Create separate config

uc-cdis · Apr 12, 2023 · 0836cfa · 0836cfa
1 parent e2f6f96
commit 0836cfa
Show file tree

Hide file tree

Showing 8 changed files with 88 additions and 103 deletions.
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -230,7 +230,7 @@
         "filename": "tests/default_test_settings.py",
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_verified": false,
-        "line_number": 26
+        "line_number": 41
       }
     ],
     "tests/postgres/migrations/test_15f2e9345ade_create_tables.py": [
@@ -391,9 +391,9 @@
         "filename": "tests/test_drs.py",
         "hashed_secret": "5666c088b494f26cd8f63ace013992f5fc391ce0",
         "is_verified": false,
-        "line_number": 31
+        "line_number": 32
       }
     ]
   },
-  "generated_at": "2023-04-10T19:43:22Z"
+  "generated_at": "2023-04-12T20:10:41Z"
 }
diff --git a/bin/indexd_settings.py b/bin/indexd_settings.py
@@ -28,6 +28,10 @@ def load_json(file_name):
 if dist:
     CONFIG["DIST"] = json.loads(dist)
 
+drs_service_info = environ.get("DRS_SERVICE_INFO", None)
+if drs_service_info:
+    CONFIG["DRS_SERVICE_INFO"] = json.loads(drs_service_info)
+
 CONFIG["INDEX"] = {
     "driver": SQLAlchemyIndexDriver(
         "postgresql+psycopg2://{usr}:{psw}@{pghost}:{pgport}/{db}".format(

diff --git a/deployment/Secrets/indexd_settings.py b/deployment/Secrets/indexd_settings.py
@@ -29,6 +29,10 @@ def load_json(file_name):
 if dist:
     CONFIG["DIST"] = json.loads(dist)
 
+drs_service_info = environ.get("DRS_SERVICE_INFO", None)
+if drs_service_info:
+    CONFIG["DRS_SERVICE_INFO"] = json.loads(drs_service_info)
+
 CONFIG["INDEX"] = {
     "driver": SQLAlchemyIndexDriver(
         "postgresql+psycopg2://{usr}:{psw}@{pghost}:{pgport}/{db}".format(

diff --git a/indexd/default_settings.py b/indexd/default_settings.py
@@ -45,24 +45,25 @@
         "hints": [],
         "type": "dos",
     },
-    {
-        "name": "DRS System",
-        "host": "https://example.com/api/ga4gh/drs/v1/",
-        "hints": [],
-        "type": {
-            "group": "org.ga4gh",
-            "artifact": "drs",
-            "version": "1.0.0",
-        },
-        "version": "1.0.0",
-        "id": "com.example",
-        "organization": {
-            "name": "Gen3",
-            "url": "http://example.com/",
-        },
-    },
 ]
 
+CONFIG["DRS_SERVICE_INFO"] = {
+    "name": "DRS System",
+    "host": "https://example.com/api/ga4gh/drs/v1/",
+    "hints": [],
+    "type": {
+        "group": "org.ga4gh",
+        "artifact": "drs",
+        "version": "1.0.3",
+    },
+    "version": "1.0.3",
+    "id": "com.example",
+    "organization": {
+        "name": "CTDS",
+        "url": "http://example.com/",
+    },
+}
+
 AUTH = SQLAlchemyAuthDriver("sqlite:///auth.sq3")
 
 settings = {"config": CONFIG, "auth": AUTH}
diff --git a/indexd/drs/blueprint.py b/indexd/drs/blueprint.py
@@ -5,60 +5,60 @@
 from indexd.errors import UserError
 from indexd.index.errors import NoRecordFound as IndexNoRecordFound
 from indexd.errors import IndexdUnexpectedError
-from indexd.utils import drs_service_info_id_url_reversal
+from indexd.utils import reverse_url
 
 blueprint = flask.Blueprint("drs", __name__)
 
 blueprint.config = dict()
 blueprint.index_driver = None
-blueprint.dist = []
+blueprint.service_info = {}
 
 
 @blueprint.route("/ga4gh/drs/v1/service-info", methods=["GET"])
 def get_drs_service_info():
     """
     Returns DRS compliant service information
     """
-    drs_dist = {}
-
-    reverse_domain_name = drs_service_info_id_url_reversal(url=os.environ["HOSTNAME"])
-
-    if len(blueprint.dist) > 0:
-        # Check to see if the information is of type drs. If not, use the available information to return DRS compliant service information
-        for dist in blueprint.dist:
-            if (
-                "type" in dist
-                and isinstance(dist["type"], dict)
-                and "artifact" in dist["type"]
-                and dist["type"]["artifact"] == "drs"
-            ):
-                drs_dist = dist
-        if drs_dist == {}:
-            drs_dist = blueprint.dist[0]
+
+    reverse_domain_name = reverse_url(url=os.environ["HOSTNAME"])
 
     ret = {
-        "id": drs_dist.get("id", reverse_domain_name),
-        "name": drs_dist.get("name", "DRS System"),
-        "version": drs_dist.get("version", "1.0.0"),
+        "id": blueprint.service_info.get("id", reverse_domain_name),
+        "name": blueprint.service_info.get("name", "DRS System"),
+        "version": blueprint.service_info.get("version", "1.0.3"),
         "type": {
-            "group": drs_dist.get("group", "org.ga4gh"),
-            "artifact": drs_dist.get("artifact", "drs"),
-        },
-        "organization": {
-            "name": "Gen3",
+            "group": blueprint.service_info.get("group", "org.ga4gh"),
+            "artifact": blueprint.service_info.get("artifact", "drs"),
         },
     }
 
