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-rw-r--r--wqflask/base/GeneralObject.py2
-rw-r--r--wqflask/tests/wqflask/show_trait/test_show_trait.py242
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py2
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py19
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py6
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css2
-rw-r--r--wqflask/wqflask/static/new/css/trait_list.css12
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js8
-rw-r--r--wqflask/wqflask/templates/collections/view.html33
-rw-r--r--wqflask/wqflask/templates/correlation_page.html4
-rw-r--r--wqflask/wqflask/templates/search_result_page.html72
11 files changed, 342 insertions, 60 deletions
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 0122ee32..249195e2 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -28,7 +28,7 @@ class GeneralObject:
"""
Base class to define an Object.
a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
- a.sort(lambda x, y: cmp(x.eggs, y.eggs))
+ a.sort(key = lambda x: x.eggs)
"""
def __init__(self, *args, **kw):
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
new file mode 100644
index 00000000..24150738
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -0,0 +1,242 @@
+"""test for wqflask/show_trait/test_show_trait.py"""
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.show_trait.show_trait import check_if_attr_exists
+from wqflask.show_trait.show_trait import get_ncbi_summary
+from wqflask.show_trait.show_trait import has_num_cases
+from wqflask.show_trait.show_trait import get_table_widths
+from wqflask.show_trait.show_trait import get_categorical_variables
+from wqflask.show_trait.show_trait import get_trait_units
+from wqflask.show_trait.show_trait import get_nearest_marker
+from wqflask.show_trait.show_trait import get_genotype_scales
+from wqflask.show_trait.show_trait import requests
+
+
+class TraitObject:
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
+
+
+class TestTraits(unittest.TestCase):
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ def test_check_if_attr_exists_truthy(self):
+ """"test if attributes exists with true return"""
+ trait_obj = TraitObject({"id_type": "id"})
+ trait_obj2 = TraitObject({"sample_name": ['samp1']})
+ results = check_if_attr_exists(trait_obj, "id_type")
+ result2 = check_if_attr_exists(trait_obj2, "sample_name")
+ self.assertIsInstance(trait_obj, TraitObject)
+ self.assertTrue(results)
+ self.assertTrue(result2)
+
+ def test_check_if_attr_exists_empty_attr(self):
+ """test if attributes exists with false return"""
+ trait_obj = TraitObject({"sample": ""})
+ trait_obj2 = TraitObject({"group": None})
+ result = check_if_attr_exists(trait_obj, "sample")
+ result2 = check_if_attr_exists(trait_obj, "group")
+ self.assertFalse(result)
+ self.assertFalse(result2)
+
+ def test_check_if_attr_exists_falsey(self):
+ """check if attribute exists with empty attributes"""
+ trait_obj = TraitObject({})
+ results = check_if_attr_exists(trait_obj, "any")
+ self.assertFalse(results)
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_success(self, mock_exists, mock_get):
+ """test for getting ncbi summary with
+ successful request"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+ get_return_obj = TraitObject({"content": content_json_string})
+ mock_get.return_value = get_return_obj
+ results = get_ncbi_summary(trait)
+ mock_exists.assert_called_once()
+ mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
+
+ self.assertEqual(results, "this is a summary of the geneid")
+
+ @mock.patch("wqflask.show_trait.show_trait.requests.get")
+ @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+ def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail):
+ """test for getting ncbi summary with request fail"""
+ trait = TraitObject({"geneid": "id"})
+ mock_exists.return_value = True
+ mock_get_fail.side_effect = Exception("an error occurred")
+ content_json_string = """{
+ "result":{
+ "id":{
+ "summary":"this is a summary of the geneid"
+ }
+ }
+ }
+ """
+ results = get_ncbi_summary(trait)
+ self.assertEqual(results, None)
+
+ def test_hash_num_cases_is_probeset(self):
+ """test for hash num_cases with dataset.type set to Probeset"""
+ create_dataset = TraitObject({"type": "ProbeSet"})
