From 8427ddfd7b60d74f4be3a453dd0b21ce7bfdb6f3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 Nov 2019 14:55:50 -0600
Subject: Added 3-letter codes to unpublished phenotype traits and fixed issue
 with ordering phenotype results from searches

---
 wqflask/base/data_set.py | 19 +++++++++----------
 wqflask/base/trait.py    |  9 +++++++--
 2 files changed, 16 insertions(+), 12 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f58367ca..6e07e383 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -26,6 +26,7 @@ import collections
 import codecs
 
 import json
+import requests
 import gzip
 import cPickle as pickle
 import itertools
@@ -63,7 +64,7 @@ logger = getLogger(__name__ )
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
+def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         logger.debug("dataset_type", dataset_type)
@@ -77,7 +78,7 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro
 
 class Dataset_Types(object):
 
-    def __init__(self):
+    def __init__(self, rebuild=False):
         """Create a dictionary of samples where the value is set to Geno,
 Publish or ProbeSet. E.g.
 
@@ -93,8 +94,10 @@ Publish or ProbeSet. E.g.
 
         """
         self.datasets = {}
-        if USE_GN_SERVER:
-            data = gen_menu.gen_dropdown_json()
+        if rebuild: #ZS: May make this the only option
+            data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
+            logger.debug("THE DATA:", data)
+            #data = gen_menu.gen_dropdown_json()
         else:
             file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
             with open(file_name, 'r') as fh:
@@ -119,12 +122,8 @@ Publish or ProbeSet. E.g.
     def __call__(self, name):
         return self.datasets[name]
 
-def rebuild_dataset_ob():
-    Dataset_Getter = Dataset_Types()
-    return Dataset_Getter
-
 # Do the intensive work at startup one time only
-Dataset_Getter = rebuild_dataset_ob()
+Dataset_Getter = Dataset_Types()
 
 def create_datasets_list():
     if USE_REDIS:
@@ -705,7 +704,7 @@ class PhenotypeDataSet(DataSet):
                             'PublishXRef.Id']
 
         # Figure out what display_fields is
-        self.display_fields = ['name',
+        self.display_fields = ['name', 'group_code',
                                'pubmed_id',
                                'pre_publication_description',
                                'post_publication_description',
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 322fb252..5fae34cf 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -352,7 +352,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     if dataset.type == 'Publish':
         query = """
                 SELECT
-                        PublishXRef.Id, Publication.PubMed_ID,
+                        PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
                         Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
                         Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
                         Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
@@ -361,12 +361,13 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                         Publication.Month, Publication.Year, PublishXRef.Sequence,
                         Phenotype.Units, PublishXRef.comments
                 FROM
-                        PublishXRef, Publication, Phenotype, PublishFreeze
+                        PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
                 WHERE
                         PublishXRef.Id = %s AND
                         Phenotype.Id = PublishXRef.PhenotypeId AND
                         Publication.Id = PublishXRef.PublicationId AND
                         PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+                        PublishXRef.InbredSetId = InbredSet.Id AND
                         PublishFreeze.Id = %s
                 """ % (trait.name, dataset.id)
 
@@ -428,6 +429,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             #     holder = unicode(trait_info[i], "utf-8", "ignore")
             setattr(trait, field, holder)
 
+        trait.display_name = trait.name
         if dataset.type == 'Publish':
             trait.confidential = 0
             if trait.pre_publication_description and not trait.pubmed_id:
@@ -462,6 +464,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             if trait.pubmed_id:
                 trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
+            else:
+                if trait.group_code:
+                    trait.display_name = trait.group_code + "_" + str(trait.name)
 
         if dataset.type == 'ProbeSet' and dataset.group:
             description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-- 
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