ start_vars.vals_hash }}</i></b>
           <br><br>
           <b>Mapping Metadata</b>
           <br>
@@ -68,6 +70,29 @@
           <div style="text-align: center;">
             <img align="center" src="/static/gif/89.gif">
           </div>
+          {% if start_vars.vals_diff|length != 0 and start_vars.transform == "" %}
+          <br><br>
+          <button id="show_full_diff">Show Full Diff</button>
+          <br>
+          <div id="diff_table_container" style="display: none; height:200px; overflow:auto;">
+          <table class="table table-hover">
+            <thead>
+              <th>Sample</th>
+              <th>New Value</th>
+              <th>Old Value</th>
+            </thead>
+            <tbody>
+              {% for sample in start_vars.vals_diff %}
+              <tr>
+                <td>{{ sample }}</td>
+                <td>{{ start_vars.vals_diff[sample].new_val }}</td>
+                <td>{{ start_vars.vals_diff[sample].old_val }}</td>
+              </tr>
+              {% endfor %}
+            </tbody>
+          </table>
+          </div>
+          {% endif %}
         </div>
       </div>
     </div>
@@ -79,4 +104,15 @@
 
 $("#loading_form").attr("action", "{{ start_vars.form_url }}");
 setTimeout(function(){ $("#loading_form").submit()}, 350);
+
+$('#show_full_diff').click(function() {
+  if ($('#diff_table_container').is(':visible')){
+    $('#diff_table_container').hide();
+  } else {
+    $('#diff_table_container').show();
+  }
+})
+
+
+
 </script>
-- 
cgit v1.2.3


From 26958694322855f4ee91beb3b01e73afe75066cf Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:50:31 +0000
Subject: Added function for getting the diff of sample values before and after
 user changes to show_trait.py

---
 wqflask/wqflask/show_trait/show_trait.py | 40 ++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 4120c801..96f6901a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1,3 +1,5 @@
+from typing import Dict
+
 import string
 import datetime
 import uuid
@@ -805,3 +807,41 @@ def get_scales_from_genofile(file_location):
         return [["physic", "Mb"], ["morgan", "cM"]]
     else:
         return [["physic", "Mb"]]
+
+
+
+def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict:
+    """ Get the diff between current sample values and the values in the DB
+
+    Given a dict of the changed values and the trait/dataset ID, return a Dict
+    with keys corresponding to each sample with a changed value and a value
+    that is a dict with keys for the old_value and new_value
+
+    """
+
+    trait_name = trait_id.split(":")[0]
+    dataset_name = trait_id.split(":")[1]
+    trait_ob = create_trait(name=trait_name, dataset_name=dataset_name)
+
+    old_vals = {sample : trait_ob.data[sample].value for sample in trait_ob.data}
+
+    shared_samples = set.union(set(new_vals.keys()), set(old_vals.keys()))
+
+    diff_dict = {}
+    for sample in shared_samples:
+        try:
+            new_val = float(new_vals[sample])
+        except:
+            new_val = "x"
+        try:
+            old_val = float(old_vals[sample])
+        except:
+            old_val = "x"
+
+        if new_val != old_val:
+            diff_dict[sample] = {
+                "new_val": new_val,
+                "old_val": old_val
+            }
+
+    return diff_dict
-- 
cgit v1.2.3


From 71e6c7483c8675e96376295927133c370478bbba Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Aug 2021 20:51:26 +0000
Subject: Removed some unnecessary empty lines from loading.html JS

---
 wqflask/wqflask/templates/loading.html | 4 ----
 1 file changed, 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index b02605ee..1edde31e 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -101,7 +101,6 @@
 <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
 <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
 <script  type="text/javascript">
-
 $("#loading_form").attr("action", "{{ start_vars.form_url }}");
 setTimeout(function(){ $("#loading_form").submit()}, 350);
 
@@ -112,7 +111,4 @@ $('#show_full_diff').click(function() {
     $('#diff_table_container').show();
   }
 })
-
-
-
 </script>
-- 
cgit v1.2.3


From ab3b838b99b58693f3f187093e78f492e7cf392b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 18 Aug 2021 00:13:55 +0000
Subject: Exclude attributes with only one distinct value as well

---
 wqflask/wqflask/templates/show_trait_transform_and_filter.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 064fd3e5..8d21b0b0 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -25,7 +25,7 @@
         <label for="exclude_column">Block samples by group:</label>
         <select id="exclude_column" size=1>
           {% for attribute in sample_groups[0].attributes %}
-          {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 %}
+          {% if sample_groups[0].attributes[attribute].distinct_values|length <= 10 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %}
           <option value="{{ loop.index }}">
               {{ sample_groups[0].attributes[attribute].name }}
           </option>
-- 
cgit v1.2.3


From 2e197bb94edb8918c256a4925652307cad941586 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 18 Aug 2021 00:14:21 +0000
Subject: Fix issues caused by the attribute keys being ids instead of names +
 fix issue caused by an attribute cell being empty

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 99397c8e..be9e2089 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -651,13 +651,14 @@ $(".corr_compute").on("click", (function(_this) {
 create_value_dropdown = function(value) {
   return "<option val=" + value + ">" + value + "</option>";
 };
+
 populate_sample_attributes_values_dropdown = function() {
   var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
   $('#attribute_values').empty();
   sample_attributes = [];
 
   var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
-    return [key, js_data.attributes[key].name.toLowerCase()];
+    return [key, js_data.attributes[key].id];
   });
 
   attributes_as_list.sort(function(first, second) {
@@ -671,7 +672,7 @@ populate_sample_attributes_values_dropdown = function() {
   });
 
   for (i=0; i < attributes_as_list.length; i++) {
-    attribute_info = js_data.attributes[attributes_as_list[i][0]]
+    attribute_info = js_data.attributes[attributes_as_list[i][1]]
     sample_attributes.push(attribute_info.distinct_values);
   }
 
@@ -710,11 +711,13 @@ block_by_attribute_value = function() {
   let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$();
 
   for (i = 0; i < exclude_val_nodes.length; i++) {
-    let this_col_value = exclude_val_nodes[i].childNodes[0].data;
-    let this_val_node = val_nodes[i].childNodes[0];
+    if (exclude_val_nodes[i].hasChildNodes()) {
+      let this_col_value = exclude_val_nodes[i].childNodes[0].data;
+      let this_val_node = val_nodes[i].childNodes[0];
 
-    if (this_col_value == exclude_by_value){
-      this_val_node.value = "x";
+      if (this_col_value == exclude_by_value){
+        this_val_node.value = "x";
+      }
     }
   }
 
-- 
cgit v1.2.3


From 8380ecba19271662c3711f8fe7928a4099988d73 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 17:26:55 +0000
Subject: Add hash of vals and diff of vals to template_vars passed to loading
 page in views.py

---
 wqflask/wqflask/views.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7095c392..b0391914 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -28,6 +28,7 @@ from zipfile import ZIP_DEFLATED
 from wqflask import app
 
 from gn3.commands import run_cmd
+from gn3.computations.gemma import generate_hash_of_string
 from gn3.db import diff_from_dict
 from gn3.db import fetchall
 from gn3.db import fetchone
@@ -63,6 +64,7 @@ from wqflask import server_side
 from base.data_set import create_dataset  # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
+from wqflask.show_trait.show_trait import get_diff_of_vals
 from wqflask.heatmap import heatmap
 from wqflask.external_tools import send_to_bnw
 from wqflask.external_tools import send_to_webgestalt
@@ -996,10 +998,10 @@ def loading_page():
             if key in wanted:
                 start_vars[key] = value
 
+        sample_vals_dict = json.loads(start_vars['sample_vals'])
         if 'n_samples' in start_vars:
             n_samples = int(start_vars['n_samples'])
         else:
-            sample_vals_dict = json.loads(start_vars['sample_vals'])
             if 'group' in start_vars:
                 dataset = create_dataset(
                     start_vars['dataset'], group_name=start_vars['group'])
@@ -1021,6 +1023,9 @@ def loading_page():
                         n_samples += 1
 
         start_vars['n_samples'] = n_samples
+        start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict))
+        start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
+
         start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
 
         start_vars_container['start_vars'] = start_vars
-- 
cgit v1.2.3


From a3718c91123316f13d22c9c5b5f7f858cd96a2cd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 17:34:01 +0000
Subject: Added type='button' to the mapping compute buttons in order to
 prevent them from being submitted twice

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index e63d0195..ddcc3edf 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -87,7 +87,7 @@
                         <div class="mapping_method_fields form-group">
                           <label class="col-xs-3 control-label"></label>
                           <div class="col-xs-6">
-                            <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
+                            <button id="gemma_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
                           </div>
                         </div>
                     </div>
@@ -190,7 +190,7 @@
                         <div class="mapping_method_fields form-group">
                             <label class="col-xs-3 control-label"></label>
                             <div class="col-xs-6">
-                              <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
+                              <button id="interval_mapping_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
                             </div>
                         </div>
                     </div>
@@ -333,7 +333,7 @@
                         <div class="mapping_method_fields form-group">
                             <label class="col-xs-3 control-label"></label>
                             <div class="col-xs-6 controls">
-                              <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
+                              <button id="rqtl_geno_compute" type="button" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
                             </div>
                         </div>
                     </div>
-- 
cgit v1.2.3


From 642c98f13c9cc4c2cf258eb960206dac79410b00 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 18:28:17 +0000
Subject: Fixed the way the drop-down for Filter by Value set values for the
 case attributes

---
 wqflask/wqflask/templates/show_trait_transform_and_filter.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 8d21b0b0..5e6ed2cf 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -74,10 +74,12 @@
         {% if js_data.se_exists %}
         <option value="stderr">SE</option>
         {% endif %}
-        {% for attribute in numerical_var_list %}
+        {% for attribute in sample_groups[0].attributes %}
+        {% if sample_groups[0].attributes[attribute].name in numerical_var_list %}
         <option value="{{ loop.index }}">
-          {{ attribute }}
+          {{ sample_groups[0].attributes[attribute].name }}
         </option>
+        {% endif %}
         {% endfor %}
       </select>
       {% endif %}
-- 
cgit v1.2.3