+ create_trait = TraitObject({"dataset": create_dataset})
+ self.assertFalse(has_num_cases(create_trait))
+
+ def test_hash_num_cases_no_probeset(self):
+ """test for hash num cases with dataset.type not Probeset"""
+ create_dataset = TraitObject({"type": "Temp"})
+ construct_data = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": True}),
+ "nm3": TraitObject({"num_cases": False})
+ }
+ construct_data2 = {
+ "nm1": TraitObject({"num_cases": False}),
+ "nm2": TraitObject({"num_cases": False}),
+ "nm3": TraitObject({"num_cases": False})
+ }
+ create_trait = TraitObject(
+ {"dataset": create_dataset, "data": construct_data})
+ create_trait2 = TraitObject(
+ {"dataset": create_dataset, "data": construct_data2})
+
+ results = has_num_cases(create_trait)
+ self.assertTrue(has_num_cases(create_trait))
+ self.assertFalse(has_num_cases(create_trait2))
+
+ def test_get_table_widths(self):
+ """test for getting table widths"""
+ sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]}
+ ), TraitObject(
+ {"se_exists": False, "attributes": ["at1", "at2"]
+ })]
+
+ results_with_numcase = get_table_widths(sample_groups, True)
+ result_no_numcase = get_table_widths(sample_groups, False)
+
+ results_one_sample = get_table_widths(
+ [TraitObject({"se_exists": True, "attributes": []})], True)
+ expected_with_numcase = (450, "750px")
+ expected_no_numcase = (450, "670px")
+ expected_one_sample = (250, "540px")
+ self.assertEqual(results_with_numcase, expected_with_numcase)
+ self.assertEqual(result_no_numcase, expected_no_numcase)
+ self.assertEqual(results_one_sample,
+ expected_one_sample)
+
+ def test_get_categorical_variables_no_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
+ trait = TraitObject({})
+ sample_list = TraitObject({"se_exists": True, "attributes": []})
+ self.assertEqual(get_categorical_variables(trait, sample_list), [])
+
+ def test_get_categorical_variables_with_sample_attributes(self):
+ """test for getting categorical variable names with no samples"""
+ this_trait = TraitObject({"data": {
+ "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}),
+ "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}),
+ "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}})
+ }})
+ sample_list = TraitObject({"attributes": {
+ "sample_attribute_1": TraitObject({"name": "ex1"}),
+ "sample_attribute_2": TraitObject({"name": "ex2"}),
+ "sample_attribute_3": TraitObject({"name": "ex3"}),
+ "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"})
+ }})
+ results = get_categorical_variables(this_trait, sample_list)
+ self.assertEqual(
+ ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results)
+
+ def test_get_trait_units(self):
+ """test for getting trait units"""
+ trait = TraitObject(
+ {"description_fmt": "[this is a description] another test [N/A]"})
+ trait_no_unit_type = TraitObject({"description_fmt": ""})
+ results = get_trait_units(trait)
+ results_no_unit = get_trait_units(trait_no_unit_type)
+ self.assertEqual(results, "this is a descriptionN/A")
+ self.assertEqual(results_no_unit, "Value")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker(self, mock_db):
+ """test for getting nearest marker with non-empty db"""
+
+ mock_db.db.execute.return_value.fetchall.return_value = [
+ ["Geno1", "Geno2"], ["Geno3"]]
+
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+ group_name = TraitObject({"name": "group_name"})
+ this_db = TraitObject({"group": group_name})
+ results_with_item_db = get_nearest_marker(trait, this_db)
+ called_with_value = """SELECT Geno.Name
+ FROM Geno, GenoXRef, GenoFreeze
+ WHERE Geno.Chr = 'test_chr' AND
+ GenoXRef.GenoId = Geno.Id AND
+ GenoFreeze.Id = GenoXRef.GenoFreezeId AND
+ GenoFreeze.Name = 'group_nameGeno'
+ ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1"""
+
+ mock_db.db.execute.assert_called_with(called_with_value)
+
+ self.assertEqual(results_with_item_db, "Geno1")
+
+ @mock.patch("wqflask.show_trait.show_trait.g")
+ def test_get_nearest_marker_empty_db(self, mock_db):
+ """test for getting nearest marker with empty db"""
+ mock_db.db.execute.return_value.fetchall.return_value = []
+ trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+ group_name = TraitObject({"name": "group_name"})
+ this_db = TraitObject({"group": group_name})
+ results_empty_db = get_nearest_marker(trait, this_db)
