Fixed collections so they can be very large (1000+ traits)

Added option to submit traits in collection to BNW

Fixed issue with "x" values for user-submitted traits

Fixed issue where post-publications descriptions were wrongly appearing in global search results

19 files changed, 348 insertions, 179 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4a422ee4..55782576 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -371,23 +371,16 @@ class DatasetGroup(object):
             result = Redis.get(key)
 
         if result is not None:
-            #logger.debug("Sample List Cache hit!!!")
-            #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
             self.samplelist = json.loads(result)
-            #logger.debug("  type: ", type(self.samplelist))
-            #logger.debug("  self.samplelist: ", self.samplelist)
         else:
             logger.debug("Cache not hit")
 
             genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
-            mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
-            if mapping_fn:
-                self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
-            elif genotype_fn:
+            if genotype_fn:
                 self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
             else:
                 self.samplelist = None
-            logger.debug("Sample list: ",self.samplelist)
+
             if USE_REDIS:
                 Redis.set(key, json.dumps(self.samplelist))
                 Redis.expire(key, 60*5)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 8f331a06..528b98cf 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -180,8 +180,8 @@ class ConvertGenoFile(object):
                 break
 
 if __name__=="__main__":
-    Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
-    New_Geno_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+    Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
+    New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
     #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
     #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index e51fa157..a04e4b13 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -85,9 +85,9 @@ class AnonCollection(object):
                 num_members = collection['num_members']
         return num_members
 
-    def add_traits(self, params):
+    def add_traits(self, unprocessed_traits):
         #assert collection_name == "Default", "Unexpected collection name for anonymous user"
-        self.traits = list(process_traits(params['traits']))
+        self.traits = list(process_traits(unprocessed_traits))
         existing_collections = Redis.get(self.key)
         logger.debug("existing_collections:", existing_collections)
         if existing_collections != None and existing_collections != "None":
@@ -144,7 +144,6 @@ class AnonCollection(object):
         return str(len_now)
 
 def process_traits(unprocessed_traits):
-    #print("unprocessed_traits are:", unprocessed_traits)
     if isinstance(unprocessed_traits, basestring):
         unprocessed_traits = unprocessed_traits.split(",")
     traits = set()
@@ -167,26 +166,38 @@ def report_change(len_before, len_now):
     else:
         logger.debug("No new traits were added.")
 
+@app.route("/collections/store_trait_list", methods=('POST',))
+def store_traits_list():
+   params = request.form
+
+   traits = params['traits']
+   hash = params['hash']
+
+   Redis.set(hash, traits)
+
+   return hash
 
 @app.route("/collections/add")
 def collections_add():
-    traits=request.args['traits']
-
     if g.user_session.logged_in:
-        user_collections = g.user_session.user_collections
-        #logger.debug("user_collections are:", user_collections)
-        return render_template("collections/add.html",
-                               traits = traits,
-                               collections = user_collections,
-                               )
+        collections = g.user_session.user_collections
     else:
         anon_collections = user_manager.AnonUser().get_collections()
-        collection_names = []
+        collections = []
         for collection in anon_collections:
-            collection_names.append({'id':collection['id'], 'name':collection['name']})
+            collections.append({'id':collection['id'], 'name':collection['name']})
+
+    if 'traits' in request.args:
+        traits=request.args['traits']
         return render_template("collections/add.html",
                                 traits = traits,
-                                collections = collection_names,
+                                collections = collections,
+                              )
+    else:
+        hash = request.args['hash']
+        return render_template("collections/add.html",
+                                hash = hash,
+                                collections = collections,
                               )
 
 @app.route("/collections/new")
@@ -231,7 +242,12 @@ def collections_new():
 def create_new(collection_name):
     params = request.args
 
-    unprocessed_traits = params['traits']
+    if "hash" in params:
+        unprocessed_traits = Redis.get(params['hash'])
+        Redis.delete(hash)
+    else:
+        unprocessed_traits = params['traits']
+
     traits = process_traits(unprocessed_traits)
 
     if g.user_session.logged_in:
@@ -241,7 +257,7 @@ def create_new(collection_name):
     else:
         ac = AnonCollection(collection_name)
         ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
-        ac.add_traits(params)
+        ac.add_traits(unprocessed_traits)
         return redirect(url_for('view_collection', collection_id=ac.id))
 
