Ran reindent.py recursively on wqflask directory

1 files changed, 122 insertions, 127 deletions

diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
index da1b8601..f8491bb1 100755
--- a/wqflask/base/webqtlDataset.py
+++ b/wqflask/base/webqtlDataset.py
@@ -31,130 +31,125 @@ import webqtlConfig
 
 
 class webqtlDataset:
-	"""
-	Database class defines a database in webqtl, can be either Microarray, 	
-	Published phenotype, genotype, or user input database(temp)
-	"""
-
-	def __init__(self, dbName, cursor=None):
-
-		assert dbName
-		self.id = 0
-		self.name = ''
-		self.type = ''
-		self.riset = ''
-		self.cursor = cursor
-
-                #temporary storage
-		if dbName.find('Temp') >= 0:
-			self.searchfield = ['name','description']
-			self.disfield = ['name','description']
-			self.type = 'Temp'
-			self.id = 1
-			self.fullname = 'Temporary Storage'
-			self.shortname = 'Temp'
-		elif dbName.find('Publish') >= 0:
-			self.searchfield = ['name','post_publication_description','abstract','title','authors']
-			self.disfield = ['name','pubmed_id', 
-					'pre_publication_description', 'post_publication_description', 'original_description', 
-					'pre_publication_abbreviation', 'post_publication_abbreviation',
-					'lab_code', 'submitter', 'owner', 'authorized_users',
-					'authors','title','abstract', 'journal','volume','pages','month',
-					'year','sequence', 'units', 'comments']
-			self.type = 'Publish'
-		elif dbName.find('Geno') >= 0:
-			self.searchfield = ['name','chr']
-			self.disfield = ['name','chr','mb', 'source2', 'sequence']
-			self.type = 'Geno'
-		else: #ProbeSet
-			self.searchfield = ['name','description','probe_target_description',
-				'symbol','alias','genbankid','unigeneid','omim',
-				'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score']
-			self.disfield = ['name','symbol','description','probe_target_description',
-				'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim',
-				'refseq_transcriptid','blatseq','targetseq','chipid', 'comments',
-				'strand_probe','strand_gene','probe_set_target_region', 
-				'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start',
-				'probe_set_blat_mb_end', 'probe_set_strand', 
-				'probe_set_note_by_rw', 'flag']
-			self.type = 'ProbeSet'
-		self.name = dbName
-		if self.cursor and self.id == 0:
-			self.retrieveName()
-	
-	def __str__(self):
-		return self.name
-	
-	__repr__ = __str__
-
-
-	def getRISet(self):
-		assert self.cursor
-		if self.type == 'Publish':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, PublishFreeze 
-					WHERE 
-						PublishFreeze.InbredSetId = InbredSet.Id AND 
-						PublishFreeze.Name = "%s"
-				''' % self.name
-		elif self.type == 'Geno':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, GenoFreeze 
-					WHERE 
-						GenoFreeze.InbredSetId = InbredSet.Id AND 
-						GenoFreeze.Name = "%s"
-				''' % self.name
-		elif self.type == 'ProbeSet':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, ProbeSetFreeze, ProbeFreeze 
-					WHERE 
-						ProbeFreeze.InbredSetId = InbredSet.Id AND 
-						ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND 
-						ProbeSetFreeze.Name = "%s"
-				''' % self.name
-		else:
-			return ""
-		self.cursor.execute(query)
-		RISet, RIID = self.cursor.fetchone()
-		if RISet == 'BXD300':
-			RISet = "BXD"
-		self.riset = RISet
-		self.risetid = RIID
-		return RISet
-
-		
-	def retrieveName(self):
-		assert self.id == 0 and self.cursor
-		query = '''
-			SELECT 
-				Id, Name, FullName, ShortName 
-			FROM 
-				%sFreeze 
-			WHERE 
-				public > %d AND 
-				(Name = "%s" OR FullName = "%s" OR ShortName = "%s")
-		  '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
-		try:
-			self.cursor.execute(query)
-			self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
-		except:
-			raise KeyError, `self.name`+' doesn\'t exist.'
-
-	
-	def genHTML(self, Class='c0dd'):
-		return  HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), 
-			url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank")
-
-
-
-
-	
+    """
+    Database class defines a database in webqtl, can be either Microarray,
+    Published phenotype, genotype, or user input database(temp)
+    """
+
+    def __init__(self, dbName, cursor=None):
+
+        assert dbName
+        self.id = 0
+        self.name = ''
+        self.type = ''
+        self.riset = ''
+        self.cursor = cursor
+
+        #temporary storage
+        if dbName.find('Temp') >= 0:
+            self.searchfield = ['name','description']
+            self.disfield = ['name','description']
+            self.type = 'Temp'
+            self.id = 1
