diff --git a/examples/external_project_upload/external_project_example.zip b/examples/external_project_upload/example.zip
similarity index 99%
rename from examples/external_project_upload/external_project_example.zip
rename to examples/external_project_upload/example.zip
index e98079834aa4ec90f3235c4e7f6d776ba58dea35..5a4bb9ebc45ca750424a1c9e21ae62a16e8ffcd7 100644
Binary files a/examples/external_project_upload/external_project_example.zip and b/examples/external_project_upload/example.zip differ
diff --git a/examples/external_project_upload/upload.py b/examples/external_project_upload/upload.py
index 6185693d7cf93fcef0d0740ad25ef3a354a27cc4..b399c2bdca572f8647fefe5f11e81215c9b2c713 100644
--- a/examples/external_project_upload/upload.py
+++ b/examples/external_project_upload/upload.py
@@ -3,29 +3,59 @@ This is a brief example demonstrating the public nomad@FAIRDI API for doing oper
that might be necessary to integrate external project data.
"""
-from bravado.requests_client import RequestsClient
+from bravado.requests_client import RequestsClient, Authenticator
from bravado.client import SwaggerClient
+from keycloak import KeycloakOpenID
from urllib.parse import urlparse
import time
import os.path
import sys
nomad_url = 'http://nomad-lab.eu/prod/rae/api'
-user = 'leonard.hofstadter@nomad-fairdi.tests.de'
-password = 'password'
+user = 'youruser'
+password = 'yourpassword'
+
+upload_file = os.path.join(os.path.dirname(__file__), 'example.zip')
+
+
+# an authenticator for NOMAD's keycloak user management
+class KeycloakAuthenticator(Authenticator):
+ def __init__(self, user, password):
+ super().__init__(host=urlparse(nomad_url).netloc)
+ self.user = user
+ self.password = password
+ self.token = None
+ self.__oidc = KeycloakOpenID(
+ server_url='https://nomad-lab.eu/fairdi/keycloak/auth/',
+ realm_name='fairdi_nomad_test',
+ client_id='nomad_public')
+
+ def apply(self, request):
+ if self.token is None:
+ self.token = self.__oidc.token(username=self.user, password=self.password)
+ self.token['time'] = time.time()
+ elif self.token['expires_in'] < int(time.time()) - self.token['time'] + 10:
+ try:
+ self.token = self.__oidc.refresh_token(self.token['refresh_token'])
+ self.token['time'] = time.time()
+ except Exception:
+ self.token = self.__oidc.token(username=self.user, password=self.password)
+ self.token['time'] = time.time()
+
+ request.headers.setdefault('Authorization', 'Bearer %s' % self.token['access_token'])
+
+ return request
-upload_file = os.path.join(os.path.dirname(__file__), 'external_project_example.zip')
# create the bravado client
-host = urlparse(nomad_url).netloc.split(':')[0]
http_client = RequestsClient()
-http_client.set_basic_auth(host, user, password)
+http_client.authenticator = KeycloakAuthenticator(user=user, password=password)
client = SwaggerClient.from_url('%s/swagger.json' % nomad_url, http_client=http_client)
# upload data
print('uploading a file with "external_id/AcAg/vasp.xml" inside ...')
with open(upload_file, 'rb') as f:
- upload = client.uploads.upload(file=f).response().result
+ upload = client.uploads.upload(file=f, publish_directly=True).response().result
print('processing ...')
while upload.tasks_running:
@@ -37,70 +67,6 @@ while upload.tasks_running:
if upload.tasks_status != 'SUCCESS':
print('something went wrong')
print('errors: %s' % str(upload.errors))
- # delete the unsuccessful upload
+ # try to delete the unsuccessful upload
client.uploads.delete_upload(upload_id=upload.upload_id).response().result
sys.exit(1)
-
-# publish data
-print('publishing ...')
