Merge pull request #35 from TheJacksonLaboratory/G3-544-gene-count-in…

…-threshold-issue

G3-544 fix to gene counts within threshold

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.5.7"
+version = "1.5.8"
 description = ""
 authors = ["Alexander Berger <[email protected]>"]
 readme = "README.md"

src/application.py

@@ -1968,7 +1968,7 @@ def render_set_threshold(gs_id):
         view = None
     # Determine if this is bi-modal, we won't display these
     is_bimodal = geneweaverdb.get_bimodal_threshold(gs_id)
-    gsv_values = geneweaverdb.get_all_geneset_values(gs_id)
+    gsv_values = geneweaverdb.get_all_geneset_values_by_gdb_id(gs_id)
     threshold_type = geneset.threshold_type
     threshold = str(geneset.threshold)
     thresh = threshold.split(',')
@@ -2804,9 +2804,9 @@ def render_viewgeneset_main(gs_id, curation_view=None, curation_team=None, curat
     threshold_type = geneset.threshold_type
     curr_threshold = threshold.split(',')
 
-    gsv_values = geneweaverdb.get_all_geneset_values(gs_id)
+    gsv_values = geneweaverdb.get_all_geneset_values_by_gdb_id(gs_id)
     # get genes count for the current threshold
-    num_genes_in_threshold = 0;
+    num_genes_in_threshold = 0
     if threshold_type == 1 or threshold_type == 2:
         gene_counts = calc_genes_count_in_threshold(gsv_values, curr_threshold)
         num_genes_in_threshold = num_genes_in_threshold if curr_threshold[0] == 'None' else gene_counts[float(curr_threshold[0])]

src/geneweaverdb.py

@@ -4273,6 +4273,28 @@ def get_all_geneset_values(gs_id):
 							  g.ode_pref='t' ORDER BY gv.gsv_value ASC''', (gs_id,))
         return list(dictify_cursor(cursor)) if cursor.rowcount != 0 else None
 
+def get_all_geneset_values_by_gdb_id(gs_id, gdb_id=7):
+    '''
+    Generic function to get all geneset values geneset_value.gs_values
+    :param geneset_id: geneset id
+    :param gdb_id: gdb id -- default is 7
+
+    :return:
+    '''
+    user_id = flask.session['user_id']
+    geneset = get_geneset(gs_id, user_id)
+    with PooledCursor() as cursor:
+        if geneset.gene_id_type < 0:
+            cursor.execute('''SELECT gv.gsv_value as gsv, g.ode_ref_id as ref FROM geneset_value gv, gene g, geneset gs WHERE
+							  g.ode_pref='t' AND gv.gs_id=%s AND gs.gs_id=gv.gs_id AND gs.sp_id=g.sp_id AND
+							  gv.ode_gene_id=g.ode_gene_id AND g.gdb_id=%s ORDER BY gv.gsv_value ASC''', (gs_id, gdb_id,))
+        else:
+            cursor.execute('''SELECT gv.gsv_value, g.ode_ref_id FROM geneset_value gv, gene g, geneset gs WHERE
+							  gv.gs_id=%s AND gs.gs_id=gv.gs_id AND gs.sp_id=g.sp_id AND gv.ode_gene_id=g.ode_gene_id AND
+							  g.ode_pref='t' AND g.gdb_id=%s ORDER BY gv.gsv_value ASC''', (gs_id, gdb_id,))
+        return list(dictify_cursor(cursor)) if cursor.rowcount != 0 else None
+
+
 def get_species_homologs(hom_id):
     """
     Uses a given homology ID to return a list of homologous species.

src/templates/viewgenesetdetails.html

@@ -114,9 +114,11 @@ <h3 class="panel-title">Gene List &bull; {{ totalGenes }} Genes</h3>
         <div class="panel-body" style="padding-top:10px;">
             <div class="row">
                 <div class="col-xs-12 col-md-9">
-                    <div class="row">
-                        <p>Genes in threshold: {{ num_genes_in_threshold }}</p>
-                    </div>
+                    {% if geneset.threshold_type != 3 %}
+                        <div class="row">
+                            <p>Genes in threshold: {{ num_genes_in_threshold }}</p>
+                        </div>
+                    {% endif %}
                 </div>
                 <div class="col-xs-6 col-md-3" style="margin:0; padding:0;">
 					{% if g.user is defined and not curation_view %}