+ mock_db.db.execute.assert_called_once()
+ self.assertEqual(results_empty_db, "")
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):
+ """test for getting genotype scales with genofile as list """
+ # where genofile is instance of list
+ genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"},
+ {"filename": "file2", "location": "~/data/files/f2"},
+ {"filename": "file3", "location": "~/data/files/f3"}]
+
+ mock_get_scales.side_effect = [[["morgan", "cM"]],
+ [["morgan", "cM"]],
+ [["physic", "Mb"]]]
+
+ results = get_genotype_scales(genofiles_list)
+ expected_results = {
+ "~/data/files/f1": [["morgan", "cM"]],
+ "~/data/files/f2": [["morgan", "cM"]],
+ "~/data/files/f3": [["physic", "Mb"]]
+ }
+
+ multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'),
+ mock.call('~/data/files/f3')]
+ mock_get_scales.assert_has_calls(multiple_calls)
+ self.assertEqual(results, expected_results)
+
+ @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+ def test_genotype_scales_with_genofile_other(self, mock_get_scales):
+ """test for getting genotype scales with genofile as a string"""
+ file_location = "~/another_file_location"
+ mock_get_scales.return_value = [["physic", "Mb"]]
+ expected_results = {f"{file_location}": [["physic", "Mb"]]}
+ self.assertEqual(get_genotype_scales(file_location), expected_results)
+ mock_get_scales.assert_called_once_with(file_location)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 04d47624..6d6572ff 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1460,7 +1460,7 @@ class DisplayMappingResults(object):
else:
continue
- smd.sort(lambda A, B: cmp(A.value, B.value))
+ smd.sort(key = lambda A: A.value)
smd.reverse()
samplelist = list(self.genotype.prgy)
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 37c1d6d5..a535c493 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -34,13 +34,18 @@ class SampleList(object):
# ZS: self.this_trait will be a list if it is a Temp trait
if isinstance(self.this_trait, list):
- if (counter <= len(self.this_trait) and
- str(self.this_trait[counter-1]).upper() != 'X'):
- sample = webqtlCaseData.webqtlCaseData(
- name=sample_name,
- value=float(self.this_trait[counter-1]))
- else:
- sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+ sample = webqtlCaseData.webqtlCaseData(name=sample_name)
+ if counter <= len(self.this_trait):
+ if isinstance(self.this_trait[counter-1], (bytes, bytearray)):
+ if (self.this_trait[counter-1].decode("utf-8").lower() != 'x'):
+ sample = webqtlCaseData.webqtlCaseData(
+ name=sample_name,
+ value=float(self.this_trait[counter-1]))
+ else:
+ if (self.this_trait[counter-1].lower() != 'x'):
+ sample = webqtlCaseData.webqtlCaseData(
+ name=sample_name,
+ value=float(self.this_trait[counter-1]))
else:
# ZS - If there's no value for the sample/strain,
# create the sample object (so samples with no value
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index edf9638c..0c6ae198 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -228,8 +228,8 @@ class ShowTrait(object):
hddn = OrderedDict()
if self.dataset.group.allsamples:
- hddn['allsamples'] = ''.join(self.dataset.group.allsamples)
- hddn['primary_samples'] = ''.join(self.primary_sample_names)
+ hddn['allsamples'] = ','.join(self.dataset.group.allsamples)
+ hddn['primary_samples'] = ','.join(self.primary_sample_names)
hddn['trait_id'] = self.trait_id
hddn['trait_display_name'] = self.this_trait.display_name
hddn['dataset'] = self.dataset.name
@@ -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-Harvested":
+ if this_group[:3] == 'BXD' and this_group != "BXD-Longevity":
this_group = 'BXD'
if this_group:
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index d8964f5d..5e1a279b 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -67,7 +67,7 @@ table.dataTable.cell-border tbody tr td:first-child {
}
.showtrait-main-div {
- min-width: 700px;
+ min-width: 1100px;
}
table.dataTable tbody td.column_name-Checkbox {
diff --git a/wqflask/wqflask/static/new/css/trait_list.css b/wqflask/wqflask/static/new/css/trait_list.css
new file mode 100644
index 00000000..691dcb12
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/trait_list.css
@@ -0,0 +1,12 @@
+div.tool-button-container {
+ min-width: 950px;
+}
+
+div.collection-table-options {
+ min-width: 1100px;
+}
+
+div.show-hide-container {
