Validation improvements

code/backend/beacon/data_types.py

@@ -43,9 +43,11 @@ def validate_input(**kwargs):
     Validates query parameters. If there's a violation,
     an `APIArgumentError` exception is raised
     """
-    def wrap(name, message, regexp, can_skip=False):
+    def wrap(name, message, regexp, optional=False):
         re_regexp = re.compile(regexp, re.IGNORECASE)
-        if not test_input_with_regex(kwargs, name, re_regexp) and not can_skip:
+        if name not in kwargs and not optional:
+            raise APIArgumentError("A required value is missing: {0}".format(name))
+        if name in kwargs and kwargs[name] is not None and not re_regexp.match(kwargs[name]):
             arg = kwargs.get(name) if kwargs.get(name) is not None else '<<None>>'
             raise APIArgumentError("Invalid {0} ({1}) - {2}".format(name, arg, message))
 
@@ -55,33 +57,33 @@ def validate_input(**kwargs):
 
     wrap('start',
          'should be a positive number',
-         r'^\d+$',
-         True)
+         r'^\d*$',
+         optional=True)
 
     wrap('startMin',
          'should be an empty string or a positive number',
          r'^\d*$',
-         True)
+         optional=True)
 
     wrap('startMax',
          'should be an empty string or a positive number',
          r'^\d*$',
-         True)
+         optional=True)
 
     wrap('end',
          'should be an empty string or a positive number',
          r'^\d*$',
-         True)
+         optional=True)
 
     wrap('endMin',
          'should be an empty string or a positive number',
          r'^\d*$',
-         True)
+         optional=True)
 
     wrap('endMax',
          'should be an empty string or a positive number',
          r'^\d*$',
-         True)
+         optional=True)
 
     wrap('assemblyId',
          'accepted ones are: GRCh38, GRCh37 and NCBI36',
@@ -94,12 +96,12 @@ def validate_input(**kwargs):
     wrap('alternateBases',
          'should contain only A, C, T, G, D',
          r'^[actgd]*$',
-         True)
+         optional=True)
 
     wrap('includeDatasetResponses',
          'accepts only "ALL", "HIT", "MISS", "NONE" and empty string',
          r'^(hit|all|miss|none)?$',
-         True)
+         optional=True)
 
     return True
 
@@ -218,9 +220,10 @@ def create_beacon_allele_request(**kwargs):
       'datasetIds', 'includeDatasetResponses'
     """
 
-    fields_required = ['referenceName', 'start', 'referenceBases',
-                       'alternateBases', 'assemblyId']
-    fields_optional = ['datasetIds', 'includeDatasetResponses',
+    fields_required = ['referenceName']
+    fields_optional = ['start', 'referenceBases',
+                       'alternateBases', 'assemblyId',
+                       'datasetIds', 'includeDatasetResponses',
                        'startMin', 'startMax',
                        'end', 'endMin', 'endMax']