def search(self):
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
for a_search in self.search_terms:
print("[kodak] item is:", pf(a_search))
search_term = a_search['search_term']
search_operator = a_search['separator']
if a_search['key']:
search_type = a_search['key'].upper()
else:
# We fall back to the dataset type as the key to get the right object
search_type = self.dataset.type
print("search_type is:", pf(search_type))
# This is throwing an error when a_search['key'] is None, so I changed above
#search_type = string.upper(a_search['key'])
#if not search_type:
# search_type = self.dataset.type
search_ob = do_search.DoSearch.get_search(search_type)
search_class = getattr(do_search, search_ob)
print("search_class is: ", pf(search_class))
the_search = search_class(search_term,
search_operator,
self.dataset,
)
self.results.extend(the_search.run())
#print("in the search results are:", self.results)
self.header_fields = the_search.header_fields
def search(self):
"""This function sets up the actual search query in the form of a SQL
statement and executes
"""
self.search_terms = parser.parse(self.search_terms)
logger.debug("After parsing:", self.search_terms)
if len(self.search_terms) > 1:
logger.debug("len(search_terms)>1")
combined_from_clause = ""
combined_where_clause = ""
previous_from_clauses = [
] #The same table can't be referenced twice in the from clause
for i, a_search in enumerate(self.search_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(the_search, "get_from_clause",
None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i + 1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
else:
logger.debug("Search failed 1")
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(
combined_from_clause, combined_where_clause)
# logger.debug("final_query",final_query)
results = the_search.execute(final_query)
self.results.extend(results)
else:
logger.debug("len(search_terms)<=1")
if self.search_terms == []:
logger.debug("Search failed 2")
self.search_term_exists = False
else:
for a_search in self.search_terms:
the_search = self.get_search_ob(a_search)
if the_search != None:
self.results.extend(the_search.run())
else:
logger.debug("Search failed 3")
self.search_term_exists = False
if self.search_term_exists:
if the_search != None:
self.header_fields = the_search.header_fields
def search(self):
"""This function sets up the actual search query in the form of a SQL
statement and executes
"""
self.search_terms = parser.parse(self.search_terms)
logger.debug("After parsing:", self.search_terms)
if len(self.search_terms) > 1:
logger.debug("len(search_terms)>1")
combined_from_clause = ""
combined_where_clause = ""
previous_from_clauses = [] #The same table can't be referenced twice in the from clause
for i, a_search in enumerate(self.search_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i+1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
else:
logger.debug("Search failed 1")
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
# logger.debug("final_query",final_query)
results = the_search.execute(final_query)
self.results.extend(results)
else:
logger.debug("len(search_terms)<=1")
if self.search_terms == []:
logger.debug("Search failed 2")
self.search_term_exists = False
else:
for a_search in self.search_terms:
the_search = self.get_search_ob(a_search)
if the_search != None:
self.results.extend(the_search.run())
else:
logger.debug("Search failed 3")
self.search_term_exists = False
if self.search_term_exists:
if the_search != None:
self.header_fields = the_search.header_fields
def search(self):
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
if len(self.search_terms) > 1:
combined_from_clause = ""
combined_where_clause = ""
previous_from_clauses = [
] #The same table can't be referenced twice in the from clause
for i, a_search in enumerate(self.search_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(the_search, "get_from_clause",
None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i + 1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
else:
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(
combined_from_clause, combined_where_clause)
results = the_search.execute(final_query)
self.results.extend(results)
else:
if self.search_terms == []:
self.search_term_exists = False
else:
for a_search in self.search_terms:
the_search = self.get_search_ob(a_search)
if the_search != None:
self.results.extend(the_search.run())
else:
self.search_term_exists = False
if self.search_term_exists:
if the_search != None:
self.header_fields = the_search.header_fields
def search(self):
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
if len(self.search_terms) > 1:
combined_from_clause = ""
combined_where_clause = ""
previous_from_clauses = [] #The same table can't be referenced twice in the from clause
for i, a_search in enumerate(self.search_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i+1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
else:
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
results = the_search.execute(final_query)
self.results.extend(results)
else:
if self.search_terms == []:
self.search_term_exists = False
else:
for a_search in self.search_terms:
the_search = self.get_search_ob(a_search)
if the_search != None:
self.results.extend(the_search.run())
else:
self.search_term_exists = False
if self.search_term_exists:
if the_search != None:
self.header_fields = the_search.header_fields
def search(self):
"""
This function sets up the actual search query in the form of a SQL statement and executes
"""
self.search_terms = parser.parse(self.search_terms)
combined_from_clause = ""
combined_where_clause = ""
# The same table can't be referenced twice in the from clause
previous_from_clauses = []
symbol_list = []
if self.dataset.type == "ProbeSet":
for a_search in self.search_terms:
if a_search['key'] == None:
symbol_list.append(a_search['search_term'][0])
alias_terms = get_aliases(symbol_list, self.dataset.group.species)
for i, a_search in enumerate(alias_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(
the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_alias_where_clause()
combined_where_clause += "(" + where_clause + ")"
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
for i, a_search in enumerate(self.search_terms):
if a_search['key'] == "GO":
self.go_term = a_search['search_term'][0]
gene_list = get_GO_symbols(a_search)
self.search_terms += gene_list
continue
else:
the_search = self.get_search_ob(a_search)
if the_search != None:
get_from_clause = getattr(
the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
pass
else:
previous_from_clauses.append(from_clause)
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
if (i + 1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
combined_where_clause += "OR"
else:
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
final_query = the_search.compile_final_query(
combined_from_clause, combined_where_clause)
results = the_search.execute(final_query)
self.results.extend(results)
if self.search_term_exists:
if the_search != None:
self.header_fields = the_search.header_fields