Merge branch 'testing' into replace-cytoscape

18 files changed, 140 insertions, 40 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 5bc30798..f28d9e7d 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -120,7 +120,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/cytoscape-panzoom/cytoscape-panzoom.js",
         "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
         "/js/cytoscape-qtip/cytoscape-qtip.js",
-
+        "/css/d3-tip/d3-tip.css",
     ]
 
     print("Checking links")
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ec8c40a0..50bd8874 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -25,19 +25,19 @@ def create_trait(**kw):
     assert bool(kw.get('dataset')) != bool(
         kw.get('dataset_name')), "Needs dataset ob. or name"
 
-    if kw.get('name'):
-        if kw.get('dataset_name'):
-            if kw.get('dataset_name') != "Temp":
-                dataset = create_dataset(kw.get('dataset_name'))
-        else:
-            dataset = kw.get('dataset')
+    assert bool(kw.get('name')), "Needs trait name"
 
+    if kw.get('dataset_name'):
         if kw.get('dataset_name') != "Temp":
-            if dataset.type == 'Publish':
-                permissions = check_resource_availability(
-                    dataset, kw.get('name'))
-            else:
-                permissions = check_resource_availability(dataset)
+            dataset = create_dataset(kw.get('dataset_name'))
+    else:
+        dataset = kw.get('dataset')
+
+    if dataset.type == 'Publish':
+        permissions = check_resource_availability(
+            dataset, kw.get('name'))
+    else:
+        permissions = check_resource_availability(dataset)
 
     if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
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 5b621264..b8c13ab4 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -43,22 +43,22 @@ class TestGemmaMapping(unittest.TestCase):
     @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
     @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/")
     @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
-    @mock.patch("wqflask.marker_regression.gemma_mapping.logger")
     @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
     @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
     @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
     @mock.patch("wqflask.marker_regression.gemma_mapping.os")
     @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
-    def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco):
+    def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco):
         """add tests for run_gemma where first run is set to true"""
-        chromosomes = []
+        this_chromosomes={}
         for i in range(1, 5):
-            chromosomes.append(AttributeSetter({"name": f"CH{i}"}))
-        chromo = AttributeSetter({"chromosomes": chromosomes})
+            this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+        chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
+
         dataset_group = MockGroup(
             {"name": "GP1", "genofile": "file_geno"})
         dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name",
-                                   "species": AttributeSetter({"chromosomes": chromo})})
+                                   "species": AttributeSetter({"chromosomes": chromosomes})})
         trait = AttributeSetter({"name": "trait1"})
         samples = []
         mock_gen_pheno_txt.return_value = None
@@ -76,7 +76,6 @@ class TestGemmaMapping(unittest.TestCase):
         mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR")
         mock_os.path.isfile.assert_called_once_with(
             ('/home/user/imgfile_output.assoc.txt'))
-        self.assertEqual(mock_logger.debug.call_count, 2)
         self.assertEqual(mock_flat_files.call_count, 4)
         self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
 
diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py
index 183f4caa..ebf75807 100644
--- a/wqflask/wqflask/markdown_routes.py
+++ b/wqflask/wqflask/markdown_routes.py
@@ -9,6 +9,7 @@ import sys
 
 from bs4 import BeautifulSoup
 
+from flask import send_from_directory
 from flask import Blueprint
 from flask import render_template
 
@@ -99,6 +100,13 @@ def environments():
             200)
 
 
+@environments_blueprint.route('/svg-dependency-graph')
+def svg_graph():
+    directory, file_name, _ = get_file_from_python_search_path(
+            "wqflask/dependency-graph.svg").partition("dependency-graph.svg")
+    return send_from_directory(directory, file_name)
+
+
 @links_blueprint.route("/")
 def links():
     return render_template(
@@ -109,7 +117,7 @@ def links():
 @policies_blueprint.route("/")
 def policies():
     return render_template(
-        "links.html",
+        "policies.html",
         rendered_markdown=render_markdown("general/policies/policies.md")), 200
 
 
diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css
index 38d664e2..859fe7fc 100644
--- a/wqflask/wqflask/static/new/css/markdown.css
+++ b/wqflask/wqflask/static/new/css/markdown.css
@@ -62,7 +62,8 @@
 }
 
 .graph-legend,
-#guix-graph {
+#guix-graph,
+#guix-svg-graph{
     width: 90%;
     margin: 10px auto;
 }
@@ -71,6 +72,10 @@
     border: solid 2px black;
 }
 
+#guix-svg-graph img {
+    width: 100%;
+}
+
 #markdown table {
     width: 100%;
 }
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index f791457f..b27a6b06 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block title %}Comparison Bar Chart{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 4e150618..96ad9c35 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -4,7 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
 {% endblock %}
 {% block content %}
 
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..68566ee5 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -345,8 +345,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -357,7 +364,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
@@ -459,8 +466,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -471,7 +485,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
@@ -506,8 +520,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -518,7 +539,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html
index 5fe01dad..89e805ce 100644
--- a/wqflask/wqflask/templates/environment.html
+++ b/wqflask/wqflask/templates/environment.html
@@ -21,6 +21,16 @@
 </div>
 
