diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 144 |
1 files changed, 54 insertions, 90 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 4ba35d63..fc65eb49 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -13,7 +13,6 @@ sys.path.append("..") from dbFunction import webqtlDatabaseFunction -from utility.benchmark import Bench class DoSearch(object): """Parent class containing parameters/functions used for all searches""" @@ -64,25 +63,17 @@ class DoSearch(object): class QuickMrnaAssaySearch(DoSearch): """A general search for mRNA assays""" - + DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch" - - base_query = """SELECT Species.Name as Species_Name, - ProbeSetFreeze.Name as DataSet_Name, - ProbeSetFreeze.FullName as DataSet_FullName, - ProbeSet.Name as ProbeSet_Name, + + base_query = """SELECT ProbeSet.Name as ProbeSet_Name, ProbeSet.Symbol as ProbeSet_Symbol, ProbeSet.description as ProbeSet_Description, ProbeSet.Chr_num as ProbeSet_Chr_Num, ProbeSet.Mb as ProbeSet_Mb, ProbeSet.name_num as ProbeSet_name_num - FROM ProbeSet, - ProbeSetXRef, - ProbeSetFreeze, - ProbeFreeze, - InbredSet, - Species """ - + FROM ProbeSet """ + header_fields = ['', 'Record ID', 'Symbol', @@ -96,12 +87,7 @@ class QuickMrnaAssaySearch(DoSearch): ProbeSet.description, ProbeSet.symbol, ProbeSet.alias) - AGAINST ('%s' IN BOOLEAN MODE)) and - ProbeSet.Id = ProbeSetXRef.ProbeSetId and - ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and - ProbeFreeze.InbredSetId = InbredSet.Id and - InbredSet.SpeciesId = Species.Id + AGAINST ('%s' IN BOOLEAN MODE)) """ % (escape(self.search_term[0])) print("final query is:", pf(query)) @@ -172,7 +158,7 @@ class MrnaAssaySearch(DoSearch): print("final query is:", pf(query)) return self.execute(query) - + class PhenotypeSearch(DoSearch): """A search within a phenotype dataset""" @@ -204,23 +190,6 @@ class PhenotypeSearch(DoSearch): 'Max LRS', 'Max LRS Location'] - #def get_fields_clause(self): - # """Generate clause for WHERE portion of query""" - # - # #Todo: Zach will figure out exactly what both these lines mean - # #and comment here - # if "'" not in self.search_term[0]: - # search_term = "[[:<:]]" + self.search_term[0] + "[[:>:]]" - # - # # This adds a clause to the query that matches the search term - # # against each field in the search_fields tuple - # fields_clause = [] - # for field in self.search_fields: - # fields_clause.append('''%s REGEXP "%s"''' % (field, search_term)) - # fields_clause = "(%s) and " % ' OR '.join(fields_clause) - # - # return fields_clause - def get_fields_clause(self): """Generate clause for WHERE portion of query""" @@ -231,13 +200,13 @@ class PhenotypeSearch(DoSearch): # This adds a clause to the query that matches the search term # against each field in the search_fields tuple - fields_clause = "MATCH(" - fields_clause += ",".join(self.search_fields) + ") " - fields_clause += "AGAINST('{}' IN BOOLEAN MODE)".format(self.search_term[0]) + fields_clause = [] + for field in self.search_fields: + fields_clause.append('''%s REGEXP "%s"''' % (field, search_term)) + fields_clause = "(%s) and " % ' OR '.join(fields_clause) return fields_clause - def compile_final_query(self, from_clause = '', where_clause = ''): """Generates the final query string""" @@ -265,61 +234,56 @@ class PhenotypeSearch(DoSearch): query = self.compile_final_query(where_clause = self.get_fields_clause()) return self.execute(query) - - -class QuickPhenotypeSearch(PhenotypeSearch): - """A search across all phenotype datasets""" - - DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch" - - base_query = """SELECT Species.Name as Species_Name, - PublishFreeze.FullName as Dataset_Name, - PublishFreeze.Name, - PublishXRef.Id, - PublishFreeze.createtime as thistable, - Publication.PubMed_ID as Publication_PubMed_ID, - Phenotype.Post_publication_description as Phenotype_Name - FROM Phenotype, - PublishFreeze, - Publication, - PublishXRef, - InbredSet, - Species """ - - 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') - - def compile_final_query(self, where_clause = ''): - """Generates the final query string""" - query = (self.base_query + - """WHERE (%s) and - PublishXRef.PhenotypeId = Phenotype.Id and - PublishXRef.PublicationId = Publication.Id and - PublishXRef.InbredSetId = InbredSet.Id and - InbredSet.SpeciesId = Species.Id""" % where_clause) - - print("query is:", pf(query)) - - return query +#class QuickPhenotypeSearch(PhenotypeSearch): +# """A search across all phenotype datasets""" +# +# DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch" +# +# base_query = """SELECT Species.Name as Species_Name, +# PublishFreeze.FullName as Dataset_Name, +# PublishFreeze.Name, +# PublishXRef.Id, +# PublishFreeze.createtime as thistable, +# Publication.PubMed_ID as Publication_PubMed_ID, +# Phenotype.Post_publication_description as Phenotype_Name +# FROM Phenotype, +# PublishFreeze, +# Publication, +# PublishXRef, +# InbredSet, +# Species """ +# +# 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') +# +# def compile_final_query(self, where_clause = ''): +# """Generates the final query string""" +# +# query = (self.base_query + +# """WHERE %s +# PublishXRef.PhenotypeId = Phenotype.Id and +# PublishXRef.PublicationId = Publication.Id and +# PublishXRef.InbredSetId = InbredSet.Id and +# InbredSet.SpeciesId = Species.Id""" % where_clause) +# +# print("query is:", pf(query)) +# +# return query def run(self): """Generates and runs a search across all phenotype datasets""" query = self.compile_final_query(where_clause = self.get_fields_clause()) - with Bench("Doing quick phenotype search"): - results = self.execute(query) - - return results - + return self.execute(query) class GenotypeSearch(DoSearch): """A search within a genotype dataset""" |