Merge pull request #168 from genenetwork/staging

Staging

5 files changed, 66 insertions, 66 deletions

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index ba82057a..039f5d1f 100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -12,30 +12,30 @@ from MySQLdb import escape_string as escape
 from pprint import pformat as pf
 
 class MrnaAssayTissueData(object):
-    
+
     def __init__(self, gene_symbols=None):
         self.gene_symbols = gene_symbols
         self.have_data = False
         if self.gene_symbols == None:
             self.gene_symbols = []
-        
+
         #print("self.gene_symbols:", self.gene_symbols)
-        
+
         self.data = collections.defaultdict(Bunch)
-            
+
         #self.gene_id_dict ={}
         #self.data_id_dict = {}
         #self.chr_dict = {}
         #self.mb_dict = {}
         #self.desc_dict = {}
         #self.probe_target_desc_dict = {}
-        
+
         query =  '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
                         from (
                         select Symbol, max(Mean) as maxmean
                         from TissueProbeSetXRef
                         where TissueProbeSetFreezeId=1 and '''
-        
+
         # Note that inner join is necessary in this query to get distinct record in one symbol group
         # with highest mean value
         # Due to the limit size of TissueProbeSetFreezeId table in DB,
@@ -43,11 +43,11 @@ class MrnaAssayTissueData(object):
         if len(gene_symbols) == 0:
             query +=  '''Symbol!='' and Symbol Is Not Null group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
-                and t.Mean = x.maxmean;  
+                and t.Mean = x.maxmean;
                     '''
         else:
             in_clause = db_tools.create_in_clause(gene_symbols)
-            
+
             #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
 
             query += ''' Symbol in {} group by Symbol)
@@ -56,7 +56,7 @@ class MrnaAssayTissueData(object):
                     '''.format(in_clause)
 
         results = g.db.execute(query).fetchall()
-        
+
         lower_symbols = []
         for gene_symbol in gene_symbols:
             if gene_symbol != None:
@@ -68,7 +68,7 @@ class MrnaAssayTissueData(object):
             if symbol.lower() in lower_symbols:
                 #gene_symbols.append(symbol)
                 symbol = symbol.lower()
-                
+
                 self.data[symbol].gene_id = result.GeneId
                 self.data[symbol].data_id = result.DataId
                 self.data[symbol].chr = result.Chr
@@ -85,21 +85,21 @@ class MrnaAssayTissueData(object):
     #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
     #Attention! All keys are lower case!
     ###########################################################################
-    
+
     def get_symbol_values_pairs(self):
         id_list = [self.data[symbol].data_id for symbol in self.data]
 
         print("id_list:", id_list)
 
         symbol_values_dict = {}
-        
+
         query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
                    FROM TissueProbeSetXRef, TissueProbeSetData
                    WHERE TissueProbeSetData.Id IN {} and
                          TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
-        
+
         print("TISSUE QUERY:", query)
-        
+
         results = g.db.execute(query).fetchall()
         for result in results:
             if result.Symbol.lower() not in symbol_values_dict:
@@ -110,11 +110,11 @@ class MrnaAssayTissueData(object):
         #for symbol in self.data:
         #    data_id = self.data[symbol].data_id
         #    symbol_values_dict[symbol] = self.get_tissue_values(data_id)
-        
-    
+
+
         return symbol_values_dict
-    
-    
+
+
     #def get_tissue_values(self, data_id):
     #    """Gets the tissue values for a particular gene"""
     #
@@ -133,7 +133,7 @@ class MrnaAssayTissueData(object):
     #    #    symbol_values_pairs[symbol] = None
     #
     #    return tissue_values
-    
+
 ########################################################################################################
 #input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
 #output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
@@ -154,7 +154,7 @@ class MrnaAssayTissueData(object):
 #    #descDict,
 #    #pTargetDescDict = getTissueProbeSetXRefInfo(
 #    #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-#    
+#
 #    if len(tissue_data.gene_symbols):
 #        return get_symbol_values_pairs(tissue_data)
-            
+
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 52bd8297..79d867c8 100755
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -24,21 +24,21 @@ class TheSpecies(object):
     #    for counter, genotype in enumerate(self.dataset.group.genotype):
     #        if len(genotype) > 1:
     #            chromosomes.append((genotype.name, counter))
-    #            
-    #    print("chromosomes is: ", pf(chromosomes))       
-    #            
+    #
+    #    print("chromosomes is: ", pf(chromosomes))
+    #
     #    return chromosomes
 
 class IndChromosome(object):
     def __init__(self, name, length):
         self.name = name
         self.length = length
-        
+
     @property
     def mb_length(self):
         """Chromosome length in megabases"""
         return self.length / 1000000
-    
+
     def set_cm_length(self, genofile_chr):
         self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
 
@@ -61,19 +61,19 @@ class Chromosomes(object):
 
         for item in results:
             self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
-        
+
         self.set_mb_graph_interval()
         #self.get_cm_length_list()
 
