Validating Ids for duplicate Issue#56 (#98)

* Validating duplicate ids are not present Issue#56

schema_salad/main.py

@@ -139,7 +139,7 @@ def main(argsl=None):  # type: (List[str]) -> int
     try:
         schema.validate_doc(metaschema_names, schema_doc,
                             metaschema_loader, args.strict,
-                            source=schema_metadata["name"])
+                            source=schema_metadata.get("name"))
     except validate.ValidationException as e:
         _logger.error("While validating schema `%s`:\n%s" %
                       (args.schema, str(e)))

schema_salad/ref_resolver.py

@@ -822,7 +822,8 @@ def resolve_all(self,
                         loader.idx[metadata[identifer]] = document
 
         if checklinks:
-            self.validate_links(document, u"")
+            all_doc_ids={}  # type: Dict[Text, Text]
+            self.validate_links(document, u"", all_doc_ids)
 
         return document, metadata
 
@@ -877,8 +878,8 @@ def validate_scoped(self, field, link, docid):
         raise validate.ValidationException(
             "Field `%s` references unknown identifier `%s`, tried %s" % (field, link, ", ".join(tried)))
 
-    def validate_link(self, field, link, docid):
-        # type: (unicode, FieldType, unicode) -> FieldType
+    def validate_link(self, field, link, docid, all_doc_ids):
+        # type: (unicode, FieldType, unicode, Dict[Text, Text]) -> FieldType
         if field in self.nolinkcheck:
             return link
         if isinstance(link, (str, unicode)):
@@ -901,14 +902,14 @@ def validate_link(self, field, link, docid):
             errors = []
             for n, i in enumerate(link):
                 try:
-                    link[n] = self.validate_link(field, i, docid)
+                    link[n] = self.validate_link(field, i, docid, all_doc_ids)
                 except validate.ValidationException as v:
                     errors.append(v)
             if bool(errors):
                 raise validate.ValidationException(
                     "\n".join([unicode(e) for e in errors]))
         elif isinstance(link, CommentedMap):
-            self.validate_links(link, docid)
+            self.validate_links(link, docid, all_doc_ids)
         else:
             raise validate.ValidationException(
                 "`%s` field is %s, expected string, list, or a dict."
@@ -924,8 +925,8 @@ def getid(self, d):  # type: (Any) -> Optional[Text]
                         return idd
         return None
 
-    def validate_links(self, document, base_url):
-        # type: (Union[CommentedMap, CommentedSeq, unicode, None], unicode) -> None
+    def validate_links(self, document, base_url, all_doc_ids):
+        # type: (Union[CommentedMap, CommentedSeq, unicode, None], unicode, Dict[Text, Text]) -> None
         docid = self.getid(document)
         if not docid:
             docid = base_url
@@ -939,7 +940,15 @@ def validate_links(self, document, base_url):
                 for d in self.url_fields:
                     sl = SourceLine(document, d, validate.ValidationException)
                     if d in document and d not in self.identity_links:
-                        document[d] = self.validate_link(d, document[d], docid)
+                        document[d] = self.validate_link(d, document[d], docid, all_doc_ids)
+                for identifier in self.identifiers:  # validate that each id is defined uniquely
+                    if identifier in document:
+                        sl = SourceLine(document, identifier, validate.ValidationException)
+                        if document[identifier] in all_doc_ids and sl.makeLead() != all_doc_ids[document[identifier]]:
+                            raise validate.ValidationException(
+                                "%s object %s `%s` previously defined" % (all_doc_ids[document[identifier]], identifier, relname(document[identifier]), ))
+                        else:
+                            all_doc_ids[document[identifier]] = sl.makeLead()
             except validate.ValidationException as v:
                 errors.append(sl.makeError(unicode(v)))
             if hasattr(document, "iteritems"):
@@ -952,7 +961,7 @@ def validate_links(self, document, base_url):
         for key, val in iterator:
             sl = SourceLine(document, key, validate.ValidationException)
             try:
-                self.validate_links(val, docid)
+                self.validate_links(val, docid, all_doc_ids)
             except validate.ValidationException as v:
                 if key not in self.nolinkcheck:
                     docid2 = self.getid(val)

