get_bundles_in_drs

indexd/drs/blueprint.py

@@ -5,7 +5,7 @@
 from indexd.errors import UnexpectedError
 
 # from indexd.index.blueprint import get_index
-from indexd.index.blueprint import get_index
+from indexd.index.blueprint import get_index, get_bundle_record_list
 
 blueprint = flask.Blueprint("drs", __name__)
 
@@ -33,8 +33,31 @@ def get_drs_object(object_id):
 
 @blueprint.route("/ga4gh/drs/v1/objects", methods=["GET"])
 def list_drs_records():
+    limit = flask.request.args.get("limit")
+    start = flask.request.args.get("start")
+    page = flask.request.args.get("page")
+
+    try:
+        limit = 100 if limit is None else int(limit)
+    except ValueError as err:
+        raise UserError("limit must be an integer")
+
+    if limit < 0 or limit > 1024:
+        raise UserError("limit must be between 0 and 1024")
+
+    if page is not None:
+        try:
+            page = int(page)
+        except ValueError as err:
+            raise UserError("page must be an integer")
+
     records = get_index()[0].json["records"]
-    ret = {"drs_objects": [indexd_to_drs(record, True) for record in records]}
+    bundles = get_bundle_record_list()[0].json
+
+    ret = {
+        "drs_objects": [indexd_to_drs(record, True) for record in records],
+        "bundles": [bundle_to_drs(bundle, is_content=True) for bundle in bundles],
+    }
 
     return flask.jsonify(ret), 200
 

indexd/index/blueprint.py

@@ -576,12 +576,9 @@ def post_bundle():
     for bundle in bundles:
         data = get_index_record(bundle)[0]
         data = data.json
-        print("------------------------data---------------------------------")
-        print(data)
         size += data["size"]
         checksums.append(get_checksum(data))
         data = bundle_to_drs(data, expand=True, is_content=True)
-        # del data["checksums"]
         bundle_data.append(data)
     checksum = (
         flask.request.json.get("checksum")
@@ -607,6 +604,8 @@ def get_bundle_record_list():
     """
 
     limit = flask.request.args.get("limit")
+    start = flask.request.args.get("start")
+    page = flask.request.args.get("page")
 
     try:
         limit = 100 if limit is None else int(limit)
@@ -616,7 +615,13 @@ def get_bundle_record_list():
     if limit < 0 or limit > 1024:
         raise UserError("limit must be between 0 and 1024")
 
-    ret = blueprint.index_driver.get_bundle_list(limit=limit)
+    if page is not None:
+        try:
+            page = int(page)
+        except ValueError as err:
+            raise UserError("page must be an integer")
+
+    ret = blueprint.index_driver.get_bundle_list(start=start, limit=limit, page=page)
 
     return flask.jsonify(ret), 200
 

indexd/index/drivers/alchemy.py

@@ -263,7 +263,7 @@ class DrsBundleRecord(Base):
     size = Column(BigInteger)
     bundle_data = Column(Text)
 
-    def to_document_dict(self, expand):
+    def to_document_dict(self, expand=False):
         """
         Get the full bundle document
         expand: True to include bundle_data
@@ -1371,22 +1371,29 @@ def add_bundle(
 
             return record.bundle_id, record.name, record.bundle_data
 
-    def get_bundle_list(self, limit=100):
+    def get_bundle_list(self, start=None, limit=100, page=None):
         """
         Returns list of all bundles
         """
         with self.session as session:
             query = session.query(DrsBundleRecord)
             query = query.limit(limit)
 
-            return [i.to_document_dict(expand=False) for i in query]
+            if start is not None:
+                query = query.filter(DrsBundleRecord.bundle_id > start)
+
+            if page is not None:
+                query = query.offset(limit * page)
+
+            return [i.to_document_dict() for i in query]
 
     def get_bundle(self, bundle_id, expand=False):
         """
         Gets a bundle record given the bundle_id.
         """
         with self.session as session:
             query = session.query(DrsBundleRecord)
+
             query = query.filter(or_(DrsBundleRecord.bundle_id == bundle_id)).order_by(
                 DrsBundleRecord.created_time.desc()
             )

tests/test_drs.py

@@ -3,6 +3,7 @@
 import requests
 import responses
 from tests.default_test_settings import settings
+from tests.test_bundles import get_bundle_doc
 
 
 def generate_presigned_url_response(did, protocol="", status=200):
@@ -102,12 +103,17 @@ def test_drs_list(client, user):
     submitted_guids = []
     for _ in range(record_length):
         res_1 = client.post("/index/", json=data, headers=user)
-        submitted_guids.append(res_1.json["did"])
+        did = res_1.json["did"]
+        submitted_guids.append(did)
+        bundle_data = get_bundle_doc(bundles=[did])
+        res2 = client.post("/bundle/", json=bundle_data, headers=user)
         assert res_1.status_code == 200
+
     res_2 = client.get("/ga4gh/drs/v1/objects")
     assert res_2.status_code == 200
     rec_2 = res_2.json
     assert len(rec_2["drs_objects"]) == record_length
+    assert len(rec_2["bundles"]) == record_length
     assert submitted_guids.sort() == [r["id"] for r in rec_2["drs_objects"]].sort()