call drs as http calls

Author: daisieh

htsget_server/database.py

@@ -330,7 +330,6 @@ def create_variantfile(obj, tries=1):
             new_variantfile.id = obj['id']
             new_variantfile.reference_genome = obj['reference_genome']
             response, status_code = drs_operations.get_object(obj['id'])
-            #new_drs = session.query(drs_database.DrsObject).filter_by(id=obj['id']).one_or_none()
             if status_code == 200:
                 new_variantfile.drs_object_id = obj['id']
             else:
@@ -346,6 +345,15 @@ def create_variantfile(obj, tries=1):
     return None
 
 
+def mark_variantfile_as_not_indexed(variantfile_id):
+    with Session() as session:
+        new_variantfile = session.query(VariantFile).filter_by(id=variantfile_id).one_or_none()
+        if new_variantfile is not None:
+            new_variantfile.indexed = 0
+            session.add(new_variantfile)
+            session.commit()
+
+
 def set_variantfile_prefix(obj):
     # obj = {'variantfile_id', 'chr_prefix'}
     with Session() as session:

htsget_server/drs_database.py

@@ -80,8 +80,12 @@ def __repr__(self):
             result['access_methods'] = json.loads(self.access_methods.__repr__())
         if self.program is not None:
             result['program'] = self.program_id
-        if self.metadata is not None:
+        if self.meta_data is not None:
             result['metadata'] = self.meta_data
+            if 'indexed' in result['metadata']:
+                result['indexed'] = result['metadata']['indexed']
+            if 'reference' in result['metadata']:
+                result['reference_genome'] = result['metadata']['reference']
         else:
             result['metadata'] = {}
         return json.dumps(result)

htsget_server/indexing.py

@@ -1,9 +1,6 @@
-import drs_operations
 import htsget_operations
 import database
 from config import INDEXING_PATH, INDEXING_SWITCH_FILE
-from pysam import VariantFile, AlignmentFile
-import argparse
 import os
 import sys
 from watchdog.observers import Observer
@@ -14,7 +11,9 @@
 from candigv2_logging.logging import initialize, CanDIGLogger
 from time import sleep
 from random import randint
-
+import requests
+from authx.auth import create_service_token
+import json
 
 logger = CanDIGLogger(__file__)
 
@@ -85,11 +84,14 @@ def index_variants(file_name=None):
 
 
 def mark_as_indexed(drs_obj_id):
-    response, status_code = drs_operations.get_object(drs_obj_id)
-    if status_code == 200:
+    headers = {
+        "X-Service-Token": create_service_token()
+    }
+    response = requests.get(url=f"{os.getenv("DRS_URL")}/ga4gh/drs/v1/objects/{drs_obj_id}", headers=headers)
+    if response.status_code == 200:
         obj = response.json()
         obj["metadata"]["indexed"] = 1
-        drs_operations.post_object(obj)
+        response = requests.post(url=f"{os.getenv("DRS_URL")}/ga4gh/drs/v1/objects", headers=headers, json=obj)
 
 
 def write_pos_bucket(obj, object_id, tries=1):

requirements.txt

@@ -17,3 +17,4 @@ uvicorn[standard]==0.30.6
 werkzeug>=3.1.0 # not directly required, pinned by Snyk to avoid a vulnerability
 zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability
 urllib3>=2.2.2 # not directly required, pinned by Snyk to avoid a vulnerability
+requests==2.32.4