diff options
Diffstat (limited to 'wqflask/wqflask/do_search.py')
| -rwxr-xr-x | wqflask/wqflask/do_search.py | 192 |
1 files changed, 162 insertions, 30 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 29f3de98..31dc11b5 100755 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -38,7 +38,6 @@ class DoSearch(object): query = self.normalize_spaces(query) print("in do_search query is:", pf(query)) results = g.db.execute(query, no_parameters=True).fetchall() - #results = self.cursor.fetchall() return results #def escape(self, stringy): @@ -139,11 +138,8 @@ class MrnaAssaySearch(DoSearch): return query - def run(self): - """Generates and runs a simple search of an mRNA expression dataset""" - - print("Running ProbeSetSearch") - query = self.base_query + """WHERE (MATCH (ProbeSet.Name, + def get_where_clause(self): + where_clause = """(MATCH (ProbeSet.Name, ProbeSet.description, ProbeSet.symbol, alias, @@ -156,6 +152,37 @@ class MrnaAssaySearch(DoSearch): """ % (escape(self.search_term[0]), escape(str(self.dataset.id))) + return where_clause + + def run_combined(self, from_clause, where_clause): + """Generates and runs a combined search of an mRNA expression dataset""" + + print("Running ProbeSetSearch") + #query = self.base_query + from_clause + " WHERE " + where_clause + + from_clause = self.normalize_spaces(from_clause) + + query = (self.base_query + + """%s + WHERE %s + and ProbeSet.Id = ProbeSetXRef.ProbeSetId + and ProbeSetXRef.ProbeSetFreezeId = %s + """ % (escape(from_clause), + where_clause, + escape(str(self.dataset.id)))) + + print("final query is:", pf(query)) + + + return self.execute(query) + + def run(self): + """Generates and runs a simple search of an mRNA expression dataset""" + + print("Running ProbeSetSearch") + where_clause = self.get_where_clause() + query = self.base_query + "WHERE " + where_clause + #print("final query is:", pf(query)) return self.execute(query) @@ -433,12 +460,15 @@ class LrsSearch(MrnaAssaySearch): DoSearch.search_types['LRS'] = 'LrsSearch' - def run(self): + def get_from_clause(self): + if self.search_operator == "=": + return ", Geno" + else: + return "" + def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] - self.from_clause = ", Geno" - if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.lrs_min, self.lrs_max = self.search_term[:2] @@ -451,7 +481,7 @@ class LrsSearch(MrnaAssaySearch): if len(self.search_term) > 2: self.chr_num = self.search_term[2] - self.sub_clause += """ Geno.Chr = %s and """ % (escape(self.chr_num)) + self.sub_clause += """ Geno.Chr = %s and """ % (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 @@ -459,21 +489,71 @@ class LrsSearch(MrnaAssaySearch): """ % self.mescape(min(self.mb_low, self.mb_high), max(self.mb_low, self.mb_high)) print("self.sub_clause is:", pf(self.sub_clause)) + + #%s.Chr = Geno.Chr + where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and + Geno.SpeciesId = %s + """ % self.mescape(self.dataset.type, + self.species_id) else: # Deal with >, <, >=, and <= print("self.search_term is:", self.search_term) - self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, + self.sub_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type, self.search_operator, self.search_term[0]) + where_clause = self.sub_clause + - self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and - Geno.SpeciesId = %s and - %s.Chr = Geno.Chr - """ % self.mescape(self.dataset.type, - self.species_id, - self.dataset.type) + return where_clause - print("where_clause is:", pf(self.where_clause)) + def get_final_query(self): + self.from_clause = self.get_from_clause() + self.where_clause = self.get_where_clause() + self.query = self.compile_final_query(self.from_clause, self.where_clause) + + return self.query + + def run(self): + + self.from_clause = self.get_from_clause() + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.lrs_min, self.lrs_max = self.search_term[:2] + # + # self.sub_clause = """ %sXRef.LRS > %s and + # %sXRef.LRS < %s and """ % self.mescape(self.dataset.type, + # min(self.lrs_min, self.lrs_max), + # self.dataset.type, + # max(self.lrs_min, self.lrs_max)) + # + # if len(self.search_term) > 