Add link to GeneCup to tool buttons

This also includes a function for converting a list of traits/datasets to symbols, which was added to trait.py

5 files changed, 58 insertions, 5 deletions

diff --git a/gn2/base/trait.py b/gn2/base/trait.py
index 701958d7..24288ba1 100644
--- a/gn2/base/trait.py
+++ b/gn2/base/trait.py
@@ -611,3 +611,34 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 f"{repr(trait.name)} information is not found in the database "
                 f"for dataset '{dataset.name}' with id '{dataset.id}'.")
         return trait
+
+def fetch_symbols(trait_db_list):
+    """
+    Fetch list of trait symbols
+
+    From a list of traits and datasets (where each item has
+    the trait and dataset name separated by a colon), return
+
+    """
+
+    trimmed_trait_list = [trait_db for trait_db in trait_db_list
+                          if 'Publish' not in trait_db and 'Geno' not in trait_db.split(":")[1]]
+
+    symbol_list = []
+    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
+        for trait_db in trimmed_trait_list:
+            symbol_query = """
+                SELECT ps.Symbol
+                FROM ProbeSet as ps
+                    INNER JOIN ProbeSetXRef psx ON psx.ProbeSetId = ps.Id
+                    INNER JOIN ProbeSetFreeze psf ON psx.ProbeSetFreezeId = psf.Id
+                WHERE
+                    ps.Name = %(trait_name)s AND
+                    psf.Name = %(db_name)s
+            """
+
+            cursor.execute(symbol_query, {'trait_name': trait_db.split(":")[0],
+                                          'db_name': trait_db.split(":")[1]})
+            symbol_list.append(cursor.fetchone()[0])
+
+    return "+".join(symbol_list)
\ No newline at end of file
diff --git a/gn2/base/webqtlConfig.py b/gn2/base/webqtlConfig.py
index 998c0efc..8018bf40 100644
--- a/gn2/base/webqtlConfig.py
+++ b/gn2/base/webqtlConfig.py
@@ -68,6 +68,8 @@ RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&
 PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn7&section=geneEQTL"
 RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
 RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
+GENE_CUP_URL = "https://genecup.org/progress?type=GWAS&type=addiction&type=drug&type=brain&type=stress&type=psychiatric&type=cell&type=function&query=%s"
+
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
diff --git a/gn2/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js
index 29050c2b..c89b4ce3 100644
--- a/gn2/wqflask/static/new/javascript/search_results.js
+++ b/gn2/wqflask/static/new/javascript/search_results.js
@@ -309,7 +309,7 @@ $(function() {
       return submit_special("/loading")
   });
 
-  $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() {
+  $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver, #send_to_genecup").on("click", function() {
       traits = getTraitsFromTable()
       $("#trait_list").val(traits)
       url = $(this).data("url")
diff --git a/gn2/wqflask/templates/tool_buttons.html b/gn2/wqflask/templates/tool_buttons.html
index c6d1476c..3e716d70 100644
--- a/gn2/wqflask/templates/tool_buttons.html
+++ b/gn2/wqflask/templates/tool_buttons.html
@@ -18,6 +18,10 @@
   BNW
 </button>
 
+<button id="send_to_genecup" class="btn btn-primary submit_special" data-url="/genecup" >
+  GeneCup
+</button>
+
 <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
     WGCNA
 </button>
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py
index 5d8a56e5..daddb442 100644
--- a/gn2/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -46,12 +46,12 @@ from gn2.wqflask import search_results
 from gn2.wqflask import server_side
 # Used by YAML in marker_regression
 from gn2.base.data_set import create_dataset
+from gn2.base.trait import fetch_symbols
 from gn2.wqflask.show_trait import show_trait
 from gn2.wqflask.show_trait import export_trait_data
 from gn2.wqflask.show_trait.show_trait import get_diff_of_vals
 from gn2.wqflask.heatmap import heatmap
-from gn2.wqflask.external_tools import send_to_bnw
-from gn2.wqflask.external_tools import send_to_webgestalt
+from gn2.wqflask.external_tools import send_to_bnw, send_to_webgestalt
 from gn2.wqflask.external_tools import send_to_geneweaver
 from gn2.wqflask.comparison_bar_chart import comparison_bar_chart
 from gn2.wqflask.marker_regression import run_mapping
@@ -88,8 +88,8 @@ from gn2.utility.redis_tools import get_redis_conn
 
 import gn2.utility.hmac as hmac
 
-from gn2.base.webqtlConfig import TMPDIR
-from gn2.base.webqtlConfig import GENERATED_IMAGE_DIR
+from gn2.base.webqtlConfig import TMPDIR, GENERATED_IMAGE_DIR
+from gn2.base.webqtlConfig import GENE_CUP_URL
 
 from gn2.wqflask.database import database_connection
 
@@ -749,6 +749,22 @@ def geneweaver_page():
     return rendered_template
 
 
+@app.route("/genecup", methods=('POST',))
+def genecup_page():
+    start_vars = request.form
+
+    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+
+    if traits[0] != "":
+        symbol_string = fetch_symbols(traits)
+        return redirect(GENE_CUP_URL % symbol_string)
+    else:
+        rendered_template = render_template(
+            "empty_collection.html", **{'tool': 'GeneWeaver'})
+
+        return rendered_template
+
+
 @app.route("/comparison_bar_chart", methods=('POST',))
 def comp_bar_chart_page():
     start_vars = request.form