Merge pull request #861 from genenetwork/feature/gnqa-search-2

Feature/gnqa search 2

2 files changed, 34 insertions, 1 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..88f199f9 100644
--- a/gn2/base/webqtlConfig.py
+++ b/gn2/base/webqtlConfig.py
@@ -34,7 +34,7 @@ MAXLRS = 460.0
 PUBLICTHRESH = 0
 
 # Groups to treat as unique when drawing correlation dropdowns (not sure if this logic even makes sense or is necessary)
-BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD']
+BXD_GROUP_EXCEPTIONS = ['BXD-Longevity', 'BXD-AE', 'BXD-Heart-Metals', 'BXD-NIA-AD', 'BXD-JAX-OFS']
 
 # EXTERNAL LINK ADDRESSES
 PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
@@ -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