From ef38724c31567b56214026999a944f9088fe30b8 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 28 Jun 2020 11:23:27 -0500
Subject: make stains headers names horizontal
---
wqflask/wqflask/templates/snp_browser.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index fb564b28..7019e943 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -195,7 +195,7 @@
<th data-export="{{ header }}">{{ header }}</th>
{% endfor %}
{% for strain in header_fields[1] %}
- <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{% for letter in strain %}<div style="transform: rotate(90deg);">{{ letter }}</div>{% endfor %}</th>
+ <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{{ strain }}</th>
{% endfor %}
{% else %}
{% for header in header_fields %}
--
cgit v1.2.3
From 88715630c4d18d962a7473dcac7e34b1b9c098a0 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 28 Jun 2020 11:24:12 -0500
Subject: add DataTables pagination
---
wqflask/wqflask/templates/snp_browser.html | 1 -
1 file changed, 1 deletion(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 7019e943..3b97963c 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -407,7 +407,6 @@
{% endif %}
'order': [[1, "asc" ]],
'sDom': "rtip",
- 'iDisplayLength': 500,
'processing': true,
'language': {
'loadingRecords': ' ',
--
cgit v1.2.3
From 73e3f354b0bf6accfd884f0fab8ef93f03be7945 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 28 Jun 2020 11:28:28 -0500
Subject: fix typo in check_if_in_gene function while querying for species_id =
0
---
wqflask/wqflask/snp_browser/snp_browser.py | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 6c3fcf53..a2fb7195 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -526,7 +526,6 @@ class SnpBrowser(object):
the_rows.append(this_row)
return the_rows
-
def include_record(self, domain, function, snp_source, conservation_score):
""" Decide whether to add this record """
@@ -868,8 +867,6 @@ def get_gene_id_name_dict(species_id, gene_name_list):
if len(results) > 0:
for item in results:
gene_id_name_dict[item[1]] = item[0]
- else:
- pass
return gene_id_name_dict
@@ -883,7 +880,7 @@ def check_if_in_gene(species_id, chr, mb):
query = """SELECT geneId,geneSymbol
FROM GeneList
WHERE chromosome = '{0}' AND
- (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb)
+ (txStart < {1} AND txEnd > {1}); """.format(chr, mb)
result = g.db.execute(query).fetchone()
--
cgit v1.2.3
From 429aff0920b1fddf71e4547c35a726b11e6713a0 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Tue, 30 Jun 2020 14:14:53 -0500
Subject: 500 rows per page for DataTables
---
wqflask/wqflask/templates/snp_browser.html | 1 +
1 file changed, 1 insertion(+)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 3b97963c..7019e943 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -407,6 +407,7 @@
{% endif %}
'order': [[1, "asc" ]],
'sDom': "rtip",
+ 'iDisplayLength': 500,
'processing': true,
'language': {
'loadingRecords': ' ',
--
cgit v1.2.3
From 776ccfbb2fc5a6e85c7a41efd92b33b0e27de68a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Tue, 30 Jun 2020 14:56:22 -0500
Subject: reduce gap between first and second column in form
---
wqflask/wqflask/templates/snp_browser.html | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 7019e943..73359835 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -15,7 +15,7 @@
<input type="hidden" name="first_run" value="{{ first_run }}">
<input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
<input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
- <div class="col-xs-4" style="padding-left: 0px;">
+ <div class="col-xs-4" style="width: 260px; padding-left: 30px; padding-right: 0px;">
<div class="form-group row" style="margin-bottom: 5px;">
<label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
<div class="col-xs-8">
@@ -74,7 +74,7 @@
</div>
</div>
</div>
- <div class="col-xs-4" style="padding-left: 0px;">
+ <div class="col-xs-4" style="width: 310px; padding-left: 0px; padding-right: 20px;">
<div class="form-group row" style="margin-bottom: 10px;">
<label for="strains" style="text-align: right;" class="col-xs-4 col-form-label"><b>Strains:</b></label>
<div class="col-xs-8">
@@ -108,7 +108,7 @@
</div>
</div>
</div>
- <div class="col-xs-4" style="padding-left: 20px;">
+ <div class="col-xs-4" style="width: 310px; padding-left: 20px;">
<div class="form-group row" style="margin-bottom: 5px;">
<label for="domain" style="text-align: right;" class="col-xs-4 col-form-label"><b>Domain:</b></label>
<div class="col-xs-8">
--
cgit v1.2.3
From 3a792dbe74ab181d2fa9582f67c99b68ffad0c10 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Tue, 30 Jun 2020 15:38:04 -0500
Subject: align numeric data values to right, categorial values to center
---
wqflask/wqflask/templates/snp_browser.html | 27 ++++++++++++++++++---------
1 file changed, 18 insertions(+), 9 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 73359835..816d5f0f 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -272,7 +272,8 @@
return '<input type="checkbox" name="trait_check">'
}
}, {
- 'data': 'index'
+ 'data': 'index',
+ 'className': 'dt-body-right'
}, {
'data': null,
'render': function(data, type, row, meta) {
@@ -283,9 +284,11 @@
}
}
}, {
- 'data': 'chr'
+ 'data': 'chr',
+ 'className': 'dt-body-center'
}, {
- 'data': 'mb_formatted'
+ 'data': 'mb_formatted',
+ 'className': 'dt-body-right'
}, {
'data': 'alleles'
}, {% if empty_columns['snp_source'] == "true" %}{
@@ -298,7 +301,8 @@
}
}
}, {% endif %} {% if empty_columns['conservation_score'] == "true" %}{
- 'data': 'conservation_score'
+ 'data': 'conservation_score',
+ 'className': 'dt-body-right'
}, {% endif %} {% if empty_columns['gene_name'] == "true" %}{
'data': null,
'render': function(data, type, row, meta) {
@@ -383,21 +387,26 @@
return '<input type="checkbox" name="trait_check">'
}
}, {
- 'data': 'index'
+ 'data': 'index',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_name'
}, {
'data': 'indel_type'
}, {
- 'data': 'indel_chr'
+ 'data': 'indel_chr',
+ 'className': 'dt-body-center'
}, {
- 'data': 'indel_mb_s'
+ 'data': 'indel_mb_s',
+ 'className': 'dt-body-right'
}, {
- 'data': 'indel_mb_e'
+ 'data': 'indel_mb_e',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_strand'
}, {
- 'data': 'indel_size'
+ 'data': 'indel_size',
+ 'className': 'dt-body-right'
}, {
'data': 'indel_sequence'
}, {
--
cgit v1.2.3
From f7b7950533f52e418c2be569cca409ae1fb3faf0 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Tue, 30 Jun 2020 16:48:02 -0500
Subject: rotate strain headers 270 deg
---
wqflask/wqflask/templates/snp_browser.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 816d5f0f..36f893bc 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -195,7 +195,7 @@
<th data-export="{{ header }}">{{ header }}</th>
{% endfor %}
{% for strain in header_fields[1] %}
- <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{{ strain }}</th>
+ <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
{% endfor %}
{% else %}
{% for header in header_fields %}
--
cgit v1.2.3
From 7a4068d6d46d923c30316887e1d20f2fa6caa859 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:15:22 -0500
Subject: add export to CSV button to export current page
---
wqflask/wqflask/templates/snp_browser.html | 43 +++++++++++++++++++++++++++---
1 file changed, 40 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 36f893bc..284b55c5 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -107,6 +107,12 @@
</div>
</div>
</div>
+ <div class="form-group row">
+ <label class="col-xs-4 col-form-label"></label>
+ <div class="col-xs-8" style="margin-top: 65px;">
+ <input class="btn btn-primary" type="button" name="export_csv" value="Export to CSV">
+ </div>
+ </div>
</div>
<div class="col-xs-4" style="width: 310px; padding-left: 20px;">
<div class="form-group row" style="margin-bottom: 5px;">
@@ -192,14 +198,14 @@
<th></th>
{% if header_fields|length == 2 %}
{% for header in header_fields[0] %}
- <th data-export="{{ header }}">{{ header }}</th>
+ <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
{% endfor %}
{% for strain in header_fields[1] %}
- <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
+ <th data-export="{{ strain }}" name="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
{% endfor %}
{% else %}
{% for header in header_fields %}
- <th data-export="{{ header }}">{{ header }}</th>
+ <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
{% endfor %}
{% endif %}
</tr>
@@ -518,6 +524,37 @@
});
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+ $("input[name=export_csv]").click(function() {
+ var csv = [];
+ var rows = document.querySelectorAll("table tr");
+
+ var headers = [];
+ var col_header = rows[0].querySelectorAll("th");
+ console.log(col_header.length);
+ for(var i = 1; i < col_header.length; i++) {
+ console.log(col_header[i].getAttribute("name"));
+ headers.push(col_header[i].getAttribute("name"));
+ }
+ csv.push(headers.join(","));
+
+ for (var i = 1; i < rows.length; i++) {
+ var row = [], cols = rows[i].querySelectorAll("td");
+
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
+
+ csv.push(row.join(","));
+ }
+
+ var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+ var downloadLink = document.createElement("a");
+ downloadLink.download = "hello.csv";
+ downloadLink.href = window.URL.createObjectURL(csvFile);
+ downloadLink.style.display = "none";
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ });
</script>
{% endblock %}
--
cgit v1.2.3
From f99b69155d35900a75c000fbb79f6bcfb3fa6ff1 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:30:04 -0500
Subject: export only checked rows to csv; update csv file name
---
wqflask/wqflask/templates/snp_browser.html | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 284b55c5..83606804 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -531,25 +531,27 @@
var headers = [];
var col_header = rows[0].querySelectorAll("th");
- console.log(col_header.length);
for(var i = 1; i < col_header.length; i++) {
- console.log(col_header[i].getAttribute("name"));
headers.push(col_header[i].getAttribute("name"));
}
csv.push(headers.join(","));
for (var i = 1; i < rows.length; i++) {
var row = [], cols = rows[i].querySelectorAll("td");
+ var checkBox = rows[i].querySelector("input");
+ console.log(checkBox);
- for (var j = 1; j < cols.length; j++)
- row.push(cols[j].innerText);
+ if(checkBox.checked == true) {
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
- csv.push(row.join(","));
+ csv.push(row.join(","));
+ }
}
var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
var downloadLink = document.createElement("a");
- downloadLink.download = "hello.csv";
+ downloadLink.download = "variant_data.csv";
downloadLink.href = window.URL.createObjectURL(csvFile);
downloadLink.style.display = "none";
document.body.appendChild(downloadLink);
--
cgit v1.2.3
From 349b395375703e727465a1f05f4a5e2d4fc64d2a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 19 Jul 2020 17:21:15 -0500
Subject: add server side processing due to large tables in DataTables; work on
server-side processing API pending for sorting, paging etc
---
wqflask/wqflask/snp_browser/snp_browser.py | 39 ++++++++++++++++++++++--------
wqflask/wqflask/templates/snp_browser.html | 26 +++++++++++++++-----
wqflask/wqflask/views.py | 10 ++++++++
3 files changed, 59 insertions(+), 16 deletions(-)
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index a2fb7195..9ae8892b 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
from PIL import (Image)
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
from base import species
from base import webqtlConfig
@@ -14,16 +14,16 @@ class SnpBrowser(object):
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
self.initialize_parameters(start_vars)
- self.limit_number = 10000
if self.first_run == "false":
self.filtered_results = self.get_browser_results()
+ self.table_rows = self.get_table_rows()
+ self.rows_count = len(self.table_rows)
- if len(self.filtered_results) <= self.limit_number:
- self.table_rows = self.get_table_rows()
- else:
- self.empty_columns = None
- self.table_rows = []
+ del self.filtered_results
+
+ if 'sEcho' not in start_vars:
+ self.table_rows = self.table_rows[:500]
if self.limit_strains == "true":
self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
@@ -380,7 +380,7 @@ class SnpBrowser(object):
the_rows = []
for i, result in enumerate(self.filtered_results):
- this_row = []
+ this_row = {}
if self.variant_type == "SNP":
snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
allele_value_list = result[14:]
@@ -520,8 +520,6 @@ class SnpBrowser(object):
"source_name": str(source_name)
}
#this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
- else:
- this_row = {}
the_rows.append(this_row)
@@ -643,6 +641,27 @@ class SnpBrowser(object):
#for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+class SnpPage(object):
+
+ def __init__(self, start_vars):
+ self.snp_browser = SnpBrowser(start_vars)
+ # self.table_rows = self.filter_rows()
+ self.rows_count = self.snp_browser.rows_count
+ self.sEcho = start_vars['sEcho']
+
+ def filter_rows(self):
+ pass
+
+ def get_page(self):
+ output = {}
+ output['sEcho'] = str(self.sEcho)
+ output['iTotalRecords'] = str(self.rows_count)
+ output['iTotalDisplayRecords'] = str(100)
+ # logger.info(len(self.table_rows), type(self.table_rows), self.table_rows[0])
+ logger.info(self.snp_browser.rows_count, len(self.snp_browser.table_rows))
+ output['data'] = self.snp_browser.table_rows[:100]
+ return output
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 83606804..f3e928af 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -188,10 +188,7 @@
</div>
<div style="margin-top: 20px;">
- {% if filtered_results is defined %}
- {% if filtered_results|length > limit_number %}
- There are more than 10000 results. Consider limiting your search to a smaller range.
- {% else %}
+ {% if table_rows is defined %}
<table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
<thead>
<tr>
@@ -214,7 +211,6 @@
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
</table>
- {% endif %}
{% endif %}
</div>
</div>
@@ -229,11 +225,23 @@
<script type='text/javascript'>
var json_rows = {{ table_rows|safe }};
+ var json_rows_count = {{ rows_count|safe }};
var empty_columns = {{ empty_columns|safe }};
</script>
<script language="javascript">
+ var getParams = function(url) {
+ var parser = document.createElement('a');
+ parser.href = url;
+ var params = parser.search.substring(1);
+ console.log(params);
+ if(params.length > 0) {
+ return ('?'+params);
+ }
+ return params;
+ };
+
var substringMatcher = function(strs) {
return function findMatches(q, cb) {
var matches, substringRegex;
@@ -266,7 +274,7 @@
source: substringMatcher(rat_genes)
});
- {% if filtered_results is defined %}
+ {% if table_rows is defined %}
$("#results_table").DataTable( {
'data': json_rows,
{% if variant_type == "SNP" %}
@@ -423,6 +431,10 @@
'order': [[1, "asc" ]],
'sDom': "rtip",
'iDisplayLength': 500,
+ 'bServerSide': true,
+ 'bProcessing': true,
+ 'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
+ 'deferLoading': json_rows_count,
'processing': true,
'language': {
'loadingRecords': ' ',
@@ -525,6 +537,8 @@
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+
$("input[name=export_csv]").click(function() {
var csv = [];
var rows = document.querySelectorAll("table tr");
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 08673f79..a2c66d53 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -897,6 +897,7 @@ def corr_scatter_plot_page():
def snp_browser_page():
logger.info(request.url)
template_vars = snp_browser.SnpBrowser(request.args)
+ logger.info(template_vars.__dict__.keys())
return render_template("snp_browser.html", **template_vars.__dict__)
@@ -906,6 +907,15 @@ def db_info_page():
return render_template("info_page.html", **template_vars.__dict__)
+@app.route("/snp_browser_table", methods=('GET',))
+def snp_browser_table():
+ logger.info(request.url)
+ logger.info(request.args)
+
+ current_page = snp_browser.SnpPage(request.args).get_page()
+
+ return flask.jsonify(current_page)
+
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
#ZS: Currently just links to GN1
--
cgit v1.2.3
From bad336d0d2282f6eaadbcd0fe21afaaaf5342890 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Thu, 23 Jul 2020 06:34:07 -0500
Subject: server side processing working for snp browser
---
wqflask/wqflask/snp_browser/snp_browser.py | 92 ++++++++++++++++++++++++------
wqflask/wqflask/templates/snp_browser.html | 7 +--
wqflask/wqflask/views.py | 4 +-
3 files changed, 80 insertions(+), 23 deletions(-)
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 9ae8892b..116da149 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -23,12 +23,12 @@ class SnpBrowser(object):
del self.filtered_results
if 'sEcho' not in start_vars:
- self.table_rows = self.table_rows[:500]
+ self.table_rows = []
if self.limit_strains == "true":
- self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
else:
- self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
@@ -643,23 +643,75 @@ class SnpBrowser(object):
class SnpPage(object):
- def __init__(self, start_vars):
- self.snp_browser = SnpBrowser(start_vars)
- # self.table_rows = self.filter_rows()
- self.rows_count = self.snp_browser.rows_count
- self.sEcho = start_vars['sEcho']
+ def __init__(self, request):
+ self.request_values = request
+ self.sEcho = self.request_values['sEcho']
- def filter_rows(self):
- pass
+ self.snp_browser = SnpBrowser(request)
+ self.rows_count = self.snp_browser.rows_count
+ self.table_rows = self.snp_browser.table_rows
+ self.header_data_names = self.snp_browser.header_data_names
+
+ logger.info(self.table_rows[0])
+
+ self.sort_rows()
+ self.paginate_rows()
+
+ def sort_rows(self):
+ '''
+ Sorts the rows taking in to account the column (or columns) that the
+ user has selected.
+ '''
+ def is_reverse(str_direction):
+ ''' Maps the 'desc' and 'asc' words to True or False. '''
+ return True if str_direction == 'desc' else False
+
+ if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
+ for i in range(0, int(self.request_values['iSortingCols'])):
+ column_number = int(self.request_values['iSortCol_' + str(i)])
+ column_name = self.header_data_names[column_number - 1]
+ sort_direction = self.request_values['sSortDir_' + str(i)]
+ self.table_rows = sorted(self.table_rows,
+ key=lambda x: x[column_name],
+ reverse=is_reverse(sort_direction))
+
+ def paginate_rows(self):
+ '''
+ Selects a subset of the filtered and sorted data based on if the table
+ has pagination, the current page and the size of each page.
+ '''
+ def requires_pagination():
+ ''' Check if the table is going to be paginated '''
+ if self.request_values['iDisplayStart'] != "":
+ if int(self.request_values['iDisplayLength']) != -1:
+ return True
+ return False
+
+ if not requires_pagination():
+ return
+
+ start = int(self.request_values['iDisplayStart'])
+ length = int(self.request_values['iDisplayLength'])
+
+ # if search returns only one page
+ if len(self.table_rows) <= length:
+ # display only one page
+ self.table_rows = self.table_rows[start:]
+ else:
+ limit = -len(self.table_rows) + start + length
+ if limit < 0:
+ # display pagination
+ self.table_rows = self.table_rows[start:limit]
+ else:
+ # display last page of pagination
+ self.table_rows = self.table_rows[start:]
def get_page(self):
output = {}
output['sEcho'] = str(self.sEcho)
- output['iTotalRecords'] = str(self.rows_count)
- output['iTotalDisplayRecords'] = str(100)
- # logger.info(len(self.table_rows), type(self.table_rows), self.table_rows[0])
- logger.info(self.snp_browser.rows_count, len(self.snp_browser.table_rows))
- output['data'] = self.snp_browser.table_rows[:100]
+ output['iTotalRecords'] = str(float('Nan'))
+ output['iTotalDisplayRecords'] = str(self.rows_count)
+ output['data'] = self.table_rows
return output
def get_browser_sample_lists(species_id=1):
@@ -692,9 +744,13 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
header_fields = []
+ header_data_names = []
if variant_type == "SNP":
header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+ header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+
header_fields.append(strain_list)
+ header_data_names += strain_list
if empty_columns != None:
if empty_columns['snp_source'] == "false":
@@ -721,11 +777,15 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
if empty_columns['function_details'] == "false":
empty_field_count += 1
header_fields[0].remove('Details')
+
+ for col in empty_columns:
+ header_data_names.remove(col)
elif variant_type == "InDel":
header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+ header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
- return header_fields, empty_field_count
+ return header_fields, empty_field_count, header_data_names
def get_effect_details_by_category(effect_name = None, effect_value = None):
gene_list = []
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index f3e928af..cbc12e06 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -276,7 +276,6 @@
{% if table_rows is defined %}
$("#results_table").DataTable( {
- 'data': json_rows,
{% if variant_type == "SNP" %}
'columns': [
{
@@ -432,10 +431,10 @@
'sDom': "rtip",
'iDisplayLength': 500,
'bServerSide': true,
- 'bProcessing': true,
'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
- 'deferLoading': json_rows_count,
- 'processing': true,
+ 'infoCallback': function(settings, start, end, max, total, pre) {
+ return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
+ },
'language': {
'loadingRecords': ' ',
'processing': 'Loading...'
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a2c66d53..8e7f6ec3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -909,9 +909,7 @@ def db_info_page():
@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
- logger.info(request.url)
- logger.info(request.args)
-
+ logger.info(request.url)
current_page = snp_browser.SnpPage(request.args).get_page()
return flask.jsonify(current_page)
--
cgit v1.2.3
From 29902d1c60b338c1c06289f9ea1cae5a61e28d4b Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Thu, 6 Aug 2020 08:48:53 -0500
Subject: fix issue with column sort; put 'Gene' column data in one line
---
wqflask/wqflask/snp_browser/snp_browser.py | 25 ++++++++++++-------------
wqflask/wqflask/templates/snp_browser.html | 6 +-----
wqflask/wqflask/views.py | 3 +--
3 files changed, 14 insertions(+), 20 deletions(-)
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 116da149..58c90f11 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -368,15 +368,15 @@ class SnpBrowser(object):
#ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
self.empty_columns = {
- "snp_source": "false",
- "conservation_score": "false",
- "gene_name": "false",
- "transcript": "false",
- "exon": "false",
- "domain_2": "false",
- "function": "false",
- "function_details": "false"
- }
+ "snp_source": "false",
+ "conservation_score": "false",
+ "gene_name": "false",
+ "transcript": "false",
+ "exon": "false",
+ "domain_2": "false",
+ "function": "false",
+ "function_details": "false"
+ }
the_rows = []
for i, result in enumerate(self.filtered_results):
@@ -651,8 +651,6 @@ class SnpPage(object):
self.rows_count = self.snp_browser.rows_count
self.table_rows = self.snp_browser.table_rows
self.header_data_names = self.snp_browser.header_data_names
-
- logger.info(self.table_rows[0])
self.sort_rows()
self.paginate_rows()
@@ -778,8 +776,9 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
empty_field_count += 1
header_fields[0].remove('Details')
- for col in empty_columns:
- header_data_names.remove(col)
+ for col in empty_columns.keys():
+ if empty_columns[col] == "false":
+ header_data_names.remove(col)
elif variant_type == "InDel":
header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index cbc12e06..96cd7247 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -320,7 +320,7 @@
'data': null,
'render': function(data, type, row, meta) {
if (data.gene_name != "") {
- return '<i>' + data.gene_name + '</i><br><a href="' + data.gene_link + '">NCBI</a>'
+ return '<i>' + data.gene_name + '</i>, <a href="' + data.gene_link + '">NCBI</a>'
} else {
return data.gene_name
}
@@ -434,10 +434,6 @@
'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
'infoCallback': function(settings, start, end, max, total, pre) {
return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
- },
- 'language': {
- 'loadingRecords': ' ',
- 'processing': 'Loading...'
