(PPS-261): (feat) Add service-info endpoint to DRS (#356)

* intial commit * Add unit tests * Add docstring * Remove unused import * move to drs * move service-info * remove unused imports * Add more test and handle edge case * remove utils stuff * Create separate config * fix things
uc-cdis · Apr 15, 2023 · 5f0435b · 5f0435b
1 parent fb21317
commit 5f0435b
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Showing 8 changed files with 166 additions and 10 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": 40
       }
     ],
     "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": "2023-03-23T20:46:39Z"
+  "generated_at": "2023-04-13T17:00:13Z"
 }
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
@@ -44,14 +44,23 @@
         "hints": [],
         "type": "dos",
     },
-    {
-        "name": "DRS System",
-        "host": "https://example.com/api/ga4gh/drs/v1/",
-        "hints": [],
-        "type": "drs",
-    },
 ]
 
+CONFIG["DRS_SERVICE_INFO"] = {
+    "name": "DRS System",
+    "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
@@ -1,14 +1,53 @@
+import os
+import re
 import flask
 import json
 from indexd.errors import AuthError, AuthzError
 from indexd.errors import UserError
 from indexd.index.errors import NoRecordFound as IndexNoRecordFound
 from indexd.errors import IndexdUnexpectedError
+from indexd.utils import reverse_url
 
 blueprint = flask.Blueprint("drs", __name__)
 
 blueprint.config = dict()
 blueprint.index_driver = None
+blueprint.service_info = {}
+
+
+@blueprint.route("/ga4gh/drs/v1/service-info", methods=["GET"])
+def get_drs_service_info():
+    """
+    Returns DRS compliant service information
+    """
+
+    reverse_domain_name = reverse_url(url=os.environ["HOSTNAME"])
+
+    ret = {
+        "id": reverse_domain_name,
+        "name": "DRS System",
+        "version": "1.0.3",
+        "type": {
+            "group": "org.ga4gh",
+            "artifact": "drs",
+            "version": "1.0.3",
+        },
+        "organization": {
+            "name": "CTDS",
+            "url": "https://" + os.environ["HOSTNAME"],
+        },
+    }
+
+    if blueprint.service_info:
+        for key, value in blueprint.service_info.items():
+            if key in ret:
+                if isinstance(value, dict):
+                    for inner_key, inner_value in value.items():
+                        ret[key][inner_key] = inner_value
+                else:
+                    ret[key] = value
+
+    return flask.jsonify(ret), 200
 
 
 @blueprint.route("/ga4gh/drs/v1/objects/<path:object_id>", methods=["GET"])
@@ -329,3 +368,9 @@ def handle_unexpected_error(err):
 def get_config(setup_state):
     index_config = setup_state.app.config["INDEX"]
     blueprint.index_driver = index_config["driver"]
+
+
+@blueprint.record
+def get_config(setup_state):
+    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
@@ -1,5 +1,6 @@
 import logging
 import re
+from urllib.parse import urlparse
 
 
 def hint_match(record, hints):
@@ -189,3 +190,23 @@ def migrate_database(driver, migrate_functions, current_schema_version, model):
             f(engine=driver.engine, session=s)
             schema_version.version += 1
             s.add(schema_version)
+
+
+def reverse_url(url):
+    """
+    Reverse the domain name for drs service-info IDs
+    Args:
+        url (str): url of the domain
+        example: drs.example.org
+
+    returns:
+        id (str): DRS service-info ID
+        example: org.example.drs
+    """
+    parsed_url = urlparse(url)
+    if parsed_url.scheme in ["http", "https"]:
+        url = parsed_url.hostname
+    segments = url.split(".")
+    reversed_segments = reversed(segments)
+    res = ".".join(reversed_segments)
+    return res
diff --git a/tests/default_test_settings.py b/tests/default_test_settings.py
@@ -9,9 +9,23 @@
         "host": "https://fictitious-commons.io/index/",
         "hints": [".*dg\\.4503.*"],
         "type": "indexd",
-    }
+    },
 ]
 
+CONFIG["DRS_SERVICE_INFO"] = {
+    "name": "DRS System",
+    "type": {
+        "group": "org.ga4gh",
+        "artifact": "drs",
+        "version": "1.0.3",
+    },
+    "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
@@ -155,3 +156,61 @@ def test_get_drs_with_encoded_slash(client, user):
         assert rec_2["checksums"][0]["type"] == k
     assert rec_2["version"]
     assert rec_2["self_uri"] == "drs://testprefix:" + rec_1["did"].split(":")[1]
+
+
+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": "1.0.3",
+        },
+        "version": "1.0.3",
+        "organization": {
+            "name": "CTDS",
+            "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_information_configured(client):
+    """
+    Test drs service info endpoint when dist is not configured in the indexd config file
+    """
+    expected_info = {
+        "id": "io.fictitious-commons",
+        "name": "DRS System",
+        "type": {
+            "group": "org.ga4gh",
+            "artifact": "drs",
+            "version": "1.0.3",
+        },
+        "version": "1.0.3",
+        "organization": {
+            "name": "CTDS",
+            "url": "https://fictitious-commons.io",
+        },
+    }
+    backup = settings["config"]["DRS_SERVICE_INFO"].copy()
+
+    try:
+        settings["config"]["DRS_SERVICE_INFO"].clear()
+
+        res = client.get("/ga4gh/drs/v1/service-info")
+
+        assert res.status_code == 200
+        assert res.json == expected_info
+    finally:
+        settings["config"]["DRS_SERVICE_INFO"] = backup