Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into HEAD

8 files changed, 72 insertions, 66 deletions

diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index bc029965..2d96c05a 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -12,12 +12,17 @@ from pprint import pformat as pf
 def export_search_results_csv(targs):
 
     table_data = json.loads(targs['export_data'])
-    table_headers = targs['headers'].split(",")
+    table_headers = table_data['headers']
     table_rows = table_data['rows']
     
     buff = StringIO.StringIO()
     writer = csv.writer(buff)
     
+    if 'file_name' in targs:
+        file_name = targs['file_name']
+    else:
+        file_name = "table_export.csv"
+
     metadata = []
 
     if 'database_name' in targs:
@@ -39,15 +44,15 @@ def export_search_results_csv(targs):
     for metadata_row in metadata:
         writer.writerow(metadata_row)
 
-    writer.writerow([""])
+    writer.writerow([])
 
     writer.writerow(table_headers)
     for trait_info in table_rows:
         writer.writerow(trait_info)
 
-    writer.writerow([""])
+    writer.writerow([])
     writer.writerow(["Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)"])
     csv_data = buff.getvalue()
     buff.close()
 
-    return csv_data
\ No newline at end of file
+    return csv_data, file_name
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index aa6ada5a..451be50b 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -55,7 +55,7 @@ class SampleList(object):
                 try:
                     sample = self.this_trait.data[sample_name]
                 except KeyError:
-                    logger.debug("No sample %s, let's create it now" % sample_name)
+                    #logger.debug("No sample %s, let's create it now" % sample_name)
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
@@ -106,7 +106,7 @@ class SampleList(object):
         self.attributes = {}
         for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
             key, name = attr
-            logger.debug("radish: %s - %s" % (key, name))
+            #logger.debug("radish: %s - %s" % (key, name))
             self.attributes[key] = Bunch()
             self.attributes[key].name = name
             self.attributes[key].distinct_values = [item.Value for item in values]
@@ -195,7 +195,7 @@ def get_transform_vals(dataset, trait):
         for sample in samples:
             sample_dict[sample['name']] = sample['qnorm']
 
-        logger.info("SAMPLE DICT:", sample_dict)
+        #logger.info("SAMPLE DICT:", sample_dict)
         return sample_dict
     else:
         return None
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 0331a141..8fa698b4 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -215,7 +215,6 @@ $(function() {
       }
     });
     table_dict['rows'] = rows;
-    console.log("TABLEDICT:", table_dict);
 
     json_table_dict = JSON.stringify(table_dict);
     $('input[name=export_data]').val(json_table_dict);
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 1be6539d..1085e432 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -70,30 +70,26 @@
                     BNW
                 </button>
 
-                <button id="delete" class="btn btn-danger submit_special" style="margin-left: 15px;" data-url="/collections/delete" title="Delete this collection" >
-                    Delete Collection
-                </button>
-
           </form>
         </div>
 