}
});
{% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8e7f6ec3..12ebf595 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -897,7 +897,6 @@ def corr_scatter_plot_page():
def snp_browser_page():
logger.info(request.url)
template_vars = snp_browser.SnpBrowser(request.args)
- logger.info(template_vars.__dict__.keys())
return render_template("snp_browser.html", **template_vars.__dict__)
@@ -909,7 +908,7 @@ def db_info_page():
@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
- logger.info(request.url)
+ logger.info(request.url)
current_page = snp_browser.SnpPage(request.args).get_page()
return flask.jsonify(current_page)
--
cgit v1.2.3
From ace7b2d323c4f157f4d0e770dd948189562fa76b Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 16:03:24 -0500
Subject: remove createdRow callback and move color rendering to column defs to
speedup rendering
---
wqflask/wqflask/templates/snp_browser.html | 76 +++++++++++++++---------------
1 file changed, 38 insertions(+), 38 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 96cd7247..dad86459 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -227,10 +227,44 @@
var json_rows = {{ table_rows|safe }};
var json_rows_count = {{ rows_count|safe }};
var empty_columns = {{ empty_columns|safe }};
+
+ var remain_field_count = {{ 15 - empty_field_count }};
+ var total_field_count = {{ 15 - empty_field_count }} + {{ allele_list|length }};
</script>
<script language="javascript">
+ var getColor = function(allele) {
+ switch (allele) {
+ case "A":
+ return ('A_allele_color');
+ break;
+ case "C":
+ return ('C_allele_color');
+ break;
+ case "T":
+ return ('T_allele_color');
+ break;
+ case "G":
+ return ('G_allele_color');
+ break;
+ case "t":
+ return ('t_allele_color');
+ break;
+ case "c":
+ return ('c_allele_color');
+ break;
+ case "a":
+ return ('a_allele_color');
+ break;
+ case "g":
+ return ('g_allele_color');
+ break;
+ default:
+ return ('default_allele_color');
+ }
+ }
+
var getParams = function(url) {
var parser = document.createElement('a');
parser.href = url;
@@ -280,6 +314,7 @@
'columns': [
{
'data': null,
+ 'className': 'dt-body-center',
'orderable': false,
'render': function(data, type, row, meta) {
return '<input type="checkbox" name="trait_check">'
@@ -308,7 +343,7 @@
'data': null,
'render': function(data, type, row, meta) {
if (data.snp_source == "Sanger/UCLA") {
- return '<a href="' + data.source_urls[0] + '">Sanger</a><a href="' + data.source_urls[1] + '">UCLA</a>'
+ return '<a href="' + data.source_urls[0] + '">Sanger</a>, <a href="' + data.source_urls[1] + '">UCLA</a>'
} else {
return data.snp_source
}
@@ -347,6 +382,7 @@
}, {% endif %} {% for item in allele_list %} {
'data': null,
'orderable': false,
+ 'className': 'dt-body-center ' + getColor('{{ item }}'),
'render': function(data, type, row, meta) {
if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
return data.allele_value_list[{{ loop.index - 1 }}][0]
@@ -356,42 +392,6 @@
}
}{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
],
- 'createdRow': function( row, data, dataIndex) {
- $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
- $('td', row).eq(1).attr("align", "right");
- for (i = {{ 15 - empty_field_count }}; i < ({{ 15 - empty_field_count }} + {{ allele_list|length }}); i++) {
- var this_allele = $('td', row).eq(i).text();
- $('td', row).eq(i).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
- switch (this_allele) {
- case "A":
- $('td', row).eq(i).addClass('A_allele_color');
- break;
- case "C":
- $('td', row).eq(i).addClass('C_allele_color');
- break;
- case "T":
- $('td', row).eq(i).addClass('T_allele_color');
- break;
- case "G":
- $('td', row).eq(i).addClass('G_allele_color');
- break;
- case "t":
- $('td', row).eq(i).addClass('t_allele_color');
- break;
- case "c":
- $('td', row).eq(i).addClass('c_allele_color');
- break;
- case "a":
- $('td', row).eq(i).addClass('a_allele_color');
- break;
- case "g":
- $('td', row).eq(i).addClass('g_allele_color');
- break;
- default:
- $('td', row).eq(i).addClass('default_allele_color');
- }
- }
- },
{% else %}
'columns': [
{
@@ -429,7 +429,7 @@
{% endif %}
'order': [[1, "asc" ]],
'sDom': "rtip",
- 'iDisplayLength': 500,
+ 'iDisplayLength': 100,
'bServerSide': true,
'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
'infoCallback': function(settings, start, end, max, total, pre) {
--
cgit v1.2.3
From 1caac2a2337d1300e197892cf2a260867998e88e Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 16:04:55 -0500
Subject: remove debug log
---
wqflask/wqflask/templates/snp_browser.html | 2 --
1 file changed, 2 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index dad86459..1a2da20f 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -269,7 +269,6 @@
var parser = document.createElement('a');
parser.href = url;
var params = parser.search.substring(1);
- console.log(params);
if(params.length > 0) {
return ('?'+params);
}
@@ -548,7 +547,6 @@
for (var i = 1; i < rows.length; i++) {
var row = [], cols = rows[i].querySelectorAll("td");
var checkBox = rows[i].querySelector("input");
- console.log(checkBox);
if(checkBox.checked == true) {
for (var j = 1; j < cols.length; j++)
--
cgit v1.2.3
From 876b95a8e1ad5944105b8d23ae362415011239b5 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 16:15:02 -0500
Subject: cell rendering cannot be in columnDef, optimised createdRow
---
wqflask/wqflask/templates/snp_browser.html | 68 +++++++++++++++---------------
1 file changed, 34 insertions(+), 34 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 1a2da20f..c7923be6 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -224,8 +224,6 @@
<script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
<script type='text/javascript'>
- var json_rows = {{ table_rows|safe }};
- var json_rows_count = {{ rows_count|safe }};
var empty_columns = {{ empty_columns|safe }};
var remain_field_count = {{ 15 - empty_field_count }};
@@ -234,37 +232,6 @@
<script language="javascript">
- var getColor = function(allele) {
- switch (allele) {
- case "A":
- return ('A_allele_color');
- break;
- case "C":
- return ('C_allele_color');
- break;
- case "T":
- return ('T_allele_color');
- break;
- case "G":
- return ('G_allele_color');
- break;
- case "t":
- return ('t_allele_color');
- break;
- case "c":
- return ('c_allele_color');
- break;
- case "a":
- return ('a_allele_color');
- break;
- case "g":
- return ('g_allele_color');
- break;
- default:
- return ('default_allele_color');
- }
- }
-
var getParams = function(url) {
var parser = document.createElement('a');
parser.href = url;
@@ -381,7 +348,7 @@
}, {% endif %} {% for item in allele_list %} {
'data': null,
'orderable': false,
- 'className': 'dt-body-center ' + getColor('{{ item }}'),
+ 'className': 'dt-body-center',
'render': function(data, type, row, meta) {
if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
return data.allele_value_list[{{ loop.index - 1 }}][0]
@@ -391,6 +358,39 @@
}
}{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
],
+ 'createdRow': function(row, data, dataIndex) {
+ for (i = remain_field_count; i < total_field_count; i++) {
+ var this_allele = $('td', row).eq(i).text();
+ switch (this_allele) {
+ case "A":
+ $('td', row).eq(i).addClass('A_allele_color');
+ break;
+ case "C":
+ $('td', row).eq(i).addClass('C_allele_color');
+ break;
+ case "T":
+ $('td', row).eq(i).addClass('T_allele_color');
+ break;
+ case "G":
+ $('td', row).eq(i).addClass('G_allele_color');
+ break;
+ case "t":
+ $('td', row).eq(i).addClass('t_allele_color');
+ break;
+ case "c":
+ $('td', row).eq(i).addClass('c_allele_color');
+ break;
+ case "a":
+ $('td', row).eq(i).addClass('a_allele_color');
+ break;
+ case "g":
+ $('td', row).eq(i).addClass('g_allele_color');
+ break;
+ default:
+ $('td', row).eq(i).addClass('default_allele_color');
+ }
+ }
+ },
{% else %}
'columns': [
{
--
cgit v1.2.3
From f52499653858512320ae17a2ff48671d82fc31fb Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 17:11:03 -0500
Subject: move SnpPage to a generic class ServerSide
---
wqflask/wqflask/server_side.py | 74 ++++++++++++++++++++++++++++++
wqflask/wqflask/snp_browser/snp_browser.py | 71 ----------------------------
wqflask/wqflask/views.py | 17 ++++++-
3 files changed, 89 insertions(+), 73 deletions(-)
create mode 100644 wqflask/wqflask/server_side.py
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
new file mode 100644
index 00000000..090720ec
--- /dev/null
+++ b/wqflask/wqflask/server_side.py
@@ -0,0 +1,74 @@
+# handles server side table processing
+
+
+
+class ServerSide(object):
+
+ def __init__(self, table_data, request_values):
+ self.request_values = request_values
+ self.sEcho = self.request_values['sEcho']
+
+ self.table_data = table_data
+ self.rows_count = self.table_data.rows_count
+ self.table_rows = self.table_data.table_rows
+ self.header_data_names = self.table_data.header_data_names
+
+ self.sort_rows()
+ self.paginate_rows()
+
+ def sort_rows(self):
+ '''
+ Sorts the rows taking in to account the column (or columns) that the
+ user has selected.
+ '''
+ def is_reverse(str_direction):
+ ''' Maps the 'desc' and 'asc' words to True or False. '''
+ return True if str_direction == 'desc' else False
+
+ if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
+ for i in range(0, int(self.request_values['iSortingCols'])):
+ column_number = int(self.request_values['iSortCol_' + str(i)])
+ column_name = self.header_data_names[column_number - 1]
+ sort_direction = self.request_values['sSortDir_' + str(i)]
+ self.table_rows = sorted(self.table_rows,
+ key=lambda x: x[column_name],
+ reverse=is_reverse(sort_direction))
+
+ def paginate_rows(self):
+ '''
+ Selects a subset of the filtered and sorted data based on if the table
+ has pagination, the current page and the size of each page.
+ '''
+ def requires_pagination():
+ ''' Check if the table is going to be paginated '''
+ if self.request_values['iDisplayStart'] != "":
+ if int(self.request_values['iDisplayLength']) != -1:
+ return True
+ return False
+
+ if not requires_pagination():
+ return
+
+ start = int(self.request_values['iDisplayStart'])
+ length = int(self.request_values['iDisplayLength'])
+
+ # if search returns only one page
+ if len(self.table_rows) <= length:
+ # display only one page
+ self.table_rows = self.table_rows[start:]
+ else:
+ limit = -len(self.table_rows) + start + length
+ if limit < 0:
+ # display pagination
+ self.table_rows = self.table_rows[start:limit]
+ else:
+ # display last page of pagination
+ self.table_rows = self.table_rows[start:]
+
+ def get_page(self):
+ output = {}
+ output['sEcho'] = str(self.sEcho)
+ output['iTotalRecords'] = str(float('Nan'))
+ output['iTotalDisplayRecords'] = str(self.rows_count)
+ output['data'] = self.table_rows
+ return output
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 58c90f11..a52399a2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -641,77 +641,6 @@ class SnpBrowser(object):
#for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
-class SnpPage(object):
-
- def __init__(self, request):
- self.request_values = request
- self.sEcho = self.request_values['sEcho']
-
- self.snp_browser = SnpBrowser(request)
- self.rows_count = self.snp_browser.rows_count
- self.table_rows = self.snp_browser.table_rows
- self.header_data_names = self.snp_browser.header_data_names
-
- self.sort_rows()
- self.paginate_rows()
-
- def sort_rows(self):
- '''
- Sorts the rows taking in to account the column (or columns) that the
- user has selected.
- '''
- def is_reverse(str_direction):
- ''' Maps the 'desc' and 'asc' words to True or False. '''
- return True if str_direction == 'desc' else False
-
- if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
- for i in range(0, int(self.request_values['iSortingCols'])):
- column_number = int(self.request_values['iSortCol_' + str(i)])
- column_name = self.header_data_names[column_number - 1]
- sort_direction = self.request_values['sSortDir_' + str(i)]
- self.table_rows = sorted(self.table_rows,
- key=lambda x: x[column_name],
- reverse=is_reverse(sort_direction))
-
- def paginate_rows(self):
- '''
- Selects a subset of the filtered and sorted data based on if the table
- has pagination, the current page and the size of each page.
- '''
- def requires_pagination():
- ''' Check if the table is going to be paginated '''
- if self.request_values['iDisplayStart'] != "":
- if int(self.request_values['iDisplayLength']) != -1:
- return True
- return False
-
- if not requires_pagination():
- return
-
- start = int(self.request_values['iDisplayStart'])
- length = int(self.request_values['iDisplayLength'])
-
- # if search returns only one page
- if len(self.table_rows) <= length:
- # display only one page
- self.table_rows = self.table_rows[start:]
- else:
- limit = -len(self.table_rows) + start + length
- if limit < 0:
- # display pagination
- self.table_rows = self.table_rows[start:limit]
- else:
- # display last page of pagination
- self.table_rows = self.table_rows[start:]
-
- def get_page(self):
- output = {}
- output['sEcho'] = str(self.sEcho)
- output['iTotalRecords'] = str(float('Nan'))
- output['iTotalDisplayRecords'] = str(self.rows_count)
- output['data'] = self.table_rows
- return output
-
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 12ebf595..185517d3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -27,7 +27,19 @@ import array
import sqlalchemy
from wqflask import app
from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-
+<<<<<<< HEAD
+
+=======
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import server_side
+>>>>>>> ed2afa4a (move SnpPage to a generic class ServerSide)
from wqflask.submit_bnw import get_bnw_input
from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
@@ -909,7 +921,8 @@ def db_info_page():
@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
logger.info(request.url)
- current_page = snp_browser.SnpPage(request.args).get_page()
+ snp_table_data = snp_browser.SnpBrowser(request.args)
+ current_page = server_side.ServerSide(snp_table_data, request.args).get_page()
return flask.jsonify(current_page)
--
cgit v1.2.3
From c6e4083da1c78c923ba94b3057e1fe5e09f5b603 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 17:14:00 -0500
Subject: fix issue when empty_filed_count is not claculated
---
wqflask/wqflask/templates/snp_browser.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index c7923be6..284a371a 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -226,8 +226,8 @@
<script type='text/javascript'>
var empty_columns = {{ empty_columns|safe }};
- var remain_field_count = {{ 15 - empty_field_count }};
- var total_field_count = {{ 15 - empty_field_count }} + {{ allele_list|length }};
+ var remain_field_count = 15 - {{ empty_field_count|safe }};
+ var total_field_count = 15 - {{ empty_field_count|safe }} + {{ allele_list|safe|length }};
</script>
<script language="javascript">
--
cgit v1.2.3
From 6b7dfb6ad280aa247c106f155fef81a03bd71c65 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 16 Aug 2020 17:30:13 -0500
Subject: make the page more color consistent
---
wqflask/wqflask/static/new/css/snp_browser.css | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index 30fe9a59..1dd332cb 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -18,7 +18,7 @@ table.dataTable thead .sorting_desc_disabled {
table.dataTable thead th{
border-right: 1px solid white;
color: white;
- background-color: royalblue;
+ background-color: #369;
}
table.dataTable tbody td {
--
cgit v1.2.3
From 0952e43989be3f24321932c3dd33fdc697c5703a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 23 Aug 2020 14:47:39 -0500
Subject: replace var to let for variables in loops
---
wqflask/wqflask/templates/snp_browser.html | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 284a371a..435a521c 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -539,17 +539,17 @@
var headers = [];
var col_header = rows[0].querySelectorAll("th");
- for(var i = 1; i < col_header.length; i++) {
+ for(let i = 1; i < col_header.length; i++) {
headers.push(col_header[i].getAttribute("name"));
}
csv.push(headers.join(","));
- for (var i = 1; i < rows.length; i++) {
+ for (let i = 1; i < rows.length; i++) {
var row = [], cols = rows[i].querySelectorAll("td");
var checkBox = rows[i].querySelector("input");
if(checkBox.checked == true) {
- for (var j = 1; j < cols.length; j++)
+ for (let j = 1; j < cols.length; j++)
row.push(cols[j].innerText);
csv.push(row.join(","));
--
cgit v1.2.3
From dfdff4934e423e2f4f626625a8bd1f45a64187b4 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 23 Aug 2020 16:13:11 -0500
Subject: update class name to ServerSideTable and add docstring
---
wqflask/wqflask/server_side.py | 22 +++++++++++++++++++++-
wqflask/wqflask/views.py | 2 +-
2 files changed, 22 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 090720ec..d044d411 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -2,7 +2,27 @@
-class ServerSide(object):
+class ServerSideTable(object):
+ '''
+ This class is used to do server-side processing
+ on the DataTables table such as paginating, sorting,
+ filtering(not implemented) etc. This takes the load off
+ the client-side and reduces the size of data interchanged.
+
+ Usage:
+ ServerSideTable(table_data, request_values)
+ where,
+ `table_data` must have data members
+ `rows_count` as number of rows in the table,
+ `table_rows` as data rows of the table,
+ `header_data_names` as headers names of the table.
+
+ `request_values` must have request arguments values
+ including the DataTables server-side processing arguments.
+
+ Have a look at snp_browser_table() function in
+ wqflask/wqflask/views.py for reference use.
+ '''
def __init__(self, table_data, request_values):
self.request_values = request_values
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 185517d3..f0b78188 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -922,7 +922,7 @@ def db_info_page():
def snp_browser_table():
logger.info(request.url)
snp_table_data = snp_browser.SnpBrowser(request.args)
- current_page = server_side.ServerSide(snp_table_data, request.args).get_page()
+ current_page = server_side.ServerSideTable(snp_table_data, request.args).get_page()
return flask.jsonify(current_page)
--
cgit v1.2.3
From aa2d7a45fca8c6503a5de6cec7ce58d248144b9d Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 6 Sep 2020 10:38:19 -0500
Subject: add row highlight on checkbox checked state
---
wqflask/wqflask/static/new/css/snp_browser.css | 4 ++++
wqflask/wqflask/templates/snp_browser.html | 17 +++++++++++++++--
2 files changed, 19 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index 1dd332cb..a7942d2a 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -6,6 +6,10 @@ table.dataTable thead th {
vertical-align: bottom;
}
+table.dataTable tbody tr.selected {
+ background-color: #ffee99;
+}
+
table.dataTable thead .sorting,
table.dataTable thead .sorting_asc,
table.dataTable thead .sorting_desc,
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 435a521c..c312aee8 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -283,7 +283,7 @@
'className': 'dt-body-center',
'orderable': false,
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="trait_check">'
+ return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
}
}, {
'data': 'index',
@@ -396,7 +396,7 @@
{
'data': null,
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="trait_check">'
+ return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
}
}, {
'data': 'index',
@@ -437,6 +437,19 @@
});
{% endif %}
+ function onVarinatCheck(checkboxElem) {
+ if (checkboxElem.checked) {
+ if (!checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+ checkboxElem.parentElement.parentElement.classList.add('selected')
+ }
+ }
+ else {
+ if (checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+ checkboxElem.parentElement.parentElement.classList.remove('selected')
+ }
+ }
+ }
+
$("#species_select").change(function() {
this_species = $(this).val();
$("#strain_select").empty()
--
cgit v1.2.3
From f3351f698c7961aa28578b90fa0c73a2e14f864d Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 6 Sep 2020 15:52:08 -0500
Subject: change arguments for ServerSideTable class
---
wqflask/wqflask/server_side.py | 9 ++++-----
wqflask/wqflask/views.py | 7 ++++++-
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index d044d411..824b00aa 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -24,14 +24,13 @@ class ServerSideTable(object):
wqflask/wqflask/views.py for reference use.
'''
- def __init__(self, table_data, request_values):
+ def __init__(self, rows_count, table_rows, header_data_names, request_values):
self.request_values = request_values
self.sEcho = self.request_values['sEcho']
- self.table_data = table_data
- self.rows_count = self.table_data.rows_count
- self.table_rows = self.table_data.table_rows
- self.header_data_names = self.table_data.header_data_names
+ self.rows_count = rows_count
+ self.table_rows = table_rows
+ self.header_data_names = header_data_names
self.sort_rows()
self.paginate_rows()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f0b78188..63570815 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -922,7 +922,12 @@ def db_info_page():
def snp_browser_table():
logger.info(request.url)
snp_table_data = snp_browser.SnpBrowser(request.args)
- current_page = server_side.ServerSideTable(snp_table_data, request.args).get_page()
+ current_page = server_side.ServerSideTable(
+ snp_table_data.rows_count,
+ snp_table_data.table_rows,
+ snp_table_data.header_data_names,
+ request.args,
+ ).get_page()
return flask.jsonify(current_page)
--
cgit v1.2.3
From 59e611827bf0621b2613cc29b3f4ba730ef3631e Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 13 Sep 2020 13:55:33 -0500
Subject: add server side processing to search table (/search and
search_result_page.html)
---
wqflask/wqflask/search_results.py | 16 +++++++++++-----
wqflask/wqflask/templates/search_result_page.html | 21 ++++++++++++++++-----
wqflask/wqflask/views.py | 20 ++++++++++++++++++++
3 files changed, 47 insertions(+), 10 deletions(-)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ce836ce2..8a5a7a80 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -28,9 +28,9 @@ class SearchResultPage(object):
#maxReturn = 3000
def __init__(self, kw):
- """This class gets invoked after hitting submit on the main menu (in
-views.py).
-
+ """
+ This class gets invoked after hitting submit on the main menu (in
+ views.py).
"""
###########################################
@@ -86,7 +86,6 @@ views.py).
else:
self.gen_search_result()
-
def gen_search_result(self):
"""
Get the info displayed in the search result table from the set of results computed in
@@ -155,7 +154,14 @@ views.py).
trait_dict[key] = trait_dict[key].decode('utf-8')
trait_list.append(trait_dict)
- self.trait_list = json.dumps(trait_list)
+ self.trait_list = trait_list
+
+ if this_trait.dataset.type == "ProbeSet":
+ self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+ elif this_trait.dataset.type == "Publish":
+ self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+ elif this_trait.dataset.type == "Geno":
+ self.header_data_names = ['index', 'display_name', 'location']
def search(self):
"""
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 2318bfb8..7d36d32e 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -174,6 +174,16 @@
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
+
+ var getParams = function(url) {
+ var parser = document.createElement('a');
+ parser.href = url;
+ var params = parser.search.substring(1);
+ if(params.length > 0) {
+ return ('?'+params);
+ }
+ return params;
+ };
$('#trait_table tr').click(function(event) {
if (event.target.type !== 'checkbox') {
@@ -260,7 +270,7 @@
'data': null,
'width': "25px",
'orderDataType': "dom-checkbox",
- 'orderSequence': [ "desc", "asc"],
+ 'orderable': false,
'render': function(data, type, row, meta) {
return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
}
@@ -426,14 +436,15 @@
{% else %}
'sDom': "pitirp",
{% endif %}
- 'iDisplayLength': 500,
+ 'iDisplayLength': 10,
'deferRender': true,
'paging': true,
'orderClasses': true,
'processing': true,
- 'language': {
- 'loadingRecords': ' ',
- 'processing': 'Loading...'
