Merge pull request #546 from biolink/issue-544-rule-set-bugfix

Issue 544 rule set bugfix
biolink · Apr 14, 2021 · 64dc644 · 64dc644
2 parents 7d0d4b1 + 0abfb2a
commit 64dc644
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/ontobio/io/assocparser.py b/ontobio/io/assocparser.py
@@ -7,6 +7,7 @@
 
 # TODO: Refactor - move some stuff out into generic parser object
 
+# from _typeshed import NoneType
 import re
 import requests
 import tempfile
@@ -21,7 +22,7 @@
 from dataclasses import dataclass
 
 from collections import namedtuple, defaultdict
-from typing import ClassVar, Iterable, Optional, List, Dict, Set, Union, Any
+from typing import Callable, ClassVar, Collection, Iterable, Optional, List, Dict, Set, TypeVar, Union, Any
 
 from ontobio import ontol
 from ontobio import ecomap
@@ -204,7 +205,6 @@ def should_run_rule(self, rule: int) -> bool:
         return rule in self.rules
 
 
-
 class AssocParserConfig():
     """
     Configuration for an association parser
@@ -262,11 +262,14 @@ def __init__(self,
         self.group_idspace = None if group_idspace is None else set(group_idspace)
         self.rule_contexts = rule_contexts
         # We'll say that the default None should run no rules, so let's set the rule_set to []
+        # print("Rule Set is {}".format(rule_set))
         if rule_set == None:
             self.rule_set = RuleSet([])
         elif rule_set == RuleSet.ALL:
             # None here means all rules
             self.rule_set = RuleSet(None)
+        else:
+            self.rule_set = RuleSet(rule_set)
 
 
         # This is a dictionary from ruleid: `gorule-0000001` to title strings
@@ -308,7 +311,6 @@ def __str__(self):
         attribute_values = ["{att}={val}".format(att=att, val=dict([(k, v) for k, v in value.items()][:8]) if isinstance(value, dict) else value) for att, value in vars(self).items()]
         return "AssocParserConfig({})".format(",".join(attribute_values))
 
-
 class Report(object):
     """
     A report object that is generated as a result of a parse

diff --git a/ontobio/io/gafparser.py b/ontobio/io/gafparser.py
@@ -188,6 +188,7 @@ def parse_line(self, line):
             assoc = self.upgrade_empty_qualifier(assoc)
 
         ## Run GO Rules, save split values into individual variables
+        # print("Config is {}".format(self.config.__dict__.keys()))
         go_rule_results = qc.test_go_rules(assoc, self.config, group=self.group)
         for rule, result in go_rule_results.all_results.items():
             if result.result_type == qc.ResultType.WARNING: