Fixed issue with getting marker info that affected heatmap and possibly other functions

Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages

6 files changed, 161 insertions, 130 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2acb3b61..79f72390 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -171,28 +171,22 @@ class Markers(object):
     def __init__(self, name):
         json_data_fh = open(locate(name + ".json",'genotype/json'))
 
-        try:
-            markers = []
-            with open(locate(name + "_snps.txt", 'r')) as bimbam_fh:
+        markers = []
+        with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
+            if len(bimbam_fh.readline().split(", ")) > 2:
+                delimiter = ", "
+            elif len(bimbam_fh.readline().split(",")) > 2:
+                delimiter = ","
+            elif len(bimbam_fh.readline().split("\t")) > 2:
+                delimiter = "\t"
+            else:
+                delimiter = " "
+            for line in bimbam_fh:
                 marker = {}
-                if len(bimbam_fh[0].split(", ")) > 2:
-                    delimiter = ", "
-                elif len(bimbam_fh[0].split(",")) > 2:
-                    delimiter = ","
-                elif len(bimbam_fh[0].split("\t")) > 2:
-                    delimiter = "\t"
-                else:
-                    delimiter = " "
-                for line in bimbam_fh:
-                    marker['name'] = line.split(delimiter)[0]
-                    marker['Mb']
-                    marker['chr'] = line.split(delimiter)[2]
-                    marker['cM']
-                    markers.append(marker)
-        #try:
-        #    markers = json.load(json_data_fh)
-        except:
-            markers = []
+                marker['name'] = line.split(delimiter)[0].rstrip()
+                marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000
+                marker['chr'] = line.split(delimiter)[2].rstrip()
+                markers.append(marker)
 
         for marker in markers:
             if (marker['chr'] != "X") and (marker['chr'] != "Y"):
@@ -334,8 +328,6 @@ class DatasetGroup(object):
         return mapping_id, mapping_names
 
     def get_markers(self):
-        logger.debug("self.species is:", self.species)
-
         def check_plink_gemma():
             if flat_file_exists("mapping"):
                 MAPPING_PATH = flat_files("mapping")+"/"
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 7b328cb5..ff589693 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -43,6 +43,9 @@ Redis = Redis()
 
 from flask import Flask, g
 
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
 class Heatmap(object):
 
     def __init__(self, start_vars, temp_uuid):
@@ -96,6 +99,7 @@ class Heatmap(object):
         for trait in self.trait_results.keys():
             lodnames.append(trait)
 
+        self.dataset.group.get_markers()
         for marker in self.dataset.group.markers.markers:
             chr_pos.append(marker['chr'])
             pos.append(marker['Mb'])
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index abcdf7e6..2277a157 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -223,6 +223,65 @@ $(function() {
     $('#export_form').submit();
   };
 
+  $("#corr_matrix").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+  $("#network_graph").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+         return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+  $("#wgcna_setup").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+  $("#ctl_setup").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+  $("#heatmap").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+  $("#comp_bar_chart").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+
+  $("#send_to_webgestalt, #send_to_bnw").on("click", function() {
+      traits = $("#trait_table input:checked").map(function() {
+          return $(this).val();
+      }).get();
+      $("#trait_list").val(traits)
+      url = $(this).data("url")
+      return submit_special(url)
+  });
+
+
   $("#select_all").click(select_all);
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index a2b63374..a219b868 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -220,64 +220,6 @@
                 url = $(this).data("url")
                 return submit_special(url)
             });
-
-            $("#corr_matrix").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#network_graph").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#wgcna_setup").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#ctl_setup").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#heatmap").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#comp_bar_chart").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-
-            $("#send_to_webgestalt, #send_to_bnw").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 2d4ed2a4..4786e379 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -20,31 +20,53 @@
         </p>    
 
         <div>
-          <form id="correlation_form" action="/corr_matrix" method="post">
-            {% if uc %}
-            <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-            {% endif %}
-            <input type="hidden" name="trait_list" id="trait_list" value= "" >
+          <form id="correlation_form" target="_blank" action="/corr_matrix" method="post">
+            <input type="hidden" name="trait_list" id="trait_list" value= "
+            {% for this_trait in trait_list %}
+                {{ this_trait.name }}:{{ this_trait.dataset }},
+            {% endfor %}" >
+
 
                 <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
                     Correlation Matrix
                 </button>
 
+
                 <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
                     Network Graph
                 </button>
 
+
                 <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
                     WGCNA Analysis
                 </button>
 
+
                 <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
                     CTL Analysis
                 </button>
 
+
                 <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
                     Heatmap
                 </button>
+
+                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+                    Comparison Bar Chart
+                </button>
+
+                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+                    WebGestalt
+                </button>
+
+                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+                    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>
@@ -465,49 +487,6 @@
                 url = $(this).data("url")
                 return submit_special(url)
             });
-
-            $("#corr_matrix").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                console.log($("#trait_list").val(traits))
-                url = $(this).data("url")
-                //return submit_special(url)
-            });
-            $("#network_graph").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#wgcna_setup").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#ctl_setup").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-            $("#heatmap").on("click", function() {
-                traits = $("#trait_table input:checked").map(function() {
-                    return $(this).val();
-                }).get();
-                $("#trait_list").val(traits)
-                url = $(this).data("url")
-                return submit_special(url)
-            });
-
         });
     </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 79a279f8..6fcbcb01 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -47,12 +47,62 @@
         <p>To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.</p>
 
         <div>
+          <form id="trait_submission_form" target="_blank" action="/corr_matrix" method="post">
+            <input type="hidden" name="trait_list" id="trait_list" value= "
+            {% for this_trait in trait_list %}
+                {{ this_trait.name }}:{{ this_trait.dataset }},
+            {% endfor %}" >
+
+
+                <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+                    Correlation Matrix
+                </button>
+
+
+                <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
+                    Network Graph
+                </button>
+
+
+                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+                    WGCNA Analysis
+                </button>
+
+
+                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+                    CTL Analysis
+                </button>
+
+
+                <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+                    Heatmap
+                </button>
+
+                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+                    Comparison Bar Chart
+                </button>
+
+                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+                    WebGestalt
+                </button>
+
+                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+                    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 />
           <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 ...">
           <br />
@@ -355,6 +405,11 @@
                 table.colReorder.reset()
             });
 
+            submit_special = function(url) {
+                $("#trait_submission_form").attr("action", url);
+                return $("#trait_submission_form").submit();
+            };
+
         });
     </script>
 {% endblock %}