-    if "type" in drs_dist and isinstance(drs_dist["type"], dict):
-        ret["type"]["version"] = drs_dist.get("type").get("version", "1.0.0")
+    ret["organization"] = {}
+
+    if "type" in blueprint.service_info and isinstance(
+        blueprint.service_info["type"], dict
+    ):
+        ret["type"]["version"] = blueprint.service_info.get("type").get(
+            "version", "1.0.3"
+        )
     else:
-        ret["type"]["version"] = "1.0.0"
+        ret["type"]["version"] = "1.0.3"
 
-    if "organization" in drs_dist and "url" in drs_dist["organization"]:
-        ret["organization"]["url"] = drs_dist["organization"]["url"]
+    if (
+        "organization" in blueprint.service_info
+        and "url" in blueprint.service_info["organization"]
+    ):
+        ret["organization"]["url"] = blueprint.service_info["organization"]["url"]
     else:
         ret["organization"]["url"] = "https://" + os.environ["HOSTNAME"]
 
+    if (
+        "organization" in blueprint.service_info
+        and "name" in blueprint.service_info["organization"]
+    ):
+        ret["organization"]["name"] = blueprint.service_info["organization"]["name"]
+    else:
+        ret["organization"]["name"] = "CTDS"
+
     return flask.jsonify(ret), 200
 
 
@@ -384,5 +384,5 @@ def get_config(setup_state):
 
 @blueprint.record
 def get_config(setup_state):
-    if "DIST" in setup_state.app.config:
-        blueprint.dist = setup_state.app.config["DIST"]
+    if "DRS_SERVICE_INFO" in setup_state.app.config:
+        blueprint.service_info = setup_state.app.config["DRS_SERVICE_INFO"]
diff --git a/indexd/utils.py b/indexd/utils.py
@@ -191,7 +191,7 @@ def migrate_database(driver, migrate_functions, current_schema_version, model):
             s.add(schema_version)
 
 
-def drs_service_info_id_url_reversal(url):
+def reverse_url(url):
     """
     Reverse the domain name for drs service-info IDs
     Args:

diff --git a/tests/default_test_settings.py b/tests/default_test_settings.py
@@ -12,6 +12,21 @@
     },
 ]
 
+CONFIG["DRS_SERVICE_INFO"] = {
+    "name": "DRS System",
+    "type": {
+        "group": "org.ga4gh",
+        "artifact": "drs",
+        "version": "1.0.3",
+    },
+    "host": "https://fictitious-commons.io/",
+    "version": "1.0.3",
+    "organization": {
+        "name": "CTDS",
+        "url": "https://fictitious-commons.io",
+    },
+}
+
 os.environ["PRESIGNED_FENCE_URL"] = "https://fictitious-commons.io/"
 os.environ["HOSTNAME"] = "fictitious-commons.io"
 settings = {"config": CONFIG, "auth": AUTH}

diff --git a/tests/test_drs.py b/tests/test_drs.py
@@ -1,3 +1,4 @@
+import flask
 import json
 import tests.conftest
 import requests
@@ -157,74 +158,34 @@ def test_get_drs_with_encoded_slash(client, user):
     assert rec_2["self_uri"] == "drs://testprefix:" + rec_1["did"].split(":")[1]
 
 
-def test_drs_service_info_without_drs_block_in_config(client):
-    """
-    Test that the non-drs related, defualt distributions convert to drs service info friendly format
-    """
-    expected_info = {
-        "id": "io.fictitious-commons",
-        "name": "testStage",
-        "type": {
-            "group": "org.ga4gh",
-            "artifact": "drs",
-            "version": "1.0.0",
-        },
-        "organization": {
-            "name": "Gen3",
-            "url": "https://fictitious-commons.io",
-        },
-        "version": "1.0.0",
-    }
-
-    res = client.get("/ga4gh/drs/v1/service-info")
-
-    assert res.status_code == 200
-    assert res.json == expected_info
-
-
 def test_drs_service_info_endpoint(client):
     """
     Test drs service endpoint with drs service info friendly distribution information
     """
+    app = flask.Flask(__name__)
+
     expected_info = {
         "id": "io.fictitious-commons",
         "name": "DRS System",
         "type": {
             "group": "org.ga4gh",
             "artifact": "drs",
-            "version": "1.0.0",
+            "version": "1.0.3",
         },
-        "version": "1.3.0",
+        "version": "1.0.3",
         "organization": {
-            "name": "Gen3",
+            "name": "CTDS",
             "url": "https://fictitious-commons.io",
         },
     }
 
-    settings["config"]["DIST"].append(
-        {
-            "name": "DRS System",
-            "type": {
-                "group": "org.ga4gh",
-                "artifact": "drs",
-                "version": "1.0.0",
-            },
-            "host": "https://fictitious-commons.io/",
-            "version": "1.3.0",
-            "organization": {
-                "name": "Gen3",
-                "url": "https://fictitious-commons.io",
-            },
-        }
-    )
-
     res = client.get("/ga4gh/drs/v1/service-info")
 
     assert res.status_code == 200
     assert res.json == expected_info
 
 
-def test_drs_service_info_no_dist_in_config(client):
+def test_drs_service_info_no_information_configured(client):
     """
     Test drs service info endpoint when dist is not configured in the indexd config file
     """
@@ -234,16 +195,16 @@ def test_drs_service_info_no_dist_in_config(client):
         "type": {
             "group": "org.ga4gh",
             "artifact": "drs",
-            "version": "1.0.0",
+            "version": "1.0.3",
         },
-        "version": "1.0.0",
+        "version": "1.0.3",
         "organization": {
-            "name": "Gen3",
+            "name": "CTDS",
             "url": "https://fictitious-commons.io",
         },
     }
 
-    settings["config"]["DIST"].clear()
+    settings["config"]["DRS_SERVICE_INFO"].clear()
 
     res = client.get("/ga4gh/drs/v1/service-info")