 @app.route("/collections/list")
diff --git a/wqflask/wqflask/external_tools/__init__.py b/wqflask/wqflask/external_tools/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/external_tools/__init__.py
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index e69de29b..e8f168f4 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -0,0 +1,72 @@
+## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import absolute_import, print_function, division
+
+from base.trait import GeneralTrait
+from utility import helper_functions, corr_result_helpers
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+class SendToBNW(object):
+    def __init__(self, start_vars):
+        trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+        helper_functions.get_trait_db_obs(self, trait_db_list)
+
+        trait_samples_list = []
+
+        for trait_db in self.trait_list:
+            trait_1 = trait_db[0]
+            this_sample_data = trait_1.data
+
+            trait1_samples = list(this_sample_data.keys())
+            trait_samples_list.append(trait1_samples)
+
+        shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list))
+
+        self.form_value = "" #ZS: string that is passed to BNW through form
+        values_list = []
+        for trait_db in self.trait_list:
+            this_trait = trait_db[0]
+            this_sample_data = this_trait.data
+
+            trait_vals = []
+            for sample in this_sample_data:
+                if sample in shared_samples:
+                    trait_vals.append(this_sample_data[sample].value)
+
+            values_list.append(trait_vals)
+            self.form_value += "_" + this_trait.name + ","
+
+        values_list = zip(*values_list)
+        self.form_value = self.form_value[:-1]
+        self.form_value += ";"
+
+        for row in values_list:
+            has_none = False
+            for cell in row:
+                if not cell:
+                    has_none = True
+                    break
+            if has_none:
+                continue
+            self.form_value += ",".join(str(cell) for cell in row)
+            self.form_value += ";"
\ No newline at end of file
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
new file mode 100644
index 00000000..956286af
--- /dev/null
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -0,0 +1,21 @@
+## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import absolute_import, print_function, division
\ No newline at end of file
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 37eb46cb..94965507 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -91,6 +91,7 @@ class GSearch(object):
                 InbredSet.`Name`,
                 PublishFreeze.`Name`,
                 PublishXRef.`Id`,
+                Phenotype.`Pre_publication_description`,
                 Phenotype.`Post_publication_description`,
                 Publication.`Authors`,
                 Publication.`Year`,
@@ -126,23 +127,26 @@ class GSearch(object):
                     this_trait['dataset'] = line[2]
                     this_trait['species'] = line[0]
                     this_trait['group'] = line[1]
-                    this_trait['description'] = line[4]
-                    this_trait['authors'] = line[5]
-                    this_trait['year'] = line[6]
+                    if line[8] != None:
+                        this_trait['description'] = line[5]
+                    else:
+                        this_trait['description'] = line[4]
+                    this_trait['authors'] = line[6]
+                    this_trait['year'] = line[7]
                     if this_trait['year'].isdigit():
                         this_trait['pubmed_text'] = this_trait['year']
                     else:
                         this_trait['pubmed_text'] = "N/A"
-                    if line[7] != "" and line[7] != None:
-                        this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[7]
+                    if line[8] != "" and line[8] != None:
+                        this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[8]
                     else:
                         this_trait['pubmed_link'] = "N/A"
                     this_trait['LRS_score_repr'] = "N/A"
-                    if line[8] != "" and line[8] != None:
-                        this_trait['LRS_score_repr'] = '%3.1f' % line[8]
+                    if line[9] != "" and line[9] != None:
+                        this_trait['LRS_score_repr'] = '%3.1f' % line[9]
                     this_trait['additive'] = "N/A"
-                    if line[9] != "":
-                        this_trait['additive'] = line[9]
+                    if line[10] != "":
+                        this_trait['additive'] = line[10]
 
                     #dataset = create_dataset(line[2], "Publish")
                     #trait_id = line[3]
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 53c96591..171fd0f9 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -44,18 +44,6 @@ views.py).
         #   Names and IDs of group / F2 set
         ###########################################
 
-        # All Phenotypes is a special case we'll deal with later
-        #if kw['dataset'] == "All Phenotypes":
-        #    self.cursor.execute("""
-        #        select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze,
-        #        InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
-        #        PublishFreeze.InbredSetId""")
-        #    results = self.cursor.fetchall()
-        #    self.dataset = map(lambda x: DataSet(x[0], self.cursor), results)
-        #    self.dataset_groups = map(lambda x: x[1], results)
-        #    self.dataset_group_ids = map(lambda x: x[2], results)
-        #else:
-
         self.uc_id = uuid.uuid4()
         logger.debug("uc_id:", self.uc_id) # contains a unique id
 
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6d9f07a0..f2259b55 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -46,7 +46,7 @@ class SampleList(object):
             sample_name = sample_name.replace("_2nd_", "")
 
             if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
-                if counter <= len(self.this_trait) and self.this_trait[counter-1] != 'X':
+                if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
                 else:
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 514c2300..2955f69a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -185,8 +185,8 @@ class ShowTrait(object):
 
         #ZS: Get list of chromosomes to select for mapping
         self.chr_list = [["All", -1]]
-        for i, this_chr in enumerate(self.species.chromosomes.chromosomes):
-            self.chr_list.append([self.species.chromosomes.chromosomes[this_chr].name, i])
+        for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes):
+            self.chr_list.append([self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
 
         self.genofiles = get_genofiles(self.dataset)
 