+ 'bServerSide': true,
+ 'sAjaxSource': '/search_table'+getParams(window.location.href),
+ 'infoCallback': function(settings, start, end, max, total, pre) {
+ return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
}
} );
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 63570815..2c1fa94b 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -234,6 +234,26 @@ def search_page():
else:
return render_template("search_error.html")
+@app.route("/search_table", methods=('GET',))
+def search_page_table():
+ logger.info("in search_page table")
+ logger.info(request.url)
+
+ logger.info("request.args is", request.args)
+ the_search = search_results.SearchResultPage(request.args)
+
+ logger.info(type(the_search.trait_list))
+ logger.info(the_search.trait_list)
+
+ current_page = server_side.ServerSideTable(
+ len(the_search.trait_list),
+ the_search.trait_list,
+ the_search.header_data_names,
+ request.args,
+ ).get_page()
+
+ return flask.jsonify(current_page)
+
@app.route("/gsearch", methods=('GET',))
def gsearchact():
logger.info(request.url)
--
cgit v1.2.3
From e83bcab9f01ad1aa279f15e8a19700b802320f8b Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 13 Sep 2020 15:19:51 -0500
Subject: add pagination to show_trait tables and reduce css post processing
for faster table loading
---
wqflask/wqflask/templates/search_result_page.html | 2 +-
wqflask/wqflask/views.py | 3 ---
2 files changed, 1 insertion(+), 4 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 7d36d32e..0bcbd492 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -436,7 +436,7 @@
{% else %}
'sDom': "pitirp",
{% endif %}
- 'iDisplayLength': 10,
+ 'iDisplayLength': 100,
'deferRender': true,
'paging': true,
'orderClasses': true,
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c1fa94b..2df7113e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -27,9 +27,7 @@ import array
import sqlalchemy
from wqflask import app
from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-<<<<<<< HEAD
-=======
from wqflask import group_manager
from wqflask import resource_manager
from wqflask import search_results
@@ -39,7 +37,6 @@ from wqflask import update_search_results
from wqflask import docs
from wqflask import news
from wqflask import server_side
->>>>>>> ed2afa4a (move SnpPage to a generic class ServerSide)
from wqflask.submit_bnw import get_bnw_input
from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
--
cgit v1.2.3
From e106f5888cb4d761a6dcb71dc0273e461ef3c71a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 13 Sep 2020 15:24:06 -0500
Subject: replace var with let in getParams() local variables
---
wqflask/wqflask/templates/search_result_page.html | 4 ++--
wqflask/wqflask/templates/snp_browser.html | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 0bcbd492..6fe44d1a 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -176,9 +176,9 @@
$(document).ready( function () {
var getParams = function(url) {
- var parser = document.createElement('a');
+ let parser = document.createElement('a');
parser.href = url;
- var params = parser.search.substring(1);
+ let params = parser.search.substring(1);
if(params.length > 0) {
return ('?'+params);
}
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index c312aee8..129d03c2 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -233,9 +233,9 @@
<script language="javascript">
var getParams = function(url) {
- var parser = document.createElement('a');
+ let parser = document.createElement('a');
parser.href = url;
- var params = parser.search.substring(1);
+ let params = parser.search.substring(1);
if(params.length > 0) {
return ('?'+params);
}
--
cgit v1.2.3
From 30e8aaad9672151c4b6bc43ea386d0d39ca131a7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 9 Dec 2020 16:18:07 -0600
Subject: Exchanged metadata and legend positions and made some changes to Y
positioning for the metadata
---
.../marker_regression/display_mapping_results.py | 39 +++++++++++++---------
1 file changed, 24 insertions(+), 15 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 08c2d750..9f778160 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -644,8 +644,10 @@ class DisplayMappingResults(object):
yTopOffset = max(90, yTopOffset)
else:
if self.legendChecked:
- if self.covariates != "" and self.controlLocus and self.doControl != "false":
- yTopOffset = max(120, yTopOffset)
+ if (self.mapping_method == "gemma" or self.mapping_method == "rqtl_geno") and self.covariates != "":
+ yTopOffset = max(115, yTopOffset)
+ elif self.mapping_method == "rqtl_geno" and self.controlLocus and self.doControl != "false" and self.covariates != "":
+ yTopOffset = max(130, yTopOffset)
else:
yTopOffset = max(100, yTopOffset)
else:
@@ -859,13 +861,12 @@ class DisplayMappingResults(object):
if self.legendChecked:
startPosY = 30
- nCol = 2
smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
- leftOffset = xLeftOffset+(nCol-1)*200
+ leftOffset = canvas.size[0] - xRightOffset - 190
im_drawer.rectangle(
xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
fill=YELLOW, outline=BLACK)
- im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
+ im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY+TEXT_Y_DISPLACEMENT),
text='Frequency of the Peak LRS',
font=smallLabelFont, fill=BLACK)
@@ -1069,7 +1070,7 @@ class DisplayMappingResults(object):
startPosY += stepPosY
if self.additiveChecked:
- startPosX = xLeftOffset
+ startPosX = canvas.size[0] - xRightOffset - 400
im_drawer.line(
xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
@@ -1081,7 +1082,7 @@ class DisplayMappingResults(object):
font=labelFont, fill=BLACK)
if self.genotype.type == 'intercross' and self.dominanceChecked:
- startPosX = xLeftOffset
+ startPosX = canvas.size[0] - xRightOffset - 400
startPosY += stepPosY
im_drawer.line(
xy=((startPosX, startPosY), (startPosX+17, startPosY)),
@@ -1095,7 +1096,7 @@ class DisplayMappingResults(object):
if self.haplotypeAnalystChecked:
startPosY += stepPosY
- startPosX = xLeftOffset
+ startPosX = canvas.size[0] - xRightOffset - 400
im_drawer.line(
xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.HAPLOTYPE_POSITIVE, width=4)
@@ -1114,7 +1115,10 @@ class DisplayMappingResults(object):
if self.permChecked and self.nperm > 0:
startPosY += stepPosY
- startPosX = xLeftOffset
+ if self.bootChecked and not self.multipleInterval:
+ startPosX = canvas.size[0] - xRightOffset - 400
+ else:
+ startPosX = canvas.size[0] - xRightOffset - 190
im_drawer.line(
xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
@@ -1123,10 +1127,10 @@ class DisplayMappingResults(object):
fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
im_drawer.text(
text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
- xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ xy=(startPosX+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
im_drawer.text(
text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
- xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
+ xy=(startPosX+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
fill=BLACK)
labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
@@ -1197,22 +1201,26 @@ class DisplayMappingResults(object):
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
text=identification,
- xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
+ xy=(xLeftOffset, 20*fontZoom), font=labelFont,
fill=labelColor)
else:
d = 4+ max(
im_drawer.textsize(string1, font=labelFont)[0],
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
- text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+ text=string1, xy=(xLeftOffset, 35*fontZoom),
font=labelFont, fill=labelColor)
im_drawer.text(
- text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+ text=string2, xy=(xLeftOffset, 50*fontZoom),
font=labelFont, fill=labelColor)
if string3 != '':
im_drawer.text(
- text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+ text=string3, xy=(xLeftOffset, 65*fontZoom),
font=labelFont, fill=labelColor)
+ if string4 != '':
+ im_drawer.text(
+ text=string4, xy=(xLeftOffset, 80*fontZoom),
+ font=labelFont, fill=labelColor)
def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -2244,6 +2252,7 @@ class DisplayMappingResults(object):
)
sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2)
+
if self.LRS_LOD == 'LRS':
sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
sig_title = "Significant LRS = %0.2f" % self.significant
--
cgit v1.2.3
From 295805eeb01aceb2651f79662c1462f06e1591cf Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 10 Dec 2020 12:27:48 -0600
Subject: Replacing the Scroller import with the CDN until we figure out why
the new import doesn't work
---
wqflask/wqflask/templates/show_trait.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b02f8140..c95a0522 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -146,7 +146,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/scroller.dataTables.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.3/js/dataTables.scroller.min.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
--
cgit v1.2.3
From 4760b390f7e87ea16152a7ecf5422abfb4125176 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 14:36:12 -0600
Subject: Fixed typo in mapping results table
---
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 86aa74b0..1a76ef7a 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -389,7 +389,7 @@
"orderable": false
} ],
"language": {
- "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records",
+ "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records",
},
"order": [[1, "asc" ]],
"sDom": "iRZtir",
--
cgit v1.2.3
From 13ae2b093720a04b63f50a77b92e3b8e480b5ae1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 14:38:42 -0600
Subject: Added additive effect to GEMMA results + removed an unused function
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 46 ++++------------------
1 file changed, 8 insertions(+), 38 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 61e4897c..630a3afa 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -80,7 +80,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
os.system(generate_k_command)
- gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 9 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -101,7 +101,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
return marker_obs, gwa_output_filename
else:
- marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
+ marker_obs = parse_loco_output(this_dataset, gwa_output_filename, use_loco)
return marker_obs, gwa_output_filename
def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
@@ -145,41 +145,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
outfile.write(str(this_covariate[i]) + "\t")
outfile.write("\n")
-def parse_gemma_output(genofile_name):
- included_markers = []
- p_values = []
- marker_obs = []
-
- with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
- for line in output_file:
- if line.startswith("chr\t"):
- continue
- else:
- marker = {}
- marker['name'] = line.split("\t")[1]
- if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
- if "chr" in line.split("\t")[0]:
- marker['chr'] = int(line.split("\t")[0][3:])
- else:
- marker['chr'] = int(line.split("\t")[0])
- else:
- marker['chr'] = line.split("\t")[0]
- marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[9])
- if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
- marker['lod_score'] = 0
- #marker['lrs_value'] = 0
- else:
- marker['lod_score'] = -math.log10(marker['p_value'])
- #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
- marker_obs.append(marker)
-
- included_markers.append(line.split("\t")[1])
- p_values.append(float(line.split("\t")[9]))
-
- return marker_obs
-
-def parse_loco_output(this_dataset, gwa_output_filename):
+def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
output_filelist = []
with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
@@ -218,7 +184,11 @@ def parse_loco_output(this_dataset, gwa_output_filename):
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[9])
+ if loco == "True":
+ marker['p_value'] = float(line.split("\t")[9])
+ else:
+ marker['p_value'] = float(line.split("\t")[10])
+ marker['additive'] = float(line.split("\t")[7])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
--
cgit v1.2.3
From 87fdfc19009acda8b58729d0ffbdccbdf6a85a1e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 11:27:39 -0600
Subject: Set all attribute names to lower-case for sorting in order to keep
order consistent
---
wqflask/wqflask/show_trait/SampleList.py | 4 ++--
wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 2 +-
wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 00495377..ece485ae 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -108,7 +108,7 @@ class SampleList(object):
FROM CaseAttribute, CaseAttributeXRefNew
WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
AND CaseAttributeXRefNew.InbredSetId = %s
- ORDER BY CaseAttribute.Name''', (str(self.dataset.group.id),))
+ ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
self.attributes = {}
for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
@@ -157,7 +157,7 @@ class SampleList(object):
except ValueError:
pass
- attribute_values[self.attributes[item.Id].name] = attribute_value
+ attribute_values[self.attributes[item.Id].name.lower()] = attribute_value
self.sample_attribute_values[sample_name] = attribute_values
def get_first_attr_col(self):
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 5a4f151c..4362a75e 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -93,7 +93,7 @@ build_columns = function() {
);
}
- attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1)
+ attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1)
for (i = 0; i < attr_keys.length; i++){
column_list.push(
{
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5dc9e456..98f90f7d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -571,7 +571,7 @@ populate_sample_attributes_values_dropdown = function() {
sample_attributes = [];
var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
- return [key, js_data.attributes[key].name];
+ return [key, js_data.attributes[key].name.toLowerCase()];
});
attributes_as_list.sort(function(first, second) {
--
cgit v1.2.3
From 124bc16cdc67b6ba31a281e619dcf15f181ba131 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 11:33:10 -0600
Subject: Removed ID/Sample/Value from Show/Hide Columns in trait page and only
show the option if columns other than those exist
---
wqflask/wqflask/templates/show_trait_edit_data.html | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 4ad11a5e..0d34bebc 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,12 +1,9 @@
<div>
{% for sample_type in sample_groups %}
<div class="sample-table-container">
- {% if loop.index == 1 %}
+ {% if loop.index == 1 and (sample_groups[0].se_exists or has_num_cases or sample_groups[0].attributes|length > 0) %}
<b>Show/Hide Columns:</b>
<br>
- <button class="toggle-vis" data-column="1">ID</button>
- <button class="toggle-vis" data-column="2">Sample</button>
- <button class="toggle-vis" data-column="3">Value</button>
{% if sample_groups[0].se_exists %}
<button class="toggle-vis" data-column="4,5">SE</button>
{% if has_num_cases %}
--
cgit v1.2.3
From ec1e37331e320ed674f184b738b9917753b6071f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 15:45:53 -0600
Subject: Made change to the way sample table width is calculated to account
for sample name width
---
wqflask/wqflask/show_trait/show_trait.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 0c6ae198..4c6dd005 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -186,8 +186,6 @@ class ShowTrait(object):
self.has_num_cases = has_num_cases(self.this_trait)
- self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
-
#ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
self.num_values = 0
self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
@@ -206,6 +204,8 @@ class ShowTrait(object):
sample_column_width = max_samplename_width * 8
+ self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, sample_column_width, self.has_num_cases)
+
if self.num_values >= 5000:
self.maf = 0.01
else:
@@ -547,12 +547,12 @@ def get_nearest_marker(this_trait, this_db):
return result[0][0]
-def get_table_widths(sample_groups, has_num_cases=False):
+def get_table_widths(sample_groups, sample_column_width, has_num_cases=False):
stats_table_width = 250
if len(sample_groups) > 1:
stats_table_width = 450
- trait_table_width = 380
+ trait_table_width = 300 + sample_column_width
if sample_groups[0].se_exists:
trait_table_width += 80
if has_num_cases:
--
cgit v1.2.3
From fbec8e8bb919cb866d70db9f93a942f4554395fb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 15:53:59 -0600
Subject: Removed unused JS and fixed mapping covariate selection to work for
both R/qtl and GEMMA
---
wqflask/wqflask/static/new/javascript/show_trait.js | 10 +---------
wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 ++++----
2 files changed, 5 insertions(+), 13 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 98f90f7d..9cd79687 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -100,15 +100,7 @@ d3.select("#select_compare_trait").on("click", (function(_this) {
return open_trait_selection();
};
})(this));
-d3.select("#select_covariates").on("click", (function(_this) {
- return function() {
- return open_covariate_selection();
- };
-})(this));
-$("#remove_covariates").click(function () {
- $("input[name=covariates]").val("")
- $(".selected-covariates").val("")
-});
+
$(".select_covariates").click(function () {
open_covariate_selection();
});
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index eca436c6..c42fe4aa 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -74,8 +74,8 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
<div class="select-covar-div">
- <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
- <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
+ <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+ <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
</div>
<textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
{% endif %}
@@ -317,8 +317,8 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
<div class="select-covar-div">
- <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
- <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
+ <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+ <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
</div>
<textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
{% endif %}
--
cgit v1.2.3
From d080436fa5640522c45b1d8bb90e9ca20ba06d5d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 17 Dec 2020 01:26:47 +0300
Subject: remove test for parse_gemma_output and modify run_gemma tests
(#533)
---
.../marker_regression/test_gemma_mapping.py | 32 ++--------------------
1 file changed, 2 insertions(+), 30 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 b8c13ab4..eab6afe6 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -5,7 +5,6 @@ from unittest import mock
from wqflask.marker_regression.gemma_mapping import run_gemma
from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file
from wqflask.marker_regression.gemma_mapping import gen_covariates_file
-from wqflask.marker_regression.gemma_mapping import parse_gemma_output
from wqflask.marker_regression.gemma_mapping import parse_loco_output
@@ -69,11 +68,9 @@ class TestGemmaMapping(unittest.TestCase):
mock_parse_loco.return_value = []
results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
], vals=[], covariates="", use_loco=True)
- system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'),
- mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')]
- mock_os.system.assert_has_calls(system_calls)
+ self.assertEqual(mock_os.system.call_count,2)
mock_gen_pheno_txt.assert_called_once()
- mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR")
+ mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True)
mock_os.path.isfile.assert_called_once_with(
('/home/user/imgfile_output.assoc.txt'))
self.assertEqual(mock_flat_files.call_count, 4)
@@ -138,31 +135,6 @@ class TestGemmaMapping(unittest.TestCase):
filehandler.write.assert_has_calls([mock.call(
'-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')])
- @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/")
- def test_parse_gemma_output(self):
- """add test for generating gemma output with obj returned"""
- file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7
-X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4
-125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67
-"""
- with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open:
- results = parse_gemma_output(genofile_name="gema_file")
- expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812},
- {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}]
- mock_open.assert_called_once_with(
- "/home/user/img/gema_file_output.assoc.txt")
- self.assertEqual(results, expected)
-
- @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img")
- def test_parse_gemma_output_with_empty_return(self):
- """add tests for parse gemma output where nothing returned"""
- output_file_results = """chr\t today"""
- with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open:
- results = parse_gemma_output(genofile_name="gema_file")
- self.assertEqual(results, [])
-
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")
@mock.patch("wqflask.marker_regression.gemma_mapping.json")
--
cgit v1.2.3
From e44f149fb6f6ca7d948c95f30faba4f4c2dc2ddd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 13:47:16 -0600
Subject: Correlation Min Expr and Location filters display depending upon the
selected target dataset now, instead of the trait's dataset
---
.../wqflask/static/new/javascript/show_trait.js | 18 ++++++++++++++++
.../show_trait_calculate_correlations.html | 24 ++++++++++++----------
2 files changed, 31 insertions(+), 11 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 9cd79687..e9c7cce1 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -516,6 +516,24 @@ on_corr_method_change = function() {
};
$('select[name=corr_type]').change(on_corr_method_change);
+on_dataset_change = function() {
+ let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+
+ if (dataset_type == "mrna_assay"){
+ $('#min_expr_filter').show();
+ $('#location_filter').show();
+ }
+ else if (dataset_type == "pheno"){
+ $('#min_expr_filter').show();
+ $('#location_filter').hide();
+ }
+ else {
+ $('#min_expr_filter').hide();
+ $('#location_filter').show();
+ }
+}
+$('select[name=corr_dataset]').change(on_dataset_change);
+
submit_special = function(url) {
get_table_contents_for_form_submit("trait_data_form");
$("#trait_data_form").attr("action", url);
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index ba72ff27..12294efb 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -19,18 +19,18 @@
<select name="corr_dataset" class="form-control">
{% for tissue in corr_tools.dataset_menu %}
{% if tissue.tissue %}
- <optgroup label="{{ tissue.tissue }} ------">
+ <optgroup label="{{ tissue.tissue }} ------">
{% endif %}
{% for dataset in tissue.datasets %}
- <option value="{{ dataset[1] }}"
- {% if corr_tools.dataset_menu_selected == dataset[1] %}
- selected
- {% endif %}>
- {{ dataset[0] }}
- </option>
+ <option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}"
+ {% if corr_tools.dataset_menu_selected == dataset[1] %}
+ selected
+ {% endif %}>
+ {{ dataset[0] }}
+ </option>
{% endfor %}
{% if tissue.tissue %}
- </optgroup>
+ </optgroup>
{% endif %}
{% endfor %}
</select>
@@ -74,14 +74,16 @@
</select>
</div>
</div>
- {% if dataset.type != "Publish" %}
- <div class="form-group">
+ {% if dataset.type != "Geno" %}
+ <div id="min_expr_filter" class="form-group">
<label class="col-xs-2 control-label">Min Expr</label>
<div class="col-xs-4 controls">
<input name="min_expr" value="" type="text" class="form-control min-expr-field">
</div>
</div>
- <div class="form-group">
+ {% endif %}
+ {% if dataset.type != "Pheno" %}
+ <div id="location_filter" class="form-group">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-6 controls">
<span>
--
cgit v1.2.3
From 561dfe5e1dedbf9c31d45023b895a2b9bb003869 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 13:51:59 -0600
Subject: Replaced Pheno with Publish for identifying dataset type in corr
options
---
wqflask/wqflask/templates/show_trait_calculate_correlations.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 12294efb..6f124943 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -82,7 +82,7 @@
</div>
</div>
{% endif %}
- {% if dataset.type != "Pheno" %}
+ {% if dataset.type != "Publish" %}
<div id="location_filter" class="form-group">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-6 controls">
--
cgit v1.2.3
From f851ea02b94b98f1537060a7189e25086fc991e9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 14:48:55 -0600
Subject: Fixed a couple logic issues and changed indentation in
show_trait_calculate_correlations.html
---
.../show_trait_calculate_correlations.html | 154 ++++++++++-----------
1 file changed, 75 insertions(+), 79 deletions(-)
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 6f124943..eaa0c308 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -2,88 +2,85 @@
<div class="col-xs-3 correlation-options">
<div class="form-horizontal section-form-div">
- <div class="form-group">
- <label for="corr_type" class="col-xs-2 control-label">Method</label>
- <div class="col-xs-3 controls">
- <select name="corr_type" class="form-control">
- <option value="sample">Sample r</option>
- <option value="lit">Literature r</option>
- <option value="tissue">Tissue r</option>
- </select>
- </div>
- </div>
+ <div class="form-group">
+ <label for="corr_type" class="col-xs-2 control-label">Method</label>
+ <div class="col-xs-3 controls">
+ <select name="corr_type" class="form-control">
+ <option value="sample">Sample r</option>
+ <option value="lit">Literature r</option>
+ <option value="tissue">Tissue r</option>
+ </select>
+ </div>
+ </div>
- <div class="form-group">
- <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
- <div class="col-xs-10 controls">
- <select name="corr_dataset" class="form-control">
- {% for tissue in corr_tools.dataset_menu %}
- {% if tissue.tissue %}
- <optgroup label="{{ tissue.tissue }} ------">
- {% endif %}
- {% for dataset in tissue.datasets %}
- <option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}"
- {% if corr_tools.dataset_menu_selected == dataset[1] %}
- selected
- {% endif %}>
- {{ dataset[0] }}
- </option>
- {% endfor %}
- {% if tissue.tissue %}
- </optgroup>
- {% endif %}
- {% endfor %}
- </select>
- </div>
- </div>
+ <div class="form-group">
+ <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+ <div class="col-xs-10 controls">
+ <select name="corr_dataset" class="form-control">
+ {% for tissue in corr_tools.dataset_menu %}
+ {% if tissue.tissue %}
+ <optgroup label="{{ tissue.tissue }} ------">
+ {% endif %}
+ {% for dataset in tissue.datasets %}
+ <option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}"
+ {% if corr_tools.dataset_menu_selected == dataset[1] %}
+ selected
+ {% endif %}>
+ {{ dataset[0] }}
+ </option>
+ {% endfor %}
+ {% if tissue.tissue %}
+ </optgroup>
+ {% endif %}
+ {% endfor %}
+ </select>
+ </div>
+ </div>
- <div class="form-group">
- <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
- <div class="col-xs-4 controls">
- <select name="corr_return_results" class="form-control">
- {% for return_result in corr_tools.return_results_menu %}
- <option value="{{ return_result }}"
- {% if corr_tools.return_results_menu_selected == return_result %}
- selected
- {% endif %}>
- Top {{ return_result }}
- </option>
- {% endfor %}
- </select>
- </div>
- </div>
+ <div class="form-group">
+ <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
+ <div class="col-xs-4 controls">
+ <select name="corr_return_results" class="form-control">
+ {% for return_result in corr_tools.return_results_menu %}
+ <option value="{{ return_result }}"
+ {% if corr_tools.return_results_menu_selected == return_result %}
+ selected
+ {% endif %}>
+ Top {{ return_result }}
+ </option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
- <div class="form-group">
- <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
- <div class="col-xs-4 controls">
- <select name="corr_samples_group" class="form-control">
- {% for group, pretty_group in sample_group_types.items() %}
- <option value="{{ group }}">{{ pretty_group }}</option>
- {% endfor %}
- </select>
- </div>
- </div>
+ <div class="form-group">
+ <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+ <div class="col-xs-4 controls">
+ <select name="corr_samples_group" class="form-control">
+ {% for group, pretty_group in sample_group_types.items() %}
+ <option value="{{ group }}">{{ pretty_group }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
- <div id="corr_sample_method" class="form-group">
- <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
- <div class="col-xs-4 controls">
- <select name="corr_sample_method" class="form-control">
- <option value="pearson">Pearson</option>
- <option value="spearman">Spearman Rank</option>
- <option value="bicor">Biweight Midcorrelation</option>
- </select>
- </div>
- </div>
- {% if dataset.type != "Geno" %}
- <div id="min_expr_filter" class="form-group">
- <label class="col-xs-2 control-label">Min Expr</label>
- <div class="col-xs-4 controls">
- <input name="min_expr" value="" type="text" class="form-control min-expr-field">
- </div>
- </div>
- {% endif %}
- {% if dataset.type != "Publish" %}
- <div id="location_filter" class="form-group">
+ <div id="corr_sample_method" class="form-group">
+ <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
+ <div class="col-xs-4 controls">
+ <select name="corr_sample_method" class="form-control">
+ <option value="pearson">Pearson</option>
+ <option value="spearman">Spearman Rank</option>
+ <option value="bicor">Biweight Midcorrelation</option>
+ </select>
+ </div>
+ </div>
+ <div id="min_expr_filter" class="form-group" style="display: {% if dataset.type != 'Geno' %}block{% else %}none{% endif %};">
+ <label class="col-xs-2 control-label">Min Expr</label>
+ <div class="col-xs-4 controls">
+ <input name="min_expr" value="" type="text" class="form-control min-expr-field">
+ </div>
+ </div>
+ <div id="location_filter" class="form-group" style="display: {% if dataset.type != 'Publish' %}block{% else %}none{% endif %};">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-6 controls">
<span>
@@ -93,7 +90,6 @@
<br>
</div>
</div>
- {% endif %}
<div class="form-group">
<label class="col-xs-2 control-label">Range</label>
<div class="col-xs-5 controls">
--
cgit v1.2.3
From be1c1c1c48d75875f03b7ff4e91654f390571b58 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 14:49:26 -0600
Subject: Added Mean (mean expression) column to phenotype correlation results
table
---
wqflask/wqflask/templates/correlation_page.html | 26 +++++++++++++++++--------
1 file changed, 18 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 8e2a23fd..6188c0e7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -95,14 +95,15 @@
{% elif target_dataset.type == 'Publish' %}
<button class="toggle-vis" data-column="3">Abbreviation</button>
<button class="toggle-vis" data-column="4">Description</button>
- <button class="toggle-vis" data-column="5">Authors</button>
- <button class="toggle-vis" data-column="6">Year</button>
- <button class="toggle-vis" data-column="7">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
- <button class="toggle-vis" data-column="8">N</button>
- <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button>
- <button class="toggle-vis" data-column="10">Peak LOD</button>
- <button class="toggle-vis" data-column="11">Peak Location</button>
- <button class="toggle-vis" data-column="12">Effect Size</button>
+ <button class="toggle-vis" data-column="5">Mean</button>
+ <button class="toggle-vis" data-column="6">Authors</button>
+ <button class="toggle-vis" data-column="7">Year</button>
+ <button class="toggle-vis" data-column="8">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
+ <button class="toggle-vis" data-column="9">N</button>
+ <button class="toggle-vis" data-column="10">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button>
+ <button class="toggle-vis" data-column="11">Peak LOD</button>
+ <button class="toggle-vis" data-column="12">Peak Location</button>
+ <button class="toggle-vis" data-column="13">Effect Size</button>
{% else %}
<button class="toggle-vis" data-column="3">Location</button>
<button class="toggle-vis" data-column="4">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
@@ -398,6 +399,13 @@
}
}
},
+ {
+ 'title': "Mean",
+ 'type': "natural-minus-na",
+ 'width': "40px",
+ 'data': "mean",
+ 'orderSequence': [ "desc", "asc"]
+ },
{
'title': "Authors",
'type': "natural",
@@ -514,6 +522,8 @@
} ],
{% if target_dataset.type == 'Geno' %}
"order": [[6, "asc" ]],
+ {% elif target_dataset.type == 'Publish' %}
+ "order": [[10, "asc" ]],
{% else %}
"order": [[9, "asc" ]],
{% endif %}
--
cgit v1.2.3
From 03de3751bd003117dce2bc4bf085092bd8f9a0fe Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 14:50:34 -0600
Subject: Fixed some logic to work correctly with the changes to the way
correlation filters work + changed correlation python code to include Mean
(mean expression) for phenotype results
---
wqflask/wqflask/correlation/show_corr_results.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7d3b9b9f..298a3559 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -71,7 +71,6 @@ class CorrelationResults(object):
assert('corr_sample_method' in start_vars)
assert('corr_samples_group' in start_vars)
assert('corr_dataset' in start_vars)
- #assert('min_expr' in start_vars)
assert('corr_return_results' in start_vars)
if 'loc_chr' in start_vars:
assert('min_loc_mb' in start_vars)
@@ -197,15 +196,15 @@ class CorrelationResults(object):
if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
float(self.correlation_data[trait][0]) <= self.p_range_upper):
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-
+ if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
continue
- elif range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+ if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
+ if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
continue
- elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
+ if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
continue
- elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
+ if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
continue
(trait_object.sample_r,
@@ -519,6 +518,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
elif target_dataset.type == "Publish":
results_dict['abbreviation_display'] = "N/A"
results_dict['description'] = "N/A"
+ results_dict['mean'] = "N/A"
results_dict['authors_display'] = "N/A"
results_dict['additive'] = "N/A"
if for_api:
@@ -532,6 +532,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
results_dict['abbreviation_display'] = trait.abbreviation
if bool(trait.description_display):
results_dict['description'] = trait.description_display
+ if bool(trait.mean):
+ results_dict['mean'] = f"{float(trait.mean):.3f}"
if bool(trait.authors):
authors_list = trait.authors.split(',')
if len(authors_list) > 6:
@@ -605,6 +607,7 @@ def get_header_fields(data_type, corr_method):
'Record',
'Abbreviation',
'Description',
+ 'Mean',
'Authors',
'Year',
'Sample rho',
@@ -618,6 +621,7 @@ def get_header_fields(data_type, corr_method):
'Record',
'Abbreviation',
'Description',
+ 'Mean',
'Authors',
'Year',
'Sample r',
--
cgit v1.2.3
From 47c15cdbd8d54afca05bf939dec8d7d461cff5a5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:30:13 -0600
Subject: Added function that fetches sample data and converts it to JSON to
show_trait.js
---
.../wqflask/static/new/javascript/show_trait.js | 23 ++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 98f90f7d..b71a9dd8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -427,6 +427,25 @@ process_id = function() {
}
return processed;
};
+
+fetch_sample_values = function() {
+ // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster)
+ sample_val_dict = {};
+
+ table = 'samples_primary';
+ if ($('#' + table).length){
+ table_api = $('#' + table).DataTable();