+            self.fullname = 'Temporary Storage'
+            self.shortname = 'Temp'
+        elif dbName.find('Publish') >= 0:
+            self.searchfield = ['name','post_publication_description','abstract','title','authors']
+            self.disfield = ['name','pubmed_id',
+                            'pre_publication_description', 'post_publication_description', 'original_description',
+                            'pre_publication_abbreviation', 'post_publication_abbreviation',
+                            'lab_code', 'submitter', 'owner', 'authorized_users',
+                            'authors','title','abstract', 'journal','volume','pages','month',
+                            'year','sequence', 'units', 'comments']
+            self.type = 'Publish'
+        elif dbName.find('Geno') >= 0:
+            self.searchfield = ['name','chr']
+            self.disfield = ['name','chr','mb', 'source2', 'sequence']
+            self.type = 'Geno'
+        else: #ProbeSet
+            self.searchfield = ['name','description','probe_target_description',
+                    'symbol','alias','genbankid','unigeneid','omim',
+                    'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score']
+            self.disfield = ['name','symbol','description','probe_target_description',
+                    'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim',
+                    'refseq_transcriptid','blatseq','targetseq','chipid', 'comments',
+                    'strand_probe','strand_gene','probe_set_target_region',
+                    'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start',
+                    'probe_set_blat_mb_end', 'probe_set_strand',
+                    'probe_set_note_by_rw', 'flag']
+            self.type = 'ProbeSet'
+        self.name = dbName
+        if self.cursor and self.id == 0:
+            self.retrieveName()
+
+    def __str__(self):
+        return self.name
+
+    __repr__ = __str__
+
+
+    def getRISet(self):
+        assert self.cursor
+        if self.type == 'Publish':
+            query = '''
+                            SELECT
+                                    InbredSet.Name, InbredSet.Id
+                            FROM
+                                    InbredSet, PublishFreeze
+                            WHERE
+                                    PublishFreeze.InbredSetId = InbredSet.Id AND
+                                    PublishFreeze.Name = "%s"
+                    ''' % self.name
+        elif self.type == 'Geno':
+            query = '''
+                            SELECT
+                                    InbredSet.Name, InbredSet.Id
+                            FROM
+                                    InbredSet, GenoFreeze
+                            WHERE
+                                    GenoFreeze.InbredSetId = InbredSet.Id AND
+                                    GenoFreeze.Name = "%s"
+                    ''' % self.name
+        elif self.type == 'ProbeSet':
+            query = '''
+                            SELECT
+                                    InbredSet.Name, InbredSet.Id
+                            FROM
+                                    InbredSet, ProbeSetFreeze, ProbeFreeze
+                            WHERE
+                                    ProbeFreeze.InbredSetId = InbredSet.Id AND
+                                    ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+                                    ProbeSetFreeze.Name = "%s"
+                    ''' % self.name
+        else:
+            return ""
+        self.cursor.execute(query)
+        RISet, RIID = self.cursor.fetchone()
+        if RISet == 'BXD300':
+            RISet = "BXD"
+        self.riset = RISet
+        self.risetid = RIID
+        return RISet
+
+
+    def retrieveName(self):
+        assert self.id == 0 and self.cursor
+        query = '''
+                SELECT
+                        Id, Name, FullName, ShortName
+                FROM
+                        %sFreeze
+                WHERE
+                        public > %d AND
+                        (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
+          '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
+        try:
+            self.cursor.execute(query)
+            self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
+        except:
+            raise KeyError, `self.name`+' doesn\'t exist.'
+
+
+    def genHTML(self, Class='c0dd'):
+        return  HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class),
+                url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank")