Got code that creates DataSets object running

Fixed one genofile that had extra quotation marks
in the comments that caused an error

Defaults mb_graph_interval to 1 for species without chromosome
lengths in megabases

5 files changed, 43 insertions, 35 deletions

diff --git a/web/genotypes/B6D2F2-PSU.geno b/web/genotypes/B6D2F2-PSU.geno
index 2c8876a0..a0c1728f 100755
--- a/web/genotypes/B6D2F2-PSU.geno
+++ b/web/genotypes/B6D2F2-PSU.geno
@@ -1,5 +1,5 @@
-"#This is B6D2F2-PSU genotype file, it should be tab-delimited"																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

-"#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive)"																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

+#This is B6D2F2-PSU genotype file, it should be tab-delimited																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

+#the first three/four columns should be ""Chr, Locus, cM, [Mb]"" (case sensitive)																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 #please save as Unix format text file.																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 #comment line always start with a '#'																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 #type riset or intercross																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

@@ -8,9 +8,9 @@
 #abbreviation of maternal or paternal parents																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 @mat:B																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 @pat:D																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

-"#heterozygous , optional, default is ""H"""																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

+#heterozygous , optional, default is ""H""																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 @het:H																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

-"#Unknown , optional, default is ""U"""																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

+#Unknown , optional, default is ""U""																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 @unk:U																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																																														