+ margin-bottom: 5px;
+ margin-top: 10px;
+} \ No newline at end of file
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 c0f36eaa..34582f21 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -147,7 +147,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
-$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
+$(".rqtl-tab, #rqtl_geno_compute").on("click", (function(_this) {
return function() {
if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
var form_data, url;
@@ -171,7 +171,7 @@ $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
};
})(this));
-$(".gemma_tab, #gemma_compute").on("click", (function(_this) {
+$(".gemma-tab, #gemma_compute").on("click", (function(_this) {
return function() {
if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
var form_data, url;
@@ -192,7 +192,7 @@ $(".gemma_tab, #gemma_compute").on("click", (function(_this) {
};
})(this));
-$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
+$(".reaper-tab, #interval_mapping_compute").on("click", (function(_this) {
return function() {
if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
var form_data, url;
@@ -260,7 +260,7 @@ $("#mapmethod_rqtl_geno").change(function() {
}
});
-$("li.mapping_tab").click(function() {
+$("li.mapping-tab").click(function() {
if ($(this).hasClass("rqtl")){
$(".rqtl_description").css("display", "block");
} else {
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 873a6703..e37f8104 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -4,6 +4,7 @@
<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('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/trait_list.css" />
{% endblock %}
{% block content %}
<!-- Start of body -->
@@ -16,7 +17,7 @@
</h1>
<h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
- <div>
+ <div class="tool-button-container">
<form id="collection_form" action="/delete" method="post">
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
<input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
@@ -68,20 +69,22 @@
<div>
<br />
- <form id="export_form" method="POST" action="/export_traits_csv">
- <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button>
- <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button>
- <button class="btn btn-success" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button>
- <input type="hidden" name="database_name" id="database_name" value="None">
- <input type="hidden" name="export_data" id="export_data" value="">
- <input type="hidden" name="file_name" id="file_name" value="collection_table">
- <button class="btn btn-default" id="export_traits">Download</button>
- <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
- <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
- <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
- <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button>
- <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
- </form>
+ <div class="collection-table-options">
+ <form id="export_form" method="POST" action="/export_traits_csv">
+ <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+ <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button>
+ <button class="btn btn-success" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button>
+ <input type="hidden" name="database_name" id="database_name" value="None">
+ <input type="hidden" name="export_data" id="export_data" value="">
+ <input type="hidden" name="file_name" id="file_name" value="collection_table">
+ <button class="btn btn-default" id="export_traits">Download</button>
+ <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
+ <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
+ <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
+ <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button>
+ <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
+ </form>
+ </div>
<div style="margin-top: 10px; margin-bottom: 5px;">
<b>Show/Hide Columns:</b>
</div>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 134f15be..bc0b592c 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -367,8 +367,8 @@
{ "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
{ "type": "natural" },
{ "type": "scientific" },
- { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
- { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
