Minor updates related to PR-1808 feedback.

4dn-dcic · Jul 19, 2023 · 55b1d76 · 55b1d76
1 parent 9219c88
commit 55b1d76
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Showing 4 changed files with 33 additions and 52 deletions.
diff --git a/src/encoded/project/authentication.py b/src/encoded/project/authentication.py
@@ -1,10 +1,12 @@
+from dcicutils.misc_utils import ignored
 from pyramid.httpexceptions import HTTPUnauthorized
 from snovault.project.authentication import SnovaultProjectAuthentication
 
 class FourfrontProjectAuthentication(SnovaultProjectAuthentication):
 
     def login(self, context, request, *, samesite):
-        samesite = "lax"  # TODO: maybe make lax = True or False (from Kent)
+        ignored(samesite)
+        samesite = "lax"
         return super().login(context, request, samesite=samesite)
 
     def namespaced_authentication_policy_authenticated_userid(self, namespaced_authentication_policy, request, set_user_info_property):

diff --git a/src/encoded/server_defaults.py b/src/encoded/server_defaults.py
@@ -1,3 +1,4 @@
+from snovault.project_app import app_project
 from snovault.server_defaults import (
     add_last_modified,
     enc_accession,
@@ -7,5 +8,5 @@
 )
 
 ACCESSION_FACTORY = __name__ + ':accession_factory'
-ACCESSION_PREFIX = '4DN'
+ACCESSION_PREFIX = app_project().ACCESSION_PREFIX
 ACCESSION_TEST_PREFIX = 'TST'
diff --git a/src/encoded/tests/test_loadxl.py b/src/encoded/tests/test_loadxl.py
@@ -8,13 +8,12 @@
 
 
 pytestmark = [pytest.mark.setone, pytest.mark.working]
-loadxl_package = "snovault.loadxl"
 
 
 def test_load_data_endpoint(testapp):
     data = {'fdn_dir': 'master-inserts',
             'itype': ['award', 'lab', 'user']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.json['status'] == 'success'
@@ -23,7 +22,7 @@ def test_load_data_endpoint(testapp):
 def test_load_data_endpoint_returns_error_if_incorrect_keyword(testapp):
     data = {'mdn_dir': 'master-inserts',
             'itype': ['user']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=422)
         assert res.json['status'] == 'error'
@@ -33,7 +32,7 @@ def test_load_data_endpoint_returns_error_if_incorrect_keyword(testapp):
 def test_load_data_endpoint_returns_error_if_incorrect_data(testapp):
     data = {'fdn_dir': 'master-inserts',
             'itype': ['user']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=422)
         assert res.json['status'] == 'error'
@@ -45,7 +44,7 @@ def test_load_data_user_specified_config(testapp):
             'itype': ['user', 'lab', 'award']}
     config_uri = 'test.ini'
     data['config_uri'] = config_uri
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.json['status'] == 'success'
@@ -54,8 +53,8 @@ def test_load_data_user_specified_config(testapp):
 