-client.uploads.exec_upload_operation(upload_id=upload.upload_id, payload={
- 'operation': 'publish',
- 'metadata': {
- # these metadata are applied to all calcs in the upload
- 'comment': 'Data from a cool external project',
- 'references': ['http://external.project.eu'],
- 'calculations': [
- {
- # these metadata are only applied to the calc identified by its 'mainfile'
- 'mainfile': 'external_id/AcAg/vasp.xml',
-
- # 'coauthors': ['sheldon.cooper@ucla.edu'], this does not YET work with emails,
- # Currently you have to use user_ids: leonard (the uploader, who is automatically an author) is 2 and sheldon is 1.
- # Ask NOMAD developers about how to find out about user_ids.
- 'coauthors': [1],
-
- # If users demand, we can implement a specific metadata keys (e.g. 'external_id', 'external_url') for external projects.
- # This could allow to directly search for, or even have API endpoints that work with external_ids
- # 'external_id': 'external_id',
- # 'external_url': 'http://external.project.eu/data/calc/external_id/'
- }
- ]
-
-
- }
-}).response().result
-
-while upload.process_running:
- upload = client.uploads.get_upload(upload_id=upload.upload_id).response().result
- time.sleep(1)
-if upload.tasks_status != 'SUCCESS' or len(upload.errors) > 0:
- print('something went wrong')
- print('errors: %s' % str(upload.errors))
- # delete the unsuccessful upload
- client.uploads.delete_upload(upload_id=upload.upload_id).response().result
- sys.exit(1)
-
-
-# search for data
-result = client.repo.search(paths=['external_id']).response().result
-if result.pagination.total == 0:
- print('not found')
- sys.exit(1)
-elif result.pagination.total > 1:
- print('my ids are not specific enough, bummer ... or did I uploaded stuff multiple times?')
-# The results key holds an array with the current page data
-print('Found the following calcs for my "external_id".')
-print(', '.join(calc['calc_id'] for calc in result.results))
-
-# download data
-calc = result.results[0]
-client.raw.get(upload_id=calc['upload_id'], path=calc['mainfile']).response()
-print('Download of first calc works.')
-
-# download urls, e.g. for curl
-print('Possible download URLs are:')
-print('%s/raw/%s/%s' % (nomad_url, calc['upload_id'], calc['mainfile']))
-print('%s/raw/%s/%s/*' % (nomad_url, calc['upload_id'], os.path.dirname(calc['mainfile'])))
-
-# direct download urls without having to search before
-print('%s/raw/query?paths=external_id' % nomad_url)
diff --git a/gui/src/components/entry/RepoEntryView.js b/gui/src/components/entry/RepoEntryView.js
index 55814aea99484908d80da152c3be3100718f4f8a..13d016dd1c98a98e36c4e19a5d7f4d13c814a8ee 100644
--- a/gui/src/components/entry/RepoEntryView.js
+++ b/gui/src/components/entry/RepoEntryView.js
@@ -75,7 +75,6 @@ export default function RepoEntryView({uploadId, calcId}) {
const loading = !state.calcData
const quantityProps = {data: calcData, loading: loading}
- const authors = loading ? null : calcData.authors
const domain = calcData.domain && domains[calcData.domain]
let entryHeader = 'Entry metadata'
@@ -117,7 +116,7 @@ export default function RepoEntryView({uploadId, calcId}) {
</Quantity>
<Quantity quantity='authors' {...quantityProps}>
<Typography>
- {authorList(authors || [])}
+ {authorList(loading ? null : calcData)}
</Typography>
</Quantity>
<Quantity quantity='datasets' placeholder='no datasets' {...quantityProps}>
diff --git a/gui/src/components/search/DatasetList.js b/gui/src/components/search/DatasetList.js
index b3ebff876350fcb35afbc863f7c408e7e5e21eae..3019bdbce72ecd16172a9d06eaa31a652255cc73 100644
--- a/gui/src/components/search/DatasetList.js
+++ b/gui/src/components/search/DatasetList.js
@@ -256,14 +256,7 @@ class DatasetListUnstyled extends React.Component {
authors: {
label: 'Authors',
description: 'Authors including the uploader and the co-authors',