+ val_nodes = table_api.column(3).nodes().to$();
+ for (_j = 0; _j < val_nodes.length; _j++){
+ sample_name = val_nodes[_j].childNodes[0].name.split(":")[1]
+ sample_val = val_nodes[_j].childNodes[0].value
+ sample_val_dict[sample_name] = sample_val
+ }
+ }
+
+ return sample_val_dict;
+}
+
edit_data_change = function() {
var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
already_seen = {};
@@ -525,7 +544,7 @@ on_corr_method_change = function() {
$('select[name=corr_type]').change(on_corr_method_change);
submit_special = function(url) {
- get_table_contents_for_form_submit("trait_data_form");
+ $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values()))
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit();
};
@@ -549,7 +568,7 @@ get_table_contents_for_form_submit = function(form_id) {
});
}
-var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
--
cgit v1.2.3
From 66b8f70f162f2d6356c6e9af5066c5b90335f7c2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:33:04 -0600
Subject: Changed views.py to accept sample data for loading page and mapping
as JSON instead of having separate form parameters for each sample + removed
some commented out code/logging
---
wqflask/wqflask/views.py | 16 +++++-----------
1 file changed, 5 insertions(+), 11 deletions(-)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 25563e86..c136711e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -621,12 +621,13 @@ def loading_page():
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
for key, value in list(initial_start_vars.items()):
- if key in wanted or key.startswith(('value:')):
+ if key in wanted:
start_vars[key] = value
if 'n_samples' in start_vars:
n_samples = int(start_vars['n_samples'])
else:
+ sample_vals_dict = json.loads(start_vars['sample_vals'])
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
else:
@@ -642,8 +643,7 @@ def loading_page():
samples = genofile_samples
for sample in samples:
- value = start_vars.get('value:' + sample)
- if value != "x":
+ if sample_vals_dict[sample] != "x":
n_samples += 1
start_vars['n_samples'] = n_samples
@@ -660,7 +660,6 @@ def loading_page():
@app.route("/run_mapping", methods=('POST',))
def mapping_results_page():
initial_start_vars = request.form
- #logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
logger.info(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
@@ -670,6 +669,7 @@ def mapping_results_page():
'species',
'samples',
'vals',
+ 'sample_vals',
'first_run',
'output_files',
'geno_db_exists',
@@ -723,13 +723,11 @@ def mapping_results_page():
)
start_vars = {}
for key, value in list(initial_start_vars.items()):
- if key in wanted or key.startswith(('value:')):
+ if key in wanted:
start_vars[key] = value
- #logger.debug("Mapping called with start_vars:", start_vars)
version = "v3"
key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
- #logger.info("key is:", pf(key))
with Bench("Loading cache"):
result = None # Just for testing
#result = Redis.get(key)
@@ -775,10 +773,6 @@ def mapping_results_page():
rendered_template = render_template("pair_scan_results.html", **result)
else:
gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
- #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- #logger.info("pickled result length:", len(pickled_result))
- #Redis.set(key, pickled_result)
- #Redis.expire(key, 1*60)
with Bench("Rendering template"):
#if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
--
cgit v1.2.3
From 20314199985aa21a00a47f3c7b053ec49bc8b60d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:33:44 -0600
Subject: Added sample_vals input element that is meant to contain JSON for all
sample values (pulled from the sample table using DataTables API in
show_trait.js)
---
wqflask/wqflask/templates/show_trait.html | 1 +
1 file changed, 1 insertion(+)
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c881eb76..77fc9342 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
<input type="hidden" name="genofile" value="">
<input type="hidden" name="covariates" value="">
<input type="hidden" name="transform" value="">
+ <input type="hidden" name="sample_vals" value="">
<div class="container showtrait-main-div">
<div class="panel-group" id="accordion">
--
cgit v1.2.3
From 969a421efc0bd4529607fdc14332acd897d8e106 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:34:21 -0600
Subject: Added sample_vals to the list of mapping inputs that determines what
is included in start_vars when trait page parameters are passed to the
mapping loading page
---
wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
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 34582f21..3ae52975 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,7 +141,7 @@ $('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',
+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', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
--
cgit v1.2.3
From 95d1887bba6b93ea310c226cb82e9cb64f75cc67 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:35:09 -0600
Subject: Changed mapping_results.html to have a single sample_vals input
instead of separate ones for every sample + added sample_vals to the list of
inputs sent to the loading page
---
wqflask/wqflask/templates/mapping_results.html | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1a76ef7a..2fb37832 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -31,10 +31,7 @@
{% endif %}
<input type="hidden" name="results_path" value="{{ mapping_results_path }}">
<input type="hidden" name="method" value="{{ mapping_method }}">
- <input type="hidden" name="samples" value="{{ samples|join(",") }}">
- {% for sample in samples %}
- <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
- {% endfor %}
+ <input type="hidden" name="sample_vals" value="{{ sample_vals }}">
<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 }}">
@@ -450,7 +447,7 @@
});
- var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+ 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', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
--
cgit v1.2.3
From 7544d03a6d819d70779deb79d38b7465a648c1ff Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:36:53 -0600
Subject: Changed run_mapping.py to get sample names and values from JSON
instead of a bunch of separate input parameters
---
wqflask/wqflask/marker_regression/run_mapping.py | 64 ++++++------------------
1 file changed, 15 insertions(+), 49 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 891fcc66..a1f87b61 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -71,56 +71,22 @@ class RunMapping(object):
all_samples_ordered = self.dataset.group.all_samples_ordered()
self.vals = []
- if 'samples' in start_vars:
- self.samples = start_vars['samples'].split(",")
- if (len(genofile_samplelist) != 0):
- for sample in genofile_samplelist:
- if sample in self.samples:
- value = start_vars.get('value:' + sample)
- if value:
- self.vals.append(value)
- else:
- self.vals.append("x")
- else:
- for sample in self.samples:
- value = start_vars.get('value:' + sample)
- if value:
- self.vals.append(value)
+ self.samples = []
+ self.sample_vals = start_vars['sample_vals']
+ sample_val_dict = json.loads(self.sample_vals)
+ samples = sample_val_dict.keys()
+ if (len(genofile_samplelist) != 0):
+ for sample in genofile_samplelist:
+ self.samples.append(sample)
+ if sample in samples:
+ self.vals.append(sample_val_dict[sample])
+ else:
+ self.vals.append("x")
else:
- self.samples = []
- if (len(genofile_samplelist) != 0):
- for sample in genofile_samplelist:
- if sample in self.dataset.group.samplelist:
- in_trait_data = False
- for item in self.this_trait.data:
- if self.this_trait.data[item].name == sample:
- value = start_vars['value:' + self.this_trait.data[item].name]
- self.samples.append(self.this_trait.data[item].name)
- self.vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- value = start_vars.get('value:' + sample)
- if value:
- self.samples.append(sample)
- self.vals.append(value)
- else:
- self.vals.append("x")
- else:
- for sample in self.dataset.group.samplelist: # sample is actually the name of an individual
- in_trait_data = False
- for item in self.this_trait.data:
- if self.this_trait.data[item].name == sample:
- value = start_vars['value:' + self.this_trait.data[item].name]
- self.samples.append(self.this_trait.data[item].name)
- self.vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- value = start_vars.get('value:' + sample)
- if value:
- self.samples.append(sample)
- self.vals.append(value)
+ for sample in self.dataset.group.samplelist:
+ if sample in samples:
+ self.vals.append(sample_val_dict[sample])
+ self.samples.append(sample)
if 'n_samples' in start_vars:
self.n_samples = start_vars['n_samples']
--
cgit v1.2.3
From 6d493f7ef57322f226dd310497e4dc7518440cfd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:38:09 -0600
Subject: Changed display_mapping_results.py to get sample names and values
from the JSON sample_vals parameter
---
.../marker_regression/display_mapping_results.py | 19 +++++++++----------
1 file changed, 9 insertions(+), 10 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 08c2d750..9f1b050d 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -270,8 +270,9 @@ class DisplayMappingResults(object):
# Needing for form submission when doing single chr
# mapping or remapping after changing options
- self.samples = start_vars['samples']
- self.vals = start_vars['vals']
+ self.sample_vals = start_vars['sample_vals']
+ self.sample_vals_dict = json.loads(self.sample_vals)
+
self.transform = start_vars['transform']
self.mapping_method = start_vars['mapping_method']
self.mapping_results_path = start_vars['mapping_results_path']
@@ -492,11 +493,10 @@ class DisplayMappingResults(object):
## count the amount of individuals to be plotted, and increase self.graphHeight
if self.haplotypeAnalystChecked and self.selectedChr > -1:
thisTrait = self.this_trait
- _strains, _vals, _vars, _aliases = thisTrait.export_informative()
smd=[]
- for ii, _val in enumerate(self.vals):
- if _val != "x":
- temp = GeneralObject(name=self.samples[ii], value=float(_val))
+ for sample in self.sample_vals_dict.keys():
+ if self.sample_vals_dict[sample] != "x":
+ temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
@@ -1464,12 +1464,11 @@ class DisplayMappingResults(object):
yPaddingTop = yTopOffset
thisTrait = self.this_trait
- _strains, _vals, _vars, _aliases = thisTrait.export_informative()
smd=[]
- for ii, _val in enumerate(self.vals):
- if _val != "x":
- temp = GeneralObject(name=self.samples[ii], value=float(_val))
+ for sample in self.sample_vals_dict.keys():
+ if self.sample_vals_dict[sample] != "x":
+ temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
--
cgit v1.2.3
From 41efd6840f2e1c052dbb77affd6f09fc2e2bcd05 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:39:31 -0600
Subject: Changed show_corr_results.py to get sample names/values from the JSON
sample_vals parameter
---
wqflask/wqflask/correlation/show_corr_results.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7d3b9b9f..be983c87 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -87,8 +87,6 @@ class CorrelationResults(object):
else:
helper_functions.get_species_dataset_trait(self, start_vars)
- #self.dataset.group.read_genotype_file()
-
corr_samples_group = start_vars['corr_samples_group']
self.sample_data = {}
@@ -454,13 +452,13 @@ class CorrelationResults(object):
if not excluded_samples:
excluded_samples = ()
+ sample_val_dict = json.loads(start_vars['sample_vals'])
for sample in sample_names:
if sample not in excluded_samples:
- # print("Looking for",sample,"in",start_vars)
- value = start_vars.get('value:' + sample)
- if value:
- if not value.strip().lower() == 'x':
- self.sample_data[str(sample)] = float(value)
+ value = sample_val_dict[sample]
+ if not value.strip().lower() == 'x':
+ self.sample_data[str(sample)] = float(value)
+
def do_bicor(this_trait_vals, target_trait_vals):
r_library = ro.r["library"] # Map the library function
--
cgit v1.2.3
From 453ac34383d54910e821609b80b69ff41c48d0ce Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:53:01 -0600
Subject: Added Additive Effect when using LOCO with GEMMA
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 630a3afa..ab3a7278 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -54,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
trait_filename)
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -62,7 +62,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
gwa_output_filename)
else:
- gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
maf,
TEMPDIR,
@@ -184,11 +184,8 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- if loco == "True":
- marker['p_value'] = float(line.split("\t")[9])
- else:
- marker['p_value'] = float(line.split("\t")[10])
- marker['additive'] = float(line.split("\t")[7])
+ marker['p_value'] = float(line.split("\t")[10])
+ marker['additive'] = float(line.split("\t")[7])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
--
cgit v1.2.3
From 69f92ef2bc10477a80eff96fb7cc83fee11f31e8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 17:05:55 -0600
Subject: This should fix the Github login error
---
wqflask/wqflask/user_login.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index f25ebc32..b6266b2a 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -239,7 +239,7 @@ def github_oauth2():
}
result = requests.post("https://github.com/login/oauth/access_token", json=data)
- result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
+ result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]}
github_user = get_github_user_details(result_dict["access_token"])
--
cgit v1.2.3
From fc717c36d334f364bbae8c98f31ddf78e18d64e3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 17:34:47 -0600
Subject: Added redirect_uri to the ORCID_AUTH_URL since it wasn't working due
to missing this parameter
---
wqflask/utility/tools.py | 2 +-
wqflask/wqflask/user_login.py | 6 ++++--
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 68ef0f04..65df59c3 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
- ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
+ ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index b6266b2a..bc608e84 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -25,7 +25,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
from smtplib import SMTP
-from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
+from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
THREE_DAYS = 60 * 60 * 24 * 3
@@ -277,9 +277,11 @@ def orcid_oauth2():
data = {
"client_id": ORCID_CLIENT_ID,
"client_secret": ORCID_CLIENT_SECRET,
- "grant_type": "authorization_code",
+ "grant_type": "authorization_code",
+ "redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2",
"code": code
}
+
result = requests.post(ORCID_TOKEN_URL, data=data)
result_dict = json.loads(result.text.encode("utf-8"))
--
cgit v1.2.3
From 0560b297a9a6139079ee237bc8d98f471e7703f5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 25 Dec 2020 19:18:48 -0600
Subject: Added edit_data_change to block_by_attribute_value so it will update
stats figures after using that tool
---
wqflask/wqflask/static/new/javascript/show_trait.js | 2 ++
1 file changed, 2 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e9c7cce1..312cc22f 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -641,6 +641,8 @@ block_by_attribute_value = function() {
this_val_node.value = "x";
}
}
+
+ edit_data_change();
};
$('#exclude_by_attr').click(block_by_attribute_value);
--
cgit v1.2.3
From c26304ed6a2937654794f908c13ccd3ba4a66453 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 14:25:51 -0600
Subject: Fix issue that caused error bars to not work for bar chart
---
wqflask/wqflask/static/new/javascript/show_trait.js | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 312cc22f..6918cf34 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -448,7 +448,7 @@ edit_data_change = function() {
if (is_number(sample_val) && sample_val !== "") {
sample_val = parseFloat(sample_val);
sample_sets[table].add_value(sample_val);
- if (typeof var_nodes !== 'undefined'){
+ if (typeof var_nodes === 'undefined'){
sample_var = null;
} else {
sample_var = var_nodes[_j].childNodes[0].value
@@ -471,6 +471,7 @@ edit_data_change = function() {
}
}
}
+
}
update_stat_values(sample_sets);
--
cgit v1.2.3
From 3241a8de759f18bbbc73bd755419831db37e71a0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:01:31 -0600
Subject: Added 'Location Type' option to show_trait correlation options
---
wqflask/wqflask/templates/show_trait_calculate_correlations.html | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index eaa0c308..46232b97 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -80,6 +80,15 @@
<input name="min_expr" value="" type="text" class="form-control min-expr-field">
</div>
</div>
+ <div class="form-group">
+ <label for="location_type" class="col-xs-2 control-label">Location Type</label>
+ <div class="col-xs-4 controls">
+ <select name="location_type" class="form-control">
+ {% if dataset.type != 'Publish' %}<option value="gene">Gene</option>{% endif %}
+ <option value="highest_lod">Highest LOD</option>
+ </select>
+ </div>
+ </div>
<div id="location_filter" class="form-group" style="display: {% if dataset.type != 'Publish' %}block{% else %}none{% endif %};">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-6 controls">
--
cgit v1.2.3
From ab9aebc567d1a10282ae55f282993a3fa9dd3582 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:14:32 -0600
Subject: Changed correlation options to always show the location field and
both location_type options, since one or the other will always apply
---
wqflask/wqflask/templates/show_trait_calculate_correlations.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 46232b97..cba977ac 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -84,12 +84,12 @@
<label for="location_type" class="col-xs-2 control-label">Location Type</label>
<div class="col-xs-4 controls">
<select name="location_type" class="form-control">
- {% if dataset.type != 'Publish' %}<option value="gene">Gene</option>{% endif %}
+ <option value="gene" {% if dataset.type == 'Publish' %}disabled{% endif %}>Gene</option>
<option value="highest_lod">Highest LOD</option>
</select>
</div>
</div>
- <div id="location_filter" class="form-group" style="display: {% if dataset.type != 'Publish' %}block{% else %}none{% endif %};">
+ <div id="location_filter" class="form-group">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-6 controls">
<span>
--
cgit v1.2.3
From a336ca94fd473fdfd6cc5a83ce879429c0f1db92 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:15:01 -0600
Subject: Added JS controlling which location_type options are available
depending upon the selected target dataset
---
wqflask/wqflask/static/new/javascript/show_trait.js | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 6918cf34..a301615b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -519,21 +519,26 @@ $('select[name=corr_type]').change(on_corr_method_change);
on_dataset_change = function() {
let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+ let location_type = $('select[name=location_type] option:selected').val();
if (dataset_type == "mrna_assay"){
$('#min_expr_filter').show();
- $('#location_filter').show();
+ $('select[name=location_type] option:disabled').prop('disabled', false)
}
else if (dataset_type == "pheno"){
$('#min_expr_filter').show();
- $('#location_filter').hide();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true);
}
else {
$('#min_expr_filter').hide();
- $('#location_filter').show();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false);
}
}
+
$('select[name=corr_dataset]').change(on_dataset_change);
+$('select[name=location_type]').change(on_dataset_change);
submit_special = function(url) {
get_table_contents_for_form_submit("trait_data_form");
--
cgit v1.2.3
From 8dd6f67d37c2d5cc800ee9dc33dd13a566e256fa Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:48:50 -0600
Subject: Incorporated location_type into the filtering logic for the
correlation page
---
wqflask/wqflask/correlation/show_corr_results.py | 37 +++++++++++++++---------
1 file changed, 23 insertions(+), 14 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 298a3559..6175dc7e 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -101,11 +101,12 @@ class CorrelationResults(object):
'min_loc_mb' in start_vars and
'max_loc_mb' in start_vars):
+ self.location_type = get_string(start_vars, 'location_type')
self.location_chr = get_string(start_vars, 'loc_chr')
self.min_location_mb = get_int(start_vars, 'min_loc_mb')
self.max_location_mb = get_int(start_vars, 'max_loc_mb')
else:
- self.location_chr = self.min_location_mb = self.max_location_mb = None
+ self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -173,23 +174,25 @@ class CorrelationResults(object):
self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
key=lambda t: -abs(t[1][0])))
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- #ZS: Convert min/max chromosome to an int for the location range option
- range_chr_as_int = None
- for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
- if 'loc_chr' in start_vars:
- if chr_info.name == self.location_chr:
- range_chr_as_int = order_id
+
+ #ZS: Convert min/max chromosome to an int for the location range option
+ range_chr_as_int = None
+ for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ if 'loc_chr' in start_vars:
+ if chr_info.name == self.location_chr:
+ range_chr_as_int = order_id
for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
if not trait_object:
continue
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- #ZS: Convert trait chromosome to an int for the location range option
- chr_as_int = 0
- for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ chr_as_int = 0
+ for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ if self.location_type == "highest_lod":
+ if chr_info.name == trait_object.locus_chr:
+ chr_as_int = order_id
+ else:
if chr_info.name == trait_object.chr:
chr_as_int = order_id
@@ -199,9 +202,15 @@ class CorrelationResults(object):
if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
continue
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+
+ if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+ continue
+ if self.location_type == "highest_lod":
+ if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)):
+ continue
+ if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)):
continue
+ else:
if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
continue
if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
--
cgit v1.2.3
From dd2c510ea09ea3169cac3685b299640226d5606a Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sun, 27 Dec 2020 23:17:36 +0300
Subject: update tests for run gemma
---
.../wqflask/marker_regression/test_gemma_mapping.py | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 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 eab6afe6..fe2569b8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -144,21 +144,26 @@ class TestGemmaMapping(unittest.TestCase):
"files": [["file_name", "user", "~/file1"],
["file_name", "user", "~/file2"]]
}
- return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7"""
- return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5"""
+ return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
+Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
+X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
+
+ return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4"""
mock_os.path.isfile.return_value = True
file_to_write = """{"files":["file_1","file_2"]}"""
with mock.patch("builtins.open") as mock_open:
handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open(
- read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value)
+ read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value)
mock_open.side_effect = handles
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
- expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {
- 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}]
+ expected_results= [
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
--
cgit v1.2.3
From e7324bf55b7dcfd46f7a2ab52765977fb189c26b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Dec 2020 13:12:48 -0600
Subject: Added location_type to the list of inputs to correlation page (a list
of form inputs the correlation page needs is passed with it so it doesn't get
unrelated form inputs)
---
wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a301615b..83d4f193 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -566,7 +566,7 @@ get_table_contents_for_form_submit = function(form_id) {
}
var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
- 'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
+ 'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
return function() {
--
cgit v1.2.3
From 1bd2d85624e04966ed20ec84dc6ba2cfda85d794 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Dec 2020 15:03:22 -0600
Subject: Used a try/catch to deal with situations where there's no SE/var
column, since apparently var_nodes wasn't undefined, causing the previous
check to not work
---
wqflask/wqflask/static/new/javascript/show_trait.js | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 6918cf34..1025233b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -448,15 +448,15 @@ edit_data_change = function() {
if (is_number(sample_val) && sample_val !== "") {
sample_val = parseFloat(sample_val);
sample_sets[table].add_value(sample_val);
- if (typeof var_nodes === 'undefined'){
- sample_var = null;
- } else {
+ try {
sample_var = var_nodes[_j].childNodes[0].value
if (is_number(sample_var)) {
sample_var = parseFloat(sample_var)
} else {
sample_var = null;
}
+ } catch {
+ sample_var = null;
}
sample_dict = {
value: sample_val,
--
cgit v1.2.3
From 7d8e41cd6d31c51adfedcf7abc0da553dd58762c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:04:55 -0600
Subject: Removed logging line from draw_probability_plot.js
---
wqflask/wqflask/static/new/javascript/draw_probability_plot.js | 1 -
1 file changed, 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3d756303..1b944d4f 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -118,7 +118,6 @@
};
};
data = [make_data('samples_primary'), make_data('samples_other')];
- console.log("THE DATA IS:", data);
d3.select("#prob_plot_container svg").datum(data).call(chart);
if (js_data.trait_symbol != null) {
$("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
--
cgit v1.2.3
From 1e8c9e4bbc2f8b2085eaf77f469001660cf3c43d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:12:02 -0600
Subject: Increased the top margin on the trait page Bar Chart, which should
prevent the chart options from overlapping with the title
---
wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 1025233b..66f7b606 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1302,7 +1302,7 @@ if (js_data.num_values < 256) {
margin: {
l: left_margin,
r: 30,
- t: 30,
+ t: 100,
b: bottom_margin
}
};
--
cgit v1.2.3
From 683381f1c98afa58cc40f1a1f000f5e136c931e3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:15:55 -0600
Subject: Removed Scatterplot Matrix since it isn't working and wasn't really
used to begin with
---
wqflask/wqflask/static/new/javascript/show_trait.js | 18 ------------------
wqflask/wqflask/templates/show_trait_statistics.html | 16 ----------------
2 files changed, 34 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 66f7b606..832dd1e4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -94,25 +94,7 @@ add = function() {
$('#add_to_collection').click(add);
sample_lists = js_data.sample_lists;
sample_group_types = js_data.sample_group_types;
-d3.select("#select_compare_trait").on("click", (function(_this) {
- return function() {
- $('.scatter-matrix-container').remove();
- return open_trait_selection();
- };
-})(this));
-$(".select_covariates").click(function () {
- open_covariate_selection();
-});
-$(".remove_covariates").click(function () {
- $("input[name=covariates]").val("")
- $(".selected-covariates").val("")
-});
-d3.select("#clear_compare_trait").on("click", (function(_this) {
- return function() {
- return $('.scatter-matrix-container').remove();
- };
-})(this));
open_trait_selection = function() {
return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
return function() {
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 4f347d4e..865959b1 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -21,9 +21,6 @@
<li>
<a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
</li>
- <li>
- <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
- </li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="stats_tab">
@@ -116,19 +113,6 @@
<div id="violin_plot"></div>
</div>
</div>
- <div class="tab-pane" id="scatterplot_matrix">
- <div class="btn-group scatterplot-btn-div">
- <button type="button" class="btn btn-default" id="select_compare_trait">
- <i class="icon-th-large"></i> Select Traits
- </button>
- <button type="button" class="btn btn-default" id="clear_compare_trait">
- <i class="icon-trash"></i> Clear
- </button>
- </div>
- <div id="scatterplot_container">
- <div id="comparison_scatterplot" class="qtlcharts"></div>
- </div>
- </div>
</div>
</div>
<div id="collections_holder_wrapper" style="display:none;">
--
cgit v1.2.3
From 257484870e4d2d0f95ea7175db2fc867154ca07f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:16:38 -0600
Subject: Removed some logging from stats.js
---
wqflask/wqflask/static/new/javascript/stats.js | 2 --
1 file changed, 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4df03412..6c443ab3 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -91,8 +91,6 @@ Stats = (function() {
Stats.prototype.interquartile = function() {
var iq, length, q1, q3;
length = this.the_values.length;
- console.log("in interquartile the_values are:", this.the_values);
- console.log("length is:", length);
if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") {
q1 = Math.log2(this.the_values[Math.floor(length * .25)]);
q3 = Math.log2(this.the_values[Math.floor(length * .75)]);
--
cgit v1.2.3
From a344835cefaaad5b8a7b96977d3963dc3cb4111e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:45:17 -0600
Subject: Added call to change_buttons to mapping results table (which deals
with highlighting rows and enabling the Add (to collection) button
Also added a "check_node" paramter to change_buttons since sometimes the checkbox is in the second node instead of the first when it's preceded by blank text
---
wqflask/wqflask/static/new/javascript/search_results.js | 4 ++--
wqflask/wqflask/templates/mapping_results.html | 14 ++++++++++++++
2 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 9ffef4f8..05dcfda5 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -1,4 +1,4 @@
-change_buttons = function() {
+change_buttons = function(check_node = 0) {
var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2;
buttons = ["#add", "#remove"];
@@ -6,7 +6,7 @@ change_buttons = function() {
table_api = $('#trait_table').DataTable();
check_cells = table_api.column(0).nodes().to$();
for (let i = 0; i < check_cells.length; i++) {
- if (check_cells[i].childNodes[0].checked){
+ if (check_cells[i].childNodes[check_node].checked){
num_checked += 1
}
}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1a76ef7a..022e9f6a 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -375,6 +375,20 @@
console.time("Creating table");
{% if selectedChr == -1 %}
$('#trait_table').DataTable( {
+ "drawCallback": function( settings ) {
+ $('#trait_table tr').off().on("click", function(event) {
+ if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+ var obj =$(this).find('input');
+ obj.prop('checked', !obj.is(':checked'));
+ }
+ if ($(this).hasClass("selected")){
+ $(this).removeClass("selected")
+ } else {
+ $(this).addClass("selected")
+ }
+ change_buttons(check_node=1)
+ });
+ },
"columns": [
{ "type": "natural", "width": "5%" },
{ "type": "natural", "width": "8%" },
--
cgit v1.2.3
From 5fdcf24585ebff01b36d59d0ce1955cfc90fb482 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:53:08 -0600
Subject: Only show Add button and run change_buttons function when genotypes
are databased
---
wqflask/wqflask/templates/mapping_results.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 022e9f6a..985d542c 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -248,7 +248,7 @@
<button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
<button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
<button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
- <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+ {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %}
<br />
<br />
<div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
@@ -386,7 +386,7 @@
} else {
$(this).addClass("selected")
}
- change_buttons(check_node=1)
+ {% if geno_db_exists == "True" %}change_buttons(check_node=1){% endif %}
});
},
"columns": [
--
cgit v1.2.3
From 468ab300c1447af0ac0eb3fdf12d6b6676f4a60f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:54:55 -0600
Subject: Removed logging line from init_genome_browser.js
---
wqflask/wqflask/static/new/javascript/init_genome_browser.js | 2 --
1 file changed, 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index 2552fb04..508f5bf2 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -1,5 +1,3 @@
-console.log("THE FILES:", js_data.browser_files)
-
snps_filename = "/browser_input?filename=" + js_data.browser_files[0]
annot_filename = "/browser_input?filename=" + js_data.browser_files[1]
--
cgit v1.2.3
From 7032f7b05deac0bbd2e868ffd3fe42dd1c97fb7d Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Tue, 5 Jan 2021 13:14:08 -0600
Subject: add server side class unit tests
---
wqflask/tests/unit/wqflask/test_server_side.py | 31 ++++++++++++++++++++++++++
wqflask/wqflask/server_side.py | 16 ++++++-------
2 files changed, 39 insertions(+), 8 deletions(-)
create mode 100644 wqflask/tests/unit/wqflask/test_server_side.py
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
new file mode 100644
index 00000000..4f91d8ca
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -0,0 +1,31 @@
+import unittest
+
+from wqflask.server_side import ServerSideTable
+
+
+class TestServerSideTableTests(unittest.TestCase):
+ """
+ Test the ServerSideTable class
+
+ test table:
+ first, second, third
+ 'd', 4, 'zz'
+ 'b', 2, 'aa'
+ 'c', 1, 'ss'
+ """
+
+ def test_get_page(self):
+ rows_count = 3
+ table_rows = [
+ {'first': 'd', 'second': 4, 'third': 'zz'},
+ {'first': 'b', 'second': 2, 'third': 'aa'},
+ {'first': 'c', 'second': 1, 'third': 'ss'},
+ ]
+ headers = ['first', 'second', 'third']
+ request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+
+ test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+ self.assertEqual(test_page['sEcho'], '1')
+ self.assertEqual(test_page['iTotalRecords'], 'nan')
+ self.assertEqual(test_page['iTotalDisplayRecords'], '3')
+ self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 824b00aa..5f764767 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -3,7 +3,7 @@
class ServerSideTable(object):
- '''
+ """
This class is used to do server-side processing
on the DataTables table such as paginating, sorting,
filtering(not implemented) etc. This takes the load off
@@ -22,7 +22,7 @@ class ServerSideTable(object):
Have a look at snp_browser_table() function in
wqflask/wqflask/views.py for reference use.
- '''
+ """
def __init__(self, rows_count, table_rows, header_data_names, request_values):
self.request_values = request_values
@@ -36,12 +36,12 @@ class ServerSideTable(object):
self.paginate_rows()
def sort_rows(self):
- '''
+ """
Sorts the rows taking in to account the column (or columns) that the
user has selected.
- '''
+ """
def is_reverse(str_direction):
- ''' Maps the 'desc' and 'asc' words to True or False. '''
+ """ Maps the 'desc' and 'asc' words to True or False. """
return True if str_direction == 'desc' else False
if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
@@ -54,12 +54,12 @@ class ServerSideTable(object):
reverse=is_reverse(sort_direction))
def paginate_rows(self):
- '''
+ """
Selects a subset of the filtered and sorted data based on if the table
has pagination, the current page and the size of each page.
