Merge pull request #255 from biothings/fix-datasets

Fix datasets with missing context or outdated names

scripts/fix_niaid_datasets.py

@@ -0,0 +1,46 @@
+from discovery.model.dataset import Dataset
+
+niaidContext = {
+"schema": "http://schema.org/",
+"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+"bioschemas": "https://discovery.biothings.io/ns/bioschemas/",
+"niaid": "https://discovery.biothings.io/ns/niaid/",
+}
+
+def updateContext():
+    """
+    Update datasets missing @context and update @types with outdated names
+    """
+    # ids = []
+    # needs_renaming =[]
+    docs = Dataset.search()
+    for doc in docs.scan():
+        context = getattr(doc, '@context', None)
+        # dataset_id = getattr(getattr(doc, 'meta', None), 'id', None)
+        clss_type = getattr(doc, "@type", None)
+        if not context:
+            if ":" not in clss_type:
+                # add context and fix class name
+                added_prefix = "niaid:" + clss_type
+                # ids.append(added_prefix)
+                doc.update(**{"@context": niaidContext, "@type": added_prefix})
+            else:
+                # add context
+                # ids.append('JUST CONTEXT')
+                doc.update(**{"@context": niaidContext})
+        if 'niaid:Niaid' in clss_type:
+            updated_name = clss_type.replace("niaid:Niaid", "niaid:")
+            # needs_renaming.append(clss_type + " >>> " + updated_name)
+            doc.update(**{"@type": updated_name})
+
+    # print(len(ids))
+    # print(ids)
+    # print("++++++++++++++++++")
+    # print(len(needs_renaming))
+    # print(needs_renaming)
+
+
+
+if __name__ == "__main__":
+    updateContext()