Merge pull request #210 from CanDIG/daisieh/error-handling

error handling, misc fixes

entrypoint.sh

@@ -24,4 +24,5 @@ if [[ -f "initial_setup" ]]; then
     rm initial_setup
 fi
 
+bash /app/htsget_server/renew_token.sh
 python3 htsget_server/server.py $@

htsget_server/drs_operations.py

@@ -54,7 +54,7 @@ def get_access_url(object_id, access_id):
             bucket = "testhtsget"
         else:
             response = requests.get(
-                AUTHZ['CANDIG_VAULT_URL'] + f"/v1/aws/{endpoint}/{bucket}",
+                AUTHZ['CANDIG_VAULT_URL'] + f"/v1/aws/{endpoint}-{bucket}",
                 headers={"Authorization": f"Bearer {VAULT_S3_TOKEN}"}
             )
             if response.status_code == 200:

htsget_server/operations.py

@@ -172,6 +172,8 @@ def _get_data(id_, reference_name=None, start=None, end=None, class_="body", for
     # get a file and index from drs, based on the id_
     gen_obj = _get_genomic_obj(request, id_)
     if gen_obj is not None:
+        if "error" in gen_obj:
+            return gen_obj, 500
         file_in = gen_obj["file"]
         ntf = tempfile.NamedTemporaryFile(prefix='htsget', suffix=format_,
                                  mode='wb', delete=False)
@@ -228,6 +230,8 @@ def _get_urls(file_type, id, reference_name=None, start=None, end=None, _class=N
 
     gen_obj = _get_genomic_obj(request, id)
     if gen_obj is not None:
+        if "error" in gen_obj:
+            return gen_obj, 500
         if _class == "header":
             urls = [{"url": f"{request.url_root}/htsget/v1/{file_type}s/data/{id}?class=header",
             "class": "header"}]
@@ -318,17 +322,20 @@ def _get_genomic_obj(request, object_id):
                 if "access_id" in method and method["access_id"] != "":
                     # we need to go to the access endpoint to get the url and file
                     (url, status_code) = drs_operations.get_access_url(sub_obj["name"], method["access_id"])
-                    f_path = os.path.join(tempdir, sub_obj["name"])
-                    with open(f_path, mode='wb') as f:
-                        with requests.get(url["url"], stream=True) as r:
-                            with r.raw as content:
-                                f.write(content.data)
-                    if index_match is not None:
-                        index_file = f_path
-                    elif read_match is not None:
-                        read_file = f_path
-                    elif variant_match is not None:
-                        variant_file = f_path
+                    if status_code < 300:
+                        f_path = os.path.join(tempdir, sub_obj["name"])
+                        with open(f_path, mode='wb') as f:
+                            with requests.get(url["url"], stream=True) as r:
+                                with r.raw as content:
+                                    f.write(content.data)
+                        if index_match is not None:
+                            index_file = f_path
+                        elif read_match is not None:
+                            read_file = f_path
+                        elif variant_match is not None:
+                            variant_file = f_path
+                    else:
+                        return {"error": url}
                 else:
                     # the access_url has all the info we need
                     url_pieces = urlparse(method["access_url"]["url"])

htsget_server/server.py

@@ -22,4 +22,4 @@ def index():
 
 if __name__ == '__main__':
     logging.basicConfig(filename='record.log', level=logging.DEBUG, format=f'%(asctime)s %(levelname)s %(name)s %(threadName)s : %(message)s')
-    app.run(port = PORT, debug=False)
+    app.run(port = PORT, debug=True)

renew_token.sh

@@ -1,3 +1,4 @@
+echo "renewing S3 token"
 curl -X "POST" "http://docker.localhost:8200/v1/auth/token/renew-self" \
      -H 'X-Vault-Token: <VAULT_S3_TOKEN>' \
      -H 'Content-Type: application/json; charset=utf-8' \