1-1 uniprot mapping

src/hub/dataload/sources/chembl/upload.py

@@ -1,18 +1,45 @@
+import copy
 import glob
 import os
 
 import biothings.hub.dataload.storage as storage
 import biothings.hub.dataload.uploader as uploader
+from biothings.utils.dataload import merge_root_keys
 
 from hub.datatransform.keylookup import MyGeneKeyLookup
 
 from .parser import load_data
 
 
+class ChemblMergerStorage(storage.RootKeyMergerStorage):
+    """
+    Just like MergerStorage, this storage deals with duplicated error
+    by appending key's content to existing document. Keys in existing
+    document will be converted to a list as needed.
+
+    Note:
+      - root keys must have the same type in each documents
+      - inner structures aren't merged together, the merge happend
+        at root key level
+    """
+
+    @classmethod
+    def merge_func(klass, doc1, doc2, **kwargs):
+        # caller popped it from doc1, let's take from doc2
+        _id = doc2["_id"]
+        # exclude_id will remove _if from doc2, that's why we kept it from before
+        # also, copy doc2 ref as the merged doc will be stored in
+        # a bulk op object, since doc2 is modified in place, this could impact
+        # the bulk op and procude empty $set error from mongo
+        doc = merge_root_keys(doc1, copy.copy(doc2), exclude=["_id", "xrefs"])
+        doc["_id"] = _id
+        return doc
+
+
 class ChemblUploader(uploader.BaseSourceUploader):
     name = "chembl"
 
-    storage_class = storage.RootKeyMergerStorage
+    storage_class = ChemblMergerStorage
     TARGET_FILENAME_PATTERN = "target.*.json"
 
     keylookup = MyGeneKeyLookup(