From 041354b4c278c4784119da60ace2c3d4ad981354 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 18:28:31 +0000
Subject: Fixed issue in JS that caused filter_by_value to not work for case
 attributes

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index be9e2089..f050d4ae 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -818,7 +818,7 @@ filter_by_value = function() {
       var this_col_value = filter_val_nodes[i].childNodes[0].value;
     } else {
       if (filter_val_nodes[i].childNodes[0] !== undefined){
-        var this_col_value = filter_val_nodes[i].childNodes[0].data;
+        var this_col_value = filter_val_nodes[i].innerText;
       } else {
         continue
       }
-- 
cgit v1.2.3


From 0e0f25a71d2fab7395af007643b908af51bd7ca2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 18:29:45 +0000
Subject: Fixed R/qtl 'select covariates' buttons to be the same as the changed
 ones for GEMMA

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index ddcc3edf..4c0efecb 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -320,9 +320,9 @@
                             No collections available. Please add traits to a collection to use them as covariates.
                             {% else %}
                             <div class="select-covar-div">
-                              <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+                              <button type="button" class="btn btn-success select-covar-button select_covariates">Select</button>
                               <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
-                              <button type="button" class="btn btn-default select-covar-button remove_all_covariates" style="width: 100px;">Remove All</button>
+                              <button type="button" class="btn btn-danger select-covar-button remove_all_covariates">Clear</button>
                             </div>
                             <select size="2" name="selected_covariates_rqtl" class="form-control selected-covariates" multiple>
                                 <option value="">No covariates selected</option>
-- 
cgit v1.2.3


From aaf28e6b2dc61469fa06816655208c0fc616f2e8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Aug 2021 18:34:23 +0000
Subject: Change color for Submit button when selecting covariates + move Back
 button to the far right

---
 .../wqflask/static/new/javascript/get_covariates_from_collection.js  | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 9aa9553c..00025a32 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -209,9 +209,8 @@ color_by_trait = function(trait_sample_data, textStatus, jqXHR) {
 process_traits = function(trait_data, textStatus, jqXHR) {
   var the_html, trait, _i, _len;
   console.log('in process_traits with trait_data:', trait_data);
-  the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>";
-  the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>";
-  the_html += "    <button class='btn btn-primary btn-small submit'> Submit </button>";
+  the_html = "<button class='btn btn-success btn-small submit'> Submit </button>";
+  the_html += "<button id='back_to_collections' class='btn btn-inverse btn-small' style='float: right;'>Back</button>";
   the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>";
   the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>";
   the_html += "<tbody>";
-- 
cgit v1.2.3


From 0fb00c0ce2e0c668508859e056f1132d67ad9243 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 19 Aug 2021 11:37:23 +0300
Subject: startup_config.py: Add DebugToobarExtension for wsgi DEBUG mode

* wqflask/utility/startup_config.py (app_config): Add
DebugToolbarExtension
---
 wqflask/utility/startup_config.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 56d0af6f..778fb64d 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -20,8 +20,12 @@ def app_config():
         import os
         app.config['SECRET_KEY'] = str(os.urandom(24))
     mode = WEBSERVER_MODE
-    if mode == "DEV" or mode == "DEBUG":
+    if mode in ["DEV", "DEBUG"]:
         app.config['TEMPLATES_AUTO_RELOAD'] = True
+        if mode == "DEBUG":
+            from flask_debugtoolbar import DebugToolbarExtension
+            app.debug = True
+            toolbar = DebugToolbarExtension(app)
 
     print("==========================================")
 
-- 
cgit v1.2.3


From d4ce7c77f9cdd73516dba6f04f03ff38be8af0a4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 20 Aug 2021 17:44:48 +0000
Subject: Fix issue where attempting to get the diff of vals for Temp traits
 was causing an error

---
 wqflask/wqflask/views.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b0391914..957c34be 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1024,7 +1024,8 @@ def loading_page():
 
         start_vars['n_samples'] = n_samples
         start_vars['vals_hash'] = generate_hash_of_string(str(sample_vals_dict))
-        start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
+        if start_vars['dataset'] != "Temp": # Currently can't get diff for temp traits
+            start_vars['vals_diff'] = get_diff_of_vals(sample_vals_dict, str(start_vars['trait_id'] + ":" + str(start_vars['dataset'])))
 
         start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
 
-- 
cgit v1.2.3


From 898b80d34442c16399366a5744cc26a157a727cb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 20 Aug 2021 17:46:20 +0000
Subject: Fixed some logic in trait.py that could cause a problem if a
 dataset_name was passed that wasn't Temp

---
 wqflask/base/trait.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 10851e00..96a09302 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -27,11 +27,13 @@ def create_trait(**kw):
 
     assert bool(kw.get('name')), "Needs trait name"
 
-    if kw.get('dataset_name'):
+    if bool(kw.get('dataset')):
+        dataset = kw.get('dataset')
+    else:
         if kw.get('dataset_name') != "Temp":
             dataset = create_dataset(kw.get('dataset_name'))
-    else:
-        dataset = kw.get('dataset')
+        else:
+            dataset = create_dataset("Temp", group_name=kw.get('group_name'))
 
     if dataset.type == 'Publish':
         permissions = check_resource_availability(
-- 
cgit v1.2.3


From 4dafd017ec1fc0cd1e78487560ed15d705a44b98 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 17:11:28 +0000
Subject: For some reason sample_data was being set twice, and the second time
 used a test function that does not exclude parents/f1s (causing the N to be
 wrong if parents/f1s exist)

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 2 --
 1 file changed, 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index f7c06a46..a78cb0b9 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -150,8 +150,6 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
     sample_data = process_samples(
         start_vars, this_dataset.group.samplelist)
 
-    sample_data = test_process_data(this_trait, this_dataset, start_vars)
-
     if target_dataset.type == "ProbeSet":
         target_dataset.get_probeset_data(list(sample_data.keys()))
     else:
-- 
cgit v1.2.3


From cbebc4ae80f77575f89df3540952f412378326dc Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:02:41 +0000
Subject: Include categorical_vars in mapping_results.html so they're included
 when recomputing

---
 wqflask/wqflask/templates/mapping_results.html | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 35d8a157..7baac000 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -44,7 +44,10 @@
         {% endif %}
         <input type="hidden" name="num_perm" value="{{ nperm }}">
         <input type="hidden" name="perm_info" value="">
+        {% if categorical_vars is defined %}
+        <input type="hidden" name="categorical_vars" value="{{ categorical_vars }}">
         <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
+        {% endif %}
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
         <input type="hidden" name="control_marker" value="{{ controlLocus }}">
-- 
cgit v1.2.3


From 0bbe9072566397942a6db034cb11203bcb43b78f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:03:10 +0000
Subject: Fix the way categorical_var_list is set to account for case attribute
 Ids being keys now instead of names

---
 wqflask/wqflask/show_trait/show_trait.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 96f6901a..36e69fa3 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -701,7 +701,7 @@ def get_categorical_variables(this_trait, sample_list) -> list:
     if len(sample_list.attributes) > 0:
         for attribute in sample_list.attributes:
             if len(sample_list.attributes[attribute].distinct_values) < 10:
-                categorical_var_list.append(sample_list.attributes[attribute].name)
+                categorical_var_list.append(str(sample_list.attributes[attribute].id))
 
     return categorical_var_list
 
-- 
cgit v1.2.3


From 654b35c2050e89f9ba533a3713d40465cf6fcd47 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:05:10 +0000
Subject: Fix get_perm_strata to usethe Ids for case attributes instead of
 names + allow perm_strata to be passed to the template

---
 wqflask/wqflask/marker_regression/run_mapping.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f601201b..ebad7d36 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -220,7 +220,7 @@ class RunMapping:
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
         elif self.mapping_method == "rqtl_geno":
-            perm_strata = []
+            self.perm_strata = []
             if "perm_strata" in start_vars and "categorical_vars" in start_vars:
                 self.categorical_vars = start_vars["categorical_vars"].split(
                     ",")
@@ -229,7 +229,7 @@ class RunMapping:
                                                  sample_names=self.samples,
                                                  this_trait=self.this_trait)
 
-                    perm_strata = get_perm_strata(
+                    self.perm_strata = get_perm_strata(
                         self.this_trait, primary_samples, self.categorical_vars, self.samples)
             self.score_type = "LOD"
             self.control_marker = start_vars['control_marker']
@@ -243,10 +243,10 @@ class RunMapping:
             #    self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
                 self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl(
-                    self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+                    self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method, self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
             else:
                 results = rqtl_mapping.run_rqtl(self.this_trait.name, self.vals, self.samples, self.dataset, self.mapping_scale, self.model, self.method,
-                                                     self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
+                                                     self.num_perm, self.perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.covariates)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars:  # ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
@@ -765,9 +765,9 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
         if sample in list(sample_list.sample_attribute_values.keys()):
             combined_string = ""
             for var in categorical_vars:
-                if var.lower() in sample_list.sample_attribute_values[sample]:
+                if var in sample_list.sample_attribute_values[sample]:
                     combined_string += str(
-                        sample_list.sample_attribute_values[sample][var.lower()])
+                        sample_list.sample_attribute_values[sample][var])
                 else:
                     combined_string += "NA"
         else:
-- 
cgit v1.2.3


From fff90d1a1b194fe5e65e99506bc4fe6fffc9a255 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:06:01 +0000
Subject: Account for situations where the minimum permutation value is also
 above webqtlConfig.MAXLRS; previously threw an error

---
 wqflask/utility/Plot.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 9b2c6735..d4256a46 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -139,7 +139,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     max_D = max(data)
     min_D = min(data)
     # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
-    if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
+    if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
         max_D = webqtlConfig.MAXLRS  # maximum LRS value
 
     xLow, xTop, stepX = detScale(min_D, max_D)
@@ -156,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
         j += step
 
     for i, item in enumerate(data):
-        if item == float('inf') or item > webqtlConfig.MAXLRS:
+        if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS:
             item = webqtlConfig.MAXLRS  # maximum LRS value
         j = int((item - xLow) / step)
         Count[j] += 1
-- 
cgit v1.2.3


