diff options
| -rw-r--r-- | wqflask/wqflask/do_search.py | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/gsearch.py | 34 |
2 files changed, 27 insertions, 18 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 5cb06305..b56a858a 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -37,10 +37,6 @@ class DoSearch(object): logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id - if self.dataset.type == "Publish": - if len(self.search_term[0].split("_")) > 1: - self.search_term[0] = self.search_term[0].split("_")[1] - self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name) def execute(self, query): @@ -234,8 +230,11 @@ class PhenotypeSearch(DoSearch): #Todo: Zach will figure out exactly what both these lines mean #and comment here - if "'" not in self.search_term[0]: - search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" + #if "'" not in self.search_term[0]: + search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]" + if "_" in self.search_term[0]: + if len(self.search_term[0].split("_")[0]) == 3: + search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]" # This adds a clause to the query that matches the search term # against each field in the search_fields tuple diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py index 9e06abfe..b3a45f45 100644 --- a/wqflask/wqflask/gsearch.py +++ b/wqflask/wqflask/gsearch.py @@ -119,6 +119,12 @@ class GSearch(object): 'Additive Effect'] elif self.type == "phenotype": + search_term = self.terms + group_clause = "" + if "_" in self.terms: + if len(self.terms.split("_")[0]) == 3: + search_term = self.terms.split("_")[1] + group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(self.terms.split("_")[0]) sql = """ SELECT Species.`Name`, @@ -138,21 +144,22 @@ class GSearch(object): WHERE PublishXRef.`InbredSetId`=InbredSet.`Id` AND PublishFreeze.`InbredSetId`=InbredSet.`Id` AND InbredSet.`SpeciesId`=Species.`Id` + {0} AND PublishXRef.`PhenotypeId`=Phenotype.`Id` AND PublishXRef.`PublicationId`=Publication.`Id` - AND (Phenotype.Post_publication_description REGEXP "[[:<:]]%s[[:>:]]" - OR Phenotype.Pre_publication_description REGEXP "[[:<:]]%s[[:>:]]" - OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" - OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]%s[[:>:]]" - OR Phenotype.Lab_code REGEXP "[[:<:]]%s[[:>:]]" - OR Publication.PubMed_ID REGEXP "[[:<:]]%s[[:>:]]" - OR Publication.Abstract REGEXP "[[:<:]]%s[[:>:]]" - OR Publication.Title REGEXP "[[:<:]]%s[[:>:]]" - OR Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" - OR PublishXRef.Id REGEXP "[[:<:]]%s[[:>:]]") + AND (Phenotype.Post_publication_description REGEXP "[[:<:]]{1}[[:>:]]" + OR Phenotype.Pre_publication_description REGEXP "[[:<:]]{1}[[:>:]]" + OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" + OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]{1}[[:>:]]" + OR Phenotype.Lab_code REGEXP "[[:<:]]{1}[[:>:]]" + OR Publication.PubMed_ID REGEXP "[[:<:]]{1}[[:>:]]" + OR Publication.Abstract REGEXP "[[:<:]]{1}[[:>:]]" + OR Publication.Title REGEXP "[[:<:]]{1}[[:>:]]" + OR Publication.Authors REGEXP "[[:<:]]{1}[[:>:]]" + OR PublishXRef.Id REGEXP "[[:<:]]{1}[[:>:]]") ORDER BY Species.`Name`, InbredSet.`Name`, PublishXRef.`Id` LIMIT 6000 - """ % (self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms, self.terms) + """.format(group_clause, search_term) logger.sql(sql) re = g.db.execute(sql).fetchall() trait_list = [] @@ -161,7 +168,10 @@ class GSearch(object): this_trait = {} this_trait['index'] = i + 1 this_trait['name'] = str(line[4]) - this_trait['display_name'] = this_trait['name'] + if len(str(line[12])) == 3: + this_trait['display_name'] = str(line[12]) + "_" + this_trait['name'] + else: + this_trait['display_name'] = this_trait['name'] this_trait['dataset'] = line[2] this_trait['dataset_fullname'] = line[3] this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[2])) |