- render: (dataset) => {
- const authors = dataset.example.authors
- if (authors.length > 3) {
- return authorList(authors.filter((_, index) => index < 2)) + ' et al'
- } else {
- return authorList(authors)
- }
- }
+ render: (dataset) => authorList(dataset.example)
}
}
diff --git a/gui/src/components/search/EntryList.js b/gui/src/components/search/EntryList.js
index 639e486eaea24e48ca05046cf2fb77a6143df9f2..19aafa03ba38d9b01b3f79e8c9e5faf237b7b101 100644
--- a/gui/src/components/search/EntryList.js
+++ b/gui/src/components/search/EntryList.js
@@ -32,7 +32,7 @@ import SharedIcon from '@material-ui/icons/SupervisedUserCircle'
import PrivateIcon from '@material-ui/icons/VisibilityOff'
import { domains } from '../domains'
import { apiContext, withApi } from '../api'
-import { authorList } from '../../utils'
+import { authorList, nameList } from '../../utils'
export function Published(props) {
const api = useContext(apiContext)
@@ -147,19 +147,19 @@ export class EntryListUnstyled extends React.Component {
},
authors: {
label: 'Authors',
- render: entry => authorList(entry.authors),
+ render: entry => authorList(entry),
supportsSort: true,
description: 'The authors of this entry. This includes the uploader and its co-authors.'
},
co_authors: {
label: 'co-Authors',
- render: entry => authorList(entry.authors),
+ render: entry => nameList(entry.authors),
supportsSort: false,
description: 'The people that this entry was co authored with'
},
shared_with: {
label: 'Shared with',
- render: entry => authorList(entry.authors),
+ render: entry => nameList(entry.authors),
supportsSort: false,
description: 'The people that this entry was shared with'
},
@@ -280,7 +280,7 @@ export class EntryListUnstyled extends React.Component {
</Quantity>
<Quantity quantity='authors' data={row}>
<Typography>
- {authorList(row.authors || [])}
+ {authorList(row)}
</Typography>
</Quantity>
<Quantity quantity='datasets' placeholder='no datasets' data={row}>
diff --git a/gui/src/utils.js b/gui/src/utils.js
index 6635eaf679135a15514e22787e1eeb1e5179acd7..552461065d6a1336e7815ddfbb83f19522633844 100644
--- a/gui/src/utils.js
+++ b/gui/src/utils.js
@@ -309,6 +309,23 @@ export function titleCase(str) {
return splitStr.join(' ')
}
-export function authorList(authors) {
- return authors.map(author => titleCase(author.name)).filter(name => name !== '').join(', ')
+export function nameList(users) {
+ const names = users.map(user => titleCase(user.name)).filter(name => name !== '')
+ if (names.length > 3) {
+ return names.slice(0, 2).join(', ') + ' et al'
+ } else {
+ return names.join(', ')
+ }
+}
+
+export function authorList(entry) {
+ if (!entry) {
+ return ''
+ }
+
+ if (entry.external_db) {
+ return entry.external_db
+ } else {
+ return nameList(entry.authors || [])
+ }
}
diff --git a/nomad/app/api/upload.py b/nomad/app/api/upload.py
index bff6180e6e95dbf17a0cfe6ea6c1e8082c8b741e..5d8fb8ca48fa59450b21b55cc0e1f7078c3390d9 100644
--- a/nomad/app/api/upload.py
+++ b/nomad/app/api/upload.py
@@ -125,6 +125,7 @@ upload_metadata_parser.add_argument('name', type=str, help='An optional name for
upload_metadata_parser.add_argument('local_path', type=str, help='Use a local file on the server.', location='args')
upload_metadata_parser.add_argument('token', type=str, help='Upload token to authenticate with curl command.', location='args')
upload_metadata_parser.add_argument('file', type=FileStorage, help='The file to upload.', location='files')
+upload_metadata_parser.add_argument('publish_directly', type=bool, help='Set this parameter to publish the upload directly after processing.', location='args')
upload_metadata_parser.add_argument('oasis_upload_id', type=str, help='Use if this is an upload from an OASIS to the central NOMAD and set it to the upload_id.', location='args')
