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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(+)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(+)

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(-)

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(-)

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(+)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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(-)

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

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 6e0ea75ca427721aed0a5f394b501b2cde9bf769 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 23 Sep 2021 13:17:55 +0300
Subject: Add script for creating/ updating groups during authorisation

---
 scripts/authentication/group.py | 130 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 scripts/authentication/group.py

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
new file mode 100644
index 00000000..b89bc3ec
--- /dev/null
+++ b/scripts/authentication/group.py
@@ -0,0 +1,130 @@
+"""A script for adding users to a specific group.
+
+Example:
+
+Assuming there are no groups and 'test@bonfacemunyoki.com' does not
+exist in Redis:
+
+.. code-block:: bash
+   python group.py -g "editors" -m "test@bonfacemunyoki.com"
+
+results in::
+
+   Successfully created the group: 'editors'
+   Data: '{"admins": [], "members": []}'
+
+If 'me@bonfacemunyoki.com' exists in 'users' in Redis and we run:
+
+.. code-block:: bash
+   python group.py -g "editors" -m "me@bonfacemunyoki.com"
+
+now results in::
+
+   No new group was created.
+   Updated Data: {'admins': [], 'members': ['me@bonfacemunyoki.com']}
+
+"""
+
+import argparse
+import redis
+import json
+
+from typing import Dict, List, Optional, Set
+from glom import glom  # type: ignore
+
+
+def create_group_data(users: Dict, target_group: str,
+                      members: Optional[str] = None,
+                      admins: Optional[str] = None) -> Dict:
+    """Return a dictionary that contains the following keys: "key",
+    "field", and "value" that can be used in a redis hash as follows:
+    HSET key field value
+
+    Parameters:
+
+    - `users`: a list of users for example:
+
+    {'8ad942fe-490d-453e-bd37-56f252e41603':
+    '{"email_address": "me@test.com",
+      "full_name": "John Doe",
+      "organization": "Genenetwork",
+      "password": {"algorithm": "pbkdf2",
+                   "hashfunc": "sha256",
+                    "salt": "gJrd1HnPSSCmzB5veMPaVk2ozzDlS1Z7Ggcyl1+pciA=",
+                    "iterations": 100000, "keylength": 32,
+                    "created_timestamp": "2021-09-22T11:32:44.971912",
+                    "password": "edcdaa60e84526c6"},
+                    "user_id": "8ad942fe", "confirmed": 1,
+                    "registration_info": {
+                        "timestamp": "2021-09-22T11:32:45.028833",
+                        "ip_address": "127.0.0.1",
+                        "user_agent": "Mozilla/5.0"}}'}
+
+    - `target_group`: the group name that will be stored inside the
+      "groups" hash in Redis.
+
+    - `members`: a comma-separated list of values that contain members
+      of the `target_group` e.g. "me@test1.com, me@test2.com,
+      me@test3.com"
+
+    - `admins`: a comma-separated list of values that contain
+      administrators of the `target_group` e.g. "me@test1.com,
+      me@test2.com, me@test3.com"
+
+    """
+    _members = "".join(members.split()).split(",") if members else []
+    _admins: List = "".join(admins.split()).split(",") if admins else []
+
+    user_emails: Set = {glom(json.loads(user_details), "email_address")
+                        for _, user_details in users.items()}
+
+    return {"key": "groups",
+            "field": target_group,
+            "value": json.dumps({
+                "admins": [admin for admin in _admins
+                           if admin in user_emails],
+                "members": [member for member in _members
+                            if member in user_emails]
+            })}
+
+
+if __name__ == "__main__":
+    # Initialising the parser CLI arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-g", "--group-name",
+                        help="This is the name of the GROUP mask")
+    parser.add_argument("-m", "--members",
+                        help="Members of the GROUP mask")
+    parser.add_argument("-a", "--admins",
+                        help="Admins of the GROUP mask")
+    args = parser.parse_args()
+
+    if not args.group_name:
+        exit("\nExiting. Please specify a group name to use!\n")
+
+    members = args.members if args.members else None
+    admins = args.admins if args.admins else None
+    REDIS_CONN = redis.Redis()
+    USERS = {key.decode(): val.decode()
+             for key, val in REDIS_CONN.hgetall("users").items()}
+
+    if not any([members, admins]):
+        exit("\nExiting. Please provide a value for "
+             "MEMBERS(-m) or ADMINS(-a)!\n")
+
+    data = create_group_data(
+        users=USERS,
+        target_group=args.group_name,
+        members=members,
+        admins=admins)
+    created_p = REDIS_CONN.hset(data.get("key", ""),
+                                data.get("field", ""),
+                                data.get("value", ""))
+
+    groups = json.loads(REDIS_CONN.hget("groups",
+                                        args.group_name))  # type: ignore
+    if created_p:
+        exit(f"\nSuccessfully created the group: '{args.group_name}'\n"
+             f"Data: {groups}\n")
+    exit("\nNo new group was created.\n"
+         f"Updated Data: {groups}\n")
-- 
cgit v1.2.3


From c585945c5516092b362efecc16325ad9ecc54291 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 23 Sep 2021 15:39:32 +0300
Subject: Add script that adds "editors" group to all resources in Redis

---
 scripts/authentication/resource.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 scripts/authentication/resource.py

diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py
new file mode 100644
index 00000000..75ef9e93
--- /dev/null
+++ b/scripts/authentication/resource.py
@@ -0,0 +1,25 @@
+"""A script that adds the group: 'editors' to every
+resource. 'editors' should have the right to edit both metadata and
+data.
+
+To use this script, simply run:
+
+.. code-block:: python
+   python resource.py
+
+"""
+import json
+import redis
+
+
+if __name__ == "__main__":
+    REDIS_CONN = redis.Redis()
+    resources = REDIS_CONN.hgetall("resources_clone")
+    for resource_id, resource in resources.items():
+        deserialized_resource = json.loads(resource)
+        deserialized_resource["group_masks"] = {
+            "editors": {"metadata": "edit",
+                        "data": "edit"}}
+        REDIS_CONN.hset("resources_clone",
+                        resource_id,
+                        json.dumps(deserialized_resource))
-- 
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(-)