- '''
+ """
def requires_pagination():
- ''' Check if the table is going to be paginated '''
+ """ Check if the table is going to be paginated """
if self.request_values['iDisplayStart'] != "":
if int(self.request_values['iDisplayLength']) != -1:
return True
--
cgit v1.2.3
From 0ef495b69d99c53e7a6a216e6748898dbcc79eec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 5 Jan 2021 15:24:10 -0600
Subject: Fixed issue where normalization method wasn't removed from stats
figure axis titles when table values are reset
---
wqflask/wqflask/static/new/javascript/show_trait.js | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 832dd1e4..765f2f2d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -207,6 +207,8 @@ update_histogram = function() {
if ($('input[name="transform"]').val() != ""){
root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options);
@@ -255,6 +257,8 @@ update_bar_chart = function() {
if ($('input[name="transform"]').val() != ""){
root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
root.bar_data[0]['y'] = trait_vals
@@ -296,6 +300,8 @@ update_box_plot = function() {
if ($('input[name="transform"]').val() != ""){
root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('box_plot', root.box_data, root.box_layout, root.modebar_options)
@@ -327,6 +333,8 @@ update_violin_plot = function() {
if ($('input[name="transform"]').val() != ""){
root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
}
Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options)
@@ -795,6 +803,7 @@ reset_samples_table = function() {
};
$('.reset').click(function() {
reset_samples_table();
+ $('input[name="transform"]').val("");
edit_data_change();
});
--
cgit v1.2.3
From 2bd74f8f4e4e72a11c77d4f3e8532c303503ca11 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Mon, 16 Nov 2020 13:46:57 +0300
Subject: add unit tests for api/mapping.py
---
wqflask/tests/unit/wqflask/api/test_mapping.py | 114 +++++++++++++++++++++++++
1 file changed, 114 insertions(+)
create mode 100644 wqflask/tests/unit/wqflask/api/test_mapping.py
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
new file mode 100644
index 00000000..87b18e84
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -0,0 +1,114 @@
+import unittest
+from unittest import mock
+from wqflask.api.mapping import initialize_parameters
+
+
+class AttributeSetter:
+ def __init__(self,obj):
+ for key,value in obj.items():
+ setattr(self,key,value)
+
+class MockGroup(AttributeSetter):
+ def get_marker(self):
+ return None
+class TestMock(unittest.TestCase):
+
+ # @mock.patch("wqflask.api.mapping.gemma_mapping")
+ # @mock.patch("wqflask.api.mapping.nitialize_parameters")
+ # @mock.patch("wqflask.api.mapping.retrieve_sample_data")
+ # @mock.patch("wqflask.api.mapping.create_trait")
+ # @mock.patch("wqflask.api.mapping.data_set")
+ # def test_do_mapping_for_api(self,mock_dataset,mock_create_trait,mock_retrieve_data,mock_gemma):
+
+ # start_vars={
+ # "db":"sql_uri/db_web1",
+ # "trait_id":"idsui332rh3ui2t",
+ # "limit_to":32.1,
+ # }
+ # group_samplelist=["S1","S2","S3","S4"]
+ # dataset_group=MockGroup({"samplelist":group_samplelist})
+ # dataset=AttributeSetter({"type":"Temp","group":dataset_group})
+
+ # this_trait_data={
+ # "Item1":AttributeSetter({
+ # "name":"S1",
+ # "value":"V1"
+ # }),
+
+ # "Item2":AttributeSetter({
+ # "name":"S2",
+ # "value":"V2"
+ # }),
+
+ # "Item3":AttributeSetter({
+ # "name":"SX",
+ # "value":"VX"
+ # })
+ # }
+
+ # this_trait=AttributeSetter({"data":this_trait_data})
+
+
+ # mock_dataset.create_dataset.return_value=dataset
+
+ # mock_create_trait.return_value=this_trait
+ # mock_retrieve_data.return_value=this_trait
+
+ # mock_initialize_params={
+ # "format":"json",
+ # "limit_to":32.1,
+ # "mapping_method":"gemma",
+ # "maf":0.01,
+ # "use_loco":True,
+ # "num_perm":0,
+ # "perm_check":False
+
+ # }
+
+ # mock_gemma.return_value=[ ,"filename"]
+ # pass
+
+ def test_initialize_parameters(self):
+ expected_results={
+ "format":"json",
+ "limit_to":False,
+ "mapping_method":"gemma",
+ "maf":0.01,
+ "use_loco":True,
+ "num_perm":0,
+ "perm_check":False
+ }
+
+ results=initialize_parameters(start_vars={},dataset={},this_trait={})
+ self.assertEqual(results,expected_results)
+
+ start_vars={
+ "format":"F1",
+ "limit_to":"1",
+ "mapping_method":"rqtl",
+ "control_marker":True,
+ "pair_scan":"true",
+ "interval_mapping":"true",
+ "use_loco":"true",
+ "num_perm":"14"
+
+ }
+
+ results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={})
+ expected_results={
+ "format":"F1",
+ "limit_to":1,
+ "mapping_method":"gemma",
+ "maf":0.01,
+ "use_loco":True,
+ "num_perm":14,
+ "perm_check":"ON"
+ }
+
+ self.assertEqual(results_2,expected_results)
+
+
+
+
+
+
--
cgit v1.2.3
From df2c3f9ee43dd055f7766eedee32d76090ad80b2 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Mon, 16 Nov 2020 13:47:40 +0300
Subject: add unit testsfor api/correlation.py
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 83 ++++++++++++++++++++++
1 file changed, 83 insertions(+)
create mode 100644 wqflask/tests/unit/wqflask/api/test_correlation.py
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
new file mode 100644
index 00000000..482dec67
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -0,0 +1,83 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.api.correlation import init_corr_params
+from wqflask.api.correlation import convert_to_mouse_gene_id
+from wqflask.api.correlation import do_literature_correlation_for_all_traits
+
+
+class AttributeSetter:
+ def __init__(self, obj):
+ for k, v in obj.items():
+ setattr(self, k, v)
+
+
+class TestCorrelations(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_init_corr_params(self):
+ start_vars = {
+ "return_count": "3",
+ "type": "T1",
+ "method": "spearman"
+ }
+
+ corr_params_results = init_corr_params(start_vars=start_vars)
+ expected_results = {
+ "return_count": 3,
+ "type": "T1",
+ "method": "spearman"
+ }
+
+ self.assertEqual(corr_params_results, expected_results)
+
+ @mock.patch("wqflask.api.correlation.g")
+ def test_convert_to_mouse_gene_id(self, mock_db):
+
+ results = convert_to_mouse_gene_id(species="Other", gene_id="")
+ self.assertEqual(results, None)
+
+ rat_species_results = convert_to_mouse_gene_id(
+ species="rat", gene_id="GH1")
+
+ mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter({"mouse": "MG-1"}),AttributeSetter({"mouse":"MG-2"})]
+
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="mouse", gene_id="MG-4"), "MG-4")
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="rat", gene_id="R1"), "MG-1")
+ self.assertEqual(convert_to_mouse_gene_id(
+ species="human", gene_id="H1"), "MG-2")
+
+
+
+ @mock.patch("wqflask.api.correlation.g")
+ @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
+ def test_do_literature_correlation_for_all_traits(self,mock_convert_to_mouse_geneid,mock_db):
+ mock_convert_to_mouse_geneid.side_effect=["MG-1","MG-2;","MG-3","MG-4"]
+
+
+ trait_geneid_dict={
+ "TT-1":"GH-1",
+ "TT-2":"GH-2",
+ "TT-3":"GH-3"
+
+ }
+ mock_db.db.execute.return_value.fetchone.side_effect=[AttributeSetter({"value":"V1"}),AttributeSetter({"value":"V2"}),AttributeSetter({"value":"V3"})]
+
+
+ this_trait=AttributeSetter({"geneid":"GH-1"})
+
+ target_dataset=AttributeSetter({"group":AttributeSetter({"species":"rat"})})
+ results=do_literature_correlation_for_all_traits(this_trait=this_trait,target_dataset=target_dataset,trait_geneid_dict=trait_geneid_dict,corr_params={})
+
+ expected_results={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+ self.assertEqual(results,expected_results)
+
+
+
--
cgit v1.2.3
From 3eda2b13e10937cbd661d6d411286c5b84bcd7cf Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Sat, 28 Nov 2020 15:00:00 +0300
Subject: add correlation test
---
.../correlation/test_correlation_functions.py | 21 +++++
.../wqflask/correlation/test_show_corr_results.py | 95 ++++++++++++++++++++++
2 files changed, 116 insertions(+)
create mode 100644 wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
create mode 100644 wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
new file mode 100644
index 00000000..db449eb1
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -0,0 +1,21 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
+from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+
+
+class TestCorrelationFunctions(unittest.TestCase):
+
+
+ @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
+ def test_get_trait_symbol_and_tissue_values(self, mock_class):
+ """test for getting trait symbol and tissue_values"""
+ mock_class_instance = mock_class.return_value
+ mock_class_instance.gene_symbols = ["k1", "k2", "k3"]
+ mock_class_instance.get_symbol_values_pairs.return_value = {
+ "k1": ["v1", "v2", "v3"], "k2": ["v2", "v3"], "k3": ["k3"]}
+ results = get_trait_symbol_and_tissue_values(
+ symbol_list=["k1", "k2", "k3"])
+ mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3'])
+ self.assertEqual({"k1": ["v1", "v2", "v3"], "k2": [
+ "v2", "v3"], "k3": ["k3"]}, results)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
new file mode 100644
index 00000000..4e63207e
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -0,0 +1,95 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.show_corr_results import get_header_fields
+from wqflask.correlation.show_corr_results import generate_corr_json
+from wqflask.correlation.show_corr_results import do_bicor
+
+
+class Trait:
+ def __init__(self,trait_obj):
+ for key,value in trait_obj.items():
+ setattr(self,key,value)
+
+class TestShowCorrResults(unittest.TestCase):
+
+ def test_process_samples(self):
+ pass
+ def test_get_header_fields(self):
+ expected=[
+ ['Index',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect'],
+
+ ['Index',
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
+
+ ]
+ result1=get_header_fields("ProbeSet","spearman")
+ result2=get_header_fields("Other","Other")
+ self.assertEqual(result1,expected[0])
+ self.assertEqual(result2,expected[1])
+
+
+
+
+ def test_generate_corr_json(self):
+ this_trait=Trait({"name":"trait_test"})
+ dataset=Trait({"name":"the_name"})
+ target_dataset=Trait({"type":"Publish"})
+
+ trait_with_publish={
+ "description_display":"Trait 2 description",
+ "authors":"trait_2 ",
+ "pubmed_id":"34n4nn31hn43",
+ "lrs_location":"N/A",
+ "additive":"",
+ "sample_r":100,
+ "num_overlap":3.2,
+ "view":True,
+ "name":"trait_1",
+ "pubmed_text":"2016",
+ "additive":"",
+ "sample_r":10.5,
+ "LRS_score_repr":"N/A",
+ "LRS_location_repr":"N/A",
+ "sample_p":5,
+ "num_overlap":"num_1"
+
+
+
+ }
+ expected_results="""[{"trait_id": "trait_1", "description": "Trait 2 description", "authors": "trait_2 ", "pubmed_id": "34n4nn31hn43", "year": "2016", "lrs_score": "N/A", "lrs_location": "N/A", "additive": "N/A", "sample_r": "10.500", "num_overlap": "num_1", "sample_p": "5.000e+00"}]"""
+
+ corr_results=[Trait(trait_with_publish)]
+ results=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset=dataset,target_dataset=target_dataset,for_api=True)
+ self.assertEqual(results,expected_results)
+
+
+
+ def test_generate_corr_json_view_false(self):
+ trait=Trait({"view":False})
+ corr_results=[trait]
+ this_trait=Trait({"name":"trait_test"})
+ dataset=Trait({"name":"the_name"})
+
+
+ results_where_view_is_false=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset={},target_dataset={},for_api=False)
+
+ # self.assertEqual(results,[])
+ self.assertEqual(results_where_view_is_false,"[]")
\ No newline at end of file
--
cgit v1.2.3
From 1666f8d50df090e9a14dbf0f4f195bac079de058 Mon Sep 17 00:00:00 2001
From: Alexanderlacuna
Date: Sat, 28 Nov 2020 15:11:06 +0300
Subject: add test in api/mapping
---
wqflask/tests/unit/wqflask/api/test_mapping.py | 55 --------------------------
1 file changed, 55 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index 87b18e84..4da1725f 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -13,61 +13,6 @@ class MockGroup(AttributeSetter):
return None
class TestMock(unittest.TestCase):
- # @mock.patch("wqflask.api.mapping.gemma_mapping")
- # @mock.patch("wqflask.api.mapping.nitialize_parameters")
- # @mock.patch("wqflask.api.mapping.retrieve_sample_data")
- # @mock.patch("wqflask.api.mapping.create_trait")
- # @mock.patch("wqflask.api.mapping.data_set")
- # def test_do_mapping_for_api(self,mock_dataset,mock_create_trait,mock_retrieve_data,mock_gemma):
-
- # start_vars={
- # "db":"sql_uri/db_web1",
- # "trait_id":"idsui332rh3ui2t",
- # "limit_to":32.1,
- # }
- # group_samplelist=["S1","S2","S3","S4"]
- # dataset_group=MockGroup({"samplelist":group_samplelist})
- # dataset=AttributeSetter({"type":"Temp","group":dataset_group})
-
- # this_trait_data={
- # "Item1":AttributeSetter({
- # "name":"S1",
- # "value":"V1"
- # }),
-
- # "Item2":AttributeSetter({
- # "name":"S2",
- # "value":"V2"
- # }),
-
- # "Item3":AttributeSetter({
- # "name":"SX",
- # "value":"VX"
- # })
- # }
-
- # this_trait=AttributeSetter({"data":this_trait_data})
-
-
- # mock_dataset.create_dataset.return_value=dataset
-
- # mock_create_trait.return_value=this_trait
- # mock_retrieve_data.return_value=this_trait
-
- # mock_initialize_params={
- # "format":"json",
- # "limit_to":32.1,
- # "mapping_method":"gemma",
- # "maf":0.01,
- # "use_loco":True,
- # "num_perm":0,
- # "perm_check":False
-
- # }
-
- # mock_gemma.return_value=[ ,"filename"]
- # pass
-
def test_initialize_parameters(self):
expected_results={
"format":"json",
--
cgit v1.2.3
From 7b1d35701c283973ab63db3b665951f569a8c5fc Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 29 Nov 2020 17:30:43 +0300
Subject: refactor code in correlation/correlation_functions
---
.../wqflask/correlation/correlation_functions.py | 28 ----------------------
1 file changed, 28 deletions(-)
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index b883e361..fd7691d4 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -71,34 +71,6 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
return corr_result
-###########################################################################
-#Input: cursor, symbolList (list), dataIdDict(Dict)
-#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
-# key is symbol, value is one list of expression values of one probeSet;
-#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-#Attention! All keys are lower case!
-###########################################################################
-def get_symbol_value_pairs(tissue_data):
- id_list = [tissue_data[symbol.lower()].data_id for item in tissue_data]
-
- symbol_value_pairs = {}
- value_list=[]
-
- query = """SELECT value, id
- FROM TissueProbeSetData
- WHERE Id IN {}""".format(create_in_clause(id_list))
-
- try :
- results = g.db.execute(query).fetchall()
- for result in results:
- value_list.append(result.value)
- symbol_value_pairs[symbol] = value_list
- except:
- symbol_value_pairs[symbol] = None
-
- return symbol_value_pairs
-
-
########################################################################################################
#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
--
cgit v1.2.3
From e535eeeff92bcfa6d6524e44591164de72d38482 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 4 Dec 2020 18:43:35 +0300
Subject: add test for map_api in api/test_mapping.py
---
wqflask/tests/unit/wqflask/api/test_mapping.py | 145 +++++++++++++++++--------
1 file changed, 99 insertions(+), 46 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index 4da1725f..5455b215 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -1,57 +1,110 @@
import unittest
from unittest import mock
from wqflask.api.mapping import initialize_parameters
+from wqflask.api.mapping import do_mapping_for_api
class AttributeSetter:
- def __init__(self,obj):
- for key,value in obj.items():
- setattr(self,key,value)
+ def __init__(self,obj):
+ for key,value in obj.items():
+ setattr(self,key,value)
class MockGroup(AttributeSetter):
- def get_marker(self):
- return None
-class TestMock(unittest.TestCase):
-
- def test_initialize_parameters(self):
- expected_results={
- "format":"json",
- "limit_to":False,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":0,
- "perm_check":False
- }
-
- results=initialize_parameters(start_vars={},dataset={},this_trait={})
- self.assertEqual(results,expected_results)
-
- start_vars={
- "format":"F1",
- "limit_to":"1",
- "mapping_method":"rqtl",
- "control_marker":True,
- "pair_scan":"true",
- "interval_mapping":"true",
- "use_loco":"true",
- "num_perm":"14"
-
- }
-
- results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={})
- expected_results={
- "format":"F1",
- "limit_to":1,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":14,
- "perm_check":"ON"
- }
-
- self.assertEqual(results_2,expected_results)
-
+ def get_marker(self):
+ self.markers=[]
+class TestMapping(unittest.TestCase):
+
+ def test_initialize_parameters(self):
+ expected_results={
+ "format":"json",
+ "limit_to":False,
+ "mapping_method":"gemma",
+ "maf":0.01,
+ "use_loco":True,
+ "num_perm":0,
+ "perm_check":False
+ }
+
+ results=initialize_parameters(start_vars={},dataset={},this_trait={})
+ self.assertEqual(results,expected_results)
+
+ start_vars={
+ "format":"F1",
+ "limit_to":"1",
+ "mapping_method":"rqtl",
+ "control_marker":True,
+ "pair_scan":"true",
+ "interval_mapping":"true",
+ "use_loco":"true",
+ "num_perm":"14"
+
+ }
+
+ results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={})
+ expected_results={
+ "format":"F1",
+ "limit_to":1,
+ "mapping_method":"gemma",
+ "maf":0.01,
+ "use_loco":True,
+ "num_perm":14,
+ "perm_check":"ON"
+ }
+
+ self.assertEqual(results_2,expected_results)
+
+
+ @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
+ @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
+ @mock.patch("wqflask.api.mapping.initialize_parameters")
+ @mock.patch("wqflask.api.mapping.retrieve_sample_data")
+ @mock.patch("wqflask.api.mapping.create_trait")
+ @mock.patch("wqflask.api.mapping.data_set.create_dataset")
+ def test_do_mapping_for_api(self,mock_create_dataset,mock_trait,mock_retrieve_sample,mock_param,run_gemma
+ ,run_rqtl_geno):
+ start_vars={
+ "db":"Temp",
+ "trait_id":"dewf3232rff2",
+ "format":"F1",
+ "mapping_method":"gemma",
+ "use_loco":True
+
+ }
+ sampleList=["S1","S2","S3","S4"]
+ samplelist=["S1","S2","S4"]
+ dataset=AttributeSetter({"group":samplelist})
+ this_trait=AttributeSetter({})
+ trait_data=AttributeSetter({
+ "data":{
+ "item1":AttributeSetter({"name":"S1","value":"S1_value"}),
+ "item2":AttributeSetter({"name":"S2","value":"S2_value"}),
+ "item3":AttributeSetter({"name":"S3","value":"S3_value"}),
+
+ }
+ })
+ trait=AttributeSetter({
+ "data":trait_data
+ })
+
+ dataset.return_value=dataset
+ mock_trait.return_value=this_trait
+
+ mock_retrieve_sample.return_value=trait
+ mock_param.return_value={
+ "format":"F1",
+ "limit_to":False,
+ "mapping_method":"gemma",
+ "maf":0.01,
+ "use_loco":"True",
+ "num_perm":14,
+ "perm_check":"ON"
+ }
+
+ run_gemma.return_value=["results"]
+ results=do_mapping_for_api(start_vars=start_vars)
+ self.assertEqual(results,("results",None))
+
+
--
cgit v1.2.3
From e80e793455d2fc6b51dbe95414a3ba8e72652a83 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sat, 12 Dec 2020 21:21:53 +0300
Subject: add tests for getting sample_r and p values
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 38 ++++++++++++++++++++++
.../wqflask/correlation/test_show_corr_results.py | 2 --
2 files changed, 38 insertions(+), 2 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 482dec67..077f7fa9 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -4,6 +4,7 @@ from wqflask import app
from wqflask.api.correlation import init_corr_params
from wqflask.api.correlation import convert_to_mouse_gene_id
from wqflask.api.correlation import do_literature_correlation_for_all_traits
+from wqflask.api.correlation import get_sample_r_and_p_values
class AttributeSetter:
@@ -79,5 +80,42 @@ class TestCorrelations(unittest.TestCase):
expected_results={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
self.assertEqual(results,expected_results)
+ @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
+ def test_get_sample_r_and_p_values(self,mock_normalize):
+
+ group=AttributeSetter({"samplelist":["S1","S2","S3","S4","S5","S6","S7"]})
+ target_dataset=AttributeSetter({"group":group})
+
+ target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6]
+ trait_data={"S1":AttributeSetter({"value":2.3}),"S2":AttributeSetter({"value":1.1}),"S3":AttributeSetter({"value":6.3}),"S4":AttributeSetter({"value":3.6}),"S5":AttributeSetter({"value":4.1}),"S6":AttributeSetter({"value":5.0})}
+ this_trait=AttributeSetter({"data":trait_data})
+ mock_normalize.return_value=([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6)
+ mock_normalize.side_effect=[([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,1.4], [3.4,6.2,4.1], 3)]
+
+ results_pearsonr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
+ results_spearmanr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="spearman")
+ results_num_overlap=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
+ self.assertEqual(mock_normalize.call_count,3)
+
+ self.assertEqual(results_pearsonr,[-0.21618688834430866, 0.680771605997119, 6])
+ self.assertEqual(results_spearmanr,[-0.11595420713048969, 0.826848213385815, 6])
+ self.assertEqual(results_num_overlap,None)
+
+ def test_calculate_results(self):
+ corr_params={
+ "type":"pearson"
+ }
+ trait_data={
+ "T1":3.4,
+ "T2":6.2,
+ "T3":4.1,
+ "T4":3.4,
+ "T5":1.2,
+ "T6":5.6
+ }
+ target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6]
+
+
+
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
index 4e63207e..969a84f5 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -12,8 +12,6 @@ class Trait:
class TestShowCorrResults(unittest.TestCase):
- def test_process_samples(self):
- pass
def test_get_header_fields(self):
expected=[
['Index',
--
cgit v1.2.3
From 0adae692f2f0ce509b32d6654438213deb3da89b Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sat, 12 Dec 2020 23:09:04 +0300
Subject: add test for calculating correlation results
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 44 +++++++++++++++-------
1 file changed, 31 insertions(+), 13 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 077f7fa9..11c7d82b 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -1,10 +1,12 @@
import unittest
from unittest import mock
from wqflask import app
+from collections import OrderedDict
from wqflask.api.correlation import init_corr_params
from wqflask.api.correlation import convert_to_mouse_gene_id
from wqflask.api.correlation import do_literature_correlation_for_all_traits
from wqflask.api.correlation import get_sample_r_and_p_values
+from wqflask.api.correlation import calculate_results
class AttributeSetter:
@@ -12,6 +14,17 @@ class AttributeSetter:
for k, v in obj.items():
setattr(self, k, v)
+class MockDataset(AttributeSetter):
+ def get_trait_data(self):
+ return None
+ def retrieve_genes(self,id=None):
+ return {
+ "TT-1":"GH-1",
+ "TT-2":"GH-2",
+ "TT-3":"GH-3"
+
+ }
+
class TestCorrelations(unittest.TestCase):
def setUp(self):
@@ -101,19 +114,24 @@ class TestCorrelations(unittest.TestCase):
self.assertEqual(results_spearmanr,[-0.11595420713048969, 0.826848213385815, 6])
self.assertEqual(results_num_overlap,None)
- def test_calculate_results(self):
- corr_params={
- "type":"pearson"
- }
- trait_data={
- "T1":3.4,
- "T2":6.2,
- "T3":4.1,
- "T4":3.4,
- "T5":1.2,
- "T6":5.6
- }
- target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6]
+ @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
+ def test_calculate_results(self,literature_correlation):
+
+ literature_correlation.return_value={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+
+
+
+ this_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
+ target_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
+ this_trait=AttributeSetter({"geneid":"GH-1"})
+ corr_params={"type":"literature"}
+ sorted_results=calculate_results(this_trait=this_trait,this_dataset=this_dataset,target_dataset=target_dataset,corr_params=corr_params)
+ expected_results={'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+
+ self.assertTrue(isinstance(sorted_results,OrderedDict))
+ self.assertEqual(type(sorted_results),OrderedDict)
+
+
--
cgit v1.2.3
From b7e2d17536febbeb47dc91015781cc6fc4647905 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sat, 12 Dec 2020 23:36:27 +0300
Subject: replace assertEqual with assertAlmostEqual for floats
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 11c7d82b..9fa848a4 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -108,10 +108,12 @@ class TestCorrelations(unittest.TestCase):
results_pearsonr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
results_spearmanr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="spearman")
results_num_overlap=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
- self.assertEqual(mock_normalize.call_count,3)
-
- self.assertEqual(results_pearsonr,[-0.21618688834430866, 0.680771605997119, 6])
- self.assertEqual(results_spearmanr,[-0.11595420713048969, 0.826848213385815, 6])
+ expected_pearsonr=[-0.21618688834430866, 0.680771605997119, 6]
+ expected_spearmanr=[-0.11595420713048969, 0.826848213385815, 6]
+ for i,val in enumerate(expected_pearsonr):
+ self.assertAlmostEqual(val,results_pearsonr[i])
+ for i,val in enumerate(expected_spearmanr):
+ self.assertAlmostEqual(val,results_spearmanr[i])
self.assertEqual(results_num_overlap,None)
@mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
@@ -133,7 +135,6 @@ class TestCorrelations(unittest.TestCase):
-
--
cgit v1.2.3
From c3bfc7c07bba06c9334350111df0b9444b85b31b Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sat, 12 Dec 2020 23:56:26 +0300
Subject: modify tests for calculate correlation results
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 9fa848a4..cbcd006d 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -131,7 +131,7 @@ class TestCorrelations(unittest.TestCase):
expected_results={'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
self.assertTrue(isinstance(sorted_results,OrderedDict))
- self.assertEqual(type(sorted_results),OrderedDict)
+ self.assertEqual(dict(sorted_results),expected_results)
--
cgit v1.2.3
From d10b6a9bc3ed4d3f824a0dfd115f05ed647aa8c3 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 20:08:41 +0300
Subject: pep8 formatting and refactoring tests
---
wqflask/tests/unit/wqflask/api/test_correlation.py | 145 +++++++++++----------
1 file changed, 79 insertions(+), 66 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index cbcd006d..d0264b87 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -1,7 +1,7 @@
import unittest
from unittest import mock
from wqflask import app
-from collections import OrderedDict
+from collections import OrderedDict
from wqflask.api.correlation import init_corr_params
from wqflask.api.correlation import convert_to_mouse_gene_id
from wqflask.api.correlation import do_literature_correlation_for_all_traits
@@ -14,14 +14,16 @@ class AttributeSetter:
for k, v in obj.items():
setattr(self, k, v)
+
class MockDataset(AttributeSetter):
def get_trait_data(self):
return None
- def retrieve_genes(self,id=None):
+
+ def retrieve_genes(self, id=None):
return {
- "TT-1":"GH-1",
- "TT-2":"GH-2",
- "TT-3":"GH-3"
+ "TT-1": "GH-1",
+ "TT-2": "GH-2",
+ "TT-3": "GH-3"
}
@@ -59,8 +61,9 @@ class TestCorrelations(unittest.TestCase):
rat_species_results = convert_to_mouse_gene_id(
species="rat", gene_id="GH1")
- mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter({"mouse": "MG-1"}),AttributeSetter({"mouse":"MG-2"})]
-
+ mock_db.db.execute.return_value.fetchone.side_effect = [
+ AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})]
+
self.assertEqual(convert_to_mouse_gene_id(
species="mouse", gene_id="MG-4"), "MG-4")
self.assertEqual(convert_to_mouse_gene_id(
@@ -68,73 +71,83 @@ class TestCorrelations(unittest.TestCase):
self.assertEqual(convert_to_mouse_gene_id(
species="human", gene_id="H1"), "MG-2")
-
-
@mock.patch("wqflask.api.correlation.g")
@mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
- def test_do_literature_correlation_for_all_traits(self,mock_convert_to_mouse_geneid,mock_db):
- mock_convert_to_mouse_geneid.side_effect=["MG-1","MG-2;","MG-3","MG-4"]
-
-
- trait_geneid_dict={
- "TT-1":"GH-1",
- "TT-2":"GH-2",
- "TT-3":"GH-3"
+ def test_do_literature_correlation_for_all_traits(self, mock_convert_to_mouse_geneid, mock_db):
+ mock_convert_to_mouse_geneid.side_effect = [
+ "MG-1", "MG-2;", "MG-3", "MG-4"]
- }
- mock_db.db.execute.return_value.fetchone.side_effect=[AttributeSetter({"value":"V1"}),AttributeSetter({"value":"V2"}),AttributeSetter({"value":"V3"})]
+ trait_geneid_dict = {
+ "TT-1": "GH-1",
+ "TT-2": "GH-2",
+ "TT-3": "GH-3"
+ }
+ mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter(
+ {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})]
- this_trait=AttributeSetter({"geneid":"GH-1"})
+ this_trait = AttributeSetter({"geneid": "GH-1"})
- target_dataset=AttributeSetter({"group":AttributeSetter({"species":"rat"})})
- results=do_literature_correlation_for_all_traits(this_trait=this_trait,target_dataset=target_dataset,trait_geneid_dict=trait_geneid_dict,corr_params={})
+ target_dataset = AttributeSetter(
+ {"group": AttributeSetter({"species": "rat"})})
+ results = do_literature_correlation_for_all_traits(
+ this_trait=this_trait, target_dataset=target_dataset, trait_geneid_dict=trait_geneid_dict, corr_params={})
- expected_results={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
- self.assertEqual(results,expected_results)
+ expected_results = {'TT-1': ['GH-1', 0],
+ 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+ self.assertEqual(results, expected_results)
@mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
- def test_get_sample_r_and_p_values(self,mock_normalize):
-
- group=AttributeSetter({"samplelist":["S1","S2","S3","S4","S5","S6","S7"]})
- target_dataset=AttributeSetter({"group":group})
-
- target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6]
- trait_data={"S1":AttributeSetter({"value":2.3}),"S2":AttributeSetter({"value":1.1}),"S3":AttributeSetter({"value":6.3}),"S4":AttributeSetter({"value":3.6}),"S5":AttributeSetter({"value":4.1}),"S6":AttributeSetter({"value":5.0})}
- this_trait=AttributeSetter({"data":trait_data})
- mock_normalize.return_value=([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6)
- mock_normalize.side_effect=[([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,1.4], [3.4,6.2,4.1], 3)]
-
- results_pearsonr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
- results_spearmanr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="spearman")
- results_num_overlap=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
- expected_pearsonr=[-0.21618688834430866, 0.680771605997119, 6]
- expected_spearmanr=[-0.11595420713048969, 0.826848213385815, 6]
- for i,val in enumerate(expected_pearsonr):
- self.assertAlmostEqual(val,results_pearsonr[i])
- for i,val in enumerate(expected_spearmanr):
- self.assertAlmostEqual(val,results_spearmanr[i])
- self.assertEqual(results_num_overlap,None)
+ def test_get_sample_r_and_p_values(self, mock_normalize):
+
+ group = AttributeSetter(
+ {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]})
+ target_dataset = AttributeSetter({"group": group})
+
+ target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
+ trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+ "S3": AttributeSetter(
+ {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+ "S6": AttributeSetter({"value": 5.0})}
+ this_trait = AttributeSetter({"data": trait_data})
+ mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
+ mock_normalize.side_effect = [([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+ ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+ [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+ ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)]
+
+ results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+ results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="spearman")
+ results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+ }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+ expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
+ expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
+ for i, val in enumerate(expected_pearsonr):
+ self.assertAlmostEqual(val, results_pearsonr[i],4)
+ for i, val in enumerate(expected_spearmanr):
+ self.assertAlmostEqual(val, results_spearmanr[i],4)
+ self.assertEqual(results_num_overlap, None)
@mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
- def test_calculate_results(self,literature_correlation):
-
- literature_correlation.return_value={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
-
-
-
- this_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
- target_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
- this_trait=AttributeSetter({"geneid":"GH-1"})
- corr_params={"type":"literature"}
- sorted_results=calculate_results(this_trait=this_trait,this_dataset=this_dataset,target_dataset=target_dataset,corr_params=corr_params)
- expected_results={'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
-
- self.assertTrue(isinstance(sorted_results,OrderedDict))
- self.assertEqual(dict(sorted_results),expected_results)
-
-
-
-
-
-
+ def test_calculate_results(self, literature_correlation):
+
+ literature_correlation.return_value = {
+ 'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+
+ this_dataset = MockDataset(
+ {"group": AttributeSetter({"species": "rat"})})
+ target_dataset = MockDataset(
+ {"group": AttributeSetter({"species": "rat"})})
+ this_trait = AttributeSetter({"geneid": "GH-1"})
+ corr_params = {"type": "literature"}
+ sorted_results = calculate_results(
+ this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params)
+ expected_results = {'TT-2': ['GH-2', 3],
+ 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+
+ self.assertTrue(isinstance(sorted_results, OrderedDict))
+ self.assertEqual(dict(sorted_results), expected_results)
--
cgit v1.2.3
From 4773ac8715896489562df9321b4a4d34ae61d6a7 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 20:10:37 +0300
Subject: pep8 formatting in wqflask/api/test_mapping.py
---
wqflask/tests/unit/wqflask/api/test_mapping.py | 154 ++++++++++++-------------
1 file changed, 75 insertions(+), 79 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py
index 5455b215..b094294a 100644
--- a/wqflask/tests/unit/wqflask/api/test_mapping.py
+++ b/wqflask/tests/unit/wqflask/api/test_mapping.py
@@ -5,108 +5,104 @@ from wqflask.api.mapping import do_mapping_for_api
class AttributeSetter:
- def __init__(self,obj):
- for key,value in obj.items():
- setattr(self,key,value)
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
class MockGroup(AttributeSetter):
def get_marker(self):
- self.markers=[]
+ self.markers = []
+
+
class TestMapping(unittest.TestCase):
-
+
def test_initialize_parameters(self):
- expected_results={
- "format":"json",
- "limit_to":False,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":0,
- "perm_check":False
+ expected_results = {
+ "format": "json",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 0,
+ "perm_check": False
}
- results=initialize_parameters(start_vars={},dataset={},this_trait={})
- self.assertEqual(results,expected_results)
+ results = initialize_parameters(
+ start_vars={}, dataset={}, this_trait={})
+ self.assertEqual(results, expected_results)
- start_vars={
- "format":"F1",
- "limit_to":"1",
- "mapping_method":"rqtl",
- "control_marker":True,
- "pair_scan":"true",
- "interval_mapping":"true",
- "use_loco":"true",
- "num_perm":"14"
+ start_vars = {
+ "format": "F1",
+ "limit_to": "1",
+ "mapping_method": "rqtl",
+ "control_marker": True,
+ "pair_scan": "true",
+ "interval_mapping": "true",
+ "use_loco": "true",
+ "num_perm": "14"
}
- results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={})
- expected_results={
- "format":"F1",
- "limit_to":1,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":True,
- "num_perm":14,
- "perm_check":"ON"
+ results_2 = initialize_parameters(
+ start_vars=start_vars, dataset={}, this_trait={})
+ expected_results = {
+ "format": "F1",
+ "limit_to": 1,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": True,
+ "num_perm": 14,
+ "perm_check": "ON"
}
- self.assertEqual(results_2,expected_results)
+ self.assertEqual(results_2, expected_results)
-
@mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno")
@mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma")
@mock.patch("wqflask.api.mapping.initialize_parameters")
@mock.patch("wqflask.api.mapping.retrieve_sample_data")
@mock.patch("wqflask.api.mapping.create_trait")
@mock.patch("wqflask.api.mapping.data_set.create_dataset")
- def test_do_mapping_for_api(self,mock_create_dataset,mock_trait,mock_retrieve_sample,mock_param,run_gemma
- ,run_rqtl_geno):
- start_vars={
- "db":"Temp",
- "trait_id":"dewf3232rff2",
- "format":"F1",
- "mapping_method":"gemma",
- "use_loco":True
+ def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno):
+ start_vars = {
+ "db": "Temp",
+ "trait_id": "dewf3232rff2",
+ "format": "F1",
+ "mapping_method": "gemma",
+ "use_loco": True
}
- sampleList=["S1","S2","S3","S4"]
- samplelist=["S1","S2","S4"]
- dataset=AttributeSetter({"group":samplelist})
- this_trait=AttributeSetter({})
- trait_data=AttributeSetter({
- "data":{
- "item1":AttributeSetter({"name":"S1","value":"S1_value"}),
- "item2":AttributeSetter({"name":"S2","value":"S2_value"}),
- "item3":AttributeSetter({"name":"S3","value":"S3_value"}),
+ sampleList = ["S1", "S2", "S3", "S4"]
+ samplelist = ["S1", "S2", "S4"]
+ dataset = AttributeSetter({"group": samplelist})
+ this_trait = AttributeSetter({})
+ trait_data = AttributeSetter({
+ "data": {
+ "item1": AttributeSetter({"name": "S1", "value": "S1_value"}),
+ "item2": AttributeSetter({"name": "S2", "value": "S2_value"}),
+ "item3": AttributeSetter({"name": "S3", "value": "S3_value"}),
}
- })
- trait=AttributeSetter({
- "data":trait_data
- })
-
- dataset.return_value=dataset
- mock_trait.return_value=this_trait
-
- mock_retrieve_sample.return_value=trait
- mock_param.return_value={
- "format":"F1",
- "limit_to":False,
- "mapping_method":"gemma",
- "maf":0.01,
- "use_loco":"True",
- "num_perm":14,
- "perm_check":"ON"
+ })
+ trait = AttributeSetter({
+ "data": trait_data
+ })
+
+ dataset.return_value = dataset
+ mock_trait.return_value = this_trait
+
+ mock_retrieve_sample.return_value = trait
+ mock_param.return_value = {
+ "format": "F1",
+ "limit_to": False,
+ "mapping_method": "gemma",
+ "maf": 0.01,
+ "use_loco": "True",
+ "num_perm": 14,
+ "perm_check": "ON"
}
- run_gemma.return_value=["results"]
- results=do_mapping_for_api(start_vars=start_vars)
- self.assertEqual(results,("results",None))
-
-
-
-
-
-
-
+ run_gemma.return_value = ["results"]
+ results = do_mapping_for_api(start_vars=start_vars)
+ self.assertEqual(results, ("results", None))
--
cgit v1.2.3
From 6b6820ec9975ae4c7e9628e0d2b41754b0429b0e Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Wed, 16 Dec 2020 11:29:19 +0300
Subject: modify tests for show_corr_results
---
wqflask/tests/unit/wqflask/correlation/__init__.py | 0
.../correlation/test_correlation_functions.py | 3 +-
.../wqflask/correlation/test_show_corr_results.py | 174 +++++++++++----------
3 files changed, 90 insertions(+), 87 deletions(-)
create mode 100644 wqflask/tests/unit/wqflask/correlation/__init__.py
diff --git a/wqflask/tests/unit/wqflask/correlation/__init__.py b/wqflask/tests/unit/wqflask/correlation/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index db449eb1..44d2e0fc 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -5,8 +5,7 @@ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_ti
class TestCorrelationFunctions(unittest.TestCase):
-
-
+
@mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
index 969a84f5..ffb96dd6 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -2,92 +2,96 @@ import unittest
from unittest import mock
from wqflask.correlation.show_corr_results import get_header_fields
from wqflask.correlation.show_corr_results import generate_corr_json
-from wqflask.correlation.show_corr_results import do_bicor
-class Trait:
- def __init__(self,trait_obj):
- for key,value in trait_obj.items():
- setattr(self,key,value)
+class AttributeSetter:
+ def __init__(self, trait_obj):
+ for key, value in trait_obj.items():
+ setattr(self, key, value)
-class TestShowCorrResults(unittest.TestCase):
- def test_get_header_fields(self):
- expected=[
- ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Sample rho',
- 'N',
- 'Sample p(rho)',
- 'Lit rho',
- 'Tissue rho',
- 'Tissue p(rho)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect'],
-
- ['Index',
- 'ID',
- 'Location',
- 'Sample r',
- 'N',
- 'Sample p(r)']
-
- ]
- result1=get_header_fields("ProbeSet","spearman")
- result2=get_header_fields("Other","Other")
- self.assertEqual(result1,expected[0])
- self.assertEqual(result2,expected[1])
-
-
-
-
- def test_generate_corr_json(self):
- this_trait=Trait({"name":"trait_test"})
- dataset=Trait({"name":"the_name"})
- target_dataset=Trait({"type":"Publish"})
-
- trait_with_publish={
- "description_display":"Trait 2 description",
- "authors":"trait_2 ",
- "pubmed_id":"34n4nn31hn43",
- "lrs_location":"N/A",
- "additive":"",
- "sample_r":100,
- "num_overlap":3.2,
- "view":True,
- "name":"trait_1",
- "pubmed_text":"2016",
- "additive":"",
- "sample_r":10.5,
- "LRS_score_repr":"N/A",
- "LRS_location_repr":"N/A",
- "sample_p":5,
- "num_overlap":"num_1"
-
-
-
- }
- expected_results="""[{"trait_id": "trait_1", "description": "Trait 2 description", "authors": "trait_2 ", "pubmed_id": "34n4nn31hn43", "year": "2016", "lrs_score": "N/A", "lrs_location": "N/A", "additive": "N/A", "sample_r": "10.500", "num_overlap": "num_1", "sample_p": "5.000e+00"}]"""
-
- corr_results=[Trait(trait_with_publish)]
- results=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset=dataset,target_dataset=target_dataset,for_api=True)
- self.assertEqual(results,expected_results)
-
-
-
- def test_generate_corr_json_view_false(self):
- trait=Trait({"view":False})
- corr_results=[trait]
- this_trait=Trait({"name":"trait_test"})
- dataset=Trait({"name":"the_name"})
-
-
- results_where_view_is_false=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset={},target_dataset={},for_api=False)
-
- # self.assertEqual(results,[])
- self.assertEqual(results_where_view_is_false,"[]")
\ No newline at end of file
+class TestShowCorrResults(unittest.TestCase):
+ def test_get_header_fields(self):
+ expected = [
+ ['Index',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect'],
+
+ ['Index',
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
+
+ ]
+ result1 = get_header_fields("ProbeSet", "spearman")
+ result2 = get_header_fields("Other", "Other")
+ self.assertEqual(result1, expected[0])
+ self.assertEqual(result2, expected[1])
+
+ @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac")
+ def test_generate_corr_json(self, mock_data_hmac):
+ mock_data_hmac.return_value = "hajsdiau"
+
+ dataset = AttributeSetter({"name": "the_name"})
+ this_trait = AttributeSetter(
+ {"name": "trait_test", "dataset": dataset})
+ target_dataset = AttributeSetter({"type": "Publish"})
+ corr_trait_1 = AttributeSetter({
+ "name": "trait_1",
+ "dataset": AttributeSetter({"name": "dataset_1"}),
+ "view": True,
+ "abbreviation": "T1",
+ "description_display": "Trait I description",
+ "authors": "JM J,JYEW",
+ "pubmed_id": "34n4nn31hn43",
+ "pubmed_text": "2016",
+ "pubmed_link": "https://www.load",
+ "lod_score": "",
+ "LRS_location_repr": "BXBS",
+ "additive": "",
+ "sample_r": 10.5,
+ "num_overlap": 2,
+ "sample_p": 5
+
+
+
+
+ })
+ corr_results = [corr_trait_1]
+
+ dataset_type_other = {
+ "location": "cx-3-4",
+ "sample_4": 12.32,
+ "num_overlap": 3,
+ "sample_p": 10.34
+ }
+
+ expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+
+ results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
+ dataset=dataset, target_dataset=target_dataset, for_api=True)
+ self.assertEqual(expected_results, results1)
+
+ def test_generate_corr_json_view_false(self):
+ trait = AttributeSetter({"view": False})
+ corr_results = [trait]
+ this_trait = AttributeSetter({"name": "trait_test"})
+ dataset = AttributeSetter({"name": "the_name"})
+
+ results_where_view_is_false = generate_corr_json(
+ corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
+ self.assertEqual(results_where_view_is_false, "[]")
--
cgit v1.2.3
From f2e4e893f5639f216f8cc6fc57984aaebffd82ef Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 14:11:23 +0300
Subject: add tests for snp browser
---
wqflask/tests/unit/wqflask/snp_browser/__init__.py | 0
.../unit/wqflask/snp_browser/test_snp_browser.py | 84 ++++++++++++++++++++++
2 files changed, 84 insertions(+)
create mode 100644 wqflask/tests/unit/wqflask/snp_browser/__init__.py
create mode 100644 wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
diff --git a/wqflask/tests/unit/wqflask/snp_browser/__init__.py b/wqflask/tests/unit/wqflask/snp_browser/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
new file mode 100644
index 00000000..e8751778
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -0,0 +1,84 @@
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.snp_browser.snp_browser import get_gene_id
+from wqflask.snp_browser.snp_browser import get_gene_id_name_dict
+from wqflask.snp_browser.snp_browser import check_if_in_gene
+from wqflask.snp_browser.snp_browser import get_browser_sample_lists
+from wqflask.snp_browser.snp_browser import get_header_list
+
+class TestSnpBrowser(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_get_gene_id(self, mock_db):
+ mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
+ called_value="\n SELECT\n geneId\n FROM\n GeneList\n WHERE\n SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'\n "
+ results = get_gene_id(
+ species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
+ mock_db.db.execute.assert_called_once_with(called_value)
+ self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_gene_id_name_dict(self,mock_db):
+ no_gene_names=[]
+ self.assertEqual("",get_gene_id_name_dict(species_id="fregb343bui43g4",gene_name_list=no_gene_names))
+ gene_name_list=["GH1","GH2","GH3"]
+ mock_db.db.execute.return_value.fetchall.side_effect=[[],[("fsdf43-fseferger-f22","GH1"),("1sdf43-fsewferger-f22","GH2"),
+ ("fwdj43-fstferger-f22","GH3")]]
+ no_results=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
+ results_found=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
+ expected_found= {'GH1': 'fsdf43-fseferger-f22', 'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
+ db_query_value="\n SELECT\n geneId, geneSymbol\n FROM\n GeneList\n WHERE\n SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')\n "
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(results_found,expected_found)
+ self.assertEqual(no_results,{})
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_check_if_in_gene(self,mock_db):
+ mock_db.db.execute.return_value.fetchone.side_effect=[("fsdf-232sdf-sdf","GHA"),""]
+ results_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
+ db_query_value="SELECT geneId, geneSymbol\n FROM GeneList\n WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND\n (txStart < 12.09 AND txEnd > 12.09); "
+ gene_not_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(gene_not_found,"")
+
+ @mock.patch("wqflask.snp_browser.snp_browser.g")
+ def test_get_browser_sample_lists(self,mock_db):
+ mock_db.db.execute.return_value.fetchall.return_value=[]
+
+ results=get_browser_sample_lists(species_id="12")
+ self.assertEqual(results, {'mouse': [], 'rat': []})
+
+ def test_get_header_list(self):
+ empty_columns={"snp_source":"false","conservation_score":"true","gene_name":"false","transcript":"false","exon":"false","domain_2":"true","function":"false","function_details":"true"}
+ strains={"mouse":["S1","S2","S3","S4","S5"],"rat":[]}
+ expected_results=([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
+
+ results_with_snp=get_header_list(variant_type="SNP",strains=strains,species="Mouse",empty_columns=empty_columns)
+ results_with_indel=get_header_list(variant_type="InDel",strains=strains,species="rat",empty_columns=[])
+ expected_results_with_indel=(['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'],0)
+
+ self.assertEqual(expected_results,results_with_snp)
+ self.assertEqual(results_with_indel,expected_results_with_indel)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
--
cgit v1.2.3
From db3170eb2fe66d8fd337803a730c18367df1b150 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 16:11:07 +0300
Subject: add tests for type checking
---
wqflask/tests/unit/utility/test_type_checking.py | 57 ++++++++++++++++++++++++
1 file changed, 57 insertions(+)
create mode 100644 wqflask/tests/unit/utility/test_type_checking.py
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
new file mode 100644
index 00000000..1ea11695
--- /dev/null
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -0,0 +1,57 @@
+import unittest
+from utility.type_checking import is_float
+from utility.type_checking import is_int
+from utility.type_checking import is_str
+from utility.type_checking import get_float
+from utility.type_checking import get_int
+from utility.type_checking import get_string
+class TestTypeChecking(unittest.TestCase):
+ def test_is_float(self):
+ floats=[2,1.2,'3.1']
+ not_floats=["String",None,[],()]
+ for flt in floats:
+ results=is_float(flt)
+ self.assertTrue(results)
+ for nflt in not_floats:
+ results=is_float(nflt)
+ self.assertFalse(results)
+
+ def test_is_int(self):
+ int_values=[1,1.1]
+ not_int_values=["1sdf",None,[],"1.1"]
+ for int_val in int_values:
+ results=is_int(int_val)
+ self.assertTrue(results)
+ for not_int in not_int_values:
+ results=is_int(not_int)
+ self.assertFalse(results)
+
+ def test_is_str(self):
+ string_values=[1,False,[],{},"string_value"]
+ falsey_values=[None]
+ for string_val in string_values:
+ results=is_str(string_val)
+ self.assertTrue(results)
+ for non_string in falsey_values:
+ results=is_str(non_string)
+ self.assertFalse(results)
+
+
+ def test_get_float(self):
+ vars_object={"min_value":"12"}
+ results=get_float(vars_object,"min_value")
+ self.assertEqual(results,12.0)
+
+ def test_get_int(self):
+ vars_object={"lx_value":"1"}
+ results=get_int(vars_object,"lx_value")
+ self.assertEqual(results,1)
+
+ def test_get_string(self):
+ string_object={"mx_value":1}
+ results=get_string(string_object,"mx_value")
+ self.assertEqual(results,"1")
+
+
+
+
--
cgit v1.2.3
From 2030cc56db878b05e5507c7c3d5ddef39ff223cb Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 16:15:01 +0300
Subject: replace vars with vars_obj which is a function name in python
---
wqflask/utility/type_checking.py | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index f15b17e2..6b029317 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -23,20 +23,20 @@ def is_str(value):
except:
return False
-def get_float(vars,name,default=None):
- if name in vars:
- if is_float(vars[name]):
- return float(vars[name])
+def get_float(vars_obj,name,default=None):
+ if name in vars_obj:
+ if is_float(vars_obj[name]):
+ return float(vars_obj[name])
return default
-def get_int(vars,name,default=None):
- if name in vars:
- if is_int(vars[name]):
- return float(vars[name])
+def get_int(vars_obj,name,default=None):
+ if name in vars_obj:
+ if is_int(vars_obj[name]):
+ return float(vars_obj[name])
return default
-def get_string(vars,name,default=None):
- if name in vars:
- if not vars[name] is None:
- return str(vars[name])
+def get_string(vars_obj,name,default=None):
+ if name in vars_obj:
+ if not vars_obj[name] is None:
+ return str(vars_obj[name])
return default
--
cgit v1.2.3
From 868b8cba1cda983d8d401e60e30794529b557c80 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Mon, 14 Dec 2020 22:36:36 +0300
Subject: modify get_header tests
---
.../unit/wqflask/snp_browser/test_snp_browser.py | 23 +++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index e8751778..9ec32c78 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -15,6 +15,18 @@ class TestSnpBrowser(unittest.TestCase):
def tearDown(self):
self.app_context.pop()
+ def test_get_header_list(self):
+ empty_columns={"snp_source":"false","conservation_score":"true","gene_name":"false","transcript":"false","exon":"false","domain_2":"true","function":"false","function_details":"true"}
+ strains={"mouse":["S1","S2","S3","S4","S5"],"rat":[]}
+ expected_results=([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
+
+ results_with_snp=get_header_list(variant_type="SNP",strains=strains,species="Mouse",empty_columns=empty_columns)
+ results_with_indel=get_header_list(variant_type="InDel",strains=strains,species="rat",empty_columns=[])
+ expected_results_with_indel=(['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'],0)
+
+ self.assertEqual(expected_results,results_with_snp)
+ self.assertEqual(results_with_indel,expected_results_with_indel)
+
@mock.patch("wqflask.snp_browser.snp_browser.g")
def test_get_gene_id(self, mock_db):
@@ -56,17 +68,6 @@ class TestSnpBrowser(unittest.TestCase):
results=get_browser_sample_lists(species_id="12")
self.assertEqual(results, {'mouse': [], 'rat': []})
- def test_get_header_list(self):
- empty_columns={"snp_source":"false","conservation_score":"true","gene_name":"false","transcript":"false","exon":"false","domain_2":"true","function":"false","function_details":"true"}
- strains={"mouse":["S1","S2","S3","S4","S5"],"rat":[]}
- expected_results=([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
-
- results_with_snp=get_header_list(variant_type="SNP",strains=strains,species="Mouse",empty_columns=empty_columns)
- results_with_indel=get_header_list(variant_type="InDel",strains=strains,species="rat",empty_columns=[])
- expected_results_with_indel=(['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'],0)
-
- self.assertEqual(expected_results,results_with_snp)
- self.assertEqual(results_with_indel,expected_results_with_indel)
--
cgit v1.2.3
From 5a73d56fdbe197e99b476d49d4adce9403c8daeb Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Fri, 18 Dec 2020 15:18:19 +0300
Subject: refactor tests and pep8 formatting
---
wqflask/tests/unit/utility/test_type_checking.py | 93 ++++++++--------
.../unit/wqflask/snp_browser/test_snp_browser.py | 120 ++++++++++++---------
2 files changed, 112 insertions(+), 101 deletions(-)
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
index 1ea11695..48d110c7 100644
--- a/wqflask/tests/unit/utility/test_type_checking.py
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -5,53 +5,50 @@ from utility.type_checking import is_str
from utility.type_checking import get_float
from utility.type_checking import get_int
from utility.type_checking import get_string
-class TestTypeChecking(unittest.TestCase):
- def test_is_float(self):
- floats=[2,1.2,'3.1']
- not_floats=["String",None,[],()]
- for flt in floats:
- results=is_float(flt)
- self.assertTrue(results)
- for nflt in not_floats:
- results=is_float(nflt)
- self.assertFalse(results)
-
- def test_is_int(self):
- int_values=[1,1.1]
- not_int_values=["1sdf",None,[],"1.1"]
- for int_val in int_values:
- results=is_int(int_val)
- self.assertTrue(results)
- for not_int in not_int_values:
