diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index bd59789aa0ddc414002407951d51dbf9a3f24f80..1ee3a46f3841203d2467c767d9e682fcd3e95fae 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -102868,47 +102868,6 @@ window.nomadArtifacts = {
]
}
},
- {
- "authors": [
- "Sbail\u00f2, Luigi",
- "Scheffler, Matthias",
- "Ghiringhelli, Luca M."
- ],
- "email": "ghiringhelli@fhi-berlin.mpg.de",
- "title": "Querying the NOMAD Archive and performing artificial-intelligence modeling",
- "description": "In this tutorial, we demonstrate how to query the NOMAD Archive from the NOMAD Analytics toolkit. We then show examples of machine learning analysis performed on the retrieved data set.",
- "notebook_name": "query_nomad_archive.ipynb",
- "url": "https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-query-nomad-archive",
- "link": "https://analytics-toolkit.nomad-coe.eu/hub/user-redirect/notebooks/tutorials/query_nomad_archive.ipynb",
- "link_public": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/query_nomad_archive.ipynb",
- "updated": "2022-04-06",
- "flags": {
- "featured": true,
- "top_of_list": false
- },
- "labels": {
- "application_section": [
- "Analysing the content of the Archive"
- ],
- "application_system": [
- "Ternaries"
- ],
- "category": [
- "query_tutorial"
- ],
- "ai_methods": [
- "Unsupervised learning",
- "Supervised learning",
- "Regression",
- "Clustering",
- "Dimension reduction",
- "Random forest"
- ],
- "platform": [
- "jupyter"
- ]
- }
- },
{
"authors": [
"Langer, Marcel F."
diff --git a/nomad/config/__init__.py b/nomad/config/__init__.py
index c1851e85b2d19550a32be7c242f2af3c9aab2729..72d8617d13684e50ced6dfcc1caaedda4c37dd15 100644
--- a/nomad/config/__init__.py
+++ b/nomad/config/__init__.py
@@ -87,8 +87,17 @@ def _load_config_env() -> Dict[str, Any]:
config_data: Dict[str, Any] = {}
prefix = 'NOMAD_'
for key, value in os.environ.items():
- if key.startswith(prefix) and key != 'NOMAD_CONFIG':
- add_deep(config_data, key[len(prefix) :].lower(), value)
+ if key == 'NOMAD_CONFIG' or not key.startswith(prefix):
+ continue
+
+ key = key[len(prefix) :].lower()
+ # Some environment variables starting with NOMAD_ are unavoidable
+ # in docker/kubernetes environments. We should ignore them here,
+ # before they cause a warning later when the config is validated.
+ if all([not key.startswith(field) for field in Config.__fields__.keys()]):
+ continue
+
+ add_deep(config_data, key, value)
return config_data
diff --git a/nomad/config/models/common.py b/nomad/config/models/common.py
index 6cc62bb32b3d2cb982962f7560d80c04f8889259..fa89af6ae44887d291c64ab9dd84872b0f4d52ea 100644
--- a/nomad/config/models/common.py
+++ b/nomad/config/models/common.py
@@ -67,7 +67,8 @@ class ConfigBaseModel(BaseModel, extra=Extra.ignore):
if extra_fields:
logger = logging.getLogger(__name__)
logger.warning(
- f'The following extra fields in the NOMAD config model "{cls.__name__}" are ignored: {list_items(extra_fields)}'
+ f'The following unsupported keys were found in your configuration, '
+ f'e.g. nomad.yaml: {list_items(extra_fields)}.'