 Chr	Locus	cM	Mb	PSU0001	PSU0004	PSU0007	PSU0022	PSU0024	PSU0042	PSU0044	PSU0045	PSU0046	PSU0048	PSU0049	PSU0050	PSU0052	PSU0053	PSU0054	PSU0055	PSU0056	PSU0057	PSU0058	PSU0059	PSU0060	PSU0061	PSU0062	PSU0063	PSU0066	PSU0067	PSU0068	PSU0069	PSU0070	PSU0071	PSU0072	PSU0074	PSU0077	PSU0079	PSU0080	PSU0082	PSU0083	PSU0084	PSU0085	PSU0086	PSU0087	PSU0089	PSU0090	PSU0091	PSU0092	PSU0093	PSU0094	PSU0095	PSU0096	PSU0097	PSU0098	PSU0099	PSU0100	PSU0102	PSU0103	PSU0104	PSU0107	PSU0108	PSU0109	PSU0110	PSU0112	PSU0113	PSU0114	PSU0116	PSU0117	PSU0118	PSU0119	PSU0122	PSU0124	PSU0126	PSU0128	PSU0130	PSU0131	PSU0132	PSU0133	PSU0134	PSU0135	PSU0136	PSU0137	PSU0138	PSU0139	PSU0140	PSU0141	PSU0142	PSU0143	PSU0146	PSU0147	PSU0148	PSU0152	PSU0153	PSU0155	PSU0158	PSU0159	PSU0163	PSU0164	PSU0165	PSU0166	PSU0167	PSU0168	PSU0169	PSU0170	PSU0172	PSU0173	PSU0174	PSU0175	PSU0177	PSU0178	PSU0179	PSU0180	PSU0182	PSU0183	PSU0187	PSU0188	PSU0190	PSU0191	PSU0193	PSU0194	PSU0196	PSU0197	PSU0198	PSU0199	PSU0205	PSU0206	PSU0207	PSU0208	PSU0209	PSU0210	PSU0211	PSU0212	PSU0213	PSU0214	PSU0216	PSU0218	PSU0219	PSU0220	PSU0222	PSU0223	PSU0225	PSU0226	PSU0227	PSU0229	PSU0230	PSU0231	PSU0234	PSU0235	PSU0236	PSU0238	PSU0239	PSU0241	PSU0242	PSU0243	PSU0244	PSU0246	PSU0247	PSU0248	PSU0250	PSU0251	PSU0255	PSU0257	PSU0258	PSU0260	PSU0261	PSU0262	PSU0263	PSU0264	PSU0271	PSU0272	PSU0273	PSU0274	PSU0275	PSU0276	PSU0278	PSU0280	PSU0282	PSU0283	PSU0285	PSU0286	PSU0287	PSU0288	PSU0289	PSU0291	PSU0292	PSU0293	PSU0295	PSU0296	PSU0299	PSU0300	PSU0301	PSU0302	PSU0304	PSU0305	PSU0306	PSU0308	PSU0309	PSU0310	PSU0311	PSU0312	PSU0313	PSU0314	PSU0315	PSU0316	PSU0317	PSU0318	PSU0319	PSU0320	PSU0321	PSU0323	PSU0325	PSU0326	PSU0327	PSU0328	PSU0329	PSU0330	PSU0331	PSU0334	PSU0336	PSU0337	PSU0338	PSU0339	PSU0340	PSU0341	PSU0342	PSU0343	PSU0344	PSU0346	PSU0349	PSU0351	PSU0352	PSU0353	PSU0355	PSU0356	PSU0357	PSU0358	PSU0359	PSU0360	PSU0361	PSU0362	PSU0363	PSU0366	PSU0367	PSU0369	PSU0370	PSU0371	PSU0372	PSU0373	PSU0374	PSU0375	PSU0376	PSU0378	PSU0379	PSU0381	PSU0382	PSU0383	PSU0384	PSU0385	PSU0388	PSU0390	PSU0391	PSU0392	PSU0393	PSU0395	PSU0397	PSU0399	PSU0400	PSU0401	PSU0403	PSU0405	PSU0406	PSU0408	PSU0410	PSU0412	PSU0413	PSU0414	PSU0416	PSU0417	PSU0418	PSU0420	PSU0421	PSU0423	PSU0425	PSU0426	PSU0430	PSU0431	PSU0434	PSU0435	PSU0437	PSU0438	PSU0441	PSU0445	PSU0449	PSU0450	PSU0451	PSU0452	PSU0454	PSU0455	PSU0458	PSU0461	PSU0462	PSU0464	PSU0466	PSU0468	PSU0470	PSU0472	PSU0478	PSU0479	PSU0480	PSU0482	PSU0483	PSU0487	PSU0488	PSU0490	PSU0492	PSU0493	PSU0494	PSU0495	PSU0499	PSU0501	PSU0502	PSU0503	PSU0504	PSU0505	PSU0506	PSU0508	PSU0511	PSU0513	PSU0514	PSU0517	PSU0519	PSU0521	PSU0522	PSU0523	PSU0524	PSU0527	PSU0529	PSU0531	PSU0533	PSU0535	PSU0536	PSU0537	PSU0540	PSU0542	PSU0543	PSU0545	PSU0546	PSU0549	PSU0551	PSU0553	PSU0554	PSU0557	PSU0561	PSU0562	PSU0565	PSU0566	PSU0568	PSU0569	PSU0570	PSU0571	PSU0575	PSU0576	PSU0586	PSU0593	PSU0597	PSU0598	PSU0603	PSU0604	PSU0606	PSU0609	PSU0610	PSU0612	PSU0616	PSU0617	PSU0620	PSU0621	PSU0623	PSU0624	PSU0626	PSU0629	PSU0630	PSU0631	PSU0632	PSU0634	PSU0637	PSU0639	PSU0641	PSU0642	PSU0643	PSU0645	PSU0646	PSU0647	PSU0648	PSU0649	PSU0650	PSU0651	PSU0652	PSU0654	PSU0655	PSU0659	PSU0661	PSU0662	PSU0663	PSU0665	PSU0667	PSU0668	PSU0669	PSU0671	PSU0672	PSU0673	PSU0674	PSU0675	PSU0677	PSU0680	PSU0682	PSU0683	PSU0684	PSU0686	PSU0687	PSU0689	PSU0690	PSU0691	PSU0696	PSU0697	PSU0699	PSU0701	PSU0702	PSU0704	PSU0705	PSU0706	PSU0709	PSU0710	PSU0712	PSU0714	PSU0716	PSU0717	PSU0718	PSU0719	PSU0720	PSU0721	PSU0724	PSU0725	PSU0727	PSU0728	PSU0729	PSU0730	PSU0731	PSU0733	PSU0734	PSU0736	PSU0737	PSU0738	PSU0741	PSU0742	PSU0743	PSU0744	PSU0745	PSU0749	PSU0750	PSU0751	PSU0753	PSU0756	PSU0757	PSU0758	PSU0759	PSU0760	PSU0763	PSU0764	PSU0765	PSU0766	PSU0767	PSU0769	PSU0770	PSU0771	PSU0772	PSU0773	PSU0776	PSU0780	PSU0781	PSU0782	PSU0783	PSU0784	PSU0787	PSU0788	PSU0789	PSU0790	PSU0791	PSU0792	PSU0794	PSU0798	PSU0799	PSU0804	PSU0806	PSU0807	PSU0808	PSU0810	PSU0811	PSU0813	PSU0814	PSU0815	PSU0816	PSU0818	PSU0821	PSU0822	PSU0824	PSU0825	PSU0828	PSU0830	PSU0831	PSU0833	PSU0834	PSU0837	PSU0840	PSU0843	PSU0844	PSU0847	PSU0849	PSU0851	PSU0853	PSU0855	PSU0856	PSU0858	PSU0860	PSU0862	PSU0863	PSU0864	PSU1060	PSU1095	PSU1372	PSU1373	PSU1374	PSU1381	PSU1392	PSU1399	PSU1414	PSU1421	PSU1422	PSU1430	PSU1432	PSU1470	PSU1473	PSU1490	PSU1526	PSU1540	PSU1549	PSU1553	PSU1556	PSU1561	PSU1564	PSU1576	PSU1591	PSU1609	PSU1613	PSU1625	PSU1626	PSU1630	PSU1638	PSU1639