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 df487791c91a5aa1a9a3b4e1a6c9ce17a58eafe6 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 4 Oct 2021 12:21:16 +0300
Subject: Modify resource editing script to enable data backups & restoration

---
 scripts/authentication/resource.py | 101 ++++++++++++++++++++++++++++++++-----
 1 file changed, 88 insertions(+), 13 deletions(-)

diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py
index 75ef9e93..8fcf09d7 100644
--- a/scripts/authentication/resource.py
+++ b/scripts/authentication/resource.py
@@ -1,25 +1,100 @@
-"""A script that adds the group: 'editors' to every
-resource. 'editors' should have the right to edit both metadata and
-data.
+"""A script that:
 
-To use this script, simply run:
+- Optionally restores data from a json file.
+
+- By default, without any args provided, adds the group: 'editors' to
+every resource. 'editors' should have the right to edit both metadata
+and data.
+
+- Optionally creates a back-up every time you edit a resource.
+
+
+To restore a back-up:
+
+.. code-block:: python
+   python resource.py --restore <PATH/TO/RESOURCE/BACK-UP/FILE>
+
+To add editors to every resource without creating a back-up:
 
 .. code-block:: python
    python resource.py
 
+To add editors to every resource while creating a back-up before any
+destructive edits:
+
+.. code-block:: python
+   python resource.py --enable-backup
+
 """
+import argparse
 import json
 import redis
+import os
+
+from datetime import datetime
+
+
+def recover_hash(name: str, file_path: str, set_function) -> bool:
+    """Recover back-ups using the `set_function`
+
+    Parameters:
+
+    - `name`: Redis hash where `file_path` will be restored
+
+    - `file_path`: File path where redis hash is sourced from
+
+    - `set_function`: Function used to do the Redis backup for
+      example: HSET
+
+    """
+    try:
+        with open(file_path, "r") as f:
+            resources = json.load(f)
+            for resource_id, resource in resources.items():
+                set_function(name=name,
+                             key=resource_id,
+                             value=resource)
+            return True
+    except Exception as e:
+        print(e)
+        return False
 
 
 if __name__ == "__main__":
-    REDIS_CONN = redis.Redis()
-    resources = REDIS_CONN.hgetall("resources_clone")
-    for resource_id, resource in resources.items():
-        deserialized_resource = json.loads(resource)
-        deserialized_resource["group_masks"] = {
-            "editors": {"metadata": "edit",
-                        "data": "edit"}}
-        REDIS_CONN.hset("resources_clone",
+    # Initialising the parser CLI arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--restore",
+                        help="Restore from a given backup")
+    parser.add_argument("--enable-backup", action="store_true",
+                        help="Create a back up before edits")
+    args = parser.parse_args()
+
+    if args.restore:
+        if recover_hash(name="resources",
+                        file_path=args.back_up,
+                        set_function=redis.Redis(decode_responses=True).hset):
+            exit(f"\n Done restoring {args.back_up}!\n")
+        else:
+            exit(f"\n There was an error restoring {args.back_up}!\n")
+
+    REDIS_CONN = redis.Redis(decode_responses=True)
+    RESOURCES = REDIS_CONN.hgetall("resources")
+    BACKUP_DIR = os.path.join(os.getenv("HOME"), "redis")
+    if args.enable_backup:
+        FILENAME = ("resources-"
+                    f"{datetime.now().strftime('%Y-%m-%d-%I:%M:%S-%p')}"
+                    ".json")
+        if not os.path.exists(BACKUP_DIR):
+            os.mkdir(BACKUP_DIR)
+        with open(os.path.join(BACKUP_DIR, FILENAME), "w") as f:
+            json.dump(RESOURCES, f, indent=4)
+        print(f"\nDone backing upto {FILENAME}")
+
+    for resource_id, resource in RESOURCES.items():
+        _resource = json.loads(resource)  # str -> dict conversion
+        _resource["group_masks"] = {"editors": {"metadata": "edit",
+                                                "data": "edit"}}
+        REDIS_CONN.hset("resources",
                         resource_id,
-                        json.dumps(deserialized_resource))
+                        json.dumps(_resource))
+    exit("Done updating `resources`\n")
-- 
cgit v1.2.3


From c5215d1ed224480a274476933beded9d2ba7f7dc Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 4 Oct 2021 13:40:06 +0300
Subject: Decode redis response by default

---
 scripts/authentication/group.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index b89bc3ec..265e8664 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -104,9 +104,8 @@ if __name__ == "__main__":
 
     members = args.members if args.members else None
     admins = args.admins if args.admins else None
-    REDIS_CONN = redis.Redis()
-    USERS = {key.decode(): val.decode()
-             for key, val in REDIS_CONN.hgetall("users").items()}
+    REDIS_CONN = redis.Redis(decode_responses=True)
+    USERS = REDIS_CONN.hgetall("users")
 
     if not any([members, admins]):
         exit("\nExiting. Please provide a value for "
-- 
cgit v1.2.3


From 8fae92c83d49042da68638319385df02061df44b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 4 Oct 2021 13:45:59 +0300
Subject: scripts: group.py: Remove "glom" dependency

