Update settings.py

Author: jawadqur

.secrets.baseline

@@ -75,6 +75,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -123,7 +127,7 @@
         "filename": "bin/settings.py",
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_verified": false,
-        "line_number": 46
+        "line_number": 54
       }
     ],
     "peregrine/blueprints/coremetadata.py": [
@@ -273,5 +277,5 @@
       }
     ]
   },
-  "generated_at": "2023-11-01T14:27:13Z"
+  "generated_at": "2024-11-01T18:38:15Z"
 }

Dockerfile

@@ -20,7 +20,6 @@ COPY poetry.lock pyproject.toml /${appname}/
 RUN poetry install -vv --only main --no-interaction
 
 COPY --chown=gen3:gen3 . /$appname
-COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py
 
 # Run poetry again so this app itself gets installed too
 RUN poetry install --without dev --no-interaction

bin/settings.py

@@ -1,6 +1,6 @@
 from peregrine.api import app, app_init
 from os import environ
-import confighelper
+import bin.confighelper as confighelper
 
 APP_NAME = "peregrine"
 
@@ -12,74 +12,60 @@ def load_json(file_name):
 conf_data = load_json("creds.json")
 config = app.config
 
-config["AUTH"] = "https://auth.service.consul:5000/v3/"
-config["AUTH_ADMIN_CREDS"] = None
-config["INTERNAL_AUTH"] = None
 
 # ARBORIST deprecated, replaced by ARBORIST_URL
 # ARBORIST_URL is initialized in app_init() directly
 config["ARBORIST"] = "http://arborist-service/"
 
-# Signpost: deprecated, replaced by index client.
-config["SIGNPOST"] = {
-    "host": environ.get("SIGNPOST_HOST") or "http://indexd-service",
-    "version": "v0",
-    "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")),
-}
+
 config["INDEX_CLIENT"] = {
     "host": environ.get("INDEX_CLIENT_HOST") or "http://indexd-service",
     "version": "v0",
-    "auth": ("gdcapi", conf_data.get("indexd_password", "{{indexd_password}}")),
+    # The user should be "sheepdog", but for legacy reasons, we use "gdcapi" instead
+    "auth": (
+        (
+            environ.get("INDEXD_USER", "gdcapi"),
+            environ.get("INDEXD_PASS")
+            or conf_data.get("indexd_password", "{{indexd_password}}"),
+        )
+    ),
 }
-config["FAKE_AUTH"] = False
+
 config["PSQLGRAPH"] = {
-    "host": conf_data.get("db_host", "{{db_host}}"),
-    "user": conf_data.get("db_username", "{{db_username}}"),
-    "password": conf_data.get("db_password", "{{db_password}}"),
-    "database": conf_data.get("db_database", "{{db_database}}"),
+    "host": environ.get("PGHOST") or conf_data.get("db_host", "{{db_host}}"),
+    "user": environ.get("PGUSER") or conf_data.get("db_username", "{{db_username}}"),
+    "password": environ.get("PGPASSWORD")
+    or conf_data.get("db_password", "{{db_password}}"),
+    "database": environ.get("PGDB") or conf_data.get("db_database", "{{db_database}}"),
 }
 
-config["HMAC_ENCRYPTION_KEY"] = conf_data.get("hmac_key", "{{hmac_key}}")
-config["FLASK_SECRET_KEY"] = conf_data.get("gdcapi_secret_key", "{{gdcapi_secret_key}}")
-config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % tuple(
-    [
-        conf_data.get(key, key)
-        for key in ["fence_username", "fence_password", "fence_host", "fence_database"]
-    ]
+fence_username = environ.get("FENCE_DB_USER") or conf_data.get(
+    "fence_username", "{{fence_username}}"
+)
+fence_password = environ.get("FENCE_DB_PASS") or conf_data.get(
+    "fence_password", "{{fence_password}}"
+)
+fence_host = environ.get("FENCE_DB_HOST") or conf_data.get(
+    "fence_host", "{{fence_host}}"
+)
+fence_database = environ.get("FENCE_DB_DBNAME") or conf_data.get(
+    "fence_database", "{{fence_database}}"
 )
+config["PSQL_USER_DB_CONNECTION"] = "postgresql://%s:%s@%s:5432/%s" % (
+    fence_username,
+    fence_password,
+    fence_host,
+    fence_database,
+)
+
 
 config["DICTIONARY_URL"] = environ.get(
     "DICTIONARY_URL",
     "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json",
 )
 
-config["SUBMISSION"] = {"bucket": conf_data.get("bagit_bucket", "{{bagit_bucket}}")}
-
-config["STORAGE"] = {
-    "s3": {
-        "access_key": conf_data.get("s3_access", "{{s3_access}}"),
-        "secret_key": conf_data.get("s3_secret", "{{s3_secret}}"),
-    }
-}
-
-config["OIDC_ISSUER"] = "https://%s/user" % conf_data["hostname"]
-
-config["OAUTH2"] = {
-    "client_id": conf_data.get("oauth2_client_id", "{{oauth2_client_id}}"),
-    "client_secret": conf_data.get("oauth2_client_secret", "{{oauth2_client_secret}}"),
-    "api_base_url": "https://%s/user/" % conf_data["hostname"],
-    "authorize_url": "https://%s/user/oauth2/authorize" % conf_data["hostname"],
-    "access_token_url": "https://%s/user/oauth2/token" % conf_data["hostname"],
-    "refresh_token_url": "https://%s/user/oauth2/token" % conf_data["hostname"],
-    "client_kwargs": {
-        "redirect_uri": "https://%s/api/v0/oauth2/authorize" % conf_data["hostname"],
-        "scope": "openid data user",
-    },
-    # deprecated key values, should be removed after all commons use new oidc
-    "internal_oauth_provider": "http://fence-service/oauth2/",
-    "oauth_provider": "https://%s/user/oauth2/" % conf_data["hostname"],
-    "redirect_uri": "https://%s/api/v0/oauth2/authorize" % conf_data["hostname"],
-}
+hostname = environ.get("CONF_HOSTNAME") or conf_data["hostname"]
+config["OIDC_ISSUER"] = "https://%s/user" % hostname
 
 config["USER_API"] = config["OIDC_ISSUER"]  # for use by authutils
 # use the USER_API URL instead of the public issuer URL to accquire JWT keys

deployment/wsgi/gunicorn.conf.py

@@ -1,4 +1,4 @@
-wsgi_app = "deployment.wsgi.wsgi:application"
+wsgi_app = "bin.settings:application"
 bind = "0.0.0.0:8000"
 workers = 1
 user = "gen3"

deployment/wsgi/wsgi.py

@@ -133,10 +133,6 @@ def app_init(app):
     submission.graphql.make_graph_traversal_dict(app)
     app.graphql_schema = submission.graphql.get_schema()
     app.schema_file = submission.generate_schema_file(app.graphql_schema, app.logger)
-    try:
-        app.secret_key = app.config["FLASK_SECRET_KEY"]
-    except KeyError:
-        app.logger.error("Secret key not set in config! Authentication will not work")
     async_pool_init(app)
 
     # ARBORIST deprecated, replaced by ARBORIST_URL