Update/versions

Dockerfile

@@ -37,12 +37,12 @@ RUN mkdir ~/.aws ~/.gen3 /root/studies
 
 RUN git clone https://github.com/bmeg/iceberg.git && \
 	cd iceberg && \
-	git checkout feature/FHIR-resource-type
+	git checkout 7f6cfdb558d05370fc645b5ab894b98b38a01e1b
 
 COPY . /root
 
 #Add jsonschemagraph exe to image
-RUN wget https://github.com/bmeg/jsonschemagraph/releases/download/v0.0.2/jsonschemagraph-linux.amd64 -P /usr/local/bin/
+RUN wget https://github.com/bmeg/jsonschemagraph/releases/download/v0.0.3/jsonschemagraph-linux.amd64 -P /usr/local/bin/
 RUN mv /usr/local/bin/jsonschemagraph-linux.amd64 /usr/local/bin/jsonschemagraph
 RUN chmod +x /usr/local/bin/jsonschemagraph
 ENV PATH="/usr/local/bin:$PATH"

bundle_service/processing/process_bundle.py

@@ -73,7 +73,7 @@ async def _can_create(access_token: str, project_id: str) -> bool | str | int:
     return True, f"HAS SERVICE create on resource {required_service}", None
 
 
-async def process(rows: List[dict], project_id: str, access_token: str) -> list[str]:
+async def process(rows: List[dict], project_id: str, access_token: str) -> List[str] | None:
     """Processes a bundle into a temp directory of NDJSON files
     that are compatible with existing loading functions
 
@@ -109,14 +109,31 @@ async def process(rows: List[dict], project_id: str, access_token: str) -> list[
             temp_file.close()
 
         if files_written:
-            subprocess.run(["jsonschemagraph", "gen-dir", "iceberg/schemas/graph", f"{temp_dir}", f"{temp_dir}/OUT", "--project_id", f"{project_id}", "--gzip_files"])
-            res = bulk_load(await _get_grip_service_name(), await _get_grip_graph_name(), project_id, f"{temp_dir}/OUT", logs, access_token)
-            if int(res[0]["status"]) != 200:
-                server_errors.append(res[0]["message"])
+            program, project = project_id.split("-")
+            project_str_dict = f'{{"auth_resource_path":"/programs/{program}/projects/{project}"}}'
+            print(f"Using project: {project_str_dict}")
+            result = subprocess.run(
+                ["jsonschemagraph", "gen-dir", "iceberg/schemas/graph", f"{temp_dir}", f"{temp_dir}/OUT", "--extraArgs", project_str_dict, "--gzip_files"],
+                capture_output=True,
+                text=True,
+                check=False
+            )
+            if result.returncode == 0:
+                print("jsonschemagraph ran successfully.")
+                res = bulk_load(await _get_grip_service_name(), await _get_grip_graph_name(), project_id, f"{temp_dir}/OUT", logs, access_token)
+                if int(res[0]["status"]) != 200:
+                    server_errors.append(res[0]["message"])
+            else:
+                print(f"jsonschemagraph failed with exit code: {result.returncode}")
+                print("Stdout:")
+                print(result.stdout)
+                print("Stderr:")
+                print(result.stderr)
+                server_errors.append(f"jsonschemagraph failed: {result.stderr.strip()}")
 
         try:
             db = LocalFHIRDatabase(db_name=f"{temp_dir}/local_fhir.db")
-            db.bulk_insert_data(resources=get_project_data(await _get_grip_service_name(), await _get_grip_graph_name(), project_id, logs, access_token))
+            db.bulk_insert_data(resources=get_project_data(await _get_grip_service_name(), await _get_grip_graph_name(), project_id, logs, access_token, 1024*1024))
 
             index_generator_dict = {
                 'researchsubject': db.flattened_research_subjects,

requirements.txt

@@ -35,7 +35,7 @@ fastapi
 uvicorn[standard]
 
 #aced submission
-aced-submission==0.0.9rc37
+aced-submission==0.0.10rc11
 
 #gen3 tracker
-gen3-tracker==0.0.5rc11
+gen3-tracker==0.0.7rc13

tests/server/test_bundle_service.py

@@ -227,13 +227,13 @@ def test_write_bundle_simple_ok(valid_bundle, valid_patient):
     vertex_id = request_bundle["entry"][0]["resource"]["id"]
     project_id = request_bundle["identifier"]["value"]
     endpoint = endpoint_from_token(ACCESS_TOKEN)
-    result = requests.get(f"{endpoint}/grip/writer/graphql/CALIPER/get-vertex/{vertex_id}/{project_id}",
+    result = requests.get(f"{endpoint}/grip/writer/CALIPER/get-vertex/{vertex_id}/{project_id}",
                           headers=HEADERS
                           ).json()
 
     print("RESULT: ", result)
     print("ENTRY: ", request_bundle["entry"][0]["resource"])
-    assert result['data']['gid'] == vertex_id
+    assert result['data']['id'] == vertex_id
 
 
 def test_write_bundle_missing_type(valid_bundle, valid_patient):