From 7546da17cc5b7a2f97b490e1593b41609b281a43 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:29:38 +0000
Subject: Fixed issue with the way categorical_vars and perm_strata were being
 passed to the template

---
 wqflask/wqflask/templates/mapping_results.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7baac000..81eb1ba1 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -45,8 +45,10 @@
         <input type="hidden" name="num_perm" value="{{ nperm }}">
         <input type="hidden" name="perm_info" value="">
         {% if categorical_vars is defined %}
-        <input type="hidden" name="categorical_vars" value="{{ categorical_vars }}">
-        <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
+        <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}">
+        {% endif %}
+        {% if perm_strata is defined %}
+        <input type="hidden" name="perm_strata" value="True">
         {% endif %}
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
-- 
cgit v1.2.3


From 629aab0ef51c2c6f7d4f479e51a7168d9aa14d41 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Aug 2021 19:31:18 +0000
Subject: Removed unused variable from list of 'wanted' variables for mapping

---
 wqflask/wqflask/views.py | 1 -
 1 file changed, 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 957c34be..11a9380c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1067,7 +1067,6 @@ def mapping_results_page():
         'num_perm',
         'permCheck',
         'perm_strata',
-        'strat_var',
         'categorical_vars',
         'perm_output',
         'num_bootstrap',
-- 
cgit v1.2.3


From 3fd1d766fcf38f5a147c01b1c397469139c9080d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Aug 2021 17:39:02 +0000
Subject: Fix issue that could cause mapping_scale to not be set correctly in
 show_trait.py

---
 wqflask/wqflask/show_trait/show_trait.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 36e69fa3..80f5d117 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -300,7 +300,7 @@ class ShowTrait:
         hddn['compare_traits'] = []
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
-        if len(self.scales_in_geno) < 2:
+        if len(self.scales_in_geno) < 2 and bool(self.scales_in_geno):
             hddn['mapping_scale'] = self.scales_in_geno[list(
                 self.scales_in_geno.keys())[0]][0][0]
 
-- 
cgit v1.2.3


From ae634a36891ddba9748e0f75ff1cf51e95e4a8a7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Aug 2021 17:39:16 +0000
Subject: Fix issue that could cause an error when doing cM mapping

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f941267e..3986c441 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2113,7 +2113,7 @@ class DisplayMappingResults:
                                 thisChr.append(
                                     [_locus.name, _locus.cM - Locus0CM])
                     else:
-                        for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1):
+                        for j in (0, round(nLoci / 4), round(nLoci / 2), round(nLoci * 3 / 4), -1):
                             while _chr[j].name == ' - ':
                                 j += 1
                             if _chr[j].cM != preLpos:
-- 
cgit v1.2.3


From 3327c9dc95d2c4d295dc8dbf4839c01294b53ada Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Aug 2021 17:46:02 +0000
Subject: Add map scale option that was missing for groups with only a single
 genotype file

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 11 +++++++++++
 1 file changed, 11 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 4c0efecb..5365140d 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -229,6 +229,17 @@
                                 </select>
                             </div>
                         </div>
+                        {% else %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
+                            <div class="col-xs-2 controls">
+                                <select id="scale_rqtl_geno" class="form-control scale-select">
+                                    {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
+                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-- 
cgit v1.2.3


From 582893c0cc87f87e5dfc7fe0209b2e4a3f85d4a4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Aug 2021 18:02:31 +0000
Subject: Fixed issue in get_diff_of_vals that caused the diff to be calculated
 wrong (due to one set of values being rounded to 3 digits and the other not

---
 wqflask/wqflask/show_trait/show_trait.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 80f5d117..3f93bae0 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -830,11 +830,11 @@ def get_diff_of_vals(new_vals: Dict, trait_id: str) -> Dict:
     diff_dict = {}
     for sample in shared_samples:
         try:
-            new_val = float(new_vals[sample])
+            new_val = round(float(new_vals[sample]), 3)
         except:
             new_val = "x"
         try:
-            old_val = float(old_vals[sample])
+            old_val = round(float(old_vals[sample]), 3)
         except:
             old_val = "x"
 
-- 
cgit v1.2.3


From cc7c392198f73ac8e8419be1367ce566d85a873c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 25 Aug 2021 19:05:07 +0000
Subject: Fix issue where correlation results weren't included parents/f1s

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index a78cb0b9..d0d4bcba 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -148,7 +148,7 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait):
 def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
 
     sample_data = process_samples(
-        start_vars, this_dataset.group.samplelist)
+        start_vars, this_dataset.group.all_samples_ordered())
 
     if target_dataset.type == "ProbeSet":
         target_dataset.get_probeset_data(list(sample_data.keys()))
-- 
cgit v1.2.3


From 5ebe36d5ff685e6b663b14c130606aa60b0123c2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 3 Sep 2021 14:58:05 +0000
Subject: Fix issue where values written to phenotype file for R/qtl sometimes
 had trailing decimal values by grounding to 3 places past the decimal

---
 wqflask/wqflask/marker_regression/rqtl_mapping.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 09afb8d1..cd578870 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -89,7 +89,7 @@ def write_phenotype_file(trait_name: str,
     for i, sample in enumerate(samples):
         this_row = [sample]
         if vals[i] != "x":
-            this_row.append(vals[i])
+            this_row.append(str(round(float(vals[i]), 3)))
         else:
             this_row.append("NA")
         for cofactor in cofactor_data:
@@ -126,7 +126,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict:
                 sample_data = trait_ob.data
                 for index, sample in enumerate(samples):
                     if sample in sample_data:
-                        sample_value = sample_data[sample].value
+                        sample_value = str(round(float(sample_data[sample].value), 3))
                         cofactor_dict[cofactor_name].append(sample_value)
                     else:
                         cofactor_dict[cofactor_name].append("NA")
-- 
cgit v1.2.3


From 8af212bc7eac5b39e8e6838df446a4003633a55e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 3 Sep 2021 14:59:14 +0000
Subject: Fix issue that caused javascript to not work on the R/qtl mapping
 result page when permutations weren't used (because it wrongly expected the
 permutation histogram to always exist)

---
 wqflask/wqflask/templates/mapping_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 81eb1ba1..d446745d 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -529,7 +529,7 @@
         });
         {% endif %}
 
-        {% if mapping_method != "gemma" and mapping_method != "plink" %}
+        {% if mapping_method != "gemma" and mapping_method != "plink" and nperm > 0 and permChecked == "ON" %}
         $('#download_perm').click(function(){
           perm_info_dict = {
             perm_data: js_data.perm_results,
-- 
cgit v1.2.3


From f4297bc9e4c49f58e0759d02d3e7aea392ba5615 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 3 Sep 2021 15:01:34 +0000
Subject: Allow categorical_var_list to be passed as a template variable

---
 wqflask/wqflask/show_trait/show_trait.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3f93bae0..c4d1ae1c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -178,11 +178,11 @@ class ShowTrait:
             self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
 
-        categorical_var_list = []
+        self.categorical_var_list = []
         self.numerical_var_list = []
         if not self.temp_trait:
             # ZS: Only using first samplelist, since I think mapping only uses those samples
-            categorical_var_list = get_categorical_variables(
+            self.categorical_var_list = get_categorical_variables(
                 self.this_trait, self.sample_groups[0])
             self.numerical_var_list = get_numerical_variables(
                 self.this_trait, self.sample_groups[0])
@@ -287,8 +287,8 @@ class ShowTrait:
         hddn['study_samplelists'] = json.dumps(study_samplelist_json)
         hddn['num_perm'] = 0
         hddn['categorical_vars'] = ""
-        if categorical_var_list:
-            hddn['categorical_vars'] = ",".join(categorical_var_list)
+        if self.categorical_var_list:
+            hddn['categorical_vars'] = ",".join(self.categorical_var_list)
         hddn['manhattan_plot'] = ""
         hddn['control_marker'] = ""
         if not self.temp_trait:
@@ -323,7 +323,7 @@ class ShowTrait:
                        has_num_cases=self.has_num_cases,
                        attributes=self.sample_groups[0].attributes,
                        categorical_attr_exists=self.categorical_attr_exists,
-                       categorical_vars=",".join(categorical_var_list),
+                       categorical_vars=",".join(self.categorical_var_list),
                        num_values=self.num_values,
                        qnorm_values=self.qnorm_vals,
                        zscore_values=self.z_scores,
-- 
cgit v1.2.3


From f81a5629ab6ea7e39893af00e59c3ac6d79d7892 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sun, 5 Sep 2021 17:03:51 +0000
Subject: Fixed issue that caused sample data to not be fetched correctly;
 there's something wrong with the 'get_probeset_data' function (not sure why
 this function exists)

---
 wqflask/wqflask/correlation/correlation_gn3_api.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index d0d4bcba..a18bceaf 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -150,10 +150,7 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
     sample_data = process_samples(
         start_vars, this_dataset.group.all_samples_ordered())
 
-    if target_dataset.type == "ProbeSet":
-        target_dataset.get_probeset_data(list(sample_data.keys()))
-    else:
-        target_dataset.get_trait_data(list(sample_data.keys()))
+    target_dataset.get_trait_data(list(sample_data.keys()))
     this_trait = retrieve_sample_data(this_trait, this_dataset)
     this_trait_data = {
         "trait_sample_data": sample_data,
-- 
cgit v1.2.3


From 25a5fe8027a00a64513855630a4365480cf567d7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 7 Sep 2021 18:21:34 +0000
Subject: Add timer to loading page to track how long the process has been
 running

