diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rw-r--r-- | wqflask/wqflask/do_search.py | 78 |
1 files changed, 38 insertions, 40 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 802cbea5..2094ed14 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -20,34 +20,32 @@ class DoSearch(object): # Used to translate search phrases into classes search_types = dict() - def __init__(self, search_term, search_operator, dataset, cursor, db_conn): + def __init__(self, search_term, search_operator, dataset): self.search_term = search_term # Make sure search_operator is something we expect assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset - self.db_conn = db_conn - self.cursor = cursor #Get group information for dataset and the species id self.dataset.get_group() - self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.dataset.group) + self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group) def execute(self, query): """Executes query and returns results""" query = self.normalize_spaces(query) print("in do_search query is:", pf(query)) - g.db.execute(query) - results = self.cursor.fetchall() + results = g.db.execute(query).fetchall() + #results = self.cursor.fetchall() return results - def escape(self, stringy): - """Shorter name than self.db_conn.escape_string""" - return escape(str(stringy)) + #def escape(self, stringy): + # """Shorter name than self.db_conn.escape_string""" + # return escape(str(stringy)) def mescape(self, *items): """Multiple escape""" - escaped = [self.escape(item) for item in items] + escaped = [escape(item) for item in items] print("escaped is:", escaped) return tuple(escaped) @@ -96,9 +94,9 @@ class ProbeSetSearch(DoSearch): WHERE %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s - """ % (self.escape(from_clause), + """ % (escape(from_clause), where_clause, - self.escape(self.dataset.id))) + escape(self.dataset.id))) print("query is:", pf(query)) @@ -118,8 +116,8 @@ class ProbeSetSearch(DoSearch): AGAINST ('%s' IN BOOLEAN MODE)) and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId = %s - """ % (self.escape(self.search_term[0]), - self.escape(self.dataset.id)) + """ % (escape(self.search_term[0]), + escape(str(self.dataset.id))) print("final query is:", pf(query)) @@ -182,14 +180,16 @@ class PhenotypeSearch(DoSearch): self.dataset.get_group() query = (self.base_query + - """WHERE %s and + """%s + WHERE %s PublishXRef.InbredSetId = %s and PublishXRef.PhenotypeId = Phenotype.Id and PublishXRef.PublicationId = Publication.Id and PublishFreeze.Id = %s""" % ( - self.get_fields_clause(), - self.escape(self.dataset.group_id), - self.escape(self.dataset.id))) + from_clause, + where_clause, + escape(str(self.dataset.group_id)), + escape(str(self.dataset.id)))) print("query is:", pf(query)) @@ -272,7 +272,7 @@ class GenotypeSearch(DoSearch): Geno.Id = GenoXRef.GenoId and GenoXRef.GenoFreezeId = GenoFreeze.Id and GenoFreeze.Id = %s"""% (where_clause, - self.escape(self.dataset.id))) + escape(self.dataset.id))) print("query is:", pf(query)) @@ -332,7 +332,7 @@ class GoSearch(ProbeSetSearch): statements = ("""%s.symbol=GOgene_product.symbol and GOassociation.gene_product_id=GOgene_product.id and GOterm.id=GOassociation.term_id""" % ( - self.db_conn.escape_string(self.dataset.type))) + escape(self.dataset.type))) where_clause = " %s = '%s' and %s " % (field, go_id, statements) @@ -377,7 +377,7 @@ class LrsSearch(ProbeSetSearch): if len(self.search_term) > 2: self.chr_num = self.search_term[2] - self.sub_clause += """ Geno.Chr = %s and """ % (self.escape(self.chr_num)) + self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num)) if len(self.search_term) == 5: self.mb_low, self.mb_high = self.search_term[3:] self.sub_clause += """ Geno.Mb > %s and @@ -429,17 +429,17 @@ class CisTransLrsSearch(LrsSearch): self.sub_clause = """ %sXRef.LRS > %s and %sXRef.LRS < %s and """ % ( - self.escape(self.dataset.type), - self.escape(min(self.lrs_min, self.lrs_max)), - self.escape(self.dataset.type), - self.escape(max(self.lrs_min, self.lrs_max)) + escape(self.dataset.type), + escape(min(self.lrs_min, self.lrs_max)), + escape(self.dataset.type), + escape(max(self.lrs_min, self.lrs_max)) ) else: # Deal with >, <, >=, and <= self.sub_clause = """ %sXRef.LRS %s %s and """ % ( - self.escape(self.dataset.type), - self.escape(self.search_operator), - self.escape(self.search_term[0]) + escape(self.dataset.type), + escape(self.search_operator), + escape(self.search_term[0]) ) self.where_clause = self.sub_clause + """ @@ -447,12 +447,12 @@ class CisTransLrsSearch(LrsSearch): %sXRef.Locus = Geno.name and Geno.SpeciesId = %s and %s.Chr = Geno.Chr""" % ( - self.escape(self.dataset.type), + escape(self.dataset.type), the_operator, - self.escape(self.mb_buffer), - self.escape(self.dataset.type), - self.escape(self.species_id), - self.escape(self.dataset.type) + escape(self.mb_buffer), + escape(self.dataset.type), + escape(self.species_id), + escape(self.dataset.type) ) print("where_clause is:", pf(self.where_clause)) @@ -559,7 +559,7 @@ class RangeSearch(ProbeSetSearch): self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) FROM ProbeSetData WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s - """ % (self.escape(self.search_term[0])) + """ % (escape(self.search_term[0])) print("where_clause is:", pf(self.where_clause)) @@ -647,16 +647,14 @@ class AuthorSearch(PhenotypeSearch): DoSearch.search_types["NAME"] = "AuthorSearch" def run(self): - - self.search_term = [float(value) for value in self.search_term] - - self.where_clause = """ Publication.Authors LIKE %s and - """ % (self.escape(self.search_term[0])) + + self.where_clause = """ Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" and + """ % (self.search_term[0]) self.query = self.compile_final_query(where_clause = self.where_clause) return self.execute(self.query) - + if __name__ == "__main__": |