)
return values
diff --git a/ops/docker-compose/nomad-oasis/docker-compose.yaml b/ops/docker-compose/nomad-oasis/docker-compose.yaml
index 87e662cd99c93dff98c2d64f692396aa6c15d829..3c418cc368fd5f95c6cf34cf0d15a33db64a9174 100644
--- a/ops/docker-compose/nomad-oasis/docker-compose.yaml
+++ b/ops/docker-compose/nomad-oasis/docker-compose.yaml
@@ -70,7 +70,7 @@ services:
# nomad worker (processing)
worker:
restart: unless-stopped
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:simplified-log-transfer
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
container_name: nomad_oasis_worker
environment:
NOMAD_SERVICE: nomad_oasis_worker
@@ -92,7 +92,7 @@ services:
# nomad app (api + proxy)
app:
restart: unless-stopped
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:simplified-log-transfer
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
container_name: nomad_oasis_app
environment:
NOMAD_SERVICE: nomad_oasis_app
@@ -130,7 +130,7 @@ services:
# nomad remote tools hub (JupyterHUB, e.g. for AI Toolkit)
north:
restart: unless-stopped
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:simplified-log-transfer
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
container_name: nomad_oasis_north
environment:
NOMAD_SERVICE: nomad_oasis_north
diff --git a/ops/kubernetes/values.yaml b/ops/kubernetes/values.yaml
index 4bd569c4d8e9ca2e8f015ea6a3305303048855e3..3a07fcfb19726e1201b5e6282769fb5ebb6bb315 100644
--- a/ops/kubernetes/values.yaml
+++ b/ops/kubernetes/values.yaml
@@ -70,6 +70,11 @@ nomad:
enabled: true
hubServiceApiTokenSecret: "nomad-hub-service-api-token"
+ plugins:
+ entry_points:
+ exclude:
+ - normalizers/simulation/soap
+
image:
tag: "prod"
pullPolicy: "Always"
diff --git a/tests/test_config.py b/tests/test_config.py
index 9325598b7c789c4977f6281e53f4ed15bebcc78c..e6103fc7b63b1f2baeed93993d4764214bcda197 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -93,21 +93,30 @@ def test_config_success(config_dict, format, mockopen, monkeypatch):
@pytest.mark.parametrize(
- 'config_dict, warning',
+ 'config_dict, warning, formats_with_warning',
[
pytest.param(
- {'does': {'not': 'exist'}},
- 'The following extra fields in the NOMAD config model "Config" are ignored: "does"',
- id='non-existing field',
- )
+ {'fs': {'does': 'not exist'}},
+ 'The following unsupported keys were found in your configuration, e.g. nomad.yaml: "does".',
+ ['yaml', 'env'],
+ id='non-existing nested field',
+ ),
+ pytest.param(
+ {'does': 'not exist'},
+ 'The following unsupported keys were found in your configuration, e.g. nomad.yaml: "does".',
+ ['yaml'],
+ id='non-existing top-level field',
+ ),
],
)
@pytest.mark.parametrize('format', ['yaml', 'env'])
-def test_config_warning(config_dict, format, warning, caplog, mockopen, monkeypatch):
+def test_config_warning(
+ config_dict, format, warning, formats_with_warning, caplog, mockopen, monkeypatch
+):
"""Tests that extra fields create a warning message."""
conf_yaml, conf_env = load_format(config_dict, format)
load_test_config(conf_yaml, conf_env, mockopen, monkeypatch)
- assert_log(caplog, 'WARNING', warning)
+ assert_log(caplog, 'WARNING', warning, negate=format not in formats_with_warning)
@pytest.mark.parametrize(
diff --git a/tests/utils.py b/tests/utils.py
index 6a6a2dcab56e808d5278695d2baebe54fa196809..4a4b347d90980bd79452c3612eb1a0ec4557a4e9 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -28,7 +28,7 @@ from typing import Any, Dict, List, Union
import pytest
-def assert_log(caplog, level: str, event_part: str) -> LogRecord:
+def assert_log(caplog, level: str, event_part: str, negate: bool = False) -> LogRecord:
"""
Assert whether a log message exists in the logs of the tests at a certain level.
@@ -42,7 +42,7 @@ def assert_log(caplog, level: str, event_part: str) -> LogRecord:
event_part : str
The error message we're after. We search the logs matching level if they
contain this string.
-
+ negate: Instead asserting that the log exist, assert that it does not exist.
"""
match = None
for record in caplog.get_records(when='call'):
@@ -58,7 +58,7 @@ def assert_log(caplog, level: str, event_part: str) -> LogRecord:
# No need to look for more matches since we aren't counting matches.
break
- assert match is not None
+ assert match is None if negate else match is not None
return match