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index a4ec6ece..3f2673c1 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -117,14 +117,14 @@
                   "Barley1 Leaf MAS 5.0 SCRI (Dec06)"
                ],
                [
-                  "125",
-                  "B30_K_1206_R",
-                  "Barley1 Leaf gcRMA SCRI (Dec06)"
-               ],
-               [
                   "126",
                   "B30_K_1206_Rn",
                   "Barley1 Leaf gcRMAn SCRI (Dec06)"
+               ],
+               [
+                  "125",
+                  "B30_K_1206_R",
+                  "Barley1 Leaf gcRMA SCRI (Dec06)"
                ]
             ],
             "Phenotypes": [
@@ -1347,14 +1347,14 @@
                   "GSE9588 Human Liver Normal (Mar11) Both Sexes"
                ],
                [
-                  "384",
-                  "HLCF_0311",
-                  "GSE9588 Human Liver Normal (Mar11) Females"
-               ],
-               [
                   "383",
                   "HLCM_0311",
                   "GSE9588 Human Liver Normal (Mar11) Males"
+               ],
+               [
+                  "384",
+                  "HLCF_0311",
+                  "GSE9588 Human Liver Normal (Mar11) Females"
                ]
             ],
             "Phenotypes": [
@@ -1608,14 +1608,14 @@
                   "NCI Mammary LMT miRNA v2 (Apr09) RMA"
                ],
                [
-                  "36",
-                  "MA_M_0704_M",
-                  "NCI Mammary mRNA M430 (July04) MAS5"
-               ],
-               [
                   "37",
                   "MA_M_0704_R",
                   "NCI Mammary mRNA M430 (July04) RMA"
+               ],
+               [
+                  "36",
+                  "MA_M_0704_M",
+                  "NCI Mammary mRNA M430 (July04) MAS5"
                ]
             ]
          },
@@ -1683,14 +1683,14 @@
             ],
             "Liver mRNA": [
                [
-                  "38",
-                  "LVF2_M_0704_M",
-                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
-               ],
-               [
                   "39",
                   "LVF2_M_0704_R",
                   "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
+               ],
+               [
+                  "38",
+                  "LVF2_M_0704_M",
+                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
                ]
             ],
             "Phenotypes": [
@@ -1713,6 +1713,11 @@
          "B6D2F2": {
             "Brain mRNA": [
                [
+                  "77",
+                  "BRF2_M_0805_R",
+                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
+               ],
+               [
                   "76",
                   "BRF2_M_0805_M",
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
@@ -1723,24 +1728,19 @@
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
                ],
                [
-                  "77",
-                  "BRF2_M_0805_R",
-                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
-               ],
-               [
                   "33",
                   "BRF2_M_0304_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
                ],
                [
-                  "31",
-                  "BRF2_M_0304_M",
-                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
-               ],
-               [
                   "32",
                   "BRF2_M_0304_R",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
+               ],
+               [
+                  "31",
+                  "BRF2_M_0304_M",
+                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
                ]
             ],
             "Genotypes": [
@@ -1819,6 +1819,11 @@
             ],
             "Striatum mRNA": [
                [
+                  "84",
+                  "SA_M2_0905_R",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
+               ],
+               [
                   "83",
                   "SA_M2_0905_M",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
@@ -1827,27 +1832,22 @@
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
-               ],
-               [
-                  "84",
-                  "SA_M2_0905_R",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
                ]
             ]
          },
          "BHF2": {
             "Adipose mRNA": [
                [
-                  "197",
-                  "UCLA_BHF2_ADIPOSE_FEMALE",
-                  "UCLA BHF2 Adipose Female mlratio"
-               ],
-               [
                   "196",
                   "UCLA_BHF2_ADIPOSE_MALE",
                   "UCLA BHF2 Adipose Male mlratio"
                ],
                [
+                  "197",
+                  "UCLA_BHF2_ADIPOSE_FEMALE",
+                  "UCLA BHF2 Adipose Female mlratio"
+               ],
+               [
                   "165",
                   "UCLA_BHF2_ADIPOSE_0605",
                   "UCLA BHF2 Adipose (June05) mlratio"
@@ -1855,16 +1855,16 @@
             ],
             "Brain mRNA": [
                [
-                  "199",
-                  "UCLA_BHF2_BRAIN_FEMALE",
-                  "UCLA BHF2 Brain Female mlratio"
-               ],
-               [
                   "198",
                   "UCLA_BHF2_BRAIN_MALE",
                   "UCLA BHF2 Brain Male mlratio"
                ],
                [
+                  "199",
+                  "UCLA_BHF2_BRAIN_FEMALE",
+                  "UCLA BHF2 Brain Female mlratio"
+               ],
+               [
                   "166",
                   "UCLA_BHF2_BRAIN_0605",