 def test_load_data_local_dir(testapp):
     expected_dir = resource_filename('encoded', 'tests/data/perf-testing/')
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
-        with mock.patch(f'{loadxl_package}.load_all') as load_all:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
+        with mock.patch(f'snovault.loadxl.load_all') as load_all:
             mocked_app.return_value = testapp.app
             load_all.return_value = None
             res = testapp.post_json('/load_data', {'fdn_dir': 'perf-testing'}, status=200)
@@ -69,7 +68,7 @@ def test_load_data_from_json(testapp):
     award_inserts = list(get_inserts('master-inserts', 'award'))
     data = {'store': {'user': user_inserts, 'lab': lab_inserts, 'award': award_inserts},
             'itype': ['user', 'lab', 'award']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.json['status'] == 'success'
@@ -78,7 +77,7 @@ def test_load_data_from_json(testapp):
 def test_load_data_local_path(testapp):
     local_path = resource_filename('encoded', 'tests/data/master-inserts/')
     data = {'local_path': local_path, 'itype': ['user', 'lab', 'award']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.json['status'] == 'success'
@@ -97,7 +96,7 @@ def test_load_data_iter_response(testapp):
     expected = len(user_inserts) + len(lab_inserts) + len(award_inserts)
     data = {'store': {'user': user_inserts, 'lab': lab_inserts, 'award': award_inserts},
             'itype': ['user', 'lab', 'award'], 'iter_response': True}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.content_type == 'text/plain'
@@ -121,7 +120,7 @@ def test_load_data_iter_response_fail(testapp):
     # the total number of items we expect
     expected = len(user_inserts)
     data = {'store': {'user': user_inserts}, 'itype': ['user'], 'iter_response': True}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         res = testapp.post_json('/load_data', data, status=200)
         assert res.content_type == 'text/plain'
@@ -147,7 +146,7 @@ def test_load_all_gen(testapp):
     expected = len(user_inserts) + len(lab_inserts) + len(award_inserts)
     data = {'store': {'user': user_inserts, 'lab': lab_inserts, 'award': award_inserts},
             'itype': ['user', 'lab', 'award']}
-    with mock.patch(f'{loadxl_package}.get_app') as mocked_app:
+    with mock.patch(f'snovault.loadxl.get_app') as mocked_app:
         mocked_app.return_value = testapp.app
         # successful load cases
         gen1 = loadxl.load_all_gen(testapp, data['store'], None,

diff --git a/src/encoded/util.py b/src/encoded/util.py
@@ -9,7 +9,7 @@
 import structlog
 import tempfile
 from typing import Any, Generator, Optional
-from dcicutils.misc_utils import url_path_join, find_association
+from dcicutils.misc_utils import exported, find_association, url_path_join
 from snovault.util import (
     beanstalk_env_from_registry,
     check_user_is_logged_in,
@@ -20,51 +20,30 @@
     delay_rerun,
     get_trusted_email,
     make_vapp_for_ingestion,
-    resolve_file_path as snovault_resolve_file_path,
+    #resolve_file_path as snovault_resolve_file_path,
     s3_local_file,
     s3_output_stream,
 )
-
-# These are now moved or reused from snovault.utils (May 2023):
-# - CONTENT_TYPE_SPECIAL_CASES
-# - register_path_content_type
-# - content_type_allowed
-# - gunzip_content
-# - deduplicate_list
-# - debuglog
-# - make_vapp_for_email
-# - vapp_for_email
-# - make_vapp_for_ingestion
-# - vapp_for_ingestion
-# - _app_from_clues
-# - make_s3_client
-# - build_s3_presigned_get_url
-# - convert_integer_to_comma_string
-# - ENCODED_ROOT_DIR
-# - resolve_file_path
-# - subrequest_object
-# - subrequest_item_creation
-# - s3_output_stream
-# - s3_local_file
-# - s3_input_stream
-# - check_user_is_logged_in
-# - create_empty_s3_file
-# - get_trusted_email
-# - beanstalk_env_from_request
-# - beanstalk_env_from_registry
-# - customized_delay_rerun
-# - delay_rerun
-# - SettingsKey
-# - ExtraArgs
-# - extra_kwargs_for_s3_encrypt_key_id
-
+exported (
+    beanstalk_env_from_registry,
+    check_user_is_logged_in,
+    content_type_allowed,
+    create_empty_s3_file,
+    customized_delay_rerun,
+    debuglog,
+    delay_rerun,
+    get_trusted_email,
+    make_vapp_for_ingestion,
+    s3_local_file,
+    s3_output_stream
+)
 
 log = structlog.getLogger(__name__)
 ENCODED_ROOT_DIR = os.path.dirname(__file__)
 
 
-def resolve_file_path(path, file_loc=None):
-    return snovault_resolve_file_path(path=path, file_loc=file_loc, root_dir=ENCODED_ROOT_DIR)
+#def resolve_file_path(path, file_loc=None):
+#    return snovault_resolve_file_path(path=path, file_loc=file_loc, root_dir=ENCODED_ROOT_DIR)
 
 
 @contextlib.contextmanager