diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 156 |
1 files changed, 78 insertions, 78 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 48527785..761ae326 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -112,7 +112,7 @@ class MrnaAssaySearch(DoSearch): match_clause = "" where_clause = (match_clause - + """ProbeSet.Id = ProbeSetXRef.ProbeSetId + + """ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(str(self.dataset.id)))) @@ -135,7 +135,7 @@ class MrnaAssaySearch(DoSearch): match_clause = "" where_clause = (match_clause - + """ProbeSet.Id = ProbeSetXRef.ProbeSetId + + """ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s """ % (escape(str(self.dataset.id)))) @@ -147,14 +147,14 @@ class MrnaAssaySearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s ORDER BY ProbeSet.symbol ASC """ % (escape(from_clause), - where_clause, - escape(str(self.dataset.id)))) + where_clause, + escape(str(self.dataset.id)))) return query def run_combined(self, from_clause='', where_clause=''): @@ -166,14 +166,14 @@ class MrnaAssaySearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s ORDER BY ProbeSet.symbol ASC """ % (escape(from_clause), - where_clause, - escape(str(self.dataset.id)))) + where_clause, + escape(str(self.dataset.id)))) return self.execute(query) @@ -199,15 +199,15 @@ class PhenotypeSearch(DoSearch): FROM Phenotype, PublishFreeze, Publication, PublishXRef """ search_fields = ('Phenotype.Post_publication_description', - 'Phenotype.Pre_publication_description', - 'Phenotype.Pre_publication_abbreviation', - 'Phenotype.Post_publication_abbreviation', - 'Phenotype.Lab_code', - 'Publication.PubMed_ID', - 'Publication.Abstract', - 'Publication.Title', - 'Publication.Authors', - 'PublishXRef.Id') + 'Phenotype.Pre_publication_description', + 'Phenotype.Pre_publication_abbreviation', + 'Phenotype.Post_publication_abbreviation', + 'Phenotype.Lab_code', + 'Publication.PubMed_ID', + 'Publication.Abstract', + 'Publication.Title', + 'Publication.Authors', + 'PublishXRef.Id') header_fields = ['Index', 'Record', @@ -250,28 +250,28 @@ class PhenotypeSearch(DoSearch): if self.search_term[0] == "*": query = (self.base_query + - """%s + """%s WHERE PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s ORDER BY PublishXRef.Id""" % ( - from_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) else: query = (self.base_query + - """%s + """%s WHERE %s and PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s ORDER BY PublishXRef.Id""" % ( - from_clause, - where_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) return query @@ -283,16 +283,16 @@ class PhenotypeSearch(DoSearch): from_clause = self.normalize_spaces(from_clause) query = (self.base_query + - """%s + """%s WHERE %s PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s""" % ( - from_clause, - where_clause, - escape(str(self.dataset.group.id)), - escape(str(self.dataset.id)))) + from_clause, + where_clause, + escape(str(self.dataset.group.id)), + escape(str(self.dataset.id)))) return self.execute(query) @@ -336,7 +336,7 @@ class GenotypeSearch(DoSearch): for field in self.search_fields: where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type, field), - self.search_term)) + self.search_term)) logger.debug("hello ;where_clause is:", pf(where_clause)) where_clause = "(%s) " % ' OR '.join(where_clause) @@ -349,16 +349,16 @@ class GenotypeSearch(DoSearch): if self.search_term[0] == "*": query = (self.base_query - + """WHERE Geno.Id = GenoXRef.GenoId + + """WHERE Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id)))) else: query = (self.base_query + - """WHERE %s + """WHERE %s and Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %s""" % (where_clause, - escape(str(self.dataset.id)))) + escape(str(self.dataset.id)))) return query @@ -526,7 +526,7 @@ class LrsSearch(DoSearch): where_clause += """ and %sXRef.Locus = Geno.name and Geno.SpeciesId = %s """ % self.mescape(self.dataset.type, - self.species_id) + self.species_id) else: # Deal with >, <, >=, and <= logger.debug("self.search_term is:", self.search_term) @@ -535,8 +535,8 @@ class LrsSearch(DoSearch): lrs_val = lrs_val * 4.61 where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, - self.search_operator, - self.search_term[0]) + self.search_operator, + self.search_term[0]) return where_clause @@ -618,18 +618,18 @@ class CisTransLrsSearch(DoSearch): sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( - escape(self.dataset.type), - escape(str(min(lrs_min, lrs_max))), - escape(self.dataset.type), - escape(str(max(lrs_min, lrs_max))) - ) + escape(self.dataset.type), + escape(str(min(lrs_min, lrs_max))), + escape(self.dataset.type), + escape(str(max(lrs_min, lrs_max))) + ) else: # Deal with >, <, >=, and <= sub_clause = """ %sXRef.LRS %s %s and """ % ( - escape(self.dataset.type), - escape(self.search_operator), - escape(self.search_term[0]) - ) + escape(self.dataset.type), + escape(self.search_operator), + escape(self.search_term[0]) + ) if cis_trans == "cis": where_clause = sub_clause + """ @@ -637,27 +637,27 @@ class CisTransLrsSearch(DoSearch): %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr""" % ( - escape(self.dataset.type), - the_operator, - escape(str(self.mb_buffer)), - escape(self.dataset.type), - escape(str(self.species_id)), - escape(self.dataset.type) - ) + escape(self.dataset.type), + the_operator, + escape(str(self.mb_buffer)), + escape(self.dataset.type), + escape(str(self.species_id)), + escape(self.dataset.type) + ) else: if chromosome: location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type), - chromosome, - escape( + chromosome, + escape( self.dataset.type), - escape( + escape( self.dataset.type), - the_operator, - escape( + the_operator, + escape( str(self.mb_buffer)), - escape( + escape( self.dataset.type), - chromosome) + chromosome) else: location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape( self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type)) @@ -665,10 +665,10 @@ class CisTransLrsSearch(DoSearch): %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and (%s)""" % ( - escape(self.dataset.type), - escape(str(self.species_id)), - location_clause - ) + escape(self.dataset.type), + escape(str(self.species_id)), + location_clause + ) return where_clause @@ -752,15 +752,15 @@ class MeanSearch(MrnaAssaySearch): where_clause = """ %sXRef.mean > %s and %sXRef.mean < %s """ % self.mescape(self.dataset.type, - min(self.mean_min, - self.mean_max), - self.dataset.type, - max(self.mean_min, self.mean_max)) + min(self.mean_min, + self.mean_max), + self.dataset.type, + max(self.mean_min, self.mean_max)) else: # Deal with >, <, >=, and <= where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, - self.search_operator, - self.search_term[0]) + self.search_operator, + self.search_term[0]) return where_clause @@ -893,17 +893,17 @@ class PvalueSearch(MrnaAssaySearch): self.pvalue_min, self.pvalue_max = self.search_term[:2] self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s """ % self.mescape( - self.dataset.type, - min(self.pvalue_min, self.pvalue_max), - self.dataset.type, - max(self.pvalue_min, self.pvalue_max)) + self.dataset.type, + min(self.pvalue_min, self.pvalue_max), + self.dataset.type, + max(self.pvalue_min, self.pvalue_max)) else: # Deal with >, <, >=, and <= self.where_clause = """ %sXRef.pValue %s %s """ % self.mescape( - self.dataset.type, - self.search_operator, - self.search_term[0]) + self.dataset.type, + self.search_operator, + self.search_term[0]) logger.debug("where_clause is:", pf(self.where_clause)) |