 
     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)
@@ -94,30 +94,30 @@ class Chromosomes(object):
 
     def get_cm_length_list(self):
         """Chromosome length in centimorgans
-        
+
         Calculates the length in centimorgans by subtracting the centimorgan position
         of the last marker in a chromosome by the position of the first marker
-        
+
         """
-        
+
         self.dataset.group.read_genotype_file()
-        
+
         self.cm_length_list = []
-        
+
         for chromosome in self.dataset.group.genotype:
             self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
-            
+
         print("self.cm_length_list:", pf(self.cm_length_list))
-        
+
         assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
         for counter, chromosome in enumerate(self.chromosomes.values()):
             chromosome.cm_length = self.cm_length_list[counter]
             #self.chromosomes[counter].cm_length = item
-            
+
         for key, value in self.chromosomes.items():
             print("bread - %s: %s" % (key, pf(vars(value))))
-        
 
-# Testing                
-#if __name__ == '__main__':    
+
+# Testing
+#if __name__ == '__main__':
 #    foo = dict(bar=dict(length))
\ No newline at end of file
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index a71d8157..b51b8c72 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -69,11 +69,11 @@ class GeneralTrait(object):
         self.retrieve_info(get_qtl_info=get_qtl_info)
         if get_sample_info != False:
             self.retrieve_sample_data()
-        
-        
+
+
     def jsonable(self):
         """Return a dict suitable for using as json
-        
+
         Actual turning into json doesn't happen here though"""
         return dict(name=self.name,
                     dataset=self.dataset.name,
@@ -258,10 +258,10 @@ class GeneralTrait(object):
                             PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                             PublishFreeze.Id = %s
                     """ % (self.name, self.dataset.id)
-        
+
             trait_info = g.db.execute(query).fetchone()
-            
-            
+
+
         #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
         #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
         elif self.dataset.type == 'ProbeSet':
@@ -310,27 +310,27 @@ class GeneralTrait(object):
                 if isinstance(trait_info[i], basestring):
                     holder = unicode(trait_info[i], "utf8", "ignore")
                 setattr(self, field, holder)
-                
+
             if self.dataset.type == 'Publish':
                 self.confidential = 0
                 if self.pre_publication_description and not self.pubmed_id:
                     self.confidential = 1
-                
+
                 description = self.post_publication_description
-            
+
                 #If the dataset is confidential and the user has access to confidential
                 #phenotype traits, then display the pre-publication description instead
                 #of the post-publication description
                 if self.confidential:
                     self.description_display = ""
-                
+
                     #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
                     #        privilege=self.dataset.privilege,
                     #        userName=self.dataset.userName,
                     #        authorized_users=self.authorized_users):
-                    #        
+                    #
                     #    description = self.pre_publication_description
-                
+
                 if description:
                     self.description_display = description.strip()
                 else:
@@ -343,8 +343,8 @@ class GeneralTrait(object):
 
                 if self.pubmed_id:
                     self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
-                    
-                    
+
+
             self.homologeneid = None
             if self.dataset.type == 'ProbeSet' and self.dataset.group:
                 if self.geneid:
@@ -374,7 +374,7 @@ class GeneralTrait(object):
 
                     if result:
                         self.homologeneid = result[0]
-                    
+
                 description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
                 target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
@@ -410,7 +410,7 @@ class GeneralTrait(object):
                     #ZS: Put this in function currently called "convert_location_to_value"
                     self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
                     self.location_value = trait_location_value
-                    
+
 
             if get_qtl_info:
                 #LRS and its location
@@ -481,7 +481,7 @@ class GeneralTrait(object):
                             self.locus = self.locus_chr = self.locus_mb = self.additive = ""
                     else:
                         self.locus = self.lrs = self.additive = ""
-                
+
                 if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "":
                     #XZ: LRS_location_value is used for sorting
                     try:
@@ -493,7 +493,7 @@ class GeneralTrait(object):
                             LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb)
 
                     self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb))
-                    if self.lrs != "":                                     
+                    if self.lrs != "":
                         self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs
                         self.LRS_score_value = LRS_score_value = self.lrs
         else:
@@ -712,7 +712,7 @@ def convert_location_to_value(chromosome, mb):
         else:
             location_value = (ord(str(chromosome).upper()[0])*1000 +
                               float(mb))
-    
+
     return location_value
 
 @app.route("/trait/get_sample_data")
@@ -720,11 +720,11 @@ def get_sample_data():
     params = request.args
     trait = params['trait']
     dataset = params['dataset']
-    
+
     trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
-    
+
     return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
-    
+
     #jsonable_sample_data = {}
     #for sample in trait_ob.data.iteritems():
     #    jsonable_sample_data[sample] = trait_ob.data[sample].value
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 99a34866..411b0d24 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -48,7 +48,7 @@ class webqtlCaseData(object):
         if self.num_cases != None:
             str += " ndata=%d" % self.num_cases
         return str
-    
+
     @property
     def class_outlier(self):
         """Template helper"""
@@ -56,14 +56,14 @@ class webqtlCaseData(object):
             return "outlier"
         else:
             return ""
-    
+
     @property
     def display_value(self):
         if self.value:
             return "%2.3f" % self.value
         else:
             return "x"
-        
+
     @property
     def display_variance(self):
         if self.variance:
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index f6140ac3..f76d8140 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -5,7 +5,7 @@
 # scripts. But rather than migrating everything in one go, we'll
 # take it a step at a time. First the hard coded paths get replaced
 # with those in utility/tools.py
-# 
+#
 #########################################
 
 from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR