fix #22

NBISweden · Oct 15, 2018 · 735231b · 735231b
1 parent 2b592c5
commit 735231b
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/EMBLmyGFF3/modules/feature.py b/EMBLmyGFF3/modules/feature.py
@@ -475,10 +475,14 @@ def add_qualifier(self, gff_qualifier, value):
             for val in value:
                 if val not in self.qualifiers[qualifier].value:
                     self.qualifiers[qualifier].add_value(val)
+                else:
+                    logging.debug('val %s alredy exist (list case)' %  val)
         # Scalar case
         else:
             if value not in self.qualifiers[qualifier].value:
                 self.qualifiers[qualifier].add_value(value)
+            else:
+                logging.debug('val %s alredy exist (scalar case)' %  val)
 
     def combine(self, other):
         """

diff --git a/EMBLmyGFF3/modules/qualifier.py b/EMBLmyGFF3/modules/qualifier.py
@@ -76,10 +76,10 @@ def _by_value_format(self, value):
             elif self.value_format.startswith("\"<database:identifier>\""): # Handle dbxref's 
                 self._load_legal_dbxref( LEGAL_DBXREF_FILE )
                 value = value if type(value) == type([]) else [value]
-                new_value=[]
+
                 for val in value:
                     if val.split(':')[0].lower() in [v.lower() for v in self.legal_dbxref]:
-                        new_value.append(val)
+                        new_value = val
                     else:
                         msg = "Unknown db_xref '%s' - removing." % (val.split(':')[0])
                         if msg not in Qualifier.PREVIOUS_ERRORS:
@@ -153,11 +153,10 @@ def add_value(self, value):
         Qualifier wihtout value is possible. e.g environmental_sample
         """
         self.value = [self.value] if type(self.value) != type([]) else self.value
-        value = [value] if type(value) != type([]) else value
 
-        new_values = [self._by_value_format(v) for v in value]
-        logging.debug("%s - Changing value: '%s' to '%s'" % (self.name, value, new_values))
-        self.value += new_values
+        new_value = self._by_value_format(value)
+        logging.debug("%s - Changing value: '%s' to '%s'" % (self.name, value, new_value))
+        self.value.append(new_value)
         logging.debug("%s - Current value: '%s'" % (self.name, self.value))
 
     def set_value(self, value):