                   "UCLA BHF2 Brain (June05) mlratio"
@@ -1879,16 +1879,16 @@
             ],
             "Liver mRNA": [
                [
-                  "201",
-                  "UCLA_BHF2_LIVER_FEMALE",
-                  "UCLA BHF2 Liver Female mlratio"
-               ],
-               [
                   "200",
                   "UCLA_BHF2_LIVER_MALE",
                   "UCLA BHF2 Liver Male mlratio"
                ],
                [
+                  "201",
+                  "UCLA_BHF2_LIVER_FEMALE",
+                  "UCLA BHF2 Liver Female mlratio"
+               ],
+               [
                   "167",
                   "UCLA_BHF2_LIVER_0605",
                   "UCLA BHF2 Liver (June05) mlratio"
@@ -2107,21 +2107,26 @@
                   "INIA Brain mRNA M430 (Jun06) RMA"
                ],
                [
-                  "101",
-                  "IBR_M_0106_P",
-                  "INIA Brain mRNA M430 (Jan06) PDNN"
-               ],
-               [
                   "102",
                   "IBR_M_0106_R",
                   "INIA Brain mRNA M430 (Jan06) RMA"
                ],
                [
+                  "101",
+                  "IBR_M_0106_P",
+                  "INIA Brain mRNA M430 (Jan06) PDNN"
+               ],
+               [
                   "95",
                   "BR_U_1105_P",
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
                ],
                [
+                  "80",
+                  "BR_U_0805_M",
+                  "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
+               ],
+               [
                   "82",
                   "BR_U_0805_R",
                   "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
@@ -2132,11 +2137,6 @@
                   "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
                ],
                [
-                  "80",
-                  "BR_U_0805_M",
-                  "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
-               ],
-               [
                   "42",
                   "CB_M_0204_P",
                   "INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2233,6 +2233,11 @@
                   "Eye M430v2 WT Gpnmb (Sep08) RMA"
                ],
                [
+                  "279",
+                  "Eye_M2_0908_R_WT",
+                  "Eye M430v2 WT Tyrp1 (Sep08) RMA"
+               ],
+               [
                   "278",
                   "Eye_M2_0908_R_MT",
                   "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
@@ -2243,11 +2248,6 @@
                   "Eye M430v2 WT WT (Sep08) RMA"
                ],
                [
-                  "279",
-                  "Eye_M2_0908_R_WT",
-                  "Eye M430v2 WT Tyrp1 (Sep08) RMA"
-               ],
-               [
                   "400",
                   "DBA2J-ONH-1212",
                   "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2531,16 +2531,16 @@
             ],
             "Kidney mRNA": [
                [
-                  "240",
-                  "MA_M2M_0706_R",
-                  "Mouse kidney M430v2 Male (Aug06) RMA"
-               ],
-               [
                   "239",
                   "MA_M2F_0706_R",
                   "Mouse kidney M430v2 Female (Aug06) RMA"
                ],
                [
+                  "240",
+                  "MA_M2M_0706_R",
+                  "Mouse kidney M430v2 Male (Aug06) RMA"
+               ],
+               [
                   "118",
                   "MA_M2_0806_R",
                   "Mouse kidney M430v2 Sex Balanced (Aug06) RMA"
@@ -2551,18 +2551,23 @@
                   "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
                ],
                [
-                  "115",
-                  "MA_M2_0706_R",
-                  "Mouse Kidney M430v2 (Jul06) RMA"
-               ],
-               [
                   "116",
                   "MA_M2_0706_P",
                   "Mouse Kidney M430v2 (Jul06) PDNN"
+               ],
+               [
+                  "115",
+                  "MA_M2_0706_R",
+                  "Mouse Kidney M430v2 (Jul06) RMA"
                ]
             ],
             "Liver Metabolome": [
                [
+                  "836",
+                  "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817",
+                  "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2"
+               ],
+               [
                   "838",
                   "UTHSC-ETHZ-EPFL_LivPMetExtBHFD0817",
                   "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2"
@@ -2578,11 +2583,6 @@
                   "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2"
                ],
                [
-                  "836",
-                  "UTHSC-ETHZ-EPFL_LivPMetExtAHFD0817",
-                  "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2"
-               ],
-               [
                   "473",
                   "EPFL-LISP_LivPMetCDHFD1213",
                   "EPFL/LISP BXD Liver Polar Metabolites CD+HFD (Jun14)"
@@ -2692,11 +2692,6 @@
                   "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
-                  "849",
-                  "EPFLMouseLiverCDEx0413",
-                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
-               ],
-               [
                   "848",
                   "EPFLMouseLiverHFCEx0413",
                   "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2707,6 +2702,11 @@
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
+                  "849",
+                  "EPFLMouseLiverCDEx0413",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
                   "433",
                   "EPFLMouseLiverBothExRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2835,16 +2835,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "374",
-                  "DevNeocortex_ILM6.2P3RInv_1111",
-                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "375",
                   "DevNeocortex_ILM6.2P14RInv_1111",
                   "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
                ],
                [
+                  "374",
+                  "DevNeocortex_ILM6.2P3RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -2860,14 +2860,14 @@
                   "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
                ],
                [
-                  "275",
-                  "DevNeocortex_ILM6.2P14RInv_1110",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
-               ],
-               [
                   "274",
                   "DevNeocortex_ILM6.2P3RInv_1110",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
+               ],
+               [
+                  "275",
+                  "DevNeocortex_ILM6.2P14RInv_1110",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
                ]
             ],
             "Nucleus Accumbens mRNA": [
@@ -3095,6 +3095,11 @@
             ],
             "Ventral Tegmental Area mRNA": [
                [
+                  "229",
+                  "VCUEtOH_0609_R",
+                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
+               ],
+               [
                   "228",
                   "VCUSal_0609_R",
                   "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
@@ -3103,11 +3108,6 @@
                   "230",
                   "VCUEtvsSal_0609_R",
                   "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
-               ],
-               [
-                  "229",
-                  "VCUEtOH_0609_R",
-                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
                ]
             ]
          },
@@ -3441,14 +3441,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "99",
-                  "HC_M2CB_1205_P",
-                  "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
-               ],
-               [
                   "100",
                   "HC_M2CB_1205_R",
                   "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
+               ],
+               [
+                  "99",
+                  "HC_M2CB_1205_P",
+                  "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
                ]
             ],
             "Liver mRNA": [
@@ -3474,6 +3474,13 @@
             ]
          },
          "D2GM": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "D2GMPublish",
+                  "D2GM Phenotypes"
+               ]
+            ],
             "Retina mRNA": [
                [
                   "847",
@@ -3532,6 +3539,16 @@
             ],
             "Hippocampus mRNA": [
                [
+                  "213",
+                  "Illum_LXS_Hipp_NOS_1008",
+                  "Hippocampus Illumina NOS (Oct08) RankInv beta"
+               ],
+               [
+                  "219",
+                  "Illum_LXS_Hipp_NON_1008",
+                  "Hippocampus Illumina NON (Oct08) RankInv beta"
+               ],
+               [
                   "212",
                   "Illum_LXS_Hipp_RSE_1008",
                   "Hippocampus Illumina RSE (Oct08) RankInv beta"
@@ -3547,16 +3564,6 @@
                   "Hippocampus Illumina RSS (Oct08) RankInv beta"
                ],
                [
-                  "213",
-                  "Illum_LXS_Hipp_NOS_1008",
-                  "Hippocampus Illumina NOS (Oct08) RankInv beta"
-               ],
-               [
-                  "219",
-                  "Illum_LXS_Hipp_NON_1008",
-                  "Hippocampus Illumina NON (Oct08) RankInv beta"
-               ],
-               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3647,14 +3654,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "272",
-                  "HC_M2_0606_MDP",
-                  "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
-               ],
-               [
                   "273",
                   "UMUTAffyExon_0209_RMA_MDP",
                   "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
+               ],
+               [
+                  "272",
+                  "HC_M2_0606_MDP",
+                  "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
                ]
             ],
             "Liver mRNA": [
@@ -3716,6 +3723,13 @@
             ]
          },
          "Retina-RGC-Rheaume": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "Retina-RGC-RheaumePublish",
+                  "Retina-RGC-Rheaume Phenotypes"
+               ]
+            ],
             "Retina Single-cell RNA-Seq": [
                [
                   "865",
@@ -5471,6 +5485,10 @@
          ],
          "D2GM": [
             [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
                "Retina mRNA",
                "Retina mRNA"
             ]
@@ -5570,6 +5588,10 @@
          ],
          "Retina-RGC-Rheaume": [
             [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
                "Retina Single-cell RNA-Seq",
                "Retina Single-cell RNA-Seq"
             ]
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 2b878087..abcdf7e6 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,12 +93,24 @@ $(function() {
     traits = $("#trait_table input:checked").map(function() {
       return $(this).val();
     }).get();
-    console.log("checked length is:", traits.length);
-    console.log("checked is:", traits);
+
+    var traits_hash = md5(traits.toString());
+
+    $.ajax({
+          type: "POST",