upload_metadata_parser.add_argument('oasis_uploader_id', type=str, help='Use if this is an upload from an OASIS to the central NOMAD and set it to the uploader\' id.', location='args')
upload_metadata_parser.add_argument('oasis_deployment_id', type=str, help='Use if this is an upload from an OASIS to the central NOMAD and set it to the OASIS\' deployment id.', location='args')
@@ -224,7 +225,7 @@ class UploadListResource(Resource):
@api.expect(upload_metadata_parser)
@api.response(400, 'To many uploads')
@marshal_with(upload_model, skip_none=True, code=200, description='Upload received')
- @authenticate(required=True, upload_token=True)
+ @authenticate(required=True, upload_token=True, basic=True)
def put(self):
'''
Upload a file and automatically create a new upload in the process.
@@ -255,6 +256,9 @@ class UploadListResource(Resource):
if Upload.user_uploads(g.user, published=False).count() >= config.services.upload_limit:
abort(400, 'Limit of unpublished uploads exceeded for user.')
+ # check if the upload is to be published directly
+ publish_directly = request.args.get('publish_directly') is not None
+
# check if allowed to perform oasis upload
oasis_upload_id = request.args.get('oasis_upload_id')
oasis_uploader_id = request.args.get('oasis_uploader_id')
@@ -344,6 +348,7 @@ class UploadListResource(Resource):
upload_time=datetime.utcnow(),
upload_path=upload_path,
temporary=local_path != upload_path,
+ publish_directly=publish_directly or from_oasis,
from_oasis=from_oasis,
oasis_deployment_id=oasis_deployment_id)
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index caab93d46c601e50f7671861283dd126eab41dca..3cd8b11063f06552ed416d8edcde37cd64aa738c 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -424,7 +424,7 @@ class EntryMetadata(metainfo.MSection):
a_search=Search())
external_db = metainfo.Quantity(
- type=metainfo.MEnum('EELSDB'), categories=[MongoMetadata, UserProvidableMetadata],
+ type=metainfo.MEnum('EELSDB', 'Materials Project'), categories=[MongoMetadata, UserProvidableMetadata],
description='The repository or external database where the original data resides',
a_search=Search())
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 7070afaddd9970cf07a412cc7cc2ba6500129fab..bf46e6b6091b3e59e50afd0ced643e2509bc186f 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -29,7 +29,8 @@ calculations, and files
'''
from typing import cast, List, Any, Tuple, Iterator, Dict, cast, Iterable
-from mongoengine import StringField, DateTimeField, DictField, BooleanField, IntField, ListField
+from mongoengine import (
+ StringField, DateTimeField, DictField, BooleanField, IntField, ListField)
import logging
from structlog import wrap_logger
from contextlib import contextmanager
@@ -44,15 +45,17 @@ from functools import lru_cache
import urllib.parse
import requests
-from nomad import utils, config, infrastructure, search, datamodel
+from nomad import utils, config, infrastructure, search, datamodel, metainfo
from nomad.files import (
PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles,
PublicUploadFiles, StagingUploadFiles)
from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
from nomad.parsing.parsers import parser_dict, match_parser
from nomad.normalizing import normalizers
-from nomad.datamodel import EntryArchive, EditableUserMetadata, OasisMetadata
-from nomad.archive import query_archive, write_partial_archive_to_mongo, delete_partial_archives_from_mongo
+from nomad.datamodel import (
+ EntryArchive, EditableUserMetadata, OasisMetadata, UserProvidableMetadata)
+from nomad.archive import (
+ query_archive, write_partial_archive_to_mongo, delete_partial_archives_from_mongo)
from nomad.datamodel.encyclopedia import EncyclopediaMetadata
@@ -60,8 +63,12 @@ section_metadata = datamodel.EntryArchive.section_metadata.name