---
 scripts/authentication/group.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 265e8664..02f782b3 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -30,7 +30,6 @@ import redis
 import json
 
 from typing import Dict, List, Optional, Set
-from glom import glom  # type: ignore
 
 
 def create_group_data(users: Dict, target_group: str,
@@ -74,10 +73,12 @@ def create_group_data(users: Dict, target_group: str,
     """
     _members = "".join(members.split()).split(",") if members else []
     _admins: List = "".join(admins.split()).split(",") if admins else []
-
-    user_emails: Set = {glom(json.loads(user_details), "email_address")
-                        for _, user_details in users.items()}
-
+    user_emails: Set = set()
+    for _, user_details in users.items():
+        _details = json.loads(user_details)
+        if _details.get("email_address"):
+            user_emails.add(_details.get("email_address"))
+    print(user_emails)
     return {"key": "groups",
             "field": target_group,
             "value": json.dumps({
-- 
cgit v1.2.3


From 7c1dd1211f96ca1021debc27a80d1700e70b9c6b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 4 Oct 2021 13:49:12 +0300
Subject: scripts: group.py: Modify exit message when displaying updated data

---
 scripts/authentication/group.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 02f782b3..cc0b037e 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -125,6 +125,6 @@ if __name__ == "__main__":
                                         args.group_name))  # type: ignore
     if created_p:
         exit(f"\nSuccessfully created the group: '{args.group_name}'\n"
-             f"Data: {groups}\n")
+             f"`HGETALL groups {args.group_name}`: {groups}\n")
     exit("\nNo new group was created.\n"
-         f"Updated Data: {groups}\n")
+         f"`HGETALL groups {args.group_name}`: {groups}\n")
-- 
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(-)

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(-)

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


From 35a970adba5ee1d60769a81b446122a60eac9494 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Oct 2021 21:03:52 +0000
Subject: Changed the group.py script to replace user e-mails with IDs and to
 include id, name, changed_timestamp, and created_timestamp in group details

---
 scripts/authentication/group.py | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index cc0b037e..a5f75aad 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -26,11 +26,13 @@ now results in::
 """
 
 import argparse
+import datetime
 import redis
 import json
 
 from typing import Dict, List, Optional, Set
 
+REDIS_CONN = redis.Redis(decode_responses=True)
 
 def create_group_data(users: Dict, target_group: str,
                       members: Optional[str] = None,
@@ -71,21 +73,26 @@ def create_group_data(users: Dict, target_group: str,
       me@test2.com, me@test3.com"
 
     """
-    _members = "".join(members.split()).split(",") if members else []
+
+    _members: List = "".join(members.split()).split(",") if members else []
     _admins: List = "".join(admins.split()).split(",") if admins else []
-    user_emails: Set = set()
-    for _, user_details in users.items():
+
+    user_ids: Dict = dict()
+    for user_id, user_details in users.items():
         _details = json.loads(user_details)
         if _details.get("email_address"):
-            user_emails.add(_details.get("email_address"))
-    print(user_emails)
+            user_ids[_details.get("email_address")] = user_id
+    print(user_ids)
     return {"key": "groups",
             "field": target_group,
             "value": json.dumps({
-                "admins": [admin for admin in _admins
-                           if admin in user_emails],
-                "members": [member for member in _members
-                            if member in user_emails]
+                "id": target_group,
+                "name": target_group,
+                "admins": [user_ids[admin] for admin in _admins
+                           if admin in user_ids],
+                "members": [user_ids[member] for member in _members
+                            if member in user_ids],
+                "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
             })}
 
 
@@ -105,7 +112,6 @@ if __name__ == "__main__":
 
     members = args.members if args.members else None
     admins = args.admins if args.admins else None
-    REDIS_CONN = redis.Redis(decode_responses=True)
     USERS = REDIS_CONN.hgetall("users")
 
     if not any([members, admins]):
@@ -117,6 +123,12 @@ if __name__ == "__main__":
         target_group=args.group_name,
         members=members,
         admins=admins)
+
+    if not REDIS_CONN.hget("groups", data.get("field", "")):
+      updated_data = json.loads(data["value"])
+      updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+      data["value"] = json.dumps(updated_data)
+
     created_p = REDIS_CONN.hset(data.get("key", ""),
                                 data.get("field", ""),
                                 data.get("value", ""))
-- 
cgit v1.2.3


From 4c6a7e46dd7afe311c0bed38c4a69ddadf3cb416 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Oct 2021 21:09:15 +0000
Subject: Moved REDIS_CONN back into if __name__ == '__main__' since it doesn't
 need to be globally accessed anymore (I think I intiially moved it because I
 was calling it in create_group_data, but that ended up being unnecessary

---
 scripts/authentication/group.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index a5f75aad..76c7fb4f 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -32,8 +32,6 @@ import json
 
 from typing import Dict, List, Optional, Set
 
-REDIS_CONN = redis.Redis(decode_responses=True)
-
 def create_group_data(users: Dict, target_group: str,
                       members: Optional[str] = None,
                       admins: Optional[str] = None) -> Dict:
@@ -112,6 +110,8 @@ if __name__ == "__main__":
 
     members = args.members if args.members else None
     admins = args.admins if args.admins else None
+
+    REDIS_CONN = redis.Redis(decode_responses=True)
     USERS = REDIS_CONN.hgetall("users")
 
     if not any([members, admins]):
-- 
cgit v1.2.3


From 2236508f24c8c266a6a9dff28a1307bb3d0dd31e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:07:09 +0300
Subject: tests: test_run_mapping: Add missing positional argument "vals_hash"

---
 wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index c220a072..31f56c07 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -181,7 +181,8 @@ class TestRunMapping(unittest.TestCase):
             with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
                                        results_path="~/results", mapping_scale="physic", score_type="-log(p)",
-                                       transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100")
+                                       transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100",
+                                       vals_hash="")
 
                 write_calls = [
                     mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
-- 
cgit v1.2.3


From 321632bf70c72ed987ba7c4f605dd92deaa62380 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:10:04 +0300
Subject: tests: test_run_mapping: Add missing attribute to "self.trait"

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

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 31f56c07..26903eed 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -47,7 +47,7 @@ class TestRunMapping(unittest.TestCase):
 
         self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
         self.trait = AttributeSetter(
-            {"symbol": "IGFI", "chr": "X1", "mb": 123313})
+            {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"})
 
     def tearDown(self):
         self.dataset = AttributeSetter(
-- 
cgit v1.2.3


From e97719eea27ede1b3e943e6d21d18e5d383679f0 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:12:29 +0300
Subject: tests: test_run_mapping: Fix failing assert when getting perm strata

---
 wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 26903eed..3e9e4ef3 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -233,25 +233,20 @@ class TestRunMapping(unittest.TestCase):
                 "c1": "c1_value",
                 "c2": "c2_value",
                 "w1": "w1_value"
-
             },
             "S2": {
                 "w1": "w2_value",
                 "w2": "w2_value"
-
             },
             "S3": {
 
                 "c1": "c1_value",
                 "c2": "c2_value"
-
             },
-
         }})
-
         results = get_perm_strata(this_trait={}, sample_list=sample_list,
                                   categorical_vars=categorical_vars, used_samples=used_samples)
-        self.assertEqual(results, [2, 1])
+        self.assertEqual(results, [1, 1])
 
     def test_get_chr_length(self):
         """test for getting chromosome length"""
-- 
cgit v1.2.3


From 1f5be42d8f090fd4fe77a9275b12a9c9b1383d09 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:19:52 +0300
Subject: tests: test_run_mapping: Add missing calls

After adding the missing attribute to "self.trait", we need to also
need to update some missing calls.
---
 wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 3e9e4ef3..3747aeb8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -188,6 +188,8 @@ class TestRunMapping(unittest.TestCase):
                     mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
                     mock.call('Population: Human GP1_\n'), mock.call(
                         'Data Set: dataser_1\n'),
+                    mock.call('Trait: Test Name\n'),
+                    mock.call('Trait Hash: \n'),
                     mock.call('N Samples: 100\n'), mock.call(
                         'Transform - Quantile Normalized\n'),
                     mock.call('Gene Symbol: IGFI\n'), mock.call(
-- 
cgit v1.2.3


From a4ec2505fb9dd6f0480c9b452fd623e038c07939 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:28:33 +0300
Subject: tests: test_run_mapping: Add missing "name" attribute to tests

---
 .../unit/wqflask/marker_regression/test_gemma_mapping.py     | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 4003d68f..58a44b2a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -81,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase):
     def test_gen_pheno_txt_file(self):
         """add tests for generating pheno txt file"""
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
-            gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[
-                               "x", "w", "q", "we", "R"], trait_filename="fitr.re")
+            gen_pheno_txt_file(
+                this_dataset=AttributeSetter({"name": "A"}),
+                genofile_name="", vals=[
+                    "x", "w", "q", "we", "R"])
             mock_open.assert_called_once_with(
-                '/home/user/data/gn2/fitr.re.txt', 'w')
+                '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w')
             filehandler = mock_open()
             values = ["x", "w", "q", "we", "R"]
             write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call(
@@ -112,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase):
         create_trait.side_effect = create_trait_side_effect
 
         group = MockGroup({"name": "group_X", "samplelist": samplelist})
-        this_dataset = AttributeSetter({"group": group})
+        this_dataset = AttributeSetter({"group": group, "name": "A"})
         flat_files.return_value = "Home/Genenetwork"
 
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
@@ -132,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase):
 
             flat_files.assert_called_once_with('mapping')
             mock_open.assert_called_once_with(
-                'Home/Genenetwork/group_X_covariates.txt', 'w')
+                'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w')
             filehandler = mock_open()
             filehandler.write.assert_has_calls([mock.call(
                 '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
-- 
cgit v1.2.3


From 7a15d24a6598f30801dd897ddc72d3773641e7bd Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 Oct 2021 11:32:17 +0300
Subject: doc: docker-container.org: Remove python2 gn2 docker set-up command

---
 doc/docker-container.org | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/doc/docker-container.org b/doc/docker-container.org
index ef0d71fc..79b8272f 100644
--- a/doc/docker-container.org
+++ b/doc/docker-container.org
@@ -28,13 +28,6 @@ which will be added to a base mariaDB image.
 First create the gn2 tar archive by running:
 
 #+begin_src sh
-# For the Python 2 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
-    ./pre-inst-env guix pack --no-grafts\
-    -S /gn2-profile=/ \
-    screen python2-genenetwork2
-
-# For the Python 3 version:
 env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
     ./pre-inst-env guix pack --no-grafts\
     -S /gn2-profile=/ \
-- 
cgit v1.2.3


From 949789a00d8e6e901cc18b939737cd42e14c0236 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 16:12:22 +0300
Subject: scripts: group: Use a unique key to identify a group

---
 scripts/authentication/group.py | 32 +++++++++++++++++++-------------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 76c7fb4f..eea13efe 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -29,6 +29,7 @@ import argparse
 import datetime
 import redis
 import json
+import uuid
 
 from typing import Dict, List, Optional, Set
 
@@ -71,26 +72,31 @@ def create_group_data(users: Dict, target_group: str,
       me@test2.com, me@test3.com"
 
     """
+    # Emails
+    _members: Set = set("".join(members.split()).split(",")
+                        if members else [])
+    _admins: Set = set("".join(admins.split()).split(",")
+                       if admins else [])
 
