diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 16 |
2 files changed, 11 insertions, 47 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 9b048346..2c6c3a14 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -52,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil +from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from wqflask import user_manager from MySQLdb import escape_string as escape @@ -77,47 +78,6 @@ def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss #print("{}: {}".format(stage, mem/1024)) -def is_float(value): - try: - float(value) - return True - except: - return False - -def is_int(value): - try: - int(value) - return True - except: - return False - -def is_str(value): - if value is None: - return False - try: - str(value) - return True - except: - return False - -def get_float(vars,name,default=None): - if name in vars: - if is_float(vars[name]): - return float(vars[name]) - return None - -def get_int(vars,name,default=None): - if name in vars: - if is_int(vars[name]): - return float(vars[name]) - return default - -def get_string(vars,name,default=None): - if name in vars: - if not vars[name] is None: - return str(vars[name]) - return default - class AuthException(Exception): pass diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index 41fcf873..53c96591 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -26,6 +26,7 @@ from db import webqtlDatabaseFunction from flask import render_template from utility import formatting +from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string from utility.logger import getLogger logger = getLogger(__name__ ) @@ -67,8 +68,9 @@ views.py). self.search_terms = kw['search_terms_and'] search = self.search_terms # check for dodgy search terms - regex = re.compile("http:|href|sql|select|update",re.IGNORECASE) - if regex.match(search): + rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE) + if rx.match(search): + logger.info("Regex failed search") self.search_term_exists = False return else: @@ -80,11 +82,10 @@ views.py). dataset_type = "Publish" elif type == "Genotypes": dataset_type = "Geno" - elif type == "ProbeSet": - dataset_type = "ProbeSet" # ProbeSet is default else: - self.search_term_exists = False - return + dataset_type = "ProbeSet" # ProbeSet is default + + assert(is_str(kw.get('dataset'))) self.dataset = create_dataset(kw['dataset'], dataset_type) logger.debug("search_terms:", self.search_terms) self.search() @@ -158,6 +159,7 @@ statement and executes 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 + ")" @@ -168,6 +170,7 @@ statement and executes 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: @@ -175,6 +178,7 @@ statement and executes 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: |