section_workflow = datamodel.EntryArchive.section_workflow.name
-_editable_metadata = {
- quantity.name: quantity for quantity in EditableUserMetadata.m_def.definitions}
+_editable_metadata: Dict[str, metainfo.Definition] = {}
+_editable_metadata.update(**{
+ quantity.name: quantity for quantity in UserProvidableMetadata.m_def.definitions})
+_editable_metadata.update(**{
+ quantity.name: quantity for quantity in EditableUserMetadata.m_def.definitions})
+
_oasis_metadata = {
quantity.name: quantity for quantity in OasisMetadata.m_def.definitions}
@@ -600,6 +607,9 @@ class Calc(Proc):
self._entry_metadata.apply_domain_metadata(self._parser_results)
self._entry_metadata.processed = True
+ if self.upload.publish_directly:
+ self._entry_metadata.published |= True
+
self._read_metadata_from_file(logger)
# persist the calc metadata
@@ -680,6 +690,7 @@ class Upload(Proc):
publish_time: Datetime when the upload was initially published on this NOMAD deployment.
last_update: Datetime of the last modifying process run (publish, re-processing, upload).
+ publish_directly: Boolean indicating that this upload should be published after initial processing.
from_oasis: Boolean indicating that this upload is coming from another NOMAD deployment.
oasis_id: The deployment id of the NOMAD that uploaded the upload.
published_to: A list of deployment ids where this upload has been successfully uploaded to.
@@ -700,6 +711,7 @@ class Upload(Proc):
publish_time = DateTimeField()
last_update = DateTimeField()
+ publish_directly = BooleanField(default=False)
from_oasis = BooleanField(default=False)
oasis_deployment_id = StringField(default=None)
published_to = ListField(StringField())
@@ -715,6 +727,7 @@ class Upload(Proc):
def __init__(self, **kwargs):
super().__init__(**kwargs)
+ self.publish_directly = self.publish_directly or self.from_oasis
self._upload_files: ArchiveBasedStagingUploadFiles = None
@lru_cache()
@@ -1297,36 +1310,33 @@ class Upload(Proc):
def _cleanup_after_processing(self):
# send email about process finish
- user = self.uploader
- name = '%s %s' % (user.first_name, user.last_name)
- message = '\n'.join([
- 'Dear %s,' % name,
- '',
- 'your data %suploaded at %s has completed processing.' % (
- '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()), # pylint: disable=no-member
- 'You can review your data on your upload page: %s' % config.gui_url(page='uploads'),
- '',
- 'If you encounter any issues with your upload, please let us know and reply to this email.',
- '',
- 'The nomad team'
- ])
- try:
- infrastructure.send_mail(
- name=name, email=user.email, message=message, subject='Processing completed')
- except Exception as e:
- # probably due to email configuration problems
- # don't fail or present this error to clients
- self.logger.error('could not send after processing email', exc_info=e)
+ if not self.publish_directly:
+ user = self.uploader
+ name = '%s %s' % (user.first_name, user.last_name)
+ message = '\n'.join([
+ 'Dear %s,' % name,
+ '',
+ 'your data %suploaded at %s has completed processing.' % (
+ '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()), # pylint: disable=no-member
+ 'You can review your data on your upload page: %s' % config.gui_url(page='uploads'),
+ '',
+ 'If you encounter any issues with your upload, please let us know and reply to this email.',
+ '',
+ 'The nomad team'
+ ])
+ try:
+ infrastructure.send_mail(
+ name=name, email=user.email, message=message, subject='Processing completed')
+ except Exception as e:
+ # probably due to email configuration problems
+ # don't fail or present this error to clients
+ self.logger.error('could not send after processing email', exc_info=e)
- def _cleanup_after_processing_oasis_upload(self):
- '''
- Moves the upload out of staging to the public area. It will
- pack the staging upload files in to public upload files.