+          url: "/collections/store_trait_list",
+          data: {
+            hash: traits_hash,
+            traits: traits.toString()
+          }
+    });
+
     return $.colorbox({
-      href: "/collections/add?traits=" + traits
+      href: "/collections/add?hash=" + traits_hash
     });
+
   };
+
   removed_traits = function() {
     console.log('in removed_traits with checked_traits:', checked_traits);
     return checked_traits.closest("tr").fadeOut();
diff --git a/wqflask/wqflask/static/new/js_external/md5.min.js b/wqflask/wqflask/static/new/js_external/md5.min.js
new file mode 100644
index 00000000..7d8a3f53
--- /dev/null
+++ b/wqflask/wqflask/static/new/js_external/md5.min.js
@@ -0,0 +1,2 @@
+!function(n){"use strict";function t(n,t){var r=(65535&n)+(65535&t);return(n>>16)+(t>>16)+(r>>16)<<16|65535&r}function r(n,t){return n<<t|n>>>32-t}function e(n,e,o,u,c,f){return t(r(t(t(e,n),t(u,f)),c),o)}function o(n,t,r,o,u,c,f){return e(t&r|~t&o,n,t,u,c,f)}function u(n,t,r,o,u,c,f){return e(t&o|r&~o,n,t,u,c,f)}function c(n,t,r,o,u,c,f){return e(t^r^o,n,t,u,c,f)}function f(n,t,r,o,u,c,f){return e(r^(t|~o),n,t,u,c,f)}function i(n,r){n[r>>5]|=128<<r%32,n[14+(r+64>>>9<<4)]=r;var e,i,a,d,h,l=1732584193,g=-271733879,v=-1732584194,m=271733878;for(e=0;e<n.length;e+=16)i=l,a=g,d=v,h=m,g=f(g=f(g=f(g=f(g=c(g=c(g=c(g=c(g=u(g=u(g=u(g=u(g=o(g=o(g=o(g=o(g,v=o(v,m=o(m,l=o(l,g,v,m,n[e],7,-680876936),g,v,n[e+1],12,-389564586),l,g,n[e+2],17,606105819),m,l,n[e+3],22,-1044525330),v=o(v,m=o(m,l=o(l,g,v,m,n[e+4],7,-176418897),g,v,n[e+5],12,1200080426),l,g,n[e+6],17,-1473231341),m,l,n[e+7],22,-45705983),v=o(v,m=o(m,l=o(l,g,v,m,n[e+8],7,1770035416),g,v,n[e+9],12,-1958414417),l,g,n[e+10],17,-42063),m,l,n[e+11],22,-1990404162),v=o(v,m=o(m,l=o(l,g,v,m,n[e+12],7,1804603682),g,v,n[e+13],12,-40341101),l,g,n[e+14],17,-1502002290),m,l,n[e+15],22,1236535329),v=u(v,m=u(m,l=u(l,g,v,m,n[e+1],5,-165796510),g,v,n[e+6],9,-1069501632),l,g,n[e+11],14,643717713),m,l,n[e],20,-373897302),v=u(v,m=u(m,l=u(l,g,v,m,n[e+5],5,-701558691),g,v,n[e+10],9,38016083),l,g,n[e+15],14,-660478335),m,l,n[e+4],20,-405537848),v=u(v,m=u(m,l=u(l,g,v,m,n[e+9],5,568446438),g,v,n[e+14],9,-1019803690),l,g,n[e+3],14,-187363961),m,l,n[e+8],20,1163531501),v=u(v,m=u(m,l=u(l,g,v,m,n[e+13],5,-1444681467),g,v,n[e+2],9,-51403784),l,g,n[e+7],14,1735328473),m,l,n[e+12],20,-1926607734),v=c(v,m=c(m,l=c(l,g,v,m,n[e+5],4,-378558),g,v,n[e+8],11,-2022574463),l,g,n[e+11],16,1839030562),m,l,n[e+14],23,-35309556),v=c(v,m=c(m,l=c(l,g,v,m,n[e+1],4,-1530992060),g,v,n[e+4],11,1272893353),l,g,n[e+7],16,-155497632),m,l,n[e+10],23,-1094730640),v=c(v,m=c(m,l=c(l,g,v,m,n[e+13],4,681279174),g,v,n[e],11,-358537222),l,g,n[e+3],16,-722521979),m,l,n[e+6],23,76029189),v=c(v,m=c(m,l=c(l,g,v,m,n[e+9],4,-640364487),g,v,n[e+12],11,-421815835),l,g,n[e+15],16,530742520),m,l,n[e+2],23,-995338651),v=f(v,m=f(m,l=f(l,g,v,m,n[e],6,-198630844),g,v,n[e+7],10,1126891415),l,g,n[e+14],15,-1416354905),m,l,n[e+5],21,-57434055),v=f(v,m=f(m,l=f(l,g,v,m,n[e+12],6,1700485571),g,v,n[e+3],10,-1894986606),l,g,n[e+10],15,-1051523),m,l,n[e+1],21,-2054922799),v=f(v,m=f(m,l=f(l,g,v,m,n[e+8],6,1873313359),g,v,n[e+15],10,-30611744),l,g,n[e+6],15,-1560198380),m,l,n[e+13],21,1309151649),v=f(v,m=f(m,l=f(l,g,v,m,n[e+4],6,-145523070),g,v,n[e+11],10,-1120210379),l,g,n[e+2],15,718787259),m,l,n[e+9],21,-343485551),l=t(l,i),g=t(g,a),v=t(v,d),m=t(m,h);return[l,g,v,m]}function a(n){var t,r="",e=32*n.length;for(t=0;t<e;t+=8)r+=String.fromCharCode(n[t>>5]>>>t%32&255);return r}function d(n){var t,r=[];for(r[(n.length>>2)-1]=void 0,t=0;t<r.length;t+=1)r[t]=0;var e=8*n.length;for(t=0;t<e;t+=8)r[t>>5]|=(255&n.charCodeAt(t/8))<<t%32;return r}function h(n){return a(i(d(n),8*n.length))}function l(n,t){var r,e,o=d(n),u=[],c=[];for(u[15]=c[15]=void 0,o.length>16&&(o=i(o,8*n.length)),r=0;r<16;r+=1)u[r]=909522486^o[r],c[r]=1549556828^o[r];return e=i(u.concat(d(t)),512+8*t.length),a(i(c.concat(e),640))}function g(n){var t,r,e="";for(r=0;r<n.length;r+=1)t=n.charCodeAt(r),e+="0123456789abcdef".charAt(t>>>4&15)+"0123456789abcdef".charAt(15&t);return e}function v(n){return unescape(encodeURIComponent(n))}function m(n){return h(v(n))}function p(n){return g(m(n))}function s(n,t){return l(v(n),v(t))}function C(n,t){return g(s(n,t))}function A(n,t,r){return t?r?s(t,n):C(t,n):r?m(n):p(n)}"function"==typeof define&&define.amd?define(function(){return A}):"object"==typeof module&&module.exports?module.exports=A:n.md5=A}(this);
+//# sourceMappingURL=md5.min.js.map
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/bnw_page.html b/wqflask/wqflask/templates/bnw_page.html
new file mode 100644
index 00000000..e506d8a8
--- /dev/null
+++ b/wqflask/wqflask/templates/bnw_page.html
@@ -0,0 +1,7 @@
+<title>Opening BNW</title>
+<form method="post" action="http://bnw.genenetwork.org/BNW/sourcecodes/bn_genenet.php" name="bnwform" id="bnwform">
+  <input type="hidden" name="My_Genenet" value="{{ form_value }}">
+</form>
+<script  type="text/javascript">
+    document.bnwform.submit();
+</script>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 889687ea..37cabdbd 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -6,7 +6,11 @@
     </div>
     <div class="modal-body" style="margin-left: 20px;">
         <form action="/collections/new" data-validate="parsley" id="add_form">
+            {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
+            {% else %}
+            <input type="hidden" name="hash" value="{{ hash }}" />
+            {% endif %}
             <fieldset>
               <legend>1. Create a new collection</legend>
               <div style="margin-left: 20px;">
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index b6ad7be8..801b58c7 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -59,6 +59,9 @@
                     Comparison Bar Chart
                 </button>
 