-    _members: List = "".join(members.split()).split(",") if members else []
-    _admins: List = "".join(admins.split()).split(",") if admins else []
+    # Unique IDs
+    member_ids: Set = set()
+    admin_ids: Set = set()
 
-    user_ids: Dict = dict()
     for user_id, user_details in users.items():
         _details = json.loads(user_details)
-        if _details.get("email_address"):
-            user_ids[_details.get("email_address")] = user_id
-    print(user_ids)
+        if _details.get("email_address") in _members:
+            member_ids.add(user_id)
+        if _details.get("email_address") in _admins:
+            admin_ids.add(user_id)
+
+    timestamp: str = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
     return {"key": "groups",
-            "field": target_group,
+            "field": str(uuid.uuid4()),
             "value": json.dumps({
-                "id": target_group,
                 "name": target_group,
-                "admins": [user_ids[admin] for admin in _admins
-                           if admin in user_ids],
-                "members": [user_ids[member] for member in _members
-                            if member in user_ids],
-                "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+                "admins": list(admin_ids),
+                "members": list(member_ids),
+                "changed_timestamp": timestamp,
             })}
 
 
-- 
cgit v1.2.3


From 931c7eb07cc995118ba808df760fd74de036853f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 16:15:31 +0300
Subject: scripts: group: Remove unused import

---
 scripts/authentication/group.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index eea13efe..d3f9a1e4 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -31,7 +31,8 @@ import redis
 import json
 import uuid
 
-from typing import Dict, List, Optional, Set
+from typing import Dict, Optional, Set
+
 
 def create_group_data(users: Dict, target_group: str,
                       members: Optional[str] = None,
-- 
cgit v1.2.3


From 870edaf2cf8ce8588ee7c58d08fc1f307f7198ec Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 16:19:04 +0300
Subject: scripts: group: Remove empty `""` value for data.get

data.get("field") will default to None if there is no value; and None
is falsy.
---
 scripts/authentication/group.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index d3f9a1e4..1919d9db 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -131,10 +131,10 @@ if __name__ == "__main__":
         members=members,
         admins=admins)
 
-    if not REDIS_CONN.hget("groups", data.get("field", "")):
       updated_data = json.loads(data["value"])
       updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
       data["value"] = json.dumps(updated_data)
+    if not REDIS_CONN.hget("groups", data.get("field")):
 
     created_p = REDIS_CONN.hset(data.get("key", ""),
                                 data.get("field", ""),
-- 
cgit v1.2.3


From c1b23a1b01071c252ddae6dbea14500e4c248d84 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:01:54 +0300
Subject: workflows: main.yml: Disable link checking

---
 .github/workflows/main.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f279a7e5..8e2c7966 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -55,11 +55,11 @@ jobs:
         GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
         etc/default_settings.py -c -m unittest discover -v
 
-    - name: Test for Broken Links
-      run: |
-        env GN2_PROFILE=/gn2-profile \
-        TMPDIR=/tmp\
-        WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
-        GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
-        etc/default_settings.py -c \
-        $PWD/test/requests/links_scraper/genelinks.py
+    # - name: Test for Broken Links
+    #   run: |
+    #     env GN2_PROFILE=/gn2-profile \
+    #     TMPDIR=/tmp\
+    #     WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+    #     GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
+    #     etc/default_settings.py -c \
+    #     $PWD/test/requests/links_scraper/genelinks.py
-- 
cgit v1.2.3


From 40dddc1a78a7808b480d26594ced689cdcc08c24 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:23:08 +0300
Subject: scripts: group: Fix indentation

---
 scripts/authentication/group.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 1919d9db..7e73be15 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -131,10 +131,10 @@ if __name__ == "__main__":
         members=members,
         admins=admins)
 
-      updated_data = json.loads(data["value"])
-      updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
-      data["value"] = json.dumps(updated_data)
     if not REDIS_CONN.hget("groups", data.get("field")):
+        updated_data = json.loads(data["value"])
+        updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        data["value"] = json.dumps(updated_data)
 
     created_p = REDIS_CONN.hset(data.get("key", ""),
                                 data.get("field", ""),
-- 
cgit v1.2.3


From 67222a6cb11995eb5a4af58f63cc9385ccfb9226 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:24:16 +0300
Subject: scripts: group: Break up long line

---
 scripts/authentication/group.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 7e73be15..ed17f260 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -133,7 +133,8 @@ if __name__ == "__main__":
 
     if not REDIS_CONN.hget("groups", data.get("field")):
         updated_data = json.loads(data["value"])
-        updated_data["created_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        updated_data["created_timestamp"] = timestamp
         data["value"] = json.dumps(updated_data)
 
     created_p = REDIS_CONN.hset(data.get("key", ""),
-- 
cgit v1.2.3


From dc378d26c003a8f0503ad69235d1685d66e4d611 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:26:03 +0300
Subject: scripts: group: Update docstrings for "create_group_data"

---
 scripts/authentication/group.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index ed17f260..08a4a2bc 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -41,6 +41,9 @@ def create_group_data(users: Dict, target_group: str,
     "field", and "value" that can be used in a redis hash as follows:
     HSET key field value
 
+    The "field" return value is a unique-id that is used to
+    distinguish the groups.
+
     Parameters:
 
     - `users`: a list of users for example:
-- 
cgit v1.2.3


From d5f6670836cbed804a00e02ec0258d0c87564006 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:40:35 +0300
Subject: scripts: group: Replace args.group_name with data["field"]