 <div id="guix-graph"></div>
+
+<!-- Display the svg graph -->
+
+<div id="guix-svg-graph">
+    <h1>The dependency graph is shown below</h1>
+
+    <p>To explore this image SVG you may want to open it in new browser page and zoom in. Or use an SVG viewing application.</p>
+
+    <img alt="Dependency graph of the tools needed to build python3-genenetwork2" src="{{url_for('environments_blueprint.svg_graph')}}"/>
+</div>
 {% endif %}
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html
index a022b657..56b127f9 100644
--- a/wqflask/wqflask/templates/facilities.html
+++ b/wqflask/wqflask/templates/facilities.html
@@ -10,7 +10,7 @@
 
  <div class="github-btn-container">
     <div class="github-btn">
-        <a href="https://github.com/genenetwork/gn-docs">
+        <a href="https://github.com/genenetwork/gn-docs/blob/master/general/help/facilities.md">
             Edit Text
             <img src="/static/images/edit.png">
         </a>
diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html
index 752c4b12..aaee7c5a 100644
--- a/wqflask/wqflask/templates/glossary.html
+++ b/wqflask/wqflask/templates/glossary.html
@@ -10,7 +10,7 @@
 
 <div class="github-btn-container">
     <div class="github-btn">
-        <a href="https://github.com/genenetwork/gn-docs">
+        <a href="https://github.com/genenetwork/gn-docs/blob/master/general/glossary/glossary.md">
             Edit Text
             <img src="/static/images/edit.png">
         </a>
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 497838dd..b16de42e 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block title %}Heatmap{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/links.html b/wqflask/wqflask/templates/links.html
index 072e8429..6e91adae 100644
--- a/wqflask/wqflask/templates/links.html
+++ b/wqflask/wqflask/templates/links.html
@@ -10,7 +10,7 @@
 
 <div class="github-btn-container">
     <div class="github-btn ">
-        <a href="https://github.com/genenetwork/gn-docs">
+        <a href="https://github.com/genenetwork/gn-docs/blob/master/general/links/links.md">
             Edit Text
             <img src="/static/images/edit.png">
         </a>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f1646af7..d64bb4b4 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -4,7 +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="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 
diff --git a/wqflask/wqflask/templates/policies.html b/wqflask/wqflask/templates/policies.html
index 4e0985d3..e36c9e08 100644
--- a/wqflask/wqflask/templates/policies.html
+++ b/wqflask/wqflask/templates/policies.html
@@ -10,7 +10,7 @@
 
  <div class="github-btn-container">
     <div class="github-btn ">
-        <a href="https://github.com/genenetwork/gn-docs">
+        <a href="https://github.com/genenetwork/gn-docs/blob/master/general/policies/policies.md">
             Edit Text
             <img src="/static/images/edit.png">
         </a>
diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html
index f723a1e8..04e60361 100644
--- a/wqflask/wqflask/templates/references.html
+++ b/wqflask/wqflask/templates/references.html
@@ -6,7 +6,7 @@
 {% block content %}
 <div class="github-btn-container">
     <div class="github-btn">
-        <a href="https://github.com/genenetwork/gn-docs">
+        <a href="https://github.com/genenetwork/gn-docs/blob/master/general/references/references.md">
             Edit Text
             <img src="/static/images/edit.png">
         </a>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..07efbe62 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -5,7 +5,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
@@ -221,6 +221,33 @@
                   primary_table.search($(this).val()).draw();
                 } );
 
+                $('.toggle-vis').on('click', function (e) {
+                    e.preventDefault();
+
+                    function toggle_column(column) {
+                        //ZS: Toggle column visibility
+                        column.visible( ! column.visible() );
+                        if (column.visible()){
+                            $(this).removeClass("active");
+                        } else {
+                            $(this).addClass("active");
+                        }
+                    }
+
+                    // Get the column API object
+                    var target_cols = $(this).attr('data-column').split(",")
+                    for (let i = 0; i < target_cols.length; i++){
+                        console.log("THE COL:", target_cols[i])
+                        var column = primary_table.column( target_cols[i] );
+                        toggle_column(column);
+
+                        {% if sample_groups|length != 1 %}
+                        var column2 = other_table.column( target_cols[i] );
+                        toggle_column(column2);
+                        {% endif %}
+                    }
+                } );
+
                 {% if sample_groups|length != 1 %}
                 $('#other_searchbox').on( 'keyup', function () {
                   other_table.search($(this).val()).draw();
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 2e730248..4ad11a5e 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,36 @@
 <div>
     {% for sample_type in sample_groups %}
       <div class="sample-table-container">
+        {% if loop.index == 1 %}
+        <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 %}
+        <button class="toggle-vis" data-column="6">N</button>
+        {% set attr_start_pos = 7 %}
+        {% else %}
+        {% set attr_start_pos = 6 %}
+        {% endif %}
+        {% else %}
+        {% if has_num_cases %}
+        <button class="toggle-vis" data-column="4">N</button>
+        {% set attr_start_pos = 5 %}
+        {% else %}
+        {% set attr_start_pos = 4 %}
+        {% endif %}
+        {% endif %}
+        {% if sample_groups[0].attributes %}
+        {% for attribute in sample_groups[0].attributes %}
+        <button class="toggle-vis" data-column="{{ loop.index + attr_start_pos - 1 }}">{{ sample_groups[0].attributes[attribute].name }}</button>
+        {% endfor %}
+        {% endif %}
+        <br>
+        <br>
+        {% endif %}
         <div class="sample-table-search-container">
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control sample-table-search" placeholder="Search This Table For ...">
         </div>