---
 wqflask/wqflask/templates/loading.html | 25 ++++++++++++++++++++++---
 1 file changed, 22 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 1edde31e..ccf810b0 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -12,6 +12,8 @@
           {% if start_vars.tool_used == "Mapping" %}
           <h1>Computing the Maps</h1>
           <br>
+          <b>Time Elapsed:</b> <span class="timer"></span>
+          <br>
           <b>Trait Metadata</b>
           <br>
           species = <b><i>{{ start_vars.species[0] | upper }}{{ start_vars.species[1:] }}</i></b>
@@ -101,9 +103,6 @@
 <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
 <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
 <script  type="text/javascript">
-$("#loading_form").attr("action", "{{ start_vars.form_url }}");
-setTimeout(function(){ $("#loading_form").submit()}, 350);
-
 $('#show_full_diff').click(function() {
   if ($('#diff_table_container').is(':visible')){
     $('#diff_table_container').hide();
@@ -111,4 +110,24 @@ $('#show_full_diff').click(function() {
     $('#diff_table_container').show();
   }
 })
+
+var start = new Date;
+
+setInterval(function() {
+  minutes = Math.floor((new Date - start) / 1000 / 60)
+  seconds = Math.round(((new Date - start) / 1000) % 60)
+  if (seconds < 10 && minutes >= 1){
+    seconds_text = "0" + seconds.toString()
+  } else {
+    seconds_text = seconds.toString()
+  }
+  if (minutes < 1) {
+    $('.timer').text(seconds_text + " seconds");
+  } else {
+    $('.timer').text(minutes.toString() + ":" + seconds_text);
+  }
+}, 100);
+
+$("#loading_form").attr("action", "{{ start_vars.form_url }}");
+setTimeout(function(){ $("#loading_form").submit()}, 350);
 </script>
-- 
cgit v1.2.3


From d243e3a69b26d60709fe10ab0b70a0e1d53ba50d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 7 Sep 2021 18:22:44 +0000
Subject: Add trait hash and datetime to mapping figure

---
 .../marker_regression/display_mapping_results.py   | 68 ++++++++++++++--------
 wqflask/wqflask/marker_regression/run_mapping.py   |  1 +
 .../new/javascript/show_trait_mapping_tools.js     | 10 ++--
 wqflask/wqflask/templates/mapping_results.html     |  1 +
 wqflask/wqflask/views.py                           |  1 +
 5 files changed, 51 insertions(+), 30 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3986c441..5f5fe6a3 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -24,6 +24,7 @@
 #
 # Last updated by Zach 12/14/2010
 
+import datetime
 import string
 from math import *
 from PIL import Image
@@ -271,6 +272,7 @@ class DisplayMappingResults:
         # Needing for form submission when doing single chr
         # mapping or remapping after changing options
         self.sample_vals = start_vars['sample_vals']
+        self.vals_hash= start_vars['vals_hash']
         self.sample_vals_dict = json.loads(self.sample_vals)
 
         self.transform = start_vars['transform']
@@ -651,7 +653,7 @@ class DisplayMappingResults:
             btminfo.append(
                 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
 
-    def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
+    def plotIntMapping(self, canvas, offset=(80, 120, 110, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
         im_drawer = ImageDraw.Draw(canvas)
         # calculating margins
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -661,7 +663,7 @@ class DisplayMappingResults:
             if self.legendChecked:
                 yTopOffset += 10
                 if self.covariates != "" and self.controlLocus and self.doControl != "false":
-                    yTopOffset += 20
+                    yTopOffset += 25
                 if len(self.transform) > 0:
                     yTopOffset += 5
             else:
@@ -1195,43 +1197,47 @@ class DisplayMappingResults:
             dataset_label = "%s - %s" % (self.dataset.group.name,
                                          self.dataset.fullname)
 
-        string1 = 'Dataset: %s' % (dataset_label)
+
+        current_datetime = datetime.datetime.now()
+        string1 = 'UTC Timestamp: %s' % (current_datetime.strftime("%b %d %Y %H:%M:%S"))
+        string2 = 'Dataset: %s' % (dataset_label)
+        string3 = 'Trait Hash: %s' % (self.vals_hash)
 
         if self.genofile_string == "":
-            string2 = 'Genotype File: %s.geno' % self.dataset.group.name
+            string4 = 'Genotype File: %s.geno' % self.dataset.group.name
         else:
-            string2 = 'Genotype File: %s' % self.genofile_string
+            string4 = 'Genotype File: %s' % self.genofile_string
 
-        string4 = ''
+        string6 = ''
         if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
             if self.use_loco == "True":
-                string3 = 'Using GEMMA mapping method with LOCO and '
+                string5 = 'Using GEMMA mapping method with LOCO and '
             else:
-                string3 = 'Using GEMMA mapping method with '
+                string5 = 'Using GEMMA mapping method with '
             if self.covariates != "":
-                string3 += 'the cofactors below:'
+                string5 += 'the cofactors below:'
                 cofactor_names = ", ".join(
                     [covar.split(":")[0] for covar in self.covariates.split(",")])
-                string4 = cofactor_names
+                string6 = cofactor_names
             else:
-                string3 += 'no cofactors'
+                string5 += 'no cofactors'
         elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
-            string3 = 'Using R/qtl mapping method with '
+            string5 = 'Using R/qtl mapping method with '
             if self.covariates != "":
-                string3 += 'the cofactors below:'
+                string5 += 'the cofactors below:'
                 cofactor_names = ", ".join(
                     [covar.split(":")[0] for covar in self.covariates.split(",")])
-                string4 = cofactor_names
+                string6 = cofactor_names
             elif self.controlLocus and self.doControl != "false":
-                string3 += '%s as control' % self.controlLocus
+                string5 += '%s as control' % self.controlLocus
             else:
-                string3 += 'no cofactors'
+                string5 += 'no cofactors'
         else:
-            string3 = 'Using Haldane mapping function with '
+            string5 = 'Using Haldane mapping function with '
             if self.controlLocus and self.doControl != "false":
-                string3 += '%s as control' % self.controlLocus
+                string5 += '%s as control' % self.controlLocus
             else:
-                string3 += 'no control for other QTLs'
+                string5 += 'no control for other QTLs'
 
         y_constant = 10
         if self.this_trait.name:
@@ -1260,7 +1266,9 @@ class DisplayMappingResults:
             d = 4 + max(
                 im_drawer.textsize(identification, font=labelFont)[0],
                 im_drawer.textsize(string1, font=labelFont)[0],
-                im_drawer.textsize(string2, font=labelFont)[0])
+                im_drawer.textsize(string2, font=labelFont)[0],
+                im_drawer.textsize(string3, font=labelFont)[0],
+                im_drawer.textsize(string4, font=labelFont)[0])
             im_drawer.text(
                 text=identification,
                 xy=(xLeftOffset, y_constant * fontZoom), font=labelFont,
@@ -1269,7 +1277,9 @@ class DisplayMappingResults:
         else:
             d = 4 + max(
                 im_drawer.textsize(string1, font=labelFont)[0],
-                im_drawer.textsize(string2, font=labelFont)[0])
+                im_drawer.textsize(string2, font=labelFont)[0],
+                im_drawer.textsize(string3, font=labelFont)[0],
+                im_drawer.textsize(string4, font=labelFont)[0])
 
         if len(self.transform) > 0:
             transform_text = "Transform - "
@@ -1296,14 +1306,22 @@ class DisplayMappingResults:
             text=string2, xy=(xLeftOffset, y_constant * fontZoom),
             font=labelFont, fill=labelColor)
         y_constant += 15
-        if string3 != '':
+        im_drawer.text(
+            text=string3, xy=(xLeftOffset, y_constant * fontZoom),
+            font=labelFont, fill=labelColor)
+        y_constant += 15
+        im_drawer.text(
+            text=string4, xy=(xLeftOffset, y_constant * fontZoom),
+            font=labelFont, fill=labelColor)
+        y_constant += 15
+        if string4 != '':
             im_drawer.text(
-                text=string3, xy=(xLeftOffset, y_constant * fontZoom),
+                text=string5, xy=(xLeftOffset, y_constant * fontZoom),
                 font=labelFont, fill=labelColor)
             y_constant += 15
-            if string4 != '':
+            if string5 != '':
                 im_drawer.text(
-                    text=string4, xy=(xLeftOffset, y_constant * fontZoom),
+                    text=string6, xy=(xLeftOffset, y_constant * fontZoom),
                     font=labelFont, fill=labelColor)
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index ebad7d36..2f90b475 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -75,6 +75,7 @@ class RunMapping:
         self.vals = []
         self.samples = []
         self.sample_vals = start_vars['sample_vals']
+        self.vals_hash = start_vars['vals_hash']
         sample_val_dict = json.loads(self.sample_vals)
         samples = sample_val_dict.keys()
         if (len(genofile_samplelist) != 0):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 09e9d024..b75d658e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,11 +141,11 @@ $('input[name=display_all]').change((function(_this) {
 })(this));
 
 //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
-                          'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
-                          'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', 'genofile',
-                          'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
-                          'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+                          'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars',
+                          'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker',
+                          'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend',
+                          'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
 
 $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) {
   return function() {
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index d446745d..162ae810 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -34,6 +34,7 @@
         <input type="hidden" name="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
         <input type="hidden" name="sample_vals" value="{{ sample_vals }}">
+        <input type="hidden" name="vals_hash" value="{{ vals_hash }}">
         <input type="hidden" name="n_samples" value="{{ n_samples }}">
         <input type="hidden" name="maf" value="{{ maf }}">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 11a9380c..707b18e1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1051,6 +1051,7 @@ def mapping_results_page():
         'samples',
         'vals',
         'sample_vals',
+        'vals_hash',
         'first_run',
         'output_files',
         'geno_db_exists',
-- 
cgit v1.2.3


From 1f2e32a91727abab77ecdf501fcc5040b17dfece Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 9 Sep 2021 17:07:06 +0000
Subject: Replaced trait name with trait display name in
 display_mapping_results so the group codes will be includes in phenotype IDs

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 5f5fe6a3..e9ba7dff 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1249,18 +1249,18 @@ class DisplayMappingResults:
 
             if self.this_trait.symbol:
                 identification += "Trait: %s - %s" % (
-                    self.this_trait.name, self.this_trait.symbol)
+                    self.this_trait.display_name, self.this_trait.symbol)
             elif self.dataset.type == "Publish":
                 if self.this_trait.post_publication_abbreviation:
                     identification += "Trait: %s - %s" % (
-                        self.this_trait.name, self.this_trait.post_publication_abbreviation)
+                        self.this_trait.display_name, self.this_trait.post_publication_abbreviation)
                 elif self.this_trait.pre_publication_abbreviation:
                     identification += "Trait: %s - %s" % (
-                        self.this_trait.name, self.this_trait.pre_publication_abbreviation)
+                        self.this_trait.display_name, self.this_trait.pre_publication_abbreviation)
                 else:
-                    identification += "Trait: %s" % (self.this_trait.name)
+                    identification += "Trait: %s" % (self.this_trait.display_name)
             else:
-                identification += "Trait: %s" % (self.this_trait.name)
+                identification += "Trait: %s" % (self.this_trait.display_name)
             identification += " with %s samples" % (self.n_samples)
 
             d = 4 + max(
-- 
cgit v1.2.3


From 5020158b3ab7cf14a5809af65d2c616d32714a22 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 9 Sep 2021 17:07:47 +0000
Subject: Change trait name to display name in the metadata at the top of the
 page (so group codes will be includes in phenotype IDs

---
 wqflask/wqflask/templates/mapping_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 162ae810..7f865056 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -68,7 +68,7 @@
               <h2>Map Viewer: Whole Genome</h2><br>
               <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
               <b>Database:</b> {{ dataset.fullname }}<br>
-              {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br>
+              {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br>
               {% if dataset.type == "ProbeSet" %}
               <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
               <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br>
-- 
cgit v1.2.3


From f51569c80a4e00ad7dcd99ed9bf3ed6d9aaf4051 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 10 Sep 2021 18:54:44 +0000
Subject: Removed encoding, since it's apparently not needed since the Python 3
 switchover (and was causing there to be no matches between user IDs and
 groups)

---
 wqflask/utility/redis_tools.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index ff125bd2..99295c67 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -135,10 +135,8 @@ def get_user_groups(user_id):
     for key in groups_list:
         try:
             group_ob = json.loads(groups_list[key])
-            group_admins = set([this_admin.encode(
-                'utf-8') if this_admin else None for this_admin in group_ob['admins']])
-            group_members = set([this_member.encode(
-                'utf-8') if this_member else None for this_member in group_ob['members']])
+            group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']])
+            group_members = set([this_member if this_member else None for this_member in group_ob['members']])
             if user_id in group_admins:
                 admin_group_ids.append(group_ob['id'])
             elif user_id in group_members:
-- 
cgit v1.2.3


From d76e1ec30195074cf8dfd0f8396285d31faa8984 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 10 Sep 2021 19:02:10 +0000
Subject: Fix issue with the way the template was checking if genofile_string
 was set; it was receiving an empty string, so the previous logic made it
 think there was a genofile string when there wasn't one

---
 wqflask/wqflask/templates/mapping_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7f865056..7a222d0c 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -73,7 +73,7 @@
               <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
               <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br>
               {% endif %}
-              {% if genofile_string is defined %}
+              {% if genofile_string != "" %}
               <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}
               {% endif %}
               <br>
-- 
cgit v1.2.3


From f414cd4109229546bfb8c56fea95b6729121f0b3 Mon Sep 17 00:00:00 2001
From: jgart
Date: Thu, 9 Sep 2021 22:28:02 -0500
Subject: Add Jupyter Notebook Launcher to Tools dropdown menu

---
 wqflask/wqflask/templates/base.html | 1 +
 1 file changed, 1 insertion(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 049ebe6d..14e6bc88 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -87,6 +87,7 @@
                                   <li><a href="https://systems-genetics.org/">Systems Genetics PheWAS</a></li>
                                   <li><a href="http://ucscbrowser.genenetwork.org/">Genome Browser</a></li>
                                   <li><a href="http://power.genenetwork.org">BXD Power Calculator</a></li>
+                                  <li><a href="http://notebook.genenetwork.org/">Jupyter Notebook Launcher</a></li>
                                   <li><a href="http://datafiles.genenetwork.org">Interplanetary File System</a></li>
                                 </ul>
                         </li>
-- 
cgit v1.2.3


From 38a8544553506651a263b0134ab5372c6a62c629 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 18:58:10 +0000
Subject: Temporarily point the View in GN1 button to gn1-lily.genenetwork.org
 since some features aren't working on gn1.genenetwork.org yet

---
 wqflask/wqflask/templates/show_trait_details.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 53e16aa0..36d3c15a 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -233,7 +233,7 @@
         <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1-lily.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
         {% if this_trait.dataset.type == 'Publish' %}
         <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
-- 
cgit v1.2.3


From 6a94f7a3a4893f087af53c2d39685d9dcb4b733d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 19:41:19 +0000
Subject: Change Genotype File text to only show the meaningful genotype
 deescription

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index e9ba7dff..a9ebeb64 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1206,7 +1206,7 @@ class DisplayMappingResults:
         if self.genofile_string == "":
             string4 = 'Genotype File: %s.geno' % self.dataset.group.name
         else:
-            string4 = 'Genotype File: %s' % self.genofile_string
+            string4 = 'Genotype File: %s' % self.genofile_string.split(":")[1]
 
         string6 = ''
         if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
-- 
cgit v1.2.3


From 75132a5382d32d9332f743aca0e406ae6137d7e5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 19:49:05 +0000
Subject: Include some extra metadata in the mapping page details (in addition
 to the figure itself)

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 4 ++--
 wqflask/wqflask/templates/mapping_results.html               | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index a9ebeb64..77d6e2db 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1198,8 +1198,8 @@ class DisplayMappingResults:
                                          self.dataset.fullname)
 
 
-        current_datetime = datetime.datetime.now()
-        string1 = 'UTC Timestamp: %s' % (current_datetime.strftime("%b %d %Y %H:%M:%S"))
+        self.current_datetime = datetime.datetime.now().strftime("%b %d %Y %H:%M:%S")
+        string1 = 'UTC Timestamp: %s' % (self.current_datetime)
         string2 = 'Dataset: %s' % (dataset_label)
         string3 = 'Trait Hash: %s' % (self.vals_hash)
 
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7a222d0c..f2d11e89 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -69,14 +69,15 @@
               <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
               <b>Database:</b> {{ dataset.fullname }}<br>
               {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br>
+              <b>Trait Hash: </b> {{ vals_hash }}<br>
               {% if dataset.type == "ProbeSet" %}
               <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
               <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br>
               {% endif %}
               {% if genofile_string != "" %}
-              <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}
+              <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}<br>
               {% endif %}
-              <br>
+              <b>Current Date/Time:</b> {{ current_datetime }}<br>
               <br>
               <a class="export_mapping_results" href="#" target="_blank" >Download Full Results</a>
           </div>
-- 
cgit v1.2.3


From 2ef7cad06cc1dcde61c91d2eafef002d25cb194e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 19:58:43 +0000
Subject: Add trait name and trait hash to exported mapping results

---
 wqflask/wqflask/marker_regression/run_mapping.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 2f90b475..b101b948 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -422,8 +422,9 @@ class RunMapping:
                 total_markers = len(self.qtl_results)
 
                 with Bench("Exporting Results"):
-                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
-                                           self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
+                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results,
+                                           self.mapping_results_path, self.mapping_scale, self.score_type,
+                                           self.transform, self.covariates, self.n_samples, self.vals_hash)
 
                 with Bench("Trimming Markers for Figure"):
                     if len(self.qtl_results) > 30000:
@@ -541,13 +542,15 @@ class RunMapping:
         return trimmed_genotype_data
 
 
-def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
+def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
     with open(results_path, "w+") as output_file:
         output_file.write(
             "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
         output_file.write(
             "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
         output_file.write("Data Set: " + dataset.fullname + "\n")
+        output_file.write("Trait: " + trait.display_name + "\n")
+        output_file.write("Trait Hash: " + vals_hash + "\n")
         output_file.write("N Samples: " + str(n_samples) + "\n")
         if len(transform) > 0:
             transform_text = "Transform - "
-- 
cgit v1.2.3


From 91d04e5b573107aead1da8482dd9184d9869b82a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 20:03:45 +0000
Subject: Change mapping export filename to use the trait hash

---
 wqflask/wqflask/marker_regression/run_mapping.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index b101b948..361c413b 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -104,9 +104,7 @@ class RunMapping:
         if "results_path" in start_vars:
             self.mapping_results_path = start_vars['results_path']
         else:
-            mapping_results_filename = self.dataset.group.name + "_" + \
-                ''.join(random.choice(string.ascii_uppercase + string.digits)
-                        for _ in range(6))
+            mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash])
             self.mapping_results_path = "{}{}.csv".format(
                 webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
-- 
cgit v1.2.3


From 24e0de14969edb220a03e22d1c9b7e6ed33f6b82 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 13 Sep 2021 20:04:30 +0000
Subject: Change mapping export filename to use the path passed from
 run_mapping, instead of the generic mapping_results.csv

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 707b18e1..54314a20 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1170,7 +1170,7 @@ def export_mapping_results():
     results_csv = open(file_path, "r").read()
     response = Response(results_csv,
                         mimetype='text/csv',
-                        headers={"Content-Disposition": "attachment;filename=mapping_results.csv"})
+                        headers={"Content-Disposition": "attachment;filename=" + os.path.basename(file_path)})
 
     return response
 
-- 
cgit v1.2.3


From c0fbbb42a79baa823b517ee8f537cec1edc057c8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 14 Sep 2021 18:09:36 +0000
Subject: Replace / with _ in the file hashes in rqtl_mapping.py, since they
 get translated to directories