- results=is_int(not_int)
- self.assertFalse(results)
-
- def test_is_str(self):
- string_values=[1,False,[],{},"string_value"]
- falsey_values=[None]
- for string_val in string_values:
- results=is_str(string_val)
- self.assertTrue(results)
- for non_string in falsey_values:
- results=is_str(non_string)
- self.assertFalse(results)
-
-
- def test_get_float(self):
- vars_object={"min_value":"12"}
- results=get_float(vars_object,"min_value")
- self.assertEqual(results,12.0)
-
- def test_get_int(self):
- vars_object={"lx_value":"1"}
- results=get_int(vars_object,"lx_value")
- self.assertEqual(results,1)
-
- def test_get_string(self):
- string_object={"mx_value":1}
- results=get_string(string_object,"mx_value")
- self.assertEqual(results,"1")
-
-
+class TestTypeChecking(unittest.TestCase):
+ def test_is_float(self):
+ floats = [2, 1.2, '3.1']
+ not_floats = ["String", None, [], ()]
+ for flt in floats:
+ results = is_float(flt)
+ self.assertTrue(results)
+ for nflt in not_floats:
+ results = is_float(nflt)
+ self.assertFalse(results)
+
+ def test_is_int(self):
+ int_values = [1, 1.1]
+ not_int_values = ["string", None, [], "1.1"]
+ for int_val in int_values:
+ results = is_int(int_val)
+ self.assertTrue(results)
+ for not_int in not_int_values:
+ results = is_int(not_int)
+ self.assertFalse(results)
+
+ def test_is_str(self):
+ string_values = [1, False, [], {}, "string_value"]
+ falsey_values = [None]
+ for string_val in string_values:
+ results = is_str(string_val)
+ self.assertTrue(results)
+ for non_string in falsey_values:
+ results = is_str(non_string)
+ self.assertFalse(results)
+
+ def test_get_float(self):
+ vars_object = {"min_value": "12"}
+ results = get_float(vars_object, "min_value")
+ self.assertEqual(results, 12.0)
+
+ def test_get_int(self):
+ vars_object = {"lx_value": "1"}
+ results = get_int(vars_object, "lx_value")
+ self.assertEqual(results, 1)
+
+ def test_get_string(self):
+ string_object = {"mx_value": 1}
+ results = get_string(string_object, "mx_value")
+ self.assertEqual(results, "1")
\ No newline at end of file
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 9ec32c78..496d228f 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -7,6 +7,7 @@ from wqflask.snp_browser.snp_browser import check_if_in_gene
from wqflask.snp_browser.snp_browser import get_browser_sample_lists
from wqflask.snp_browser.snp_browser import get_header_list
+
class TestSnpBrowser(unittest.TestCase):
def setUp(self):
self.app_context = app.app_context()
@@ -16,70 +17,83 @@ class TestSnpBrowser(unittest.TestCase):
self.app_context.pop()
def test_get_header_list(self):
- empty_columns={"snp_source":"false","conservation_score":"true","gene_name":"false","transcript":"false","exon":"false","domain_2":"true","function":"false","function_details":"true"}
- strains={"mouse":["S1","S2","S3","S4","S5"],"rat":[]}
- expected_results=([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
-
- results_with_snp=get_header_list(variant_type="SNP",strains=strains,species="Mouse",empty_columns=empty_columns)
- results_with_indel=get_header_list(variant_type="InDel",strains=strains,species="rat",empty_columns=[])
- expected_results_with_indel=(['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'],0)
-
- self.assertEqual(expected_results,results_with_snp)
- self.assertEqual(results_with_indel,expected_results_with_indel)
-
+ empty_columns = {"snp_source": "false", "conservation_score": "true", "gene_name": "false",
+ "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
+ strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
+ expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
+ 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
+
+ results_with_snp = get_header_list(
+ variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
+ results_with_indel = get_header_list(
+ variant_type="InDel", strains=strains, species="rat", empty_columns=[])
+ expected_results_with_indel = (
+ ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0)
+
+ self.assertEqual(expected_results, results_with_snp)
+ self.assertEqual(results_with_indel, expected_results_with_indel)
@mock.patch("wqflask.snp_browser.snp_browser.g")
def test_get_gene_id(self, mock_db):
mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
- called_value="\n SELECT\n geneId\n FROM\n GeneList\n WHERE\n SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'\n "
+ db_query_value = """
+ SELECT
+ geneId
+ FROM
+ GeneList
+ WHERE
+ SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'
+ """
results = get_gene_id(
species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
- mock_db.db.execute.assert_called_once_with(called_value)
+ mock_db.db.execute.assert_called_once_with(db_query_value)
self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
@mock.patch("wqflask.snp_browser.snp_browser.g")
- def test_gene_id_name_dict(self,mock_db):
- no_gene_names=[]
- self.assertEqual("",get_gene_id_name_dict(species_id="fregb343bui43g4",gene_name_list=no_gene_names))
- gene_name_list=["GH1","GH2","GH3"]
- mock_db.db.execute.return_value.fetchall.side_effect=[[],[("fsdf43-fseferger-f22","GH1"),("1sdf43-fsewferger-f22","GH2"),
- ("fwdj43-fstferger-f22","GH3")]]
- no_results=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
- results_found=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
- expected_found= {'GH1': 'fsdf43-fseferger-f22', 'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
- db_query_value="\n SELECT\n geneId, geneSymbol\n FROM\n GeneList\n WHERE\n SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')\n "
- mock_db.db.execute.assert_called_with(db_query_value)
- self.assertEqual(results_found,expected_found)
- self.assertEqual(no_results,{})
+ def test_gene_id_name_dict(self, mock_db):
+ no_gene_names = []
+ self.assertEqual("", get_gene_id_name_dict(
+ species_id="fregb343bui43g4", gene_name_list=no_gene_names))
+ gene_name_list = ["GH1", "GH2", "GH3"]
+ mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"),
+ ("fwdj43-fstferger-f22", "GH3")]]
+ no_results = get_gene_id_name_dict(
+ species_id="ret3-32rf32", gene_name_list=gene_name_list)
+ results_found = get_gene_id_name_dict(
+ species_id="ret3-32rf32", gene_name_list=gene_name_list)
+ expected_found = {'GH1': 'fsdf43-fseferger-f22',
+ 'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
+ db_query_value = """
+ SELECT
+ geneId, geneSymbol
+ FROM
+ GeneList
+ WHERE
+ SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')
+ """
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(results_found, expected_found)
+ self.assertEqual(no_results, {})
@mock.patch("wqflask.snp_browser.snp_browser.g")
- def test_check_if_in_gene(self,mock_db):
- mock_db.db.execute.return_value.fetchone.side_effect=[("fsdf-232sdf-sdf","GHA"),""]
- results_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
- db_query_value="SELECT geneId, geneSymbol\n FROM GeneList\n WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND\n (txStart < 12.09 AND txEnd > 12.09); "
- gene_not_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
- mock_db.db.execute.assert_called_with(db_query_value)
- self.assertEqual(gene_not_found,"")
+ def test_check_if_in_gene(self, mock_db):
+ mock_db.db.execute.return_value.fetchone.side_effect = [
+ ("fsdf-232sdf-sdf", "GHA"), ""]
+ results_found = check_if_in_gene(
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+ db_query_value = """SELECT geneId, geneSymbol
+ FROM GeneList
+ WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND
+ (txStart < 12.09 AND txEnd > 12.09); """
+ gene_not_found = check_if_in_gene(
+ species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+ mock_db.db.execute.assert_called_with(db_query_value)
+ self.assertEqual(gene_not_found, "")
@mock.patch("wqflask.snp_browser.snp_browser.g")
- def test_get_browser_sample_lists(self,mock_db):
- mock_db.db.execute.return_value.fetchall.return_value=[]
-
- results=get_browser_sample_lists(species_id="12")
- self.assertEqual(results, {'mouse': [], 'rat': []})
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+ def test_get_browser_sample_lists(self, mock_db):
+ mock_db.db.execute.return_value.fetchall.return_value = []
+ results = get_browser_sample_lists(species_id="12")
+ self.assertEqual(results, {'mouse': [], 'rat': []})
--
cgit v1.2.3
From 47d6c4d9c39b8a506f65ce86a11ff394be76f3d0 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Thu, 17 Dec 2020 20:59:54 +0300
Subject: replace scroller/css/scroller.dataTables.min.css with
scrollerStyle/css/scroller.dataTables.min.css
---
wqflask/wqflask/templates/search_result_page.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 765c4ab8..411a6628 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -3,7 +3,7 @@
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
--
cgit v1.2.3
From 6781bda17452ee5b948fd0deb217df464a4a7202 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Thu, 17 Dec 2020 21:12:26 +0300
Subject: add scroller.dataTables.min.css and dataTables.scroller.min.js to
mechanical rob
---
test/requests/link_checker.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index bc3b5861..f162ec84 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -103,9 +103,9 @@ def check_packaged_js_files(args_obj, parser):
"/js/DataTablesExtensions/colResize/dataTables.colResize.js",
"/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js",
"/js/DataTablesExtensions/buttons/js/buttons.colVis.min.js",
- "/js/DataTablesExtensions/scroller/js/scroller.dataTables.min.js",
+ "/js/DataTablesExtensions/scroller/js/dataTables.scroller.min.js",
"/js/DataTables/js/jquery.dataTables.js",
- "/css/DataTablesExtensions/scroller/css/scroller.dataTables.min.css",
+ "/js/DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css",
# Datatables plugins:
"/js/DataTablesExtensions/plugins/sorting/natural.js",
"/js/DataTablesExtensions/plugins/sorting/scientific.js",
--
cgit v1.2.3
From b605f52440e84909631b6afdf510a9e513260901 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Wed, 6 Jan 2021 08:21:44 +0300
Subject: fix tests for show_corr_results
---
wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
index ffb96dd6..33601990 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -61,6 +61,7 @@ class TestShowCorrResults(unittest.TestCase):
"pubmed_text": "2016",
"pubmed_link": "https://www.load",
"lod_score": "",
+ "mean": "",
"LRS_location_repr": "BXBS",
"additive": "",
"sample_r": 10.5,
@@ -80,7 +81,7 @@ class TestShowCorrResults(unittest.TestCase):
"sample_p": 10.34
}
- expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+ expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
dataset=dataset, target_dataset=target_dataset, for_api=True)
--
cgit v1.2.3
From 4203e9609dcf59fa7369e9e0dde02d0da3c8e32f Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Wed, 6 Jan 2021 08:50:30 +0300
Subject: update tests for snp_browser
---
.../tests/unit/wqflask/snp_browser/test_snp_browser.py | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 496d228f..7fa96dba 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -21,18 +21,25 @@ class TestSnpBrowser(unittest.TestCase):
"transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
- 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
+ 'Domain 1', 'Domain 2', 'Details'],
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'conservation_score', 'domain_1', 'domain_2',
+ 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
results_with_snp = get_header_list(
variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
results_with_indel = get_header_list(
variant_type="InDel", strains=strains, species="rat", empty_columns=[])
expected_results_with_indel = (
- ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
- 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0)
+ ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+ ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
self.assertEqual(expected_results, results_with_snp)
- self.assertEqual(results_with_indel, expected_results_with_indel)
+ # self.assertEqual(results_with_indel, expected_results_with_indel)
+ self.assertEqual(expected_results_with_indel, results_with_indel)
@mock.patch("wqflask.snp_browser.snp_browser.g")
def test_get_gene_id(self, mock_db):
--
cgit v1.2.3
From e55aa51937abf03897a20a52dd7dbf3cfc4ac6c8 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Wed, 6 Jan 2021 08:54:47 +0300
Subject: remove comments
---
wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py | 1 -
1 file changed, 1 deletion(-)
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 7fa96dba..ce3e7b83 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -38,7 +38,6 @@ class TestSnpBrowser(unittest.TestCase):
'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
self.assertEqual(expected_results, results_with_snp)
- # self.assertEqual(results_with_indel, expected_results_with_indel)
self.assertEqual(expected_results_with_indel, results_with_indel)
@mock.patch("wqflask.snp_browser.snp_browser.g")
--
cgit v1.2.3
From 7bcc5d1e8111d7c74299c7f017c4a0427f8b4830 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 6 Jan 2021 11:51:01 -0600
Subject: Changes to the way R/qtl deals with 4-way crosses so it will work
with new HET3-ITP genotypes
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 10 ++--------
1 file changed, 2 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 0a5758af..4117a0e5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -94,9 +94,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
- #logger.info("Saving");
- #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
- #logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
if pair_scan:
@@ -159,7 +156,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur
toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
type <- getGenoCode(header, 'type')
if(type == '4-way'){
- genocodes <- c('1','2','3','4')
+ genocodes <- NULL
} else {
genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
@@ -174,7 +171,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur
require(qtl)
if(type == '4-way'){
cat('Loading in as 4-WAY\n')
- cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ cross = read.cross(file=out, 'csvr', genotypes=NULL, crosstype="4way") # Load the created cross file using R/qtl read.cross
}else if(type == 'f2'){
cat('Loading in as F2\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2") # Load the created cross file using R/qtl read.cross
@@ -332,8 +329,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_name_string += '"' + col_name + '", '
else:
covar_name_string += '"' + col_name + '"'
-
- logger.info("covar_name_string:" + covar_name_string)
else:
col_name = "covar_" + str(i)
cross = add_phenotype(cross, covar_as_string, col_name)
@@ -343,7 +338,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_name_string += '"' + col_name + '"'
covar_name_string += ")"
- logger.info("covar_name_string:" + covar_name_string);
covars_ob = pull_var("trait_covars", cross, covar_name_string)
return cross, covars_ob
--
cgit v1.2.3
From f617bca3f5298454f8944205f84ae77e0c59ca4b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 6 Jan 2021 11:53:04 -0600
Subject: Added line to views.py to fixes error if the genotype file contains
samples not listed in the DB
---
wqflask/wqflask/views.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index c136711e..6b706b3f 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -643,8 +643,9 @@ def loading_page():
samples = genofile_samples
for sample in samples:
- if sample_vals_dict[sample] != "x":
- n_samples += 1
+ if sample in sample_vals_dict:
+ if sample_vals_dict[sample] != "x":
+ n_samples += 1
start_vars['n_samples'] = n_samples
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
@@ -749,10 +750,9 @@ def mapping_results_page():
rendered_template = render_template("mapping_error.html")
return rendered_template
except:
- rendered_template = render_template("mapping_error.html")
- return rendered_template
+ rendered_template = render_template("mapping_error.html")
+ return rendered_template
- #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")
--
cgit v1.2.3
From 6c63b869d047daca44ff5facee44833f52b0d861 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 11 Jan 2021 13:49:04 -0600
Subject: Added something to line accounting for certain BXD individual groups
when building the correlation drop-down
---
wqflask/wqflask/show_trait/show_trait.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 4c6dd005..9b4a8fa4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -372,7 +372,7 @@ class ShowTrait(object):
# We're checking a string here!
assert isinstance(this_group, str), "We need a string type thing here"
- if this_group[:3] == 'BXD' and this_group != "BXD-Longevity":
+ if this_group[:3] == 'BXD' and this_group != "BXD-Longevity" and this_group != "BXD-AE":
this_group = 'BXD'
if this_group:
--
cgit v1.2.3
From 2016470a13945e6bb833d28583de9e0877fe91eb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 11 Jan 2021 14:21:47 -0600
Subject: Fixed error with JS that adds text to footer showing how long it took
to render the page
---
wqflask/wqflask/templates/base.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index e368a4be..facebdff 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -264,7 +264,7 @@
{% endblock %}
<script type="text/javascript">
- $(window).load(function() {
+ document.addEventListener('DOMContentLoaded', function() {
let timeToLoad = document.createElement("p");
timeToLoad.innerHTML = "It took your browser " + ((Date.now() - pageLoadStart)/1000) + " second(s) to render this page";
document.querySelector("footer .row .col-xs-6").appendChild(timeToLoad);
--
cgit v1.2.3
From 3c0715dc52dc583d8a84907a9ba41a799ed3068a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 Jan 2021 11:09:11 -0600
Subject: Added a line that redraws the DataTable, which fixes its initial
scroll height
---
wqflask/wqflask/templates/search_result_page.html | 37 ++++++-----------------
1 file changed, 9 insertions(+), 28 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 411a6628..5fe65c00 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -146,6 +146,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
@@ -383,36 +384,16 @@
}{% endif %}
],
"order": [[1, "asc" ]],
- {% if dataset.type != 'Geno' %}
- buttons: [
- {
- extend: 'columnsToggle',
- columns: function( idx, data, node ) {
- if (idx != 0) {
- return true;
- } else {
- return false;
- }
- },
- postfixButtons: [ 'colvisRestore' ]
- }
- ],
- 'sDom': "Bpitirp",
- {% else %}
- 'sDom': "pitirp",
- {% endif %}
- 'iDisplayLength': 500,
- 'deferRender': true,
- 'paging': true,
- 'orderClasses': true,
- 'processing': true,
- 'bServerSide': true,
- 'sAjaxSource': '/search_table'+getParams(window.location.href),
- 'infoCallback': function(settings, start, end, max, total, pre) {
- return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
- }
+ 'sDom': "itir",
+ "autoWidth": true,
+ "bSortClasses": false,
+ "scrollY": "100vh",
+ "scroller": true,
+ "scrollCollapse": true
} );
+ trait_table.draw(); //ZS: This makes the table adjust its height properly on initial load
+
$('.toggle-vis').on( 'click', function (e) {
e.preventDefault();
--
cgit v1.2.3
From b3aba44e452fbfeb9f79c91f94b00061057937a4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 Jan 2021 17:51:06 -0600
Subject: Fixed issue causing interval mapping to not be displayed correctly
---
wqflask/wqflask/marker_regression/run_mapping.py | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 891fcc66..38f8c26d 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -138,15 +138,15 @@ class RunMapping(object):
mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
- if start_vars['manhattan_plot']:
- self.color_scheme = "alternating"
- if "color_scheme" in start_vars:
- self.color_scheme = start_vars['color_scheme']
- if self.color_scheme == "single":
- self.manhattan_single_color = start_vars['manhattan_single_color']
- self.manhattan_plot = True
- else:
- self.manhattan_plot = False
+ self.manhattan_plot = False
+ if 'manhattan_plot' in start_vars:
+ if start_vars['manhattan_plot'].lower() != "false":
+ self.color_scheme = "alternating"
+ if "color_scheme" in start_vars:
+ self.color_scheme = start_vars['color_scheme']
+ if self.color_scheme == "single":
+ self.manhattan_single_color = start_vars['manhattan_single_color']
+ self.manhattan_plot = True
self.maf = start_vars['maf'] # Minor allele frequency
if "use_loco" in start_vars:
--
cgit v1.2.3
From 7d97698ca88460c2f66b67ada31085b02cbc9ee4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 Jan 2021 17:56:52 -0600
Subject: Fixed a bunch fo remaining issues with positioning legend items on
the right side of the mapping figure
---
.../marker_regression/display_mapping_results.py | 87 +++++++++++-----------
1 file changed, 43 insertions(+), 44 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 9f778160..bba08f63 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -860,7 +860,10 @@ class DisplayMappingResults(object):
text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
if self.legendChecked:
- startPosY = 30
+ if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
+ startPosY = 30
+ else:
+ startPosY = 15
smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
leftOffset = canvas.size[0] - xRightOffset - 190
im_drawer.rectangle(
@@ -942,28 +945,6 @@ class DisplayMappingResults(object):
draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
fill=self.TRANSCRIPT_LOCATION_COLOR)
- if self.legendChecked:
- startPosY = 15
- nCol = 2
- smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
- if self.manhattan_plot:
- leftOffset = xLeftOffset
- else:
- leftOffset = xLeftOffset+(nCol-1)*200*fontZoom
- draw_open_polygon(
- canvas,
- xy=(
- (leftOffset+7, startPosY-7),
- (leftOffset, startPosY+7),
- (leftOffset+14, startPosY+7)),
- outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR
- )
- TEXT_Y_DISPLACEMENT = -8
- im_drawer.text(
- text="Sequence Site",
- xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
- fill=self.TOP_RIGHT_INFO_COLOR)
-
def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
@@ -1060,17 +1041,38 @@ class DisplayMappingResults(object):
labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
startPosY = 15
stepPosY = 12*fontZoom
+
+ startPosX = canvas.size[0] - xRightOffset - 415
+ if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
+ startPosY = 15
+ nCol = 2
+ smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
+
+ leftOffset = canvas.size[0] - xRightOffset - 190
+ draw_open_polygon(
+ canvas,
+ xy=(
+ (leftOffset + 6, startPosY-7),
+ (leftOffset - 1, startPosY+7),
+ (leftOffset + 13, startPosY+7)),
+ outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR
+ )
+ TEXT_Y_DISPLACEMENT = -8
+ im_drawer.text(
+ text="Sequence Site",
+ xy=(leftOffset + 20, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+ fill=self.TOP_RIGHT_INFO_COLOR)
+
if self.manhattan_plot != True:
im_drawer.line(
- xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
+ xy=((startPosX, startPosY), (startPosX+32, startPosY)),
fill=self.LRS_COLOR, width=2)
im_drawer.text(
- text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+ text=self.LRS_LOD, xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.additiveChecked:
- startPosX = canvas.size[0] - xRightOffset - 400
im_drawer.line(
xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
@@ -1080,10 +1082,9 @@ class DisplayMappingResults(object):
im_drawer.text(
text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
font=labelFont, fill=BLACK)
+ startPosY += stepPosY
if self.genotype.type == 'intercross' and self.dominanceChecked:
- startPosX = canvas.size[0] - xRightOffset - 400
- startPosY += stepPosY
im_drawer.line(
xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
@@ -1093,44 +1094,42 @@ class DisplayMappingResults(object):
im_drawer.text(
text='Dominance Effect', xy=(startPosX+42, startPosY+5),
font=labelFont, fill=BLACK)
+ startPosY += stepPosY
if self.haplotypeAnalystChecked:
- startPosY += stepPosY
- startPosX = canvas.size[0] - xRightOffset - 400
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX+17, startPosY)),
+ xy=((startPosX-34, startPosY), (startPosX-17, startPosY)),
fill=self.HAPLOTYPE_POSITIVE, width=4)
im_drawer.line(
- xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
+ xy=((startPosX-17, startPosY), (startPosX, startPosY)),
fill=self.HAPLOTYPE_NEGATIVE, width=4)
im_drawer.line(
- xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
+ xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
im_drawer.line(
- xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
+ xy=((startPosX+17, startPosY), (startPosX+34, startPosY)),
fill=self.HAPLOTYPE_RECOMBINATION, width=4)
im_drawer.text(
text='Haplotypes (Pat, Mat, Het, Unk)',
- xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
+ xy=(startPosX+41, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ startPosY += stepPosY
if self.permChecked and self.nperm > 0:
- startPosY += stepPosY
- if self.bootChecked and not self.multipleInterval:
- startPosX = canvas.size[0] - xRightOffset - 400
- else:
- startPosX = canvas.size[0] - xRightOffset - 190
+ thisStartX = startPosX
+ if self.multipleInterval and not self.bootChecked:
+ thisStartX = canvas.size[0] - xRightOffset - 205
im_drawer.line(
- xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
+ xy=((thisStartX, startPosY), ( startPosX + 32, startPosY)),
fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
im_drawer.line(
- xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
+ xy=((thisStartX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
im_drawer.text(
text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
- xy=(startPosX+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ xy=(thisStartX+40, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
im_drawer.text(
text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
- xy=(startPosX+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
+ xy=(thisStartX+40, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
fill=BLACK)
labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
--
cgit v1.2.3
From 4e8a9dfabf3580f1dd2cfeaa407bae726e7659a0 Mon Sep 17 00:00:00 2001
From: robwwilliams
Date: Wed, 13 Jan 2021 11:56:32 -0600
Subject: Just some tweaks to first paragrfaph
---
README.md | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/README.md b/README.md
index cd35defb..bfb16ddb 100644
--- a/README.md
+++ b/README.md
@@ -3,13 +3,12 @@
# GeneNetwork
-This repository contains the source code for the GeneNetwork (GN)
-server http://gn2.genenetwork.org/ (version 2 aka GN2). GN is a Web
-2.0 style framework with included tools for doing genetics online
-using high-throughput data. GN is used for a wide range of studies. An
-exhaustive list of publications mentioning GN and its previous
-incarnation WebQTL can be found
-[here](http://www.genenetwork.org/reference.html).
+This repository contains the current source code for GeneNetwork (GN)
+(https://www.genenetwork.org/ (version 2). GN2 is a Web
+2.0-style framework that includes data and computational tools for online genetics and genomic analysis of
+many different populations and many types of molecular, cellular, and physiological data.
+The system is used by scientists and clinians in the field of precision health care and systems genetics.
+GN and its predecessors have been in operation since Jan 1994, making it one of the longest-lived web services in biomedical research (https://en.wikipedia.org/wiki/GeneNetwork, and see a partial list of publications using GN and its predecessor, WebQTL (https://genenetwork.org/references/).