schema_salad/schema.py

@@ -242,7 +242,7 @@ def load_and_validate(document_loader,  # type: Loader
 
     validationErrors = u""
     try:
-        document_loader.validate_links(data, u"")
+        document_loader.validate_links(data, u"", {})
     except validate.ValidationException as v:
         validationErrors = unicode(v) + "\n"
 

schema_salad/sourceline.py

@@ -149,18 +149,21 @@ def __exit__(self,
             return
         raise self.makeError(unicode(exc_value))
 
-    def makeError(self, msg):  # type: (Text) -> Any
-        if not isinstance(self.item, ruamel.yaml.comments.CommentedBase):
-            return self.raise_type(msg)
-        errs = []
+    def makeLead(self):  # type: () -> Text
         if self.key is None or self.item.lc.data is None or self.key not in self.item.lc.data:
-            lead = "%s:%i:%i:" % (self.item.lc.filename if hasattr(self.item.lc, "filename") else "",
+            return "%s:%i:%i:" % (self.item.lc.filename if hasattr(self.item.lc, "filename") else "",
                                   (self.item.lc.line or 0)+1,
                                   (self.item.lc.col or 0)+1)
         else:
-            lead = "%s:%i:%i:" % (self.item.lc.filename if hasattr(self.item.lc, "filename") else "",
+            return "%s:%i:%i:" % (self.item.lc.filename if hasattr(self.item.lc, "filename") else "",
                                   (self.item.lc.data[self.key][0] or 0)+1,
                                   (self.item.lc.data[self.key][1] or 0)+1)
+
+    def makeError(self, msg):  # type: (Text) -> Any
+        if not isinstance(self.item, ruamel.yaml.comments.CommentedBase):
+            return self.raise_type(msg)
+        errs = []
+        lead = self.makeLead()
         for m in msg.splitlines():
             if bool(lineno_re.match(m)):
                 errs.append(m)

schema_salad/tests/test_errors.py

@@ -21,7 +21,10 @@ def test_errors(self):
                   "test_schema/test8.cwl",
                   "test_schema/test9.cwl",
                   "test_schema/test10.cwl",
-                  "test_schema/test11.cwl"):
+                  "test_schema/test11.cwl",
+                  "test_schema/test12.cwl",
+                  "test_schema/test13.cwl",
+                  "test_schema/test14.cwl"):
             with self.assertRaises(ValidationException):
                 try:
                     load_and_validate(document_loader, avsc_names,

schema_salad/tests/test_schema/test12.cwl

@@ -0,0 +1,16 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+  - id: example_flag
+    type: boolean
+    inputBinding:
+      position: 1
+      prefix: -f
+  - id: example_flag
+    type: int
+    inputBinding:
+      position: 3
+      prefix: --example-string
+
+outputs: []

schema_salad/tests/test_schema/test13.cwl

@@ -0,0 +1,20 @@
+cwlVersion: v1.0
+class: Workflow
+inputs:
+  example_flag:
+    type: boolean
+    inputBinding:
+      position: 1
+      prefix: -f
+
+outputs: []
+
+steps:
+  example_flag:
+    in: []
+    out: []
+    run:
+      id: blah
+      class: CommandLineTool
+      inputs: []
+      outputs: []

schema_salad/tests/test_schema/test14.cwl

@@ -0,0 +1,11 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+inputs:
+  example_flag:
+    type: boolean
+    inputBinding:
+      position: 1
+      prefix: -f
+outputs:
+  example_flag: int

setup.py

@@ -47,7 +47,7 @@
 extras_require = {}               # TODO: to be removed when the above is added
 
 setup(name='schema-salad',
-      version='2.4',
+      version='2.5',
       description='Schema Annotations for Linked Avro Data (SALAD)',
       long_description=open(README).read(),
       author='Common workflow language working group',