2: + # self.chr_num = self.search_term[2] + # 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 + # Geno.Mb < %s and + # """ % self.mescape(min(self.mb_low, self.mb_high), + # max(self.mb_low, self.mb_high)) + # print("self.sub_clause is:", pf(self.sub_clause)) + #else: + # # Deal with >, <, >=, and <= + # print("self.search_term is:", self.search_term) + # self.sub_clause = """ %sXRef.LRS %s %s and """ % self.mescape(self.dataset.type, + # self.search_operator, + # self.search_term[0]) + # + #self.where_clause = self.sub_clause + """ %sXRef.Locus = Geno.name and + # Geno.SpeciesId = %s and + # %s.Chr = Geno.Chr + # """ % self.mescape(self.dataset.type, + # self.species_id, + # self.dataset.type) + + self.where_clause = self.get_where_clause() self.query = self.compile_final_query(self.from_clause, self.where_clause) @@ -586,25 +666,54 @@ class MeanSearch(MrnaAssaySearch): DoSearch.search_types['MEAN'] = "MeanSearch" - def run(self): - + def get_where_clause(self): self.search_term = [float(value) for value in self.search_term] if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.mean_min, self.mean_max = self.search_term[:2] - self.where_clause = """ %sXRef.mean > %s and + 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)) else: # Deal with >, <, >=, and <= - self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, + where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, self.search_operator, - self.search_term[0]) + self.search_term[0]) + + return where_clause + def get_final_query(self): + self.where_clause = self.get_where_clause() + print("where_clause is:", pf(self.where_clause)) + + self.query = self.compile_final_query(where_clause = self.where_clause) + + return self.query + + def run(self): + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.mean_min, self.mean_max = self.search_term[:2] + # + # self.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)) + #else: + # # Deal with >, <, >=, and <= + # self.where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type, + # self.search_operator, + # self.search_term[0]) + + self.where_clause = self.get_where_clause() print("where_clause is:", pf(self.where_clause)) self.query = self.compile_final_query(where_clause = self.where_clause) @@ -616,14 +725,11 @@ class RangeSearch(MrnaAssaySearch): DoSearch.search_types['RANGE'] = "RangeSearch" - def run(self): - - self.search_term = [float(value) for value in self.search_term] - + def get_where_clause(self): if self.search_operator == "=": assert isinstance(self.search_term, (list, tuple)) self.range_min, self.range_max = self.search_term[:2] - self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + where_clause = """ (SELECT Pow(2, max(value) -min(value)) FROM ProbeSetData WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND (SELECT Pow(2, max(value) -min(value)) @@ -633,12 +739,38 @@ class RangeSearch(MrnaAssaySearch): max(self.range_min, self.range_max)) else: # Deal with >, <, >=, and <= - self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + where_clause = """ (SELECT Pow(2, max(value) -min(value)) FROM ProbeSetData WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s """ % (escape(self.search_term[0])) - print("where_clause is:", pf(self.where_clause)) + print("where_clause is:", pf(where_clause)) + + return where_clause + + def run(self): + + #self.search_term = [float(value) for value in self.search_term] + # + #if self.search_operator == "=": + # assert isinstance(self.search_term, (list, tuple)) + # self.range_min, self.range_max = self.search_term[:2] + # self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s AND + # (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) < %s + # """ % self.mescape(min(self.range_min, self.range_max), + # max(self.range_min, self.range_max)) + #else: + # # Deal with >, <, >=, and <= + # self.where_clause = """ (SELECT Pow(2, max(value) -min(value)) + # FROM ProbeSetData + # WHERE ProbeSetData.Id = ProbeSetXRef.dataId) > %s + # """ % (escape(self.search_term[0])) + + self.where_clause = self.get_where_clause() self.query = self.compile_final_query(where_clause = self.where_clause) |