---
 wqflask/wqflask/marker_regression/rqtl_mapping.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index cd578870..a148b49c 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -61,6 +61,7 @@ def get_hash_of_textio(the_file: TextIO) -> str:
 
     the_file.seek(0)
     hash_of_file = hashlib.md5(the_file.read().encode()).hexdigest()
+    hash_of_file = hash_of_file.replace("/", "_") # Replace / with _ to prevent issue with filenames being translated to directories
 
     return hash_of_file
 
-- 
cgit v1.2.3


From 8d54d1871e1319f7db46132d3eed61a817d5dc4c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 14 Sep 2021 18:14:33 +0000
Subject: Replace / with _ in the mapping results filename, due to / causing
 issues with being translated to directories

---
 wqflask/wqflask/marker_regression/run_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 361c413b..1df53fef 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -104,7 +104,7 @@ class RunMapping:
         if "results_path" in start_vars:
             self.mapping_results_path = start_vars['results_path']
         else:
-            mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash])
+            mapping_results_filename = "_".join([self.dataset.group.name, self.vals_hash]).replace("/", "_")
             self.mapping_results_path = "{}{}.csv".format(
                 webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
-- 
cgit v1.2.3


From b6c0885007d516b257d1027b97df66c11b8672dd Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 16 Sep 2021 13:26:53 +0300
Subject: wqflask: views: Redirect to the correct URL after phenotype update

---
 wqflask/wqflask/views.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 54314a20..85aa6b17 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -633,7 +633,7 @@ def update_phenotype():
                                   json_data=json.dumps(diff_data)))
         flash(f"Diff-data: \n{diff_data}\nhas been uploaded", "success")
     return redirect(f"/trait/{data_.get('dataset-name')}"
-                    f"/edit/phenotype-id/{data_.get('phenotype-id')}")
+                    f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
 
 
 @app.route("/probeset/update", methods=["POST"])
-- 
cgit v1.2.3


From 719b256996facb1f4bee2a0288bce1f18168f99b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 16 Sep 2021 17:59:49 +0000
Subject: Added back the option to edit privileges on trait pages, since the
 metadata edit button had replaced it

---
 wqflask/wqflask/templates/show_trait_details.html | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 36d3c15a..6a541c8c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -242,6 +242,9 @@
         {% if this_trait.dataset.type == 'ProbeSet' %}
         <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/edit/probeset-name/{{ this_trait.name }}', '_blank')">Edit</button>
         {% endif %}
+        {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+        <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit Privileges</button>
+        {% endif %}
         {% endif %}
     </div>
 </div>
-- 
cgit v1.2.3


From a9509a01191883e61cd5013453d18e89db022df2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 20 Sep 2021 17:34:26 +0000
Subject: Removed the reaper_version selection option, since original qtlreaper
 is no longer supported

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 9 ---------
 1 file changed, 9 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 5365140d..c6b6c0e1 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -95,15 +95,6 @@
                 {% elif mapping_method == "QTLReaper" %}
                 <div class="tab-pane" id="interval_mapping">
                     <div class="form-horizontal section-form-div">
-                        <div class="mapping_method_fields form-group">
-                            <label for="reaper_version" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
-                            <div class="col-xs-3 controls">
-                                <select name="reaper_version" class="form-control reaper-ver-select">
-                                    <option value="new">New</option>
-                                    <option value="original">Original</option>
-                                </select>
-                            </div>
-                        </div>
                         <div class="mapping_method_fields form-group">
                             <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
                             <div class="col-xs-2 controls">
-- 
cgit v1.2.3


From 2ad5b87f1c9bc5ce5bd3f54f7d83f18123ce3c3e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 20 Sep 2021 17:37:18 +0000
Subject: Returned the GN1 url to gn1.genenetwork.org since it's apparently
 working well enough again now that some issues have been fixed

---
 wqflask/wqflask/templates/show_trait_details.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 6a541c8c..2a21dd24 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -233,7 +233,7 @@
         <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1-lily.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
         {% if this_trait.dataset.type == 'Publish' %}
         <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('/trait/{{ this_trait.name }}/edit/inbredset-id/{{ this_trait.dataset.id }}', '_blank')">Edit</button>
-- 
cgit v1.2.3


From 92df90d68c3d3067f6856c6894be92c7c5dbcaa6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Sep 2021 17:41:53 +0000
Subject: Remove references to reaper_version and code for running old
 qtlreaper

---
 .../marker_regression/display_mapping_results.py   |  3 +-
 .../wqflask/marker_regression/qtlreaper_mapping.py | 95 ----------------------
 wqflask/wqflask/marker_regression/run_mapping.py   | 59 +++++---------
 .../new/javascript/show_trait_mapping_tools.js     |  2 +-
 wqflask/wqflask/views.py                           |  1 -
 5 files changed, 24 insertions(+), 136 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 77d6e2db..6254b9b9 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -357,8 +357,7 @@ class DisplayMappingResults:
         if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma":
             self.use_loco = start_vars['use_loco']
 
-        if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
-            self.reaper_version = start_vars['reaper_version']
+        if self.mapping_method == "reaper":
             if 'output_files' in start_vars:
                 self.output_files = ",".join(
                     [(the_file if the_file is not None else "") for the_file in start_vars['output_files']])
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 4d6715ba..801674e1 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -178,101 +178,6 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
     return marker_obs, permu_vals, bootstrap_vals
 
 
-def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
-    genotype = dataset.group.read_genotype_file(use_reaper=True)
-
-    if manhattan_plot != True:
-        genotype = genotype.addinterval()
-
-    trimmed_samples = []
-    trimmed_values = []
-    for i in range(0, len(samples_before)):
-        try:
-            trimmed_values.append(float(trait_vals[i]))
-            trimmed_samples.append(str(samples_before[i]))
-        except:
-            pass
-
-    perm_output = []
-    bootstrap_results = []
-
-    if num_perm < 100:
-        suggestive = 0
-        significant = 0
-    else:
-        perm_output = genotype.permutation(
-            strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
-        suggestive = perm_output[int(num_perm * 0.37 - 1)]
-        significant = perm_output[int(num_perm * 0.95 - 1)]
-        # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
-
-    json_data['suggestive'] = suggestive
-    json_data['significant'] = significant
-
-    if control_marker != "" and do_control == "true":
-        reaper_results = genotype.regression(strains=trimmed_samples,
-                                             trait=trimmed_values,
-                                             control=str(control_marker))
-        if bootCheck:
-            control_geno = []
-            control_geno2 = []
-            _FIND = 0
-            for _chr in genotype:
-                for _locus in _chr:
-                    if _locus.name == control_marker:
-                        control_geno2 = _locus.genotype
-                        _FIND = 1
-                        break
-                if _FIND:
-                    break
-            if control_geno2:
-                _prgy = list(genotype.prgy)
-                for _strain in trimmed_samples:
-                    _idx = _prgy.index(_strain)
-                    control_geno.append(control_geno2[_idx])
-
-            bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
-                                                   trait=trimmed_values,
-                                                   control=control_geno,
-                                                   nboot=num_bootstrap)
-    else:
-        reaper_results = genotype.regression(strains=trimmed_samples,
-                                             trait=trimmed_values)
-
-        if bootCheck:
-            bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
-                                                   trait=trimmed_values,
-                                                   nboot=num_bootstrap)
-
-    json_data['chr'] = []
-    json_data['pos'] = []
-    json_data['lod.hk'] = []
-    json_data['markernames'] = []
-    # if self.additive:
-    #    self.json_data['additive'] = []
-
-    # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-    qtl_results = []
-    for qtl in reaper_results:
-        reaper_locus = qtl.locus
-        # ZS: Convert chr to int
-        converted_chr = reaper_locus.chr
-        if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
-            converted_chr = int(reaper_locus.chr)
-        json_data['chr'].append(converted_chr)
-        json_data['pos'].append(reaper_locus.Mb)
-        json_data['lod.hk'].append(qtl.lrs)
-        json_data['markernames'].append(reaper_locus.name)
-        # if self.additive:
-        #    self.json_data['additive'].append(qtl.additive)
-        locus = {"name": reaper_locus.name, "chr": reaper_locus.chr,
-                 "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
-        qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
-               "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance}
-        qtl_results.append(qtl)
-    return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
-
-
 def natural_sort(marker_list):
     """
     Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 1df53fef..290c4a14 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -271,47 +271,32 @@ class RunMapping:
                     self.bootCheck = False
                     self.num_bootstrap = 0
 
-            self.reaper_version = start_vars['reaper_version']
-
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
             logger.info("Running qtlreaper")
 
-            if self.reaper_version == "new":
-                self.first_run = True
-                self.output_files = None
-                # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
-                if 'first_run' in start_vars:
-                    self.first_run = False
-                    if 'output_files' in start_vars:
-                        self.output_files = start_vars['output_files'].split(
-                            ",")
-
-                results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
-                                                                                                                                                       self.dataset,
-                                                                                                                                                       self.samples,
-                                                                                                                                                       self.vals,
-                                                                                                                                                       self.json_data,
-                                                                                                                                                       self.num_perm,
-                                                                                                                                                       self.bootCheck,
-                                                                                                                                                       self.num_bootstrap,
-                                                                                                                                                       self.do_control,
-                                                                                                                                                       self.control_marker,
-                                                                                                                                                       self.manhattan_plot,
-                                                                                                                                                       self.first_run,
-                                                                                                                                                       self.output_files)
-            else:
-                results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait,
-                                                                                                                                                             self.dataset,
-                                                                                                                                                             self.samples,
-                                                                                                                                                             self.vals,
-                                                                                                                                                             self.json_data,
-                                                                                                                                                             self.num_perm,
-                                                                                                                                                             self.bootCheck,
-                                                                                                                                                             self.num_bootstrap,
-                                                                                                                                                             self.do_control,
-                                                                                                                                                             self.control_marker,
-                                                                                                                                                             self.manhattan_plot)
+            self.first_run = True
+            self.output_files = None
+            # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+            if 'first_run' in start_vars:
+                self.first_run = False
+                if 'output_files' in start_vars:
+                    self.output_files = start_vars['output_files'].split(
+                        ",")
+
+            results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
+                                                                                                                                                    self.dataset,
+                                                                                                                                                    self.samples,
+                                                                                                                                                    self.vals,
+                                                                                                                                                    self.json_data,
+                                                                                                                                                    self.num_perm,
+                                                                                                                                                    self.bootCheck,
+                                                                                                                                                    self.num_bootstrap,
+                                                                                                                                                    self.do_control,
+                                                                                                                                                    self.control_marker,
+                                                                                                                                                    self.manhattan_plot,
+                                                                                                                                                    self.first_run,
+                                                                                                                                                    self.output_files)
         elif self.mapping_method == "plink":
             self.score_type = "-logP"
             self.manhattan_plot = True
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index b75d658e..e42fe8c4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -145,7 +145,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form
                           'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars',
                           'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker',
                           'do_control', 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend',
-                          'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
+                          'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples']
 