+ { "type": "natural-minus-na", 'orderSequence': [ "desc", "asc"] },
+ { "type": "natural-minus-na", 'orderSequence': [ "desc", "asc"] },
{ "type": "scientific" },
{ "type": "natural-minus-na" },
{ "type": "natural-minus-na" },
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 6d9ea8fe..36f144c2 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -5,6 +5,7 @@
<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/buttonStyles/css/buttons.dataTables.min.css') }}">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+ <link rel="stylesheet" type="text/css" href="static/new/css/trait_list.css" />
{% endblock %}
{% block content %}
<!-- Start of body -->
@@ -40,10 +41,10 @@
{% elif word.search_term|length == 5 %}
with <u>{{ word.key|upper }}</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
{% endif %}
- {% elif word.key|lower == "position" %}
- with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
+ {% elif word.key|lower == "position" or word.key|lower == "mb" %}
+ with <u>target genes</u> on chromosome <strong>{% if (word.search_term[0]|lower).split('chr')|length > 1 %}{{ (word.search_term[0]|lower).split('chr')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
{% else %}
- {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>"{{ word.search_term[0] }}"</b>{% if loop.last %}{% else %} and {% endif %}{% endif %}
+ {% if word.search_term[0] == "*" %} in the dataset.{% else %}{% if loop.first %}that match:<br>{% endif %}<b>{{ word.search_term[0] }}</b>{% if loop.last %}{% else %} and {% endif %}{% endif %}
{% endif %}
{% endfor %}
{% endif %}
@@ -133,11 +134,29 @@
<button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
</div>
</form>
- <br />
{% if dataset.type != 'Geno' %}
- <br />
- <div style="margin-bottom: 5px;">
+ <div class="show-hide-container">
<b>Show/Hide Columns:</b>
+ <br>
+ <button class="toggle-vis" data-column="1">Index</button>
+ <button class="toggle-vis" data-column="2">Record</button>
+ {% if dataset.type == 'ProbeSet' %}
+ <button class="toggle-vis" data-column="3">Symbol</button>
+ <button class="toggle-vis" data-column="4">Description</button>
+ <button class="toggle-vis" data-column="5">Location</button>
+ <button class="toggle-vis" data-column="6">Mean</button>
+ <button class="toggle-vis" data-column="7">High P</button>
+ <button class="toggle-vis" data-column="8">Peak Location</button>
+ <button class="toggle-vis" data-column="9">Effect Size</button>
+ {% elif dataset.type == 'Publish' %}
+ <button class="toggle-vis" data-column="3">Description</button>
+ <button class="toggle-vis" data-column="4">Mean</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">High P</button>
+ <button class="toggle-vis" data-column="8">Peak Location</button>
+ <button class="toggle-vis" data-column="9">Effect Size</button>
+ {% endif %}
</div>
{% endif %}
<div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
@@ -209,7 +228,7 @@
}
//ZS: Need to make sort by symbol, also need to make sure blank symbol fields at the bottom and symbols starting with numbers below letters
- $('#trait_table').DataTable( {
+ trait_table = $('#trait_table').DataTable( {
'drawCallback': function( settings ) {
$('#trait_table tr').click(function(event) {
if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
@@ -381,7 +400,7 @@
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Max LRS<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
+ 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
'type': "natural-minus-na",
'data': "lrs_score",
'width': "80px",
@@ -408,24 +427,7 @@
}{% 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 %}
+ 'sDom': "itirp",
'iDisplayLength': 500,
'deferRender': true,
'paging': true,
@@ -439,6 +441,23 @@
console.timeEnd("Creating table");
+ $('.toggle-vis').on( 'click', function (e) {
+ e.preventDefault();
+
+ // Get the column API object
+ var column = trait_table.column( $(this).attr('data-column') );
+
+ // Toggle the visibility
+ column.visible( ! column.visible() );
+
+ if (column.visible()){
+ $(this).removeClass("active");
+ } else {
+ $(this).addClass("active");
+ }
+ } );
+
+
$('#redraw').click(function() {
var table = $('#trait_table').DataTable();
table.colReorder.reset()
@@ -452,3 +471,4 @@
});
</script>
{% endblock %}
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 20:07:52 +0000