optional fields

indexd/drs/blueprint.py

@@ -103,7 +103,13 @@ def indexd_to_drs(record, expand=False, list_drs=False):
         record["created_date"] if "created_date" in record else record["created_time"]
     )
 
-    version = record["rev"] if "rev" in record else ""
+    version = (
+        record["rev"]
+        if "rev" in record
+        else record["version"]
+        if "version" in record
+        else ""
+    )
 
     updated_date = (
         record["updated_date"] if "updated_date" in record else record["updated_time"]
@@ -113,7 +119,13 @@ def indexd_to_drs(record, expand=False, list_drs=False):
 
     description = record["description"] if "description" in record else None
 
-    alias = record["alias"] if "alias" in record else []
+    alias = (
+        record["alias"]
+        if "alias" in record
+        else eval(record["aliases"])
+        if "aliases" in record
+        else []
+    )
 
     drs_object = {
         "id": did,
@@ -123,14 +135,13 @@ def indexd_to_drs(record, expand=False, list_drs=False):
         "created_time": created_time,
         "updated_time": updated_date,
         "size": record["size"],
-        "aliases": [],
+        "aliases": alias,
         "contents": [],
         "self_uri": self_uri,
         "version": version,
         "form": form,
         "checksums": [],
         "description": description,
-        "aliases": alias,
     }
 
     if "description" in record:
@@ -202,6 +213,15 @@ def bundle_to_drs(record, expand=False, is_content=False):
 
     if not is_content:
         # Show these only if its the leading bundle
+        description = record["description"] if "description" in record else ""
+        aliases = (
+            record["alias"]
+            if "alias" in record
+            else eval(record["aliases"])
+            if "aliases" in record
+            else []
+        )
+        version = record["version"] if "version" in record else ""
         drs_object["checksums"] = []
         parse_checksums(record, drs_object)
 
@@ -219,6 +239,9 @@ def bundle_to_drs(record, expand=False, is_content=False):
         drs_object["created_time"] = created_time
         drs_object["updated_time"] = updated_time
         drs_object["size"] = record["size"]
+        drs_object["aliases"] = aliases
+        drs_object["description"] = description
+        drs_object["version"] = version
 
     return drs_object
 

indexd/index/blueprint.py

@@ -640,6 +640,17 @@ def post_bundle():
     bundles = flask.request.json.get("bundles")
     bundle_id = flask.request.json.get("bundle_id")
     size = flask.request.json.get("size") if flask.request.json.get("size") else 0
+    description = (
+        flask.request.json.get("description")
+        if flask.request.json.get("description")
+        else ""
+    )
+    version = (
+        flask.request.json.get("version") if flask.request.json.get("version") else ""
+    )
+    aliases = (
+        flask.request.json.get("aliases") if flask.request.json.get("aliases") else []
+    )
 
     if len(bundles) == 0:
         raise UserError("Bundle data required.")
@@ -652,6 +663,8 @@ def post_bundle():
 
     bundle_data = []
     checksums = []
+
+    # get bundles/records that already exists and add it to bundle_data
     for bundle in bundles:
         data = get_index_record(bundle)[0]
         data = data.json
@@ -671,6 +684,9 @@ def post_bundle():
         size=size,
         bundle_data=json.dumps(bundle_data),
         checksum=checksum,
+        description=description,
+        version=version,
+        aliases=json.dumps(aliases),
     )
 
     return flask.jsonify({"bundle_id": ret[0], "name": ret[1], "contents": ret[2]}), 200
@@ -694,7 +710,6 @@ def get_bundle_record_with_id(bundle_id):
     """
     Returns a record given bundle_id
     """
-    from indexd.drs.blueprint import indexd_to_drs, bundle_to_drs
 
     expand = True if flask.request.args.get("expand") == "true" else False
 

indexd/index/drivers/alchemy.py

@@ -1522,7 +1522,15 @@ def len(self):
             ).scalar()
 
     def add_bundle(
-        self, bundle_id=None, name=None, checksum=None, size=None, bundle_data=None
+        self,
+        bundle_id=None,
+        name=None,
+        checksum=None,
+        size=None,
+        bundle_data=None,
+        description=None,
+        version=None,
+        aliases=None,
     ):
         """
         Add a bundle record 
@@ -1546,6 +1554,12 @@ def add_bundle(
 
             record.bundle_data = bundle_data
 
+            record.description = description
+
+            record.version = version
+
+            record.aliases = aliases
+
             try:
                 session.add(record)
                 session.commit()
@@ -1591,6 +1605,7 @@ def get_bundle(self, bundle_id, expand=False):
                 raise NoRecordFound("No bundle found")
 
             doc = record.to_document_dict(expand)
+
             return doc
 
     def get_bundle_and_object_list(

indexd/index/schema.py

@@ -122,7 +122,7 @@
             "description": "optional version string of the object",
             "type": "string",
         },
-        "aliases": {"type": "array"},
+        "aliases": {"description": "Optional", "type": "array",},
     },
 }
 

tests/test_bundles.py

@@ -59,6 +59,56 @@ def test_bundle_post(client, user):
     assert res2.status_code == 200
 
 
+def test_bundle_get_post_with_optional_fields(client, user):
+    """
+    Bundle 1
+        +-object1
+
+    Bundel 2
+        +-Bundle 1 
+            +-object1 
+        +-object1 
+    """
+    did_list, _ = create_index(client, user)
+
+    data = get_bundle_doc(bundles=did_list)
+    data["description"] = "This is a cool bundle."
+    data["version"] = "v13cde"
+    data["aliases"] = ["123", "456"]
+
+    res2 = client.post("/bundle/", json=data, headers=user)
+    rec2 = res2.json
+    did = rec2["bundle_id"]
+    assert res2.status_code == 200
+
+    res3 = client.get("/ga4gh/drs/v1/objects/" + did)
+    rec3 = res3.json
+    assert res3.status_code == 200
+    assert rec3["description"] == data["description"]
+    assert rec3["version"] == data["version"]
+    assert rec3["aliases"] == data["aliases"]
+
+    res4 = client.get("/bundle/" + did)
+    rec4 = res4.json
+    assert res4.status_code == 200
+    assert rec4["description"] == data["description"]
+    assert rec4["version"] == data["version"]
+    assert rec4["aliases"] == data["aliases"]
+
+    # Nested bundle shouldn't contain optional fields
+    data2 = get_bundle_doc(bundles=[did, did_list[0]])
+    res5 = client.post("/bundle/", json=data2, headers=user)
+    did2 = res5.json["bundle_id"]
+    assert res5.status_code == 200
+    res6 = client.get("/bundle/" + did2 + "?expand=true")
+    rec6 = res6.json
+    contents = rec6["contents"]
+    for content in contents:
+        assert "description" not in content
+        assert "version" not in content
+        assert "aliases" not in content
+
+
 def test_bundle_post_self_reference(client, user):
     """
     Make sure this doesnt exist