 $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) {
   return function() {
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 85aa6b17..980b9362 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1097,7 +1097,6 @@ def mapping_results_page():
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno',
         'temp_trait',
-        'reaper_version',
         'n_samples',
         'transform'
     )
-- 
cgit v1.2.3


From 7cb23fe9c03e4f8051340e2a8f32645e88acce3a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Sep 2021 17:52:37 +0000
Subject: Added type='button' to the Delete Collection button within
 collections/view, since without it it attempts to submit the form
 encapsulating the button (export in this case)

---
 wqflask/wqflask/templates/collections/view.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 9ec98ab1..a3090bcf 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -49,7 +49,7 @@
                     <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
                     <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
                     <button id="remove" class="btn btn-danger" data-url="/collections/remove" type="button" disabled><i class="icon-minus-sign"></i> Delete Rows</button>
-                    <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
+                    <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" type="button" title="Delete this collection" > Delete Collection</button>
                 </form>
             </div>
             <div style="margin-top: 10px; margin-bottom: 5px;">
-- 
cgit v1.2.3


From 9bd85361d58eb67ef9e59eff6031ed9fd00a3411 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Sep 2021 18:30:13 +0000
Subject: Only show most search page options if results exist; otherwise
 provide a link back to the home page

---
 wqflask/wqflask/templates/search_result_page.html | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 7ec335d5..c499aa8f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -53,6 +53,7 @@
                 A total of {{ results|count }} records were found.
         </p>
 
+        {% if results|count > 0 %}
         {% if go_term is not none %}
         <p><b>The associated genes include:</b><br><br>{% for word in search_terms %}{{ word.search_term[0] }}{% endfor %}</p>
         {% endif %}
@@ -133,8 +134,11 @@
           </div>
         </div>
         {% endif %}
+        {% else %}
+        <br>
+        <button type="button" onclick="window.location.href='/'">Return To Index Page</button>
+        {% endif %}
     </div>
-
     <div id="myModal"></div>
 
 <!-- End of body -->
@@ -171,6 +175,7 @@
                 return params;
             };
 
+            {% if results|count > 0 %}
             //ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters
             trait_table = $('#trait_table').DataTable( {
                 'drawCallback': function( settings ) {
@@ -412,6 +417,7 @@
                 var table = $('#trait_table').DataTable();
                 table.colReorder.reset()
             });
+            {% endif %}
 
             submit_special = function(url) {
                 $("#trait_submission_form").attr("action", url);
-- 
cgit v1.2.3


From cbb9905aa4406551973bfe47dcdb00f6b8ce9628 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Sep 2021 18:39:38 +0000
Subject: Fixed issue where the control marker parameter was being passed
 incorrectly to GN3 (should be just 'control' but was previously passed as
 'control_marker')

---
 wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index a148b49c..1dca1b1b 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -39,7 +39,7 @@ def run_rqtl(trait_name, vals, samples, dataset, mapping_scale, model, method, n
     }
 
     if do_control == "true" and control_marker:
-        post_data["control_marker"] = control_marker
+        post_data["control"] = control_marker
 
     if not manhattan_plot:
         post_data["interval"] = True
-- 
cgit v1.2.3


From cb9422ec5fc985530fcb4fb44d2729e460424d60 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Sep 2021 18:44:01 +0000
Subject: Removed the Control for (marker) option from R/qtl for now since
 Danny mentioned it isn't working correctly

---
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 15 ---------------
 1 file changed, 15 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c6b6c0e1..3af94ed6 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -253,21 +253,6 @@
                             </div>
                         </div>
                         {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div class="col-xs-6 controls">
-                              <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
-                              <label class="radio-inline">
-                                  <input type="radio" name="do_control_rqtl" value="true">
-                                  Yes
-                              </label>
-                              <label class="radio-inline">
-                                  <input type="radio" name="do_control_rqtl" value="false" checked="">
-                                  No
-                              </label>
-                            </div>
-                        </div>
-
                         <div class="mapping_method_fields form-group">
                             <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
                             <div class="col-xs-4 controls">
-- 
cgit v1.2.3


From 3494a9af7f82691f419ba1e3bd616be5ce68a00a Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 27 Sep 2021 13:07:11 +0300
Subject: Remove lengthy stack trace for 404, 400, 408 status codes

The stack trace causes the log file to grow into unmanageable sizes
over time.
---
 wqflask/wqflask/views.py | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 980b9362..1139ad43 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -160,18 +160,26 @@ def shutdown_session(exception=None):
 
 
 @app.errorhandler(Exception)
-def handle_bad_request(e):
+def handle_generic_exceptions(e):
+    import werkzeug
     err_msg = str(e)
-    logger.error(err_msg)
-    logger.error(request.url)
-    # get the stack trace and send it to the logger
-    exc_type, exc_value, exc_traceback = sys.exc_info()
-    logger.error(traceback.format_exc())
     now = datetime.datetime.utcnow()
     time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
-    formatted_lines = [request.url
-                       + " (" + time_str + ")"] + traceback.format_exc().splitlines()
-
+    # get the stack trace and send it to the logger
+    exc_type, exc_value, exc_traceback = sys.exc_info()
+    formatted_lines = {f"{request.url} ({time_str}) "
+                       f" {traceback.format_exc().splitlines()}"}
+
+    _message_templates = {
+        werkzeug.exceptions.NotFound: ("404: Not Found: "
+                                       f"{time_str}: {request.url}"),
+        werkzeug.exceptions.BadRequest: ("400: Bad Request: "
+                                         f"{time_str}: {request.url}"),
+        werkzeug.exceptions.RequestTimeout: ("408: Request Timeout: "
+                                             f"{time_str}: {request.url}")}
+    # Default to the lengthy stack trace!
+    logger.error(_message_templates.get(exc_type,
+                                        formatted_lines))
     # Handle random animations
     # Use a cookie to have one animation on refresh
     animation = request.cookies.get(err_msg[:32])
-- 
cgit v1.2.3


From 8135bd22898130ae6f58aa74cb80c83ab334d0d4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 27 Sep 2021 13:08:49 +0300
Subject: Remove variable-- named after a python keyword-- called "list"

---
 wqflask/wqflask/views.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1139ad43..007b0f9e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -184,9 +184,8 @@ def handle_generic_exceptions(e):
     # Use a cookie to have one animation on refresh
     animation = request.cookies.get(err_msg[:32])
     if not animation:
-        list = [fn for fn in os.listdir(
-            "./wqflask/static/gif/error") if fn.endswith(".gif")]
-        animation = random.choice(list)
+        animation = random.choice([fn for fn in os.listdir(
+            "./wqflask/static/gif/error") if fn.endswith(".gif")])
 
     resp = make_response(render_template("error.html", message=err_msg,
                                          stack=formatted_lines, error_image=animation, version=GN_VERSION))
-- 
cgit v1.2.3


From 16947a15bd955be7da45bb5f078870649b1b63e5 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 27 Sep 2021 13:09:24 +0300
Subject: Apply pep-8 formatting

---
 wqflask/wqflask/views.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 007b0f9e..b297da08 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -188,7 +188,9 @@ def handle_generic_exceptions(e):
             "./wqflask/static/gif/error") if fn.endswith(".gif")])
 
     resp = make_response(render_template("error.html", message=err_msg,
-                                         stack=formatted_lines, error_image=animation, version=GN_VERSION))
+                                         stack=formatted_lines,
+                                         error_image=animation,
+                                         version=GN_VERSION))
 
     # logger.error("Set cookie %s with %s" % (err_msg, animation))
     resp.set_cookie(err_msg[:32], animation)
-- 
cgit v1.2.3


From 266d4c4a425ca0a215c8d789e2978d213d5ff37d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 21 Sep 2021 21:25:13 +0300
Subject: Rename "admin_login_required" to "edit_access_required"

---
 wqflask/wqflask/decorators.py |  2 +-
 wqflask/wqflask/views.py      | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py
index f0978fd3..f6e3eb8a 100644
--- a/wqflask/wqflask/decorators.py
+++ b/wqflask/wqflask/decorators.py
@@ -3,7 +3,7 @@ from flask import g
 from functools import wraps
 
 
-def admin_login_required(f):
+def edit_access_required(f):
     """Use this for endpoints where admins are required"""
     @wraps(f)
     def wrap(*args, **kwargs):
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b297da08..5067ca0e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -85,7 +85,7 @@ from wqflask.export_traits import export_search_results_csv
 from wqflask.gsearch import GSearch
 from wqflask.update_search_results import GSearch as UpdateGSearch
 from wqflask.docs import Docs, update_text
-from wqflask.decorators import admin_login_required
+from wqflask.decorators import edit_access_required
 from wqflask.db_info import InfoPage
 
 from utility import temp_data
@@ -420,7 +420,7 @@ def submit_trait_form():
 
 
 @app.route("/trait/<name>/edit/inbredset-id/<inbredset_id>")
-@admin_login_required
+@edit_access_required
 def edit_phenotype(name, inbredset_id):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -477,7 +477,7 @@ def edit_phenotype(name, inbredset_id):
 
