Wildcard search (*) works for regular mRNA assay and phenotype searches and fixed issue with black columns in correlation page

3 files changed, 53 insertions, 33 deletions

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index f966b564..4cd87270 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -128,18 +128,24 @@ class MrnaAssaySearch(DoSearch):
                      'Additive Effect']
 
     def get_where_clause(self):
-        where_clause = """(MATCH (ProbeSet.Name,
-                    ProbeSet.description,
-                    ProbeSet.symbol,
-                    alias,
-                    GenbankId,
-                    UniGeneId,
-                    Probe_Target_Description)
-                    AGAINST ('%s' IN BOOLEAN MODE))
-                    and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                    and ProbeSetXRef.ProbeSetFreezeId = %s
-                            """ % (escape(self.search_term[0]),
-                            escape(str(self.dataset.id)))
+
+        if self.search_term[0] != "*":
+            match_clause = """(MATCH (ProbeSet.Name,
+                        ProbeSet.description,
+                        ProbeSet.symbol,
+                        alias,
+                        GenbankId,
+                        UniGeneId,
+                        Probe_Target_Description)
+                        AGAINST ('%s' IN BOOLEAN MODE)) and
+                                """ % (escape(self.search_term[0]))
+        else:
+            match_clause = ""
+
+        where_clause = (match_clause + 
+            """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+               and ProbeSetXRef.ProbeSetFreezeId = %s
+                        """ % (escape(str(self.dataset.id))))
 
         return where_clause
 
@@ -235,29 +241,40 @@ class PhenotypeSearch(DoSearch):
 
         # This adds a clause to the query that matches the search term
         # against each field in the search_fields tuple
-        fields_clause_list = []
+        where_clause_list = []
         for field in self.search_fields:
-            fields_clause_list.append('''%s REGEXP "%s"''' % (field, search_term))
-        fields_clause = "(%s) " % ' OR '.join(fields_clause_list)
+            where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term))
+        where_clause = "(%s) " % ' OR '.join(where_clause_list)
 
-        return fields_clause
+        return where_clause
 
     def compile_final_query(self, from_clause = '', where_clause = ''):
         """Generates the final query string"""
 
         from_clause = self.normalize_spaces(from_clause)
 
-        query = (self.base_query +
-                """%s
-                    WHERE %s
-                    and PublishXRef.InbredSetId = %s
-                    and PublishXRef.PhenotypeId = Phenotype.Id
-                    and PublishXRef.PublicationId = Publication.Id
-                    and PublishFreeze.Id = %s""" % (
-                        from_clause,
-                        where_clause,
-                        escape(str(self.dataset.group.id)),
-                        escape(str(self.dataset.id))))
+        if self.search_term[0] == "*":
+            query = (self.base_query +
+                    """%s
+                        WHERE PublishXRef.InbredSetId = %s
+                        and PublishXRef.PhenotypeId = Phenotype.Id
+                        and PublishXRef.PublicationId = Publication.Id
+                        and PublishFreeze.Id = %s""" % (
+                            from_clause,
+                            escape(str(self.dataset.group.id)),
+                            escape(str(self.dataset.id))))
+        else:
+            query = (self.base_query +
+                    """%s
+                        WHERE %s
+                        and PublishXRef.InbredSetId = %s
+                        and PublishXRef.PhenotypeId = Phenotype.Id
+                        and PublishXRef.PublicationId = Publication.Id
+                        and PublishFreeze.Id = %s""" % (
+                            from_clause,
+                            where_clause,
+                            escape(str(self.dataset.group.id)),
+                            escape(str(self.dataset.id))))
 
         print("query is:", pf(query))
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 6614520e..2e0299f2 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -249,12 +249,7 @@ class SearchResultPage(object):
         search_type = {}
         search_type['dataset_type'] = self.dataset.type
         if a_search['key']:
-            search_type['key'] = a_search['key'].upper()
-            #search_type = a_search['key'].upper()
-        #else:
-        #    # We fall back to the dataset type as the key to get the right object
-        #    search_type = self.dataset.type
-                
+            search_type['key'] = a_search['key'].upper()       
         print("search_type is:", pf(search_type))
 
         search_ob = do_search.DoSearch.get_search(search_type)
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 74919c88..445ad428 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -98,8 +98,16 @@
                         <td><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>{{ trait.num_overlap }}</td>
                         <td>{{'%0.3e'|format(trait.sample_p)}}</td>
+                        {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
+                        <td>--</td>
+                        {% else %}
                         <td>{{'%0.3f'|format(trait.lit_corr)}}</td>
+                        {% endif %}
+                        {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
+                        <td>--</td>
+                        {% else %}
                         <td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
+                        {% endif %}
                         <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
                     {% elif target_dataset.type == "Publish" %}
                         <td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>