## Install
--
cgit v1.2.3
From ac28594a4eba9c73b836170ef81beb93f40a11d6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 13 Jan 2021 14:18:02 -0600
Subject: The Scroller CSS was removed because it forces all row text onto one
line; Scroller still seems to function fine without it, which is a little
strange
---
wqflask/wqflask/templates/search_result_page.html | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5fe65c00..b8f89121 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -3,7 +3,6 @@
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
- <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scrollerStyle/css/scroller.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -125,7 +124,7 @@
{% endif %}
</div>
{% endif %}
- <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
+ <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px; max-width:100%;"{% endif %}>
<table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
<tbody>
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
@@ -310,7 +309,6 @@
{
'title': "Description",
'type': "natural",
- 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
--
cgit v1.2.3
From 4a67b437215b04a089449f93cfa9ebcaed5640dd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 14 Jan 2021 14:22:02 -0600
Subject: Re-added some code that was accidentally removed that was needed for
adding cofactors to mapping
---
wqflask/wqflask/static/new/javascript/show_trait.js | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 2ec9d6d5..1c8e328d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -95,6 +95,14 @@ $('#add_to_collection').click(add);
sample_lists = js_data.sample_lists;
sample_group_types = js_data.sample_group_types;
+$(".select_covariates").click(function () {
+ open_covariate_selection();
+});
+$(".remove_covariates").click(function () {
+ $("input[name=covariates]").val("")
+ $(".selected-covariates").val("")
+});
+
open_trait_selection = function() {
return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
return function() {
--
cgit v1.2.3
From aa5d3d6bfedd7df8c6e35465d60bba1c11c8fa79 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 14 Jan 2021 14:22:47 -0600
Subject: Added transform text to mapping figure and fixed an issue where
cofactors weren't appearing in the metadata
---
.../marker_regression/display_mapping_results.py | 46 +++++++++++++++++-----
1 file changed, 37 insertions(+), 9 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 9f1b050d..0de9b9a1 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -636,7 +636,7 @@ class DisplayMappingResults(object):
btminfo.append(HtmlGenWrapper.create_br_tag())
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, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+ def plotIntMapping(self, canvas, offset= (80, 120, 90, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
im_drawer = ImageDraw.Draw(canvas)
#calculating margins
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -644,10 +644,11 @@ class DisplayMappingResults(object):
yTopOffset = max(90, yTopOffset)
else:
if self.legendChecked:
+ yTopOffset += 10
if self.covariates != "" and self.controlLocus and self.doControl != "false":
- yTopOffset = max(120, yTopOffset)
- else:
- yTopOffset = max(100, yTopOffset)
+ yTopOffset += 20
+ if len(self.transform) > 0:
+ yTopOffset += 5
else:
pass
@@ -1131,6 +1132,7 @@ class DisplayMappingResults(object):
labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
labelColor = BLACK
+
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
dataset_label = self.dataset.fullname
else:
@@ -1172,6 +1174,7 @@ class DisplayMappingResults(object):
else:
string3 += 'no control for other QTLs'
+ y_constant = 10
if self.this_trait.name:
if self.selectedChr == -1:
identification = "Mapping on All Chromosomes for "
@@ -1197,23 +1200,48 @@ class DisplayMappingResults(object):
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
text=identification,
- xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
+ xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom), font=labelFont,
fill=labelColor)
+ y_constant += 15
else:
d = 4+ max(
im_drawer.textsize(string1, font=labelFont)[0],
im_drawer.textsize(string2, font=labelFont)[0])
+
+ if len(self.transform) > 0:
+ transform_text = "Transform - "
+ if self.transform == "qnorm":
+ transform_text += "Quantile Normalized"
+ elif self.transform == "log2" or self.transform == "log10":
+ transform_text += self.transform.capitalize()
+ elif self.transform == "sqrt":
+ transform_text += "Square Root"
+ elif self.transform == "zscore":
+ transform_text += "Z-Score"
+ elif self.transform == "invert":
+ transform_text += "Invert +/-"
+
+ im_drawer.text(
+ text=transform_text, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
+ font=labelFont, fill=labelColor)
+ y_constant += 15
im_drawer.text(
- text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+ text=string1, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
font=labelFont, fill=labelColor)
+ y_constant += 15
im_drawer.text(
- text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+ text=string2, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
font=labelFont, fill=labelColor)
+ y_constant += 15
if string3 != '':
im_drawer.text(
- text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+ text=string3, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
font=labelFont, fill=labelColor)
-
+ y_constant += 15
+ if string4 != '':
+ im_drawer.text(
+ text=string4, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
+ font=labelFont, fill=labelColor)
def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
--
cgit v1.2.3
From 355e5337330f57ee173aaf309805ca1b0ec0503c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 14 Jan 2021 15:35:35 -0600
Subject: Fixed mistake where the mapping figure Transform text didn't have its
X position set correctly
---
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 864f3264..4df56190 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1223,7 +1223,7 @@ class DisplayMappingResults(object):
transform_text += "Invert +/-"
im_drawer.text(
- text=transform_text, xy=(canvas.size[0] - xRightOffset-d, y_constant*fontZoom),
+ text=transform_text, xy=(xLeftOffset, y_constant*fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
im_drawer.text(
--
cgit v1.2.3
From 0bac313ba6a6c4cf04acf230641cc4208a386275 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 14 Jan 2021 15:53:53 -0600
Subject: Added some lines that check if salt is already bytes and convert it
if necessary (this is caused by salt being passed to a function as bytes when
an account is registered but being passed as a string when logging in)
---
wqflask/wqflask/pbkdf2.py | 4 ++--
wqflask/wqflask/user_login.py | 6 +++++-
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index aea5b06c..6346df03 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -2,15 +2,15 @@ import hashlib
from werkzeug.security import safe_str_cmp as ssc
-
# Replace this because it just wraps around Python3's internal
# functions. Added this during migration.
def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
"""Wrapper function of python's hashlib.pbkdf2_hmac.
"""
+
dk = hashlib.pbkdf2_hmac(hashfunc,
bytes(data, "utf-8"), # password
- bytes(salt, "utf-8"), # salt
+ salt,
iterations,
keylen)
return dk.hex()
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index bc608e84..041f1f11 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -39,8 +39,12 @@ def basic_info():
def encode_password(pass_gen_fields, unencrypted_password):
+ if isinstance(pass_gen_fields['salt'], bytes):
+ salt = pass_gen_fields['salt']
+ else:
+ salt = bytes(pass_gen_fields['salt'], "utf-8")
encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
- pass_gen_fields['salt'],
+ salt,
pass_gen_fields['iterations'],
pass_gen_fields['keylength'],
pass_gen_fields['hashfunc'])
--
cgit v1.2.3
From db31d53421c033a9907d2c67bc8a0c3c911b5402 Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Thu, 14 Jan 2021 21:13:01 +0300
Subject: resize image in facilities page
---
wqflask/wqflask/templates/facilities.html | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html
index 56b127f9..dc8d0ded 100644
--- a/wqflask/wqflask/templates/facilities.html
+++ b/wqflask/wqflask/templates/facilities.html
@@ -4,6 +4,14 @@
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
+
+<style>
+ img[src="https://github.com/genenetwork/gn-docs/raw/master/general/help/octopus.jpg"] {
+ width:100%;
+ margin:20px 0px;
+}
+</style>
+
{% endblock %}
{% block content %}
--
cgit v1.2.3
From c228aff0cc9480f7b9ee46e54c9fef0f46299a3d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sun, 17 Jan 2021 14:57:52 -0600
Subject: Set default description to avoid error in situations where
description is None
---
wqflask/wqflask/search_results.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c4ea2921..9e8001cf 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -120,7 +120,9 @@ class SearchResultPage(object):
trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
if this_trait.dataset.type == "ProbeSet":
trait_dict['symbol'] = this_trait.symbol
- trait_dict['description'] = this_trait.description_display
+ trait_dict['description'] = "N/A"
+ if this_trait.description_display:
+ trait_dict['description'] = this_trait.description_display
trait_dict['location'] = this_trait.location_repr
trait_dict['mean'] = "N/A"
trait_dict['additive'] = "N/A"
@@ -136,7 +138,9 @@ class SearchResultPage(object):
elif this_trait.dataset.type == "Geno":
trait_dict['location'] = this_trait.location_repr
elif this_trait.dataset.type == "Publish":
- trait_dict['description'] = this_trait.description_display
+ trait_dict['description'] = "N/A"
+ if this_trait.description_display:
+ trait_dict['description'] = this_trait.description_display
trait_dict['authors'] = this_trait.authors
trait_dict['pubmed_id'] = "N/A"
if this_trait.pubmed_id:
--
cgit v1.2.3
From 715d9137038887c6654a14d22dc0512bb01aaf86 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 17 Jan 2021 08:51:06 -0600
Subject: modify the main query in gene global search to add locus chr, locus
mb and optimize the speed of query
---
wqflask/wqflask/gsearch.py | 37 ++++++++++++++++++++++---------------
1 file changed, 22 insertions(+), 15 deletions(-)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9e46c0c5..6ff57563 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,4 +1,6 @@
import json
+import datetime as dt
+from types import SimpleNamespace
from flask import Flask, g
from base.data_set import create_dataset
@@ -9,8 +11,9 @@ from base import webqtlConfig
from utility import hmac
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.benchmark import Bench
+from utility.authentication_tools import check_resource_availability
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -42,15 +45,19 @@ class GSearch(object):
ProbeSetXRef.LRS AS lrs,
ProbeSetXRef.`Locus` AS locus,
ProbeSetXRef.`pValue` AS pvalue,
- ProbeSetXRef.`additive` AS additive
- FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
- WHERE InbredSet.`SpeciesId`=Species.`Id`
- AND ProbeFreeze.InbredSetId=InbredSet.`Id`
- AND ProbeFreeze.`TissueId`=Tissue.`Id`
- AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
- AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
- AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
- AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+ ProbeSetXRef.`additive` AS additive,
+ ProbeSetFreeze.Id AS probesetfreeze_id,
+ Geno.Chr as geno_chr,
+ Geno.Mb as geno_mb
+ FROM Species
+ INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id`
+ INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId=InbredSet.`Id`
+ INNER JOIN Tissue ON ProbeFreeze.`TissueId`=Tissue.`Id`
+ INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
+ INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+ INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+ WHERE ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,ProbeSet.alias,ProbeSet.GenbankId, ProbeSet.UniGeneId, ProbeSet.Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
AND ProbeSetFreeze.confidentiality < 1
AND ProbeSetFreeze.public > 0
ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
@@ -90,16 +97,16 @@ class GSearch(object):
this_trait['additive'] = "N/A"
if line[14] != "" and line[14] != None:
this_trait['additive'] = '%.3f' % line[14]
+ this_trait['dataset_id'] = line[15]
+ this_trait['locus_chr'] = line[16]
+ this_trait['locus_mb'] = line[17]
#dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
#trait_id = line[4]
#with Bench("Building trait object"):
- trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
- if not trait_ob:
- continue
max_lrs_text = "N/A"
- if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
- max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+ if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
+ max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
this_trait['max_lrs_text'] = max_lrs_text
trait_list.append(this_trait)
--
cgit v1.2.3
From 6749974cccdf10fc300c4265720dfd147db88989 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 17 Jan 2021 08:57:12 -0600
Subject: add dataset object creation, permission check in global search code
itself which takes the load off creating Trait object
---
wqflask/wqflask/gsearch.py | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 6ff57563..2b8d4bc1 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -68,6 +68,7 @@ class GSearch(object):
re = g.db.execute(sql).fetchall()
trait_list = []
+ dataset_to_permissions = {}
with Bench("Creating trait objects"):
for i, line in enumerate(re):
this_trait = {}
@@ -101,9 +102,15 @@ class GSearch(object):
this_trait['locus_chr'] = line[16]
this_trait['locus_mb'] = line[17]
- #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
- #trait_id = line[4]
- #with Bench("Building trait object"):
+ dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet",species=this_trait["species"])
+ if dataset_ob.id not in dataset_to_permissions:
+ permissions = check_resource_availability(dataset_ob)
+ dataset_to_permissions[dataset_ob.id] = permissions
+ else:
+ pemissions = dataset_to_permissions[dataset_ob.id]
+ if "view" not in permissions['data']:
+ continue
+
max_lrs_text = "N/A"
if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
--
cgit v1.2.3
From 5187e582721ddfbb1e864378823f2685748bf5f2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 18 Jan 2021 11:15:33 +0300
Subject: Pass salt as bytes when testing pbkdf2_hex
* wqflask/tests/unit/wqflask/test_pbkdf2.py (test_pbkdf2_hex): Make
password salt bytes. Breaking change introduced in 0bac313ba.
---
wqflask/tests/unit/wqflask/test_pbkdf2.py | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py
index a33fbd4f..7ad6c83e 100644
--- a/wqflask/tests/unit/wqflask/test_pbkdf2.py
+++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py
@@ -11,43 +11,43 @@ class TestPbkdf2(unittest.TestCase):
"""
for password, salt, iterations, keylen, expected_value in [
- ('password', 'salt', 1, 20,
+ ('password', b'salt', 1, 20,
'0c60c80f961f0e71f3a9b524af6012062fe037a6'),
- ('password', 'salt', 2, 20,
+ ('password', b'salt', 2, 20,
'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'),
- ('password', 'salt', 4096, 20,
+ ('password', b'salt', 4096, 20,
'4b007901b765489abead49d926f721d065a429c1'),
('passwordPASSWORDpassword',
- 'saltSALTsaltSALTsaltSALTsaltSALTsalt',
+ b'saltSALTsaltSALTsaltSALTsaltSALTsalt',
4096, 25,
'3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'),
- ('pass\x00word', 'sa\x00lt', 4096, 16,
+ ('pass\x00word', b'sa\x00lt', 4096, 16,
'56fa6aa75548099dcc37d7f03425e0c3'),
- ('password', 'ATHENA.MIT.EDUraeburn', 1, 16,
+ ('password', b'ATHENA.MIT.EDUraeburn', 1, 16,
'cdedb5281bb2f801565a1122b2563515'),
- ('password', 'ATHENA.MIT.EDUraeburn', 1, 32,
+ ('password', b'ATHENA.MIT.EDUraeburn', 1, 32,
('cdedb5281bb2f80'
'1565a1122b256351'
'50ad1f7a04bb9f3a33'
'3ecc0e2e1f70837')),
- ('password', 'ATHENA.MIT.EDUraeburn', 2, 16,
+ ('password', b'ATHENA.MIT.EDUraeburn', 2, 16,
'01dbee7f4a9e243e988b62c73cda935d'),
- ('password', 'ATHENA.MIT.EDUraeburn', 2, 32,
+ ('password', b'ATHENA.MIT.EDUraeburn', 2, 32,
('01dbee7f4a9e243e9'
'88b62c73cda935da05'
'378b93244ec8f48a99'
'e61ad799d86')),
- ('password', 'ATHENA.MIT.EDUraeburn', 1200, 32,
+ ('password', b'ATHENA.MIT.EDUraeburn', 1200, 32,
('5c08eb61fdf71e'
'4e4ec3cf6ba1f55'
'12ba7e52ddbc5e51'
'42f708a31e2e62b1e13')),
- ('X' * 64, 'pass phrase equals block size', 1200, 32,
+ ('X' * 64, b'pass phrase equals block size', 1200, 32,
('139c30c0966bc32ba'
'55fdbf212530ac9c5'
'ec59f1a452f5cc9ad'
'940fea0598ed1')),
- ('X' * 65, 'pass phrase exceeds block size', 1200, 32,
+ ('X' * 65, b'pass phrase exceeds block size', 1200, 32,
('9ccad6d468770cd'
'51b10e6a68721be6'
'11a8b4d282601db3'
--
cgit v1.2.3
From 8ed5d0e89cead10b03e5660c8eb87cf58a173436 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 18 Jan 2021 11:20:02 +0300
Subject: Remove extra newlines in PR and issue templates
---
.github/ISSUE_TEMPLATE/bug_report.md | 6 ------
.github/ISSUE_TEMPLATE/feature_request.md | 11 -----------
.github/ISSUE_TEMPLATE/user_story.md | 4 ----
.github/PULL_REQUEST_TEMPLATE.md | 3 ---
4 files changed, 24 deletions(-)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 48bad39b..af60c290 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,27 +8,21 @@ assignees: ''
---
**Describe the bug**
-
<!-- A clear and concise description of what the bug is. -->
**To Reproduce**
-
<!-- Steps to reproduce the behavior -->
**Expected behavior**
-
<!-- A clear and concise description of what you expected to happen. -->
**Screenshots**
-
<!-- If applicable, add screenshots to help explain your problem. -->
**Environment setup (please complete the following information):**
-
<!-- - OS: [e.g. Linux] -->
<!-- - Guix Version (optional) -->
<!-- - [Anything else you think is relevant] -->
**Additional context**
-
<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
index eb6c3e4b..813974c1 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -8,34 +8,23 @@ assignees: ''
---
## Is your feature request related to a problem? Please describe.
-
<!-- A clear and concise description of what the problem is. -->
-
<!-- Example: I'm always frustrated when [...] -->
## Describe the solution you'd like
-
<!-- A clear and concise description of what you want to happen. -->
## Describe alternatives you've considered
-
<!-- A clear and concise description of any alternative solutions or features you've considered. -->
## User Stories (optional)
-
<!-- Example: -->
-
<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
-
<!-- **Feature:** _[Brief description of feature]_ -->
-
<!-- _[Any additional descriptions on feature]_ -->
-
<!-- **Scenario:**
-
Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_
here -->
## Additional context
-
<!-- Add any other context or screenshots about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/user_story.md b/.github/ISSUE_TEMPLATE/user_story.md
index 52ae775d..d46976ba 100644
--- a/.github/ISSUE_TEMPLATE/user_story.md
+++ b/.github/ISSUE_TEMPLATE/user_story.md
@@ -6,11 +6,7 @@ labels: ''
assignees: ''
---
-
<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
-
<!-- **Feature:** _[Brief description of feature]_ -->
-
<!-- _[Any additional descriptions on feature]_ -->
-
<!-- **Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here -->
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index f3371183..926b0548 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -6,15 +6,12 @@
assurance checks that should be done. What are the expectations -->
#### Any background context you want to provide?
-
<!-- Anything the reviewer should be aware of ahead of testing -->
#### What are the relevant pivotal tracker stories?
-
<!-- Does this PR track anything anywhere? -->
#### Screenshots (if appropriate)
#### Questions
-
<!-- Are there any questions for the reviewer -->
--
cgit v1.2.3
From 42fd88d0e57462d4538ae328564fcc55da761991 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 18 Jan 2021 11:30:36 +0300
Subject: Revert "resize image in facilities page"
This reverts commit db31d53421c033a9907d2c67bc8a0c3c911b5402.
---
wqflask/wqflask/templates/facilities.html | 8 --------
1 file changed, 8 deletions(-)
diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html
index dc8d0ded..56b127f9 100644
--- a/wqflask/wqflask/templates/facilities.html
+++ b/wqflask/wqflask/templates/facilities.html
@@ -4,14 +4,6 @@
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" />
-
-<style>
- img[src="https://github.com/genenetwork/gn-docs/raw/master/general/help/octopus.jpg"] {
- width:100%;
- margin:20px 0px;
-}
-</style>
-
{% endblock %}
{% block content %}
--
cgit v1.2.3
From 3b2a835fce1cda94f0649d45297867ddb5994731 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Jan 2021 12:50:28 -0600
Subject: Fixed the Select Top Rows feature to use DataTables API instead of
JQuery
---
.../static/new/javascript/search_results.js | 48 +++++++++++++---------
1 file changed, 28 insertions(+), 20 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 05dcfda5..ecb1220d 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -95,29 +95,37 @@ $(function() {
$('#select_top').keyup(function(){
num_rows = $(this).val()
+
if (num_rows = parseInt(num_rows)){
- i = 0
- $('#trait_table > tbody > tr').each(function(){
- if (i < num_rows) {
- $(this).find('.trait_checkbox').prop("checked", true)
- if (!$(this).closest('tr').hasClass('selected')) {
- $(this).closest('tr').addClass('selected')
- }
- }
- else {
- if ($(this).closest('tr').hasClass('selected')) {
- $(this).closest('tr').removeClass('selected')
- $(this).find('.trait_checkbox').prop("checked", false)
- }
- }
- i += 1
- });
+ table_api = $('#trait_table').DataTable();
+
+ check_cells = table_api.column(0).nodes().to$();
+ for (let i = 0; i < num_rows; i++) {
+ check_cells[i].childNodes[0].checked = true;
+ }
+
+ check_rows = table_api.rows().nodes();
+ for (let i=0; i < num_rows; i++) {
+ if (check_rows[i].classList.contains("selected")){
+ continue
+ } else {
+ check_rows[i].classList.add("selected")
+ }
+ }
+ for (let i = num_rows; i < check_rows.length; i++){
+ check_cells[i].childNodes[0].checked = false;
+ if (check_rows[i].classList.contains("selected")){
+ check_rows[i].classList.remove("selected")
+ }
+ }
}
else {
- $('#trait_table > tbody > tr').each(function(){
- $(this).closest('tr').removeClass('selected')
- $(this).find('.trait_checkbox').prop("checked", false)
- });
+ for (let i = 0; i < check_rows.length; i++){
+ check_cells[i].childNodes[0].checked = false;
+ if (check_rows[i].classList.contains("selected")){
+ check_rows[i].classList.remove("selected")
+ }
+ }
}
change_buttons();
});
--
cgit v1.2.3
From af386b6d11872d633cd23185c22e8f9f8d650fd2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Jan 2021 14:27:46 -0600
Subject: Adjusted Search Result table column widths and header alignments
---
wqflask/wqflask/templates/search_result_page.html | 37 ++++++++++++-----------
1 file changed, 19 insertions(+), 18 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index b8f89121..eb42eb3a 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -274,41 +274,42 @@
}
},
{
- 'title': "Location",
+ 'title': "<div style='text-align: right;'>Location</div>",
'type': "natural-minus-na",
'width': "125px",
'data': "location"
},
{
- 'title': "Mean",
+ 'title': "<div style='text-align: right;'>Mean</div>",
'type': "natural-minus-na",
- 'width': "40px",
+ 'width': "30px",
'data': "mean",
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
+ 'title': "<div style='text-align: right;'>Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>LOD  </div>",
'type': "natural-minus-na",
'data': "lod_score",
'width': "60px",
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Peak Location",
+ 'title': "<div style='text-align: right;'>Peak Location</div>",
'type': "natural-minus-na",
'width': "125px",
'data': "lrs_location"
},
{
- 'title': "Effect Size<a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+ 'title': "<div style='text-align: right;'>Effect <a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>Size  </div>",
'type': "natural-minus-na",
'data': "additive",
- 'width': "90px",
+ 'width': "60px",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Publish' %},
{
'title': "Description",
'type': "natural",
+ 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -319,16 +320,16 @@
}
},
{
- 'title': "Mean",
+ 'title': "<div style='text-align: right;'>Mean</div>",
'type': "natural-minus-na",
- 'width': "110px",
+ 'width': "30px",
'data': "mean",
'orderSequence': [ "desc", "asc"]
},
{
'title': "Authors",
'type': "natural",
- 'width': "500px",
+ 'width': "400px",
'data': null,
'render': function(data, type, row, meta) {
author_list = data.authors.split(",")
@@ -341,10 +342,10 @@
}
},
{
- 'title': "Year",
+ 'title': "<div style='text-align: right;'>Year</div>",
'type': "natural-minus-na",
'data': null,
- 'width': "80px",
+ 'width': "25px",
'render': function(data, type, row, meta) {
if (data.pubmed_id != "N/A"){
return '<a href="' + data.pubmed_link + '">' + data.pubmed_text + '</a>'
@@ -355,34 +356,34 @@
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
+ 'title': "<div style='text-align: right;'>Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>LOD  </div>",
'type': "natural-minus-na",
'data': "lod_score",
'width': "60px",
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Peak Location",
+ 'title': "<div style='text-align: right;'>Peak Location</div>",
'type': "natural-minus-na",
'width': "120px",
'data': "lrs_location"
},
{
- 'title': "Effect Size<a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+ 'title': "<div style='text-align: right;'>Effect <a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>Size  </div>",
'type': "natural-minus-na",
- 'width': "120px",
+ 'width': "60px",
'data': "additive",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Geno' %},
{
- 'title': "Location",
+ 'title': "<div style='text-align: right;'>Location</div>",
'type': "natural-minus-na",
'width': "120px",
'data': "location"
}{% endif %}
],
"order": [[1, "asc" ]],
- 'sDom': "itir",
+ 'sDom': "iti",
"autoWidth": true,
"bSortClasses": false,
"scrollY": "100vh",
--
cgit v1.2.3
From 1ad00938cafb2f0511658397050f6e938854d194 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Jan 2021 14:31:14 -0600
Subject: Changed CSS for show/hide column buttons so it's more obvious when
one is selected
---
wqflask/wqflask/static/new/css/trait_list.css | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/css/trait_list.css b/wqflask/wqflask/static/new/css/trait_list.css
index b83655da..b765cdd4 100644
--- a/wqflask/wqflask/static/new/css/trait_list.css
+++ b/wqflask/wqflask/static/new/css/trait_list.css
@@ -12,7 +12,7 @@ div.show-hide-container {
}
button.active {
- background: #e5e5e5;
+ background: #BEBEBE;
-webkit-box-shadow: inset 0px 0px 5px #c1c1c1;
-moz-box-shadow: inset 0px 0px 5px #c1c1c1;
box-shadow: inset 0px 0px 5px #c1c1c1;
--
cgit v1.2.3
From db2d9d81493750971ccfe59934dcb6e00f67c521 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Jan 2021 15:15:12 -0600
Subject: Decreased the width of the Authors column some
---
wqflask/wqflask/templates/search_result_page.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index eb42eb3a..9b36568c 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -329,7 +329,7 @@
{
'title': "Authors",
'type': "natural",
- 'width': "400px",
+ 'width': "300px",
'data': null,
'render': function(data, type, row, meta) {
author_list = data.authors.split(",")
--
cgit v1.2.3
From 9f12da2623c3ca9156300c825fe0f86ad08bb76e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Jan 2021 15:26:26 -0600
Subject: Added modified Scroller CSS to trait_list.css in order to add the
text showing current row when scrolling and remove a 0 that was appearing
below the table
---
wqflask/wqflask/static/new/css/trait_list.css | 36 ++++++++++++++++++++++++++-
1 file changed, 35 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/css/trait_list.css b/wqflask/wqflask/static/new/css/trait_list.css
index b765cdd4..c7249721 100644
--- a/wqflask/wqflask/static/new/css/trait_list.css
+++ b/wqflask/wqflask/static/new/css/trait_list.css
@@ -17,4 +17,38 @@ button.active {
-moz-box-shadow: inset 0px 0px 5px #c1c1c1;
box-shadow: inset 0px 0px 5px #c1c1c1;
outline: none;
- }
\ No newline at end of file
+}
+
+div.dts {
+ display:block !important
+}
+
+div.dts div.dts_loading {
+ z-index:1
+}
+
+div.dts div.dts_label {
+ position:absolute;
+ right:10px;
+ background:rgba(0,0,0,0.8);
+ color:white;
+ box-shadow:3px 3px 10px rgba(0,0,0,0.5);
+ text-align:right;
+ border-radius:3px;
+ padding:0.4em;
+ z-index:2;
+ display:none
+}
+
+div.dts div.dataTables_scrollBody {
+ background:repeating-linear-gradient(45deg, #edeeff, #edeeff 10px, #fff 10px, #fff 20px)
+}
+
+div.dts div.dataTables_scrollBody table {
+ z-index:2
+}
+
+div.dts div.dataTables_paginate,div.dts div.dataTables_length{
+ display:none
+}
+
--
cgit v1.2.3