 
 @app.route("/trait/edit/probeset-name/<dataset_name>")
-@admin_login_required
+@edit_access_required
 def edit_probeset(dataset_name):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -520,7 +520,7 @@ def edit_probeset(dataset_name):
 
 
 @app.route("/trait/update", methods=["POST"])
-@admin_login_required
+@edit_access_required
 def update_phenotype():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -646,7 +646,7 @@ def update_phenotype():
 
 
 @app.route("/probeset/update", methods=["POST"])
-@admin_login_required
+@edit_access_required
 def update_probeset():
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -1381,7 +1381,7 @@ def get_sample_data_as_csv(trait_name: int, phenotype_id: int):
 
 
 @app.route("/admin/data-sample/diffs/")
-@admin_login_required
+@edit_access_required
 def display_diffs_admin():
     TMPDIR = current_app.config.get("TMPDIR")
     DIFF_DIR = f"{TMPDIR}/sample-data/diffs"
-- 
cgit v1.2.3


From 7f317126d7d422b073cb4e4a8698757fe1e763f3 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 21 Sep 2021 21:36:32 +0300
Subject: Replace hard-coded e-mails with gn-proxy queries

* wqflask/wqflask/decorators.py (edit_access_required.wrap): Query the
proxy to see the access rights of a given user.
---
 wqflask/wqflask/decorators.py | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/decorators.py b/wqflask/wqflask/decorators.py
index f6e3eb8a..54aa6795 100644
--- a/wqflask/wqflask/decorators.py
+++ b/wqflask/wqflask/decorators.py
@@ -1,14 +1,36 @@
 """This module contains gn2 decorators"""
 from flask import g
+from typing import Dict
 from functools import wraps
+from utility.hmac import hmac_creation
+
+import json
+import requests
 
 
 def edit_access_required(f):
     """Use this for endpoints where admins are required"""
     @wraps(f)
     def wrap(*args, **kwargs):
-        if g.user_session.record.get(b"user_email_address") not in [
-                b"labwilliams@gmail.com"]:
+        resource_id: str = ""
+        if kwargs.get("inbredset_id"):  # data type: dataset-publish
+            resource_id = hmac_creation("dataset-publish:"
+                                        f"{kwargs.get('inbredset_id')}:"
+                                        f"{kwargs.get('name')}")
+        if kwargs.get("dataset_name"):  # data type: dataset-probe
+            resource_id = hmac_creation("dataset-probeset:"
+                                        f"{kwargs.get('dataset_name')}")
+        response: Dict = {}
+        try:
+            _user_id = g.user_session.record.get(b"user_id",
+                                                 "").decode("utf-8")
+            response = json.loads(
+                requests.get("http://localhost:8080/"
+                             "available?resource="
+                             f"{resource_id}&user={_user_id}").content)
+        except:
+            response = {}
+        if "edit" not in response.get("data", []):
             return "You need to be admin", 401
         return f(*args, **kwargs)
     return wrap
-- 
cgit v1.2.3


From ac14326be6695f185f843d29bf3ff016f5eb3016 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 22 Sep 2021 14:30:09 +0300
Subject: new_security: login_user.html: Delete commented out block

---
 .../wqflask/templates/new_security/login_user.html | 26 ----------------------
 1 file changed, 26 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 095036f0..88eab6bc 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -114,31 +114,5 @@ label.error,div.error{
 {% endblock %}
 
 {% block js %}
-    <!-- Disable plugin, see https://github.com/genenetwork/genenetwork2/issues/310
-
-    <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
-    <script>
-    $(document).ready(function () {
-        $("#loginUserForm").validate({
-            onkeyup: false,
-            onsubmit: true,
-            onfocusout: function(element) { $(element).valid(); },
-            rules: {
-                email_address: {
-                    required: true,
-                    email: true
-                },
-                password: {
-                    required: true
-                }
-            }
-        });
-    });
-
-    </script>
-
-    -->
-
-    {% include "new_security/_scripts.html" %}
 
 {% endblock %}
-- 
cgit v1.2.3


From 84a0cce8a341b8b45b3b0037379818c32d5614b2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 22 Sep 2021 14:32:03 +0300
Subject: Remove "_scripts.html" and all it's references

---
 wqflask/wqflask/templates/new_security/_scripts.html                  | 1 -
 wqflask/wqflask/templates/new_security/forgot_password.html           | 1 -
 wqflask/wqflask/templates/new_security/forgot_password_step2.html     | 1 -
 wqflask/wqflask/templates/new_security/password_reset.html            | 1 -
 wqflask/wqflask/templates/new_security/register_user.html             | 1 -
 wqflask/wqflask/templates/new_security/registered.html                | 1 -
 wqflask/wqflask/templates/new_security/thank_you.html                 | 1 -
 wqflask/wqflask/templates/new_security/verification_still_needed.html | 1 -
 8 files changed, 8 deletions(-)
 delete mode 100644 wqflask/wqflask/templates/new_security/_scripts.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/new_security/_scripts.html b/wqflask/wqflask/templates/new_security/_scripts.html
deleted file mode 100644
index 5fefe305..00000000
--- a/wqflask/wqflask/templates/new_security/_scripts.html
+++ /dev/null
@@ -1 +0,0 @@
-<!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
diff --git a/wqflask/wqflask/templates/new_security/forgot_password.html b/wqflask/wqflask/templates/new_security/forgot_password.html
index e5c42a45..60a221da 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password.html
@@ -48,6 +48,5 @@
   {% endblock %}
 
 {% block js %}
-    {% include "new_security/_scripts.html" %}
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
index b4bf41c7..1835fd4c 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
@@ -20,7 +20,6 @@
 {% endblock %}
 
 {% block js %}
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html
index 684c12b1..e21f075c 100644
--- a/wqflask/wqflask/templates/new_security/password_reset.html
+++ b/wqflask/wqflask/templates/new_security/password_reset.html
@@ -73,7 +73,6 @@
 
 {% block js %}
 
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html
index 3ae4488b..c2895517 100644
--- a/wqflask/wqflask/templates/new_security/register_user.html
+++ b/wqflask/wqflask/templates/new_security/register_user.html
@@ -100,7 +100,6 @@
 
 {% block js %}
 
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html
index f2f58ec1..29889a97 100644
--- a/wqflask/wqflask/templates/new_security/registered.html
+++ b/wqflask/wqflask/templates/new_security/registered.html
@@ -19,7 +19,6 @@
 
 {% block js %}
 
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html
index 0ff7ee8d..d4f5e574 100644
--- a/wqflask/wqflask/templates/new_security/thank_you.html
+++ b/wqflask/wqflask/templates/new_security/thank_you.html
@@ -18,7 +18,6 @@
 {% endblock %}
 
 {% block js %}
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html
index dc0f9e68..1f91fd8d 100644
--- a/wqflask/wqflask/templates/new_security/verification_still_needed.html
+++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html
@@ -21,7 +21,6 @@
 {% endblock %}
 
 {% block js %}
-    {% include "new_security/_scripts.html" %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn/zxcvbn.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
-- 
cgit v1.2.3


From edb6fe1b9dd98d84deb0925a2d83726e739d8677 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 27 Sep 2021 16:28:12 +0300
Subject: wqflask: resource_manager: Remove logger

---
 wqflask/wqflask/resource_manager.py | 2 --
 1 file changed, 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index b28c1b04..c54dd0b3 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -8,8 +8,6 @@ from wqflask import app
 from utility.authentication_tools import check_owner_or_admin
 from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner
 
-from utility.logger import getLogger
-logger = getLogger(__name__)
 
 
 @app.route("/resources/manage", methods=('GET', 'POST'))
-- 
cgit v1.2.3


From 609865fc42b7436d8c34cdcefd159c3352c5d91c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Oct 2021 20:58:14 +0000
Subject: Add group link for user member groups

---
 wqflask/wqflask/templates/admin/group_manager.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index c0b99e75..692a7abc 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -81,7 +81,7 @@
                         <tr>
                             <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
                             <td>{{ loop.index }}</td>
-                            <td>{{ group.name }}</td>
+                            <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td>
                             <td>{{ group.admins|length + group.members|length }}</td>
                             <td>{{ group.created_timestamp }}</td>
                             <td>{{ group.changed_timestamp }}</td>
-- 
cgit v1.2.3


From 5b116de4aaf796be138ee0ad06c2242b3f3c33c7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Oct 2021 21:02:37 +0000
Subject: Changed get_user_groups to pull both the ID and details in the for
 loop from group_list by using group_list.items()

---
 wqflask/utility/redis_tools.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 99295c67..de9dde46 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -127,20 +127,20 @@ def check_verification_code(code):
 
 
 def get_user_groups(user_id):
-    # ZS: Get the groups where a user is an admin or a member and
+    # Get the groups where a user is an admin or a member and
     # return lists corresponding to those two sets of groups
-    admin_group_ids = []  # ZS: Group IDs where user is an admin
-    user_group_ids = []  # ZS: Group IDs where user is a regular user
+    admin_group_ids = []  # Group IDs where user is an admin
+    user_group_ids = []  # Group IDs where user is a regular user
     groups_list = Redis.hgetall("groups")
-    for key in groups_list:
+    for group_id, group_details in groups_list.items():
         try:
-            group_ob = json.loads(groups_list[key])
-            group_admins = set([this_admin if this_admin else None for this_admin in group_ob['admins']])
-            group_members = set([this_member if this_member else None for this_member in group_ob['members']])
+            _details = json.loads(group_details)
+            group_admins = set([this_admin if this_admin else None for this_admin in _details['admins']])
+            group_members = set([this_member if this_member else None for this_member in _details['members']])
             if user_id in group_admins:
-                admin_group_ids.append(group_ob['id'])
+                admin_group_ids.append(group_id)
             elif user_id in group_members:
-                user_group_ids.append(group_ob['id'])
+                user_group_ids.append(group_id)
             else:
                 continue
         except:
-- 
cgit v1.2.3