Committing some in-progress changes related to loading correlation page from JSON

5 files changed, 115 insertions, 18 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 4d7fea61..9b048346 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -32,6 +32,7 @@ import pp
 import math
 import collections
 import resource
+import json
 
 import scipy
 
@@ -51,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only.
 from wqflask.correlation import correlation_functions
 from utility.benchmark import Bench
 import utility.webqtlUtil
+from wqflask import user_manager
 
 from MySQLdb import escape_string as escape
 
@@ -248,7 +250,7 @@ class CorrelationResults(object):
                         else:
                             self.this_trait_vals.append("None")
                     num_overlap = len(self.this_trait_vals)
-
+                    logger.debug("DOING PARALLEL")
                     self.do_parallel_correlation(db_filename, num_overlap)
                 else:
                     for trait, values in self.target_dataset.trait_data.iteritems():
@@ -335,6 +337,7 @@ class CorrelationResults(object):
 
             #print("self.correlation_results: ", pf(self.correlation_results))
 
+        self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
 
         #XZ, 09/18/2008: get all information about the user selected database.
         #target_db_name = fd.corr_dataset
@@ -1431,3 +1434,61 @@ class CorrelationResults(object):
         # for one_result in results:
             # for one_traitinfo in one_result:
                 # allcorrelations.append( one_traitinfo )
+
+def generate_corr_json(corr_results, this_trait, dataset, target_dataset):
+    results_list = []
+    for i, trait in enumerate(corr_results):
+        results_dict = {}
+        results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + user_manager.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + "'>"
+        results_dict['index'] = i + 1
+        results_dict['trait_id'] = "<a href='/show_trait?trait_id="+str(trait.name)+"&dataset="+str(dataset.name)+"'>"+str(trait.name)+"</a>"
+        if target_dataset.type == "ProbeSet":
+            results_dict['symbol'] = trait.symbol
+            results_dict['description'] = trait.description_display
+            results_dict['location'] = trait.location_repr
+            results_dict['mean'] = float(trait.mean)
+            if trait.LRS_score_repr != "N/A":
+                results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr)
+            else:
+                results_dict['lrs_score'] = "N/A"
+            results_dict['lrs_location'] = trait.LRS_location_repr
+            if trait.additive != "":
+                results_dict['additive'] = "%0.3f" % float(trait.additive)
+            else:
+                results_dict['additive'] = "N/A"
+            results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+            if trait.lit_corr == "" or trait.lit_corr == 0:
+                results_dict['lit_corr'] = "--"
+            else:
+                results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr)
+            if trait.tissue_corr == "" or trait.tissue_corr == 0:
+                results_dict['tissue_corr'] = "--"
+            else:
+                results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr)
+        elif target_dataset.type == "Publish":
+            results_dict['description'] = trait.description_display
+            results_dict['authors'] = trait.authors
+            if trait.pubmed_id:
+                results_dict['pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>"
+            else:
+                results_dict['pubmed'] = "N/A"
+            results_dict['lrs_score'] = trait.LRS_score_repr
+            results_dict['lrs_location'] = trait.LRS_location_repr
+            if trait.additive != "":
+                results_dict['additive'] = "%0.3f" % float(trait.additive)
+            else:
+                results_dict['additive'] = "N/A"
+            results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % trait.sample_r + "</a>"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+        else:
+            results_dict['lrs_location'] = trait.LRS_location_repr
+            results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>"
+            results_dict['num_overlap'] = trait.num_overlap
+            results_dict['sample_p'] = "%0.3e" % float(trait.sample_p)
+
+        results_list.append(results_dict)
+
+    return json.dumps(results_list)
diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md
new file mode 100644
index 00000000..c0a8bab7
--- /dev/null
+++ b/wqflask/wqflask/static/dbdoc/TODO.md
@@ -0,0 +1 @@
+TODO: Add all database documentation into this folder
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 629724c0..1254ea6a 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -65,8 +65,10 @@
 
         <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
             <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;">
+<!--
                 <thead>
                     <tr>
+                        <th></th>
                     {% for header in target_dataset.header_fields %}
                         {% if header == 'Year' %}
                         <th>{{header}}</th>
@@ -129,7 +131,8 @@
                 <tbody>
                 {% for trait in correlation_results %}
                     <tr>
-                        <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center; display: inline;">{{ loop.index }}<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
+                        <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; display: inline;">{{ loop.index }}</td>
                         <td>
                             <a href="{{ url_for('show_trait_page',
                                     trait_id = trait.name,
@@ -182,6 +185,7 @@
                     </tr>
                 {% endfor %}
                 </tbody>
+-->
             </table>
         </div>
     </div>
@@ -267,24 +271,55 @@
 