---
 scripts/authentication/group.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/authentication/group.py b/scripts/authentication/group.py
index 08a4a2bc..c8c2caad 100644
--- a/scripts/authentication/group.py
+++ b/scripts/authentication/group.py
@@ -145,7 +145,7 @@ if __name__ == "__main__":
                                 data.get("value", ""))
 
     groups = json.loads(REDIS_CONN.hget("groups",
-                                        args.group_name))  # type: ignore
+                                        data.get("field")))  # type: ignore
     if created_p:
         exit(f"\nSuccessfully created the group: '{args.group_name}'\n"
              f"`HGETALL groups {args.group_name}`: {groups}\n")
-- 
cgit v1.2.3


From 70f8ed53f85cfb42ca81ed6c3b4c9cf1060940e5 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 Oct 2021 21:44:51 +0300
Subject: scripts: resource: Add option for specifying a groups uuid

---
 scripts/authentication/resource.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/scripts/authentication/resource.py b/scripts/authentication/resource.py
index 8fcf09d7..4996f34c 100644
--- a/scripts/authentication/resource.py
+++ b/scripts/authentication/resource.py
@@ -63,12 +63,16 @@ def recover_hash(name: str, file_path: str, set_function) -> bool:
 if __name__ == "__main__":
     # Initialising the parser CLI arguments
     parser = argparse.ArgumentParser()
+    parser.add_argument("--group-id",
+                        help="Add the group id to all resources")
     parser.add_argument("--restore",
                         help="Restore from a given backup")
     parser.add_argument("--enable-backup", action="store_true",
                         help="Create a back up before edits")
     args = parser.parse_args()
 
+    if not args.group_id:
+        exit("Please specify the group-id!\n")
     if args.restore:
         if recover_hash(name="resources",
                         file_path=args.back_up,
@@ -92,8 +96,8 @@ if __name__ == "__main__":
 
     for resource_id, resource in RESOURCES.items():
         _resource = json.loads(resource)  # str -> dict conversion
-        _resource["group_masks"] = {"editors": {"metadata": "edit",
-                                                "data": "edit"}}
+        _resource["group_masks"] = {args.group_id: {"metadata": "edit",
+                                                    "data": "edit"}}
         REDIS_CONN.hset("resources",
                         resource_id,
                         json.dumps(_resource))
-- 
cgit v1.2.3


From 7805a48172ada364d3783db043dbcf637445a7fe Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 22:07:43 +0000
Subject: Adding convert_dol_genotypes.py to scripts; everything is hard-coded
 in it since I was only writing it to generate a specific file and it probably
 won't be re-used

---
 scripts/convert_dol_genotypes.py | 68 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 scripts/convert_dol_genotypes.py

diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py
new file mode 100644
index 00000000..353f1b53
--- /dev/null
+++ b/scripts/convert_dol_genotypes.py
@@ -0,0 +1,68 @@
+# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file
+# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly
+
+import os
+
+geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/"
+markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt"
+gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno"
+
+marker_data = {}
+with open(markers_file, "r") as markers_fh:
+    for i, line in enumerate(markers_fh):
+        if i == 0:
+            continue
+        else:
+            line_items = line.split("\t")
+            this_marker = {}
+            this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M"
+            this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}'
+            marker_data[line_items[1]] = this_marker
+
+sample_names = []
+for filename in os.listdir(geno_dir):
+    if "gm4qtl2_geno" in filename:
+        with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh:
+            for i, line in enumerate(rqtl_geno_fh):
+                line_items = line.split(",")
+                if i < 3:
+                    continue
+                elif not len(sample_names) and i == 3:
+                    sample_names = [item.replace("TLB", "TB") for item in line_items[1:]]
+                elif i > 3:
+                    marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]]
+
+def sort_func(e):
+    try:
+        return int(e['chr'])
+    except:
+        if e['chr'] == "X":
+            return 20
+        elif e['chr'] == "Y":
+            return 21
+        elif e['chr'] == "M":
+            return 22
+
+marker_list = []
+for key, value in marker_data.items():
+    if 'genotypes' in value:
+        this_marker = {
+            'chr': value['chr'],
+            'locus': key,
+            'pos': value['pos'],
+            'genotypes': value['genotypes']
+        }
+        marker_list.append(this_marker)
+
+marker_list.sort(key=sort_func)
+
+with open(gn_geno_path, "w") as gn_geno_fh:
+    gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names)))
+    for marker in marker_list:
+        row_contents = [
+            marker['chr'],
+            marker['locus'],
+            marker['pos'],
+            marker['pos']
+        ] + marker['genotypes']
+        gn_geno_fh.write("\t".join(row_contents) + "\n")
-- 
cgit v1.2.3


From b37a9c6c495d142852d0cee54d83f5c9e815e37b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 22:19:07 +0000
Subject: Fixed the sort to account for both chr and pos in a kind of hack-y
 way + added some comments + changed EOL to LF because the file suddenly
 started including EOL characters

---
 scripts/convert_dol_genotypes.py | 142 ++++++++++++++++++++-------------------
 1 file changed, 74 insertions(+), 68 deletions(-)