         <div>
             <br />
+            <form id="export_form" method="POST" action="/export_traits_csv">
             <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" id="add" disabled="disabled"><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 CSV</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"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
             <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete Rows</button>
-            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy to Other Collection</button>
-            <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
-            <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
-            <br />
-            <br />
-            <form id="export_form" method="POST" action="/export_traits_csv">
-              <input type="hidden" name="database_name" id="database_name" value="None">
-              <input type="hidden" name="export_data" id="export_data" value="">
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+            <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
             </form>
             <br />
+            <br />
             <div>
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index f52f20e1..829c5c29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -73,13 +73,18 @@
         </div>
         <br />
         <div>
-            <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-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-            <button id="redraw" class="btn btn-default">Reset Columns</button>
-            <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
-            <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
+            <form id="export_form" method="POST" action="/export_traits_csv">
+                <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+                <button class="btn btn-default" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+                <input type="hidden" name="database_name" id="database_name" value="None">
+                <input type="hidden" name="export_data" id="export_data" value="">
+                <input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation.csv">
+                <button class="btn btn-default" id="export_traits">Download CSV</button>
+                <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ...">
+                <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
+                <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
+                <button id="redraw" class="btn btn-default">Reset Columns</button>
+            </form>
             <br />
             <br />
             <button id="more_options" class="btn btn-primary">More Options...</button>
@@ -116,7 +121,7 @@
                     <tr>
                         <th></th>
                     {% for header in header_fields %}
-                        <th>{{header}}</th>
+                        <th {% if header != "" %}data-export="{{ header }}"{% endif %}>{{header}}</th>
                     {% endfor %}
                     </tr>
                 </thead>
@@ -125,8 +130,8 @@
                 {% for trait in correlation_results %}
                     <tr>
                         <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
-                        <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;">{{ loop.index }}</td>
-                        <td>
+                        <td data-export="{{ loop.index }}" style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;">{{ loop.index }}</td>
+                        <td data-export="{{ trait.name }}">
                             <a href="{{ url_for('show_trait_page',
                                     trait_id = trait.name,
                                     dataset = trait.dataset.name
@@ -135,47 +140,47 @@
                             </a>
                         </td>
                       {% if target_dataset.type == 'ProbeSet' %}
-                        <td>{{ trait.symbol }}</td>
-                        <td>{{ trait.description_display }}</TD>
-                        <td style="white-space: nowrap;">{{ trait.location_repr }}</td>
-                        <td align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right">{{ trait.num_overlap }}</td>
-                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td data-export="{{ trait.symbol }}">{{ trait.symbol }}</td>
+                        <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
+                        <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
+                        <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }} align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
+                        <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
-                        <td align="right">--</td>
+                        <td data-export="--" align="right">--</td>
                         {% else %}
-                        <td align="right">{{'%0.3f'|format(trait.lit_corr)}}</td>
+                        <td data-export="{{ '%0.3f'|format(trait.lit_corr) }}" align="right">{{ '%0.3f'|format(trait.lit_corr) }}</td>
                         {% endif %}
                         {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
-                        <td align="right">--</td>
-                        <td align="right">--</td>
+                        <td data-export="--" align="right">--</td>
+                        <td data-export="--" align="right">--</td>
                         {% else %}
-                        <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
-                        <td align="right">{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
+                        <td data-export="{{ '%0.3f'|format(trait.tissue_corr) }}" align="right">{{ '%0.3f'|format(trait.tissue_corr) }}</td>
+                        <td data-export="{{ '%0.3e'|format(trait.tissue_pvalue) }}" align="right">{{ '%0.3e'|format(trait.tissue_pvalue) }}</td>
                         {% endif %}
-                        <td align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td align="right">{{ trait.LRS_location_repr }}</td>
-                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+                        <td data-export={% if trait.LRS_score_repr != "N/A" %}"{{ '%0.1f' % trait.LRS_score_repr|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
+                        <td data-export="{{ trait.LRS_location_repr }}" align="right">{{ trait.LRS_location_repr }}</td>
+                        <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Publish" %}
-                        <td>{{ trait.description_display }}</td>
-                        <td>{{ trait.authors }}</td>
-                        <td>
+                        <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</td>
+                        <td data-export="{{ trait.authors }}">{{ trait.authors }}</td>
+                        <td data-export="{{ trait.pubmed_text }}">
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
                             </a>
                         </td>
-                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right">{{ trait.num_overlap }}</td>
-                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
-                        <td align="right">{{ trait.LRS_score_repr }}</td>
-                        <td align="right">{{ trait.LRS_location_repr }}</td>
-                        <td align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
+                        <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
+                        <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
+                        <td data-export="{{ trait.LRS_location_repr }}" align="right">{{ trait.LRS_location_repr }}</td>
+                        <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Geno" %}
-                        <td align="right">{{ trait.location_repr }}</TD>
-                        <td align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
-                        <td align="right">{{ trait.num_overlap }}</td>
-                        <td align="right">{{'%0.3e'|format(trait.sample_p)}}</td>
+                        <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
+                        <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                       {% endif %}
                     </tr>
                 {% endfor %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index c11b2533..6fc19be1 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -122,6 +122,7 @@
             <input type="hidden" name="headers" id="headers" value="{% for field in header_fields %}{{ field }},{% endfor %}">
             <input type="hidden" name="search_string" id="search_string" value="{{ original_search_string }}">
             <input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}">
+            <input type="hidden" name="file_name" id="file_name" value="search_results">
             <input type="hidden" name="filter_term" id="filter_term" value="None">
             {% if dataset.accession_id is defined %}
             <input type="hidden" name="accession_id" id="accession_id" value="{{ dataset.accession_id }}">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index ad7412b2..6da25a5d 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -6,7 +6,7 @@
             <ul class="nav nav-pills">
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
-                <li class="gemma_tab mapping_tab {% if dataset.group.mapping_id == '1' %}active{% endif %}">
+                <li class="gemma_tab mapping_tab {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}">
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
                 {% elif mapping_method == "R/qtl" %}
@@ -27,7 +27,7 @@
             <div class="tab-content">
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
-                <div class="tab-pane {% if dataset.group.mapping_id == '1' %}active{% endif %}" id="gemma">
+                <div class="tab-pane {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
                             <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8a80c26c..c4a1b85c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -377,11 +377,11 @@ def export_traits_csv():
     logger.info("In export_traits_csv")
     logger.info("request.form:", request.form)
     logger.info(request.url)
-    csv_data = export_traits.export_search_results_csv(request.form)
+    csv_data, file_name = export_traits.export_search_results_csv(request.form)
 
     return Response(csv_data,
                     mimetype='text/csv',
-                    headers={"Content-Disposition":"attachment;filename=trait_list.csv"})
+                    headers={"Content-Disposition":"attachment;filename=" + file_name})
 
 @app.route('/export_perm_data', methods=('POST',))
 def export_perm_data():