From b27e6a7bb1c0cf4fa6cd85aa471302ee5dc13cab Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Wed, 13 Nov 2019 14:59:46 +0100
Subject: [PATCH] Fixes to migration in cli mirror command.
---
nomad/cli/client/mirror.py | 10 ++++++++--
nomad/datamodel/metainfo.py | 2 +-
nomad/infrastructure.py | 13 +++++++------
nomad/metainfo/metainfo.py | 2 +-
ops/deployments/nomad.testing-major.env.sh | 12 ++++++++++++
5 files changed, 29 insertions(+), 10 deletions(-)
create mode 100644 ops/deployments/nomad.testing-major.env.sh
diff --git a/nomad/cli/client/mirror.py b/nomad/cli/client/mirror.py
index a3a3c0ab63..2ea586ba1f 100644
--- a/nomad/cli/client/mirror.py
+++ b/nomad/cli/client/mirror.py
@@ -37,7 +37,7 @@ def v0Dot6(upload_data):
""" Inplace transforms v0.6.x upload data into v0.7.x upload data. """
def tarnsform_user_id(source_user_id):
- target_user = User.repo_users.get(source_user_id)
+ target_user = User.repo_users().get(str(source_user_id))
if target_user is None:
__logger.error('user does not exist in target', source_user_id=source_user_id)
raise KeyError
@@ -61,11 +61,14 @@ def v0Dot6(upload_data):
return target_dataset.dataset_id
+ def transform_reference(reference):
+ return reference['value']
+
upload = json.loads(upload_data.upload)
upload['user_id'] = tarnsform_user_id(upload['user_id'])
upload_data.upload = json.dumps(upload)
- for calc_data_json, i in enumerate(upload_data.calcs):
+ for i, calc_data_json in enumerate(upload_data.calcs):
calc_data = json.loads(calc_data_json)
metadata = calc_data['metadata']
@@ -77,6 +80,9 @@ def v0Dot6(upload_data):
# transform datasets
metadata['datasets'] = [transform_dataset(dataset) for dataset in metadata['datasets']]
+ # transform references
+ metadata['references'] = [transform_reference(reference) for reference in metadata['references']]
+
upload_data.calcs[i] = json.dumps(calc_data)
return upload_data
diff --git a/nomad/datamodel/metainfo.py b/nomad/datamodel/metainfo.py
index ac49269626..0a6c3ef5dd 100644
--- a/nomad/datamodel/metainfo.py
+++ b/nomad/datamodel/metainfo.py
@@ -70,7 +70,7 @@ class User(metainfo.MSection):
def repo_users() -> Dict[str, 'User']:
from nomad import infrastructure
return {
- user.repo_user_id: user
+ str(user.repo_user_id): user
for user in infrastructure.keycloak.search_user()
if user.repo_user_id is not None
}
diff --git a/nomad/infrastructure.py b/nomad/infrastructure.py
index 51cecb4c39..6bc273ac7d 100644
--- a/nomad/infrastructure.py
+++ b/nomad/infrastructure.py
@@ -270,17 +270,18 @@ class Keycloak():
kwargs = {key: value[0] for key, value in keycloak_user.get('attributes', {}).items()}
return datamodel.User(
user_id=keycloak_user['id'],
- email=keycloak_user['email'],
- username=keycloak_user.get('username', None),
- first_name=keycloak_user.get('firstName', None),
- last_name=keycloak_user.get('lastName', None),
+ email=keycloak_user.get('email'),
+ username=keycloak_user.get('username'),
+ first_name=keycloak_user.get('firstName'),
+ last_name=keycloak_user.get('lastName'),
created=datetime.fromtimestamp(keycloak_user['createdTimestamp'] / 1000),
**kwargs)
- def search_user(self, query: str = None):
- kwargs = {}
+ def search_user(self, query: str = None, **kwargs):
if query is not None:
kwargs['query'] = dict(search=query)
+ else:
+ kwargs['query'] = dict(max=1000)
try:
keycloak_results = self._admin_client.get_users(**kwargs)
except Exception as e:
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index c89d090785..608cb01533 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -805,7 +805,7 @@ class MSection(metaclass=MObjectMeta):
return bool(value)
else:
- if type(value) != quantity_def.type:
+ if value is not None and type(value) != quantity_def.type:
raise TypeError(
'The value %s with type %s for quantity %s is not of type %s' %
(value, type(value), quantity_def, quantity_def.type))
diff --git a/ops/deployments/nomad.testing-major.env.sh b/ops/deployments/nomad.testing-major.env.sh
new file mode 100644
index 0000000000..17b8777ae9
--- /dev/null
+++ b/ops/deployments/nomad.testing-major.env.sh
@@ -0,0 +1,12 @@
+export NOMAD_CLIENT_URL=https://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/testing-major/api
+export NOMAD_CLIENT_USER=admin
+export NOMAD_FS_LOCAL_TMP=/nomad/fairdi/testing_major/fs/tmp
+export NOMAD_MONGO_DB_NAME=fairdi_nomad_testing_major
+export NOMAD_ELASTIC_INDEX_NAME=fairdi_nomad_testing_major
+export NOMAD_FS_LOCAL_TMP=/nomad/fairdi/testing_major/fs/tmp
+export NOMAD_FS_STAGING=/nomad/fairdi/testing_major/fs/staging
+export NOMAD_FS_PUBLIC=/nomad/fairdi/testing_major/fs/public
+export NOMAD_FS_TMP=/nomad/fairdi/testing_major/fs/tmp
+export NOMAD_SERVICE_ADMIN_USER_ID="82efac55-6187-408c-8027-b98580c0e1c5"
+export NOMAD_KEYCLOAK_REALM_NAME=fairdi_nomad_prod
+export NOMAD_FS_PREFIX_SIZE=1
--
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