diff --git a/scripts/convert_dol_genotypes.py b/scripts/convert_dol_genotypes.py
index 353f1b53..81b3bd6d 100644
--- a/scripts/convert_dol_genotypes.py
+++ b/scripts/convert_dol_genotypes.py
@@ -1,68 +1,74 @@
-# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file
-# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly
-
-import os
-
-geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/"
-markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt"
-gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno"
-
-marker_data = {}
-with open(markers_file, "r") as markers_fh:
-    for i, line in enumerate(markers_fh):
-        if i == 0:
-            continue
-        else:
-            line_items = line.split("\t")
-            this_marker = {}
-            this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M"
-            this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}'
-            marker_data[line_items[1]] = this_marker
-
-sample_names = []
-for filename in os.listdir(geno_dir):
-    if "gm4qtl2_geno" in filename:
-        with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh:
-            for i, line in enumerate(rqtl_geno_fh):
-                line_items = line.split(",")
-                if i < 3:
-                    continue
-                elif not len(sample_names) and i == 3:
-                    sample_names = [item.replace("TLB", "TB") for item in line_items[1:]]
-                elif i > 3:
-                    marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]]
-
-def sort_func(e):
-    try:
-        return int(e['chr'])
-    except:
-        if e['chr'] == "X":
-            return 20
-        elif e['chr'] == "Y":
-            return 21
-        elif e['chr'] == "M":
-            return 22
-
-marker_list = []
-for key, value in marker_data.items():
-    if 'genotypes' in value:
-        this_marker = {
-            'chr': value['chr'],
-            'locus': key,
-            'pos': value['pos'],
-            'genotypes': value['genotypes']
-        }
-        marker_list.append(this_marker)
-
-marker_list.sort(key=sort_func)
-
-with open(gn_geno_path, "w") as gn_geno_fh:
-    gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names)))
-    for marker in marker_list:
-        row_contents = [
-            marker['chr'],
-            marker['locus'],
-            marker['pos'],
-            marker['pos']
-        ] + marker['genotypes']
-        gn_geno_fh.write("\t".join(row_contents) + "\n")
+# This is just to convert the Rqtl2 format genotype files for DOL into a .geno file
+# Everything is hard-coded since I doubt this will be re-used and I just wanted to generate the file quickly
+
+import os
+
+geno_dir = "/home/zas1024/gn2-zach/DO_genotypes/"
+markers_file = "/home/zas1024/gn2-zach/DO_genotypes/SNP_Map.txt"
+gn_geno_path = "/home/zas1024/gn2-zach/DO_genotypes/DOL.geno"
+
+# Iterate through the SNP_Map.txt file to get marker positions
+marker_data = {}
+with open(markers_file, "r") as markers_fh:
+    for i, line in enumerate(markers_fh):
+        if i == 0:
+            continue
+        else:
+            line_items = line.split("\t")
+            this_marker = {}
+            this_marker['chr'] = line_items[2] if line_items[2] != "0" else "M"
+            this_marker['pos'] = f'{float(line_items[3])/1000000:.6f}'
+            marker_data[line_items[1]] = this_marker
+
+# Iterate through R/qtl2 format genotype files and pull out the samplelist and genotypes for each marker
+sample_names = []
+for filename in os.listdir(geno_dir):
+    if "gm4qtl2_geno" in filename:
+        with open(geno_dir + "/" + filename, "r") as rqtl_geno_fh:
+            for i, line in enumerate(rqtl_geno_fh):
+                line_items = line.split(",")
+                if i < 3:
+                    continue
+                elif not len(sample_names) and i == 3:
+                    sample_names = [item.replace("TLB", "TB") for item in line_items[1:]]
+                elif i > 3:
+                    marker_data[line_items[0]]['genotypes'] = ["X" if item.strip() == "-" else item.strip() for item in line_items[1:]]
+
+# Generate list of marker obs to iterate through when writing to .geno file
+marker_list = []
+for key, value in marker_data.items():
+    if 'genotypes' in value:
+        this_marker = {
+            'chr': value['chr'],
+            'locus': key,
+            'pos': value['pos'],
+            'genotypes': value['genotypes']
+        }
+        marker_list.append(this_marker)
+
+def sort_func(e):
+    """For ensuring that X/Y chromosomes/mitochondria are sorted to the end correctly"""
+    try:
+        return float((e['chr']))*1000 + float(e['pos'])
+    except:
+        if e['chr'] == "X":
+            return 20000 + float(e['pos'])
+        elif e['chr'] == "Y":
+            return 21000 + float(e['pos'])
+        elif e['chr'] == "M":
+            return 22000 + float(e['pos'])
+
+# Sort markers by chromosome
+marker_list.sort(key=sort_func)
+
+# Write lines to .geno file
+with open(gn_geno_path, "w") as gn_geno_fh:
+    gn_geno_fh.write("\t".join((["Chr", "Locus", "cM", "Mb"] + sample_names)))
+    for marker in marker_list:
+        row_contents = [
+            marker['chr'],
+            marker['locus'],
+            marker['pos'],
+            marker['pos']
+        ] + marker['genotypes']
+        gn_geno_fh.write("\t".join(row_contents) + "\n")
-- 
cgit v1.2.3


From e473a210491620477898ba69f33f69f14fdf5893 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 22:49:20 +0000
Subject: Fix issue where outliers weren't being highlighted for rows drawn by
 Scroller (so all rows beyond a certain point)

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

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 4de1b0ac..0a060cdc 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -130,6 +130,7 @@ var primary_table = $('#samples_primary').DataTable( {
       $(row).addClass("value_se");
       if (data.outlier) {
         $(row).addClass("outlier");
+        $(row).attr("style", "background-color: orange;");
       }
       $('td', row).eq(1).addClass("column_name-Index")
       $('td', row).eq(2).addClass("column_name-Sample")
@@ -189,6 +190,7 @@ if (js_data.sample_lists.length > 1){
         $(row).addClass("value_se");
         if (data.outlier) {
           $(row).addClass("outlier");
+          $(row).attr("style", "background-color: orange;");
         }
         $('td', row).eq(1).addClass("column_name-Index")
         $('td', row).eq(2).addClass("column_name-Sample")
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 3dbf5f57..f3fa1332 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -254,8 +254,6 @@
                 } );
                 {% endif %}
 
-                $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'orange')
-
                 $('.edit_sample_checkbox:checkbox').change(function() {
                     if ($(this).is(":checked")) {
                         if (!$(this).closest('tr').hasClass('selected')) {
-- 
cgit v1.2.3