         $(document).ready( function () {
             
+            var table_json = {{ json_results | safe }}
+
+
+            {% if target_dataset.type == "ProbeSet" %}
+            var json_array = new Array();
+
+            for (i=0; i < table_json.length; i++){
+                json_array.push({
+                      checkbox: table_json[i]["checkbox"],
+                      index: table_json[i]["index"],
+                      trait_id: table_json[i]["trait_id"],
+                      symbol: table_json[i]["symbol"],
+                      description: table_json[i]["description"],
+                      location: table_json[i]["location"],
+                      mean: table_json[i]["mean"],
+                      lrs_score: table_json[i]["lrs_score"],
+                      lrs_location: table_json[i]["lrs_location"],
+                      additive: table_json[i]["additive"],
+                      sample_r: table_json[i]["sample_r"],
+                      num_overlap: table_json[i]["num_overlap"],
+                      sample_p: table_json[i]["sample_p"],
+                      lit_corr: table_json[i]["lit_corr"],
+                      tissue_corr: table_json[i]["tissue_corr"]
+                });
+                console.log("JSON_DATA:", json_array);
+            }
+            //console.log("JSON_DATA:", json_array)
+
             $("#trait_table").tabulator({
+                data: json_array,
                 columns:[
-                    {title:"Index", formatter:"html"},
-                    {title:"Record", formatter:"html"},
-                    {title:"Symbol", formatter:"plaintext"},
-                    {title:"Description", formatter:"textarea", width:"25%"},
-                    {title:"Location", formatter:"plaintext"},
-                    {title:"Mean", formatter:"plaintext"},
-                    {title:"Max LRS", formatter:"plaintext"},
-                    {title:"Max LRS Location", formatter:"plaintext"},
-                    {title:"Additive Effect", formatter:"plaintext"},
-                    {title:"Sample r", formatter:"html"},
-                    {title:"N", formatter:"plaintext"},
-                    {title:"Sample p(r)", formatter:"plaintext"},
-                    {title:"Lit r", formatter:"plaintext"},
-                    {title:"Tissue r", formatter:"plaintext"}
+                    {title:"", field:"checkbox", formatter:"html"},
+                    {title:"Index", field:"index", formatter:"plaintext"},
+                    {title:"Record", field:"trait_id", formatter:"html"},
+                    {title:"Symbol", field:"symbol", formatter:"plaintext"},
+                    {title:"Description", field:"description", formatter:"textarea", width:"25%"},
+                    {title:"Location", field:"location", formatter:"plaintext"},
+                    {title:"Mean", field:"mean", formatter:"plaintext"},
+                    {title:"Max LRS", field:"lrs_score", formatter:"plaintext"},
+                    {title:"Max LRS Location", field:"lrs_location", formatter:"plaintext"},
+                    {title:"Additive Effect", field:"additive", formatter:"plaintext"},
+                    {title:"Sample r", field:"sample_r", formatter:"html"},
+                    {title:"N", field:"num_overlap", formatter:"plaintext"},
+                    {title:"Sample p(r)", field:"sample_p", formatter:"plaintext"},
+                    {title:"Lit r", field:"lit_corr", formatter:"plaintext"},
+                    {title:"Tissue r", field:"tissue_corr", formatter:"plaintext"}
                 ]
             });
+            {% endif %}
 
             $('#trait_table tr').click(function(event) {
                 if (event.target.type !== 'checkbox') {
diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html
index 3f2b3786..d1b779ef 100644
--- a/wqflask/wqflask/templates/empty_collection.html
+++ b/wqflask/wqflask/templates/empty_collection.html
@@ -6,7 +6,7 @@
 
     <div class="container">
         <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
-        <p>You must select at least one trait to use the {{ tool }}.</p>
+        <p>You must select at least two traits to use the {{ tool }}.</p>
     </div>
 
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 4e81c29c..187b60dc 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -743,7 +743,7 @@ def corr_matrix_page():
 
     start_vars = request.form
     traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
-    if traits[0] != "":
+    if len(traits) > 1:
         template_vars = show_corr_matrix.CorrelationMatrix(start_vars)
         template_vars.js_data = json.dumps(template_vars.js_data,
                                            default=json_default_handler,