 1	rs13475697	0.01	3.385827	U	H	H	H	H	B	D	B	H	B	H	H	D	H	H	H	H	H	H	H	H	B	H	H	H	H	D	H	D	B	B	D	H	H	B	H	D	H	B	H	H	H	B	B	B	D	B	H	H	D	H	D	B	H	H	H	B	H	B	B	B	B	B	B	H	H	B	D	D	H	H	D	D	H	D	D	H	H	B	D	D	B	B	D	B	B	D	B	B	H	B	B	H	D	B	H	H	H	D	H	D	B	D	B	D	H	H	D	B	D	D	H	H	H	D	B	H	B	H	D	H	D	H	D	B	D	D	D	H	H	D	H	B	B	H	H	B	H	B	H	B	D	H	D	D	D	D	H	D	H	H	H	D	B	D	H	D	H	H	D	B	D	B	B	B	D	H	H	B	D	H	H	H	H	D	H	D	H	D	H	D	H	D	D	B	H	D	B	H	D	H	D	D	H	H	H	H	H	D	D	B	H	H	D	B	H	H	H	H	D	H	H	H	D	H	B	D	D	D	H	H	H	H	B	D	H	H	H	D	H	B	B	B	D	B	H	H	H	H	B	H	H	B	H	B	D	D	D	D	H	D	H	D	H	D	B	H	H	H	B	B	B	B	B	H	U	B	H	H	B	D	H	D	H	D	H	H	B	B	B	H	H	H	H	H	D	B	H	H	H	B	H	D	H	D	B	B	D	B	H	H	B	D	H	H	H	B	B	H	H	H	D	H	B	H	B	D	H	B	H	D	B	H	B	H	H	H	B	H	B	H	D	D	B	H	D	B	H	H	D	H	H	D	D	H	H	H	H	B	B	H	D	H	D	H	H	D	D	B	D	D	H	H	D	D	H	H	B	H	H	H	H	B	H	H	D	H	D	H	B	H	D	D	H	H	D	D	B	H	H	H	H	H	H	D	B	D	H	H	B	H	B	H	H	H	H	H	D	H	B	B	D	H	H	D	D	D	B	B	H	H	B	H	H	B	H	B	B	H	B	D	H	H	H	B	B	H	D	B	B	B	D	D	B	D	H	H	B	H	D	D	H	H	H	B	H	H	D	B	D	H	B	H	D	D	B	H	H	D	H	D	H	B	H	H	H	H	H	D	H	B	D	B	H	H	H	D	H	H	B	H	H	B	D	H	D	D	B	H	D	H	D	B	H	H	H	D	H	D	H	D	D	H	B	B	D	B	H	D	B	H	D	H	H	B	B	H	H	H	H	B	H	D	H	H	B	D	B	D	H	D	D	H	B	D	H	B	H	H	H	D	D	H	D	H

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index f301cc05..e4bdb5c3 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -46,17 +46,18 @@ from pprint import pformat as pf
 # Used by create_database to instantiate objects
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name):
+def create_dataset(dataset_name, dataset_type = None):
     #print("dataset_name:", dataset_name)
 