From 9b28d111ad156f3862286e88bc220e02d5e1312b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Oct 2021 23:31:19 +0000
Subject: Fixed some issues with scale and score_type in mapping export +
 include mapping method in export filename

---
 wqflask/wqflask/marker_regression/run_mapping.py | 25 ++++++++++++------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 290c4a14..80094057 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]).replace("/", "_")
+            mapping_results_filename = "_".join([self.dataset.group.name, self.mapping_method, self.vals_hash]).replace("/", "_")
             self.mapping_results_path = "{}{}.csv".format(
                 webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
@@ -405,8 +405,8 @@ 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,
+                    export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+                                           self.mapping_method, self.mapping_scale, self.score_type,
                                            self.transform, self.covariates, self.n_samples, self.vals_hash)
 
                 with Bench("Trimming Markers for Figure"):
@@ -525,7 +525,11 @@ class RunMapping:
         return trimmed_genotype_data
 
 
-def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
+def export_mapping_results(dataset, trait, markers, results_path, mapping_method, mapping_scale, score_type, transform, covariates, n_samples, vals_hash):
+    if mapping_scale == "physic":
+        scale_string = "Mb"
+    else:
+        scale_string = "cM"
     with open(results_path, "w+") as output_file:
         output_file.write(
             "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
@@ -535,6 +539,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         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")
+        output_file.write("Mapping Tool: " + str(mapping_method) + "\n")
         if len(transform) > 0:
             transform_text = "Transform - "
             if transform == "qnorm":
@@ -564,10 +569,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("Name,Chr,")
         if score_type.lower() == "-logP":
             score_type = "-logP"
-        if 'Mb' in markers[0]:
-            output_file.write("Mb," + score_type)
-        if 'cM' in markers[0]:
-            output_file.write("Cm," + score_type)
+        output_file.write(scale_string + "," + score_type)
         if "additive" in list(markers[0].keys()):
             output_file.write(",Additive")
         if "dominance" in list(markers[0].keys()):
@@ -575,11 +577,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("\n")
         for i, marker in enumerate(markers):
             output_file.write(marker['name'] + "," + str(marker['chr']) + ",")
-            if 'Mb' in marker:
-                output_file.write(str(marker['Mb']) + ",")
-            if 'cM' in marker:
-                output_file.write(str(marker['cM']) + ",")
-            if "lod_score" in marker.keys():
+            output_file.write(str(marker[scale_string]) + ",")
+            if score_type == "-logP":
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
-- 
cgit v1.2.3


From a212ad123f902b6a9c74bcac1d98bc274cebbdda Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 Oct 2021 17:36:02 +0000
Subject: Fixed export_mapping_results test in test_run_mapping.py

---
 .../wqflask/marker_regression/test_run_mapping.py  | 33 +++++++++++-----------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index 3747aeb8..868b0b0b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -43,7 +43,7 @@ class TestRunMapping(unittest.TestCase):
             })
         }
         self.dataset = AttributeSetter(
-            {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+            {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"})
 
         self.chromosomes = AttributeSetter({"chromosomes": chromosomes})
         self.trait = AttributeSetter(
@@ -180,37 +180,36 @@ class TestRunMapping(unittest.TestCase):
 
             with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
                 export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
-                                       results_path="~/results", mapping_scale="physic", score_type="-log(p)",
-                                       transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100",
-                                       vals_hash="")
+                                       results_path="~/results", mapping_method="gemma", mapping_scale="physic",
+                                       score_type="-logP", transform="qnorm",
+                                       covariates="Dataset1:Trait1,Dataset2:Trait2",
+                                       n_samples="100", vals_hash="")
 
                 write_calls = [
                     mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
                     mock.call('Population: Human GP1_\n'), mock.call(
-                        'Data Set: dataser_1\n'),
+                        'Data Set: dataset_1\n'),
                     mock.call('Trait: Test Name\n'),
                     mock.call('Trait Hash: \n'),
-                    mock.call('N Samples: 100\n'), mock.call(
-                        'Transform - Quantile Normalized\n'),
+                    mock.call('N Samples: 100\n'),
+                    mock.call('Mapping Tool: gemma\n'),
+                    mock.call('Transform - Quantile Normalized\n'),
                     mock.call('Gene Symbol: IGFI\n'), mock.call(
                         'Location: X1 @ 123313 Mb\n'),
                     mock.call('Cofactors (dataset - trait):\n'),
                     mock.call('Trait1 - Dataset1\n'),
                     mock.call('Trait2 - Dataset2\n'),
                     mock.call('\n'), mock.call('Name,Chr,'),
-                    mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+                    mock.call('Mb,-logP'),
                     mock.call(',Additive'), mock.call(',Dominance'),
                     mock.call('\n'), mock.call('MK1,C1,'),
-                    mock.call('12000,'), mock.call('1,'),
-                    mock.call('3'), mock.call(',VA'),
-                    mock.call(',TT'), mock.call('\n'),
-                    mock.call('MK2,C2,'), mock.call('10000,'),
-                    mock.call('15,'), mock.call('7'),
+                    mock.call('12000,'), mock.call('3'),
+                    mock.call(',VA'), mock.call(',TT'),
+                    mock.call('\n'), mock.call('MK2,C2,'),
+                    mock.call('10000,'), mock.call('7'),
                     mock.call('\n'), mock.call('MK1,C3,'),
-                    mock.call('1,'), mock.call('45,'),
-                    mock.call('7'), mock.call(',VE'),
-                    mock.call(',Tt')
-
+                    mock.call('1,'), mock.call('7'),
+                    mock.call(',VE'), mock.call(',Tt')
                 ]
                 mock_open.assert_called_once_with("~/results", "w+")
                 filehandler = mock_open()
-- 
cgit v1.2.3