Added 3-letter codes to unpublished phenotype traits and fixed issue with ordering phenotype results from searches

11 files changed, 47 insertions, 29 deletions

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')
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b6580bbe..0df72b0d 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -251,7 +251,8 @@ class PhenotypeSearch(DoSearch):
                         WHERE PublishXRef.InbredSetId = %s
                         and PublishXRef.PhenotypeId = Phenotype.Id
                         and PublishXRef.PublicationId = Publication.Id
-                        and PublishFreeze.Id = %s""" % (
+                        and PublishFreeze.Id = %s
+                        ORDER BY PublishXRef.Id""" % (
                             from_clause,
                             escape(str(self.dataset.group.id)),
                             escape(str(self.dataset.id))))
@@ -262,7 +263,8 @@ class PhenotypeSearch(DoSearch):
                         and PublishXRef.InbredSetId = %s
                         and PublishXRef.PhenotypeId = Phenotype.Id
                         and PublishXRef.PublicationId = Publication.Id
-                        and PublishFreeze.Id = %s""" % (
+                        and PublishFreeze.Id = %s
+                        ORDER BY PublishXRef.Id""" % (
                             from_clause,
                             where_clause,
                             escape(str(self.dataset.group.id)),
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index dbb77826..53e5f2b7 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -118,7 +118,8 @@ class GSearch(object):
                 Publication.`Year`,
                 Publication.`PubMed_ID`,
                 PublishXRef.`LRS`,
-                PublishXRef.`additive`
+                PublishXRef.`additive`,
+                InbredSet.`InbredSetCode`
                 FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
                 WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
                 AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
@@ -146,6 +147,7 @@ class GSearch(object):
                     this_trait = {}
                     this_trait['index'] = i + 1
                     this_trait['name'] = str(line[4])
+                    this_trait['display_name'] = this_trait['name']
                     this_trait['dataset'] = line[2]
                     this_trait['dataset_fullname'] = line[3]
                     this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[2]))
@@ -167,6 +169,8 @@ class GSearch(object):
                         this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
                     else:
                         this_trait['pubmed_link'] = "N/A"
+                        if line[12]:
+                            this_trait['display_name'] = line[12] + "_" + str(this_trait['name'])
                     this_trait['LRS_score_repr'] = "N/A"
                     if line[10] != "" and line[10] != None:
                         this_trait['LRS_score_repr'] = '%3.1f' % line[10]
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5a5a850b..2ac6d4b5 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -110,6 +110,10 @@ views.py).
             trait_dict['index'] = index + 1
             this_trait = trait.GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
             trait_dict['name'] = this_trait.name
+            if this_trait.dataset.type == "Publish":
+                trait_dict['display_name'] = this_trait.display_name
+            else:
+                trait_dict['display_name'] = this_trait.name
             trait_dict['dataset'] = this_trait.dataset.name
             trait_dict['hmac'] = user_manager.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
             if this_trait.dataset.type == "ProbeSet":
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 64597711..09004396 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -45,7 +45,6 @@ class ShowTrait(object):
         if 'trait_id' in kw and kw['dataset'] != "Temp":
             self.temp_trait = False
             self.trait_id = kw['trait_id']
-            data_set.rebuild_dataset_ob()
             helper_functions.get_species_dataset_trait(self, kw)
         elif 'group' in kw:
             self.temp_trait = True
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 1a4ff752..85127e99 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -9,8 +9,10 @@
 
     <div class="container" style="width: 2000px;">
 
-        <h3>GN searched 754 datasets and 39,765,944 traits across 10 species, and found {{ trait_count }} results that match your query.
-        You can filter these results by adding key words in the fields below and you can also sort results on most columns.</h3>
+        <h3>GN searched for the term(s) <b>"{{ terms }}"</b> in 754 datasets and 39,765,944 traits across 10 species<br/>
+            and found <b>{{ trait_count }}</b> results that match your query.<br/>
+            You can filter these results by adding key words in the fields below<br/>
+            and you can also sort results on most columns.</h3>
         <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p>
 
         <div>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index c626a589..bc88a76e 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -9,8 +9,10 @@
 
     <div class="container">
 
-        <h3>GN searched 51 datasets and 13763 traits across 10 species, and found {{ trait_count }} results that match your query.
-        You can filter these results by adding key words in the fields below and you can also sort results on most columns.</h3>
+        <h3>GN searched for the term(s) <b>"{{ terms }}"</b> in 51 datasets and 13763 traits across 10 species<br/>
+            and found <b>{{ trait_count }}</b> results that match your query.<br/>
+            You can filter these results by adding key words in the fields below<br/>
+            and you can also sort results on most columns.</h3>
         <p>To study a record, click on its ID below.<br />Check records below and click Add button to add to selection.</p>
 
         <div>
@@ -160,7 +162,7 @@
                       'type': "natural",
                       'data': null,
                       'render': function(data, type, row, meta) {
-                        return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
+                        return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
                     },
                     {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 262a563d..b66540d7 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -276,7 +276,7 @@
                       'width': "60px",
                       'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
-                        return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
+                        return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
                     }{% if dataset.type == 'ProbeSet' %},
                     {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 0f49b092..0b4618f1 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -15,7 +15,7 @@
 {% block content %} <!-- Start of body -->
 
     <div class="container">
-        <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2>
+        <h2>Trait Data and Analysis for <b>{{ this_trait.display_name }}</b></h2>
         {% if this_trait.dataset.type != 'Publish' %}
         <h3>{{ this_trait.description_fmt[0]|upper }}{{ this_trait.description_fmt[1:] }}</h3>
         {% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index bff9f9d2..1c513591 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -125,12 +125,13 @@ def index_page():
         import_collections = params['import_collections']
         if import_collections == "true":
             g.cookie_session.import_traits_to_user()
-    if USE_GN_SERVER:
-        # The menu is generated using GN_SERVER
-        return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION)
-    else:
-        # Old style static menu (OBSOLETE)
-        return render_template("index_page_orig.html", version=GN_VERSION)
+    #if USE_GN_SERVER:
+    #    # The menu is generated using GN_SERVER
+    #    return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION)
+    #else:
+
+    # Old style static menu (OBSOLETE)
+    return render_template("index_page_orig.html", version=GN_VERSION)
 
 
 @app.route("/tmp/<img_path>")