-    query = """
-        SELECT DBType.Name
-        FROM DBList, DBType
-        WHERE DBList.Name = '{}' and
-              DBType.Id = DBList.DBTypeId
-        """.format(escape(dataset_name))
-    #print("query is: ", pf(query))
-    dataset_type = g.db.execute(query).fetchone().Name
+    if not dataset_type:
+        query = """
+            SELECT DBType.Name
+            FROM DBList, DBType
+            WHERE DBList.Name = '{}' and
+                  DBType.Id = DBList.DBTypeId
+            """.format(escape(dataset_name))
+        #print("query is: ", pf(query))
+        dataset_type = g.db.execute(query).fetchone().Name
 
     #dataset_type = cursor.fetchone()[0]
     #print("[blubber] dataset_type:", pf(dataset_type))
@@ -228,16 +229,17 @@ class DataSets(object):
     def __init__(self):
         self.datasets = list()
         
-        type_dict = {'phenotype': 'PublishFreeze',
-                   'mrna_assay': 'ProbeSetFreeze',
-                   'genotype': 'GenoFreeze'}
+        type_dict = {'Publish': 'PublishFreeze',
+                   'ProbeSet': 'ProbeSetFreeze',
+                   'Geno': 'GenoFreeze'}
         
         for dataset_type in type_dict:
             query = "SELECT Name FROM {}".format(type_dict[dataset_type])
             for result in g.db.execute(query).fetchall():
                 #The query at the beginning of this function isn't necessary here, but still would
                 #rather just reuse it
-                create_dataset(result.Name)
+                print("type: {}\tname: {}".format(dataset_type, result.Name))
+                create_dataset(result.Name, dataset_type)
         
         
         #query = """SELECT Name FROM ProbeSetFreeze
@@ -265,6 +267,8 @@ class DataSet(object):
         assert name, "Need a name"
         self.name = name
         self.id = None
+        self.shortname = None
+        self.fullname = None
         self.type = None
 
         self.setup()
@@ -324,7 +328,7 @@ class DataSet(object):
             self.name,
             self.name,
             self.name))
-        #print("query_args are:", query_args)
+        print("query_args are:", query_args)
 
         #print("""
         #        SELECT Id, Name, FullName, ShortName
@@ -332,17 +336,17 @@ class DataSet(object):
         #        WHERE public > %s AND
         #             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
         #  """ % (query_args))
-
-        self.id, self.name, self.fullname, self.shortname = g.db.execute("""
-                SELECT Id, Name, FullName, ShortName
-                FROM %s
-                WHERE public > %s AND
-                     (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-          """ % (query_args)).fetchone()
-
-        #self.cursor.execute(query)
-        #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
         
+        try:
+            self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+                    SELECT Id, Name, FullName, ShortName
+                    FROM %s
+                    WHERE public > %s AND
+                         (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+              """ % (query_args)).fetchone()
+        except TypeError:
+            print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+            pass
 
 class PhenotypeDataSet(DataSet):
     DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
@@ -971,6 +975,5 @@ def geno_mrna_confidentiality(ob):
      authorized_users) = result.fetchall()[0]
 
     if confidential:
-        # Allow confidential data later
-        NoConfindetialDataForYouTodaySorry
+        return True
 
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 191f4535..ebc2bfed 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -56,6 +56,7 @@ class Chromosomes(object):
                         InbredSet.Name = %s
                 Order by OrderId
                 """, self.dataset.group.name).fetchall()
+        print("group: ", self.dataset.group.name)
         print("bike:", results)
 
         for item in results:
@@ -68,9 +69,14 @@ class Chromosomes(object):
     def set_mb_graph_interval(self):
         """Empirical megabase interval"""
         
+        if self.chromosomes:
+            self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        else:
+            self.mb_graph_interval = 1
+            
         #if self.chromosomes:
-        assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
-        self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        #assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+        #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
         #else:
             #self.mb_graph_interval = 1
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f76af374..504a67ce 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -162,8 +162,6 @@ class SearchResultPage(object):
         import redis
         Redis = redis.Redis()
         
-        
-        
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fcb34d31..e48506ab 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -54,7 +54,8 @@ def connect_db():
 @app.route("/")
 def index_page():
     print("Sending index_page")
-    ds = DataSets()
+    with Bench("Creating DataSets object"):
+        ds = DataSets()
     print("[orange] ds:", ds.datasets)
     return render_template("index_page.html")