+                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+                    BNW
+                </button>
 
                 <button id="delete" class="btn btn-danger submit_special" style="margin-left: 15px;" data-url="/collections/delete" title="Delete this collection" >
                     Delete Collection
@@ -138,6 +141,7 @@
 {% endblock %}
 
 {% block js %}
+    <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
@@ -261,6 +265,15 @@
                 url = $(this).data("url")
                 return submit_special(url)
             });
+
+            $("#send_to_bnw").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index eaeb7e6b..7096a18b 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -122,6 +122,7 @@
 {% endblock %}
 
 {% block js %}
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 0192bff1..96675306 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -129,11 +129,6 @@
         <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
         </a>
         {% endif %}
-        {% if UTHSC_BLAT_URL != "" %}
-        <a href="{{ UTHSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="View probes, SNPs, and RNA-seq at UTHSC">RNA-seq</button>
-        </a>
-        {% endif %}
         {% if show_probes == "True" %}
         <a href="http://genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
         <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 27e6eed1..a97679db 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -43,6 +43,7 @@ from base.data_set import DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.heatmap import heatmap
+from wqflask.external_tools import send_to_bnw
 from wqflask.comparison_bar_chart import comparison_bar_chart
 from wqflask.marker_regression import run_mapping
 from wqflask.marker_regression import display_mapping_results
@@ -466,6 +467,24 @@ def heatmap_page():
 
     return rendered_template
 
+@app.route("/bnw_page", methods=('POST',))
+def bnw_page():
+    logger.info("In run BNW, request.form is:", pf(request.form))
+    logger.info(request.url)
+
+    start_vars = request.form
+
+    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+    if traits[0] != "":
+        template_vars = send_to_bnw.SendToBNW(request.form)
+
+        result = template_vars.__dict__
+        rendered_template = render_template("bnw_page.html", **result)
+    else:
+        rendered_template = render_template("empty_collection.html", **{'tool':'BNW'})
+
+    return rendered_template
+
 @app.route("/comparison_bar_chart", methods=('POST',))
 def comp_bar_chart_page():
     logger.info("In comp bar chart, request.form is:", pf(request.form))