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-rw-r--r--wqflask/wqflask/do_search.py69
1 files changed, 46 insertions, 23 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 7442dc72..e50ff50b 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -26,14 +26,16 @@ class DoSearch:
def __init__(self, search_term, search_operator=None, dataset=None, search_type=None):
self.search_term = search_term
# Make sure search_operator is something we expect
- assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
+ assert search_operator in (
+ None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
self.search_type = search_type
if self.dataset:
# Get group information for dataset and the species id
- self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
+ self.species_id = webqtlDatabaseFunction.retrieve_species_id(
+ self.dataset.group.name)
def execute(self, query):
"""Executes query and returns results"""
@@ -104,7 +106,8 @@ class MrnaAssaySearch(DoSearch):
search_string = escape(self.search_term[0])
if self.search_term[0] != "*":
- match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (search_string)
+ match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (
+ search_string)
else:
match_clause = ""
@@ -223,16 +226,19 @@ class PhenotypeSearch(DoSearch):
# and comment here
# if "'" not in self.search_term[0]:
- search_term = "[[:<:]]" + self.handle_wildcard(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]) + "[[:>:]]"
+ 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
where_clause_list = []
for field in self.search_fields:
- where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term))
+ where_clause_list.append('''%s REGEXP "%s"''' %
+ (field, search_term))
where_clause = "(%s) " % ' OR '.join(where_clause_list)
return where_clause
@@ -364,7 +370,8 @@ class GenotypeSearch(DoSearch):
if self.search_term[0] == "*":
self.query = self.compile_final_query()
else:
- self.query = self.compile_final_query(where_clause=self.get_where_clause())
+ self.query = self.compile_final_query(
+ where_clause=self.get_where_clause())
return self.execute(self.query)
@@ -497,7 +504,8 @@ class LrsSearch(DoSearch):
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s """ % self.mescape(self.dataset.type,
- min(lrs_min, lrs_max),
+ min(lrs_min,
+ lrs_max),
self.dataset.type,
max(lrs_min, lrs_max))
@@ -537,7 +545,8 @@ class LrsSearch(DoSearch):
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)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -551,7 +560,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
+ self.query = self.compile_final_query(
+ from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -566,7 +576,8 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
+ self.query = self.compile_final_query(
+ from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -593,7 +604,8 @@ class CisTransLrsSearch(DoSearch):
elif len(self.search_term) == 3:
lrs_min, lrs_max, self.mb_buffer = self.search_term
elif len(self.search_term) == 4:
- lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]]
+ lrs_min, lrs_max, self.mb_buffer = [
+ float(value) for value in self.search_term[:3]]
chromosome = self.search_term[3]
if "Chr" in chromosome or "chr" in chromosome:
chromosome = int(chromosome[3:])
@@ -636,14 +648,19 @@ class CisTransLrsSearch(DoSearch):
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(self.dataset.type),
- escape(self.dataset.type),
+ escape(
+ self.dataset.type),
+ escape(
+ self.dataset.type),
the_operator,
- escape(str(self.mb_buffer)),
- escape(self.dataset.type),
+ escape(
+ str(self.mb_buffer)),
+ escape(
+ self.dataset.type),
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))
+ 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))
where_clause = sub_clause + """
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
@@ -683,7 +700,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
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)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -714,7 +732,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
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)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -733,7 +752,8 @@ class MeanSearch(MrnaAssaySearch):
where_clause = """ %sXRef.mean > %s and
%sXRef.mean < %s """ % self.mescape(self.dataset.type,
- min(self.mean_min, self.mean_max),
+ min(self.mean_min,
+ self.mean_max),
self.dataset.type,
max(self.mean_min, self.mean_max))
else:
@@ -796,7 +816,8 @@ class PositionSearch(DoSearch):
DoSearch.search_types[search_key] = "PositionSearch"
def get_where_clause(self):
- self.search_term = [float(value) if is_number(value) else value for value in self.search_term]
+ self.search_term = [float(value) if is_number(
+ value) else value for value in self.search_term]
chr, self.mb_min, self.mb_max = self.search_term[:3]
self.chr = str(chr).lower()
self.get_chr()
@@ -806,7 +827,8 @@ class PositionSearch(DoSearch):
%s.Mb < %s """ % self.mescape(self.dataset.type,
self.chr,
self.dataset.type,
- min(self.mb_min, self.mb_max),
+ min(self.mb_min,
+ self.mb_max),
self.dataset.type,
max(self.mb_min, self.mb_max))
@@ -923,7 +945,8 @@ def get_aliases(symbol, species):
return []
filtered_aliases = []
- response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
+ response = requests.get(
+ GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
if response:
alias_list = json.loads(response.content)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-29 10:32:05 +0000