- '''
- assert self.processed_calcs > 0
+ if not self.publish_directly or self.processed_calcs == 0:
+ return
logger = self.get_logger()
- logger.info('started to publish oasis upload')
+ logger.info('started to publish upload directly')
with utils.lnr(logger, 'publish failed'):
metadata = self.metadata_file_cached(
@@ -1343,12 +1353,13 @@ class Upload(Proc):
upload_size=self.upload_files.size):
self.upload_files.delete()
- if metadata is not None:
- self.upload_time = metadata.get('upload_time')
+ if self.from_oasis:
+ if metadata is not None:
+ self.upload_time = metadata.get('upload_time')
- if self.upload_time is None:
- self.upload_time = datetime.utcnow()
- logger.warn('oasis upload without upload time')
+ if self.upload_time is None:
+ self.upload_time = datetime.utcnow()
+ logger.warn('oasis upload without upload time')
self.publish_time = datetime.utcnow()
self.published = True
@@ -1389,10 +1400,7 @@ class Upload(Proc):
if self.current_process == 're_process_upload':
self._cleanup_after_re_processing()
else:
- if self.from_oasis:
- self._cleanup_after_processing_oasis_upload()
- else:
- self._cleanup_after_processing()
+ self._cleanup_after_processing()
def get_calc(self, calc_id) -> Calc:
''' Returns the upload calc with the given id or ``None``. '''
diff --git a/nomad/utils/structlogging.py b/nomad/utils/structlogging.py
index 3d9ff90168a70545189f6f01cdf6fc325c72ae8c..02314714a56d897bc263bd001c29608f359df27b 100644
--- a/nomad/utils/structlogging.py
+++ b/nomad/utils/structlogging.py
@@ -37,6 +37,7 @@ Depending on the configuration all logs will also be send to a central logstash.
.. autofunc::nomad.utils.lnr
'''
+from typing import cast, Any
import logging
import structlog
from structlog.processors import StackInfoRenderer, format_exc_info, TimeStamper, JSONRenderer
@@ -277,7 +278,7 @@ def logger_factory(*args):
structlog.configure(
- processors=log_processors,
+ processors=cast(Any, log_processors),
logger_factory=logger_factory,
wrapper_class=structlog.stdlib.BoundLogger)
diff --git a/tests/app/test_api.py b/tests/app/test_api.py
index 4e032afe2a3cbf425ab0ffad259cffe8c6eee9ee..86b4621d69fc0c96eadafa1a38731e05fdca72f9 100644
--- a/tests/app/test_api.py
+++ b/tests/app/test_api.py
@@ -532,6 +532,29 @@ class TestUploads:
rv = api.get('/raw/%s/examples_potcar/POTCAR%s.stripped' % (upload_id, ending))
assert rv.status_code == 200
+ def test_put_publish_directly(self, api, test_user_auth, non_empty_example_upload, proc_infra, no_warn):
+ rv = api.put('/uploads/?%s' % urlencode(dict(
+ local_path=non_empty_example_upload,
+ publish_directly=True)), headers=test_user_auth)
+ assert rv.status_code == 200, rv.data
+ upload = self.assert_upload(rv.data)
+ upload_id = upload['upload_id']
+
+ # poll until completed
+ upload = self.block_until_completed(api, upload_id, test_user_auth)
+
+ assert len(upload['tasks']) == 4
+ assert upload['tasks_status'] == SUCCESS
+ assert upload['current_task'] == 'cleanup'
+ assert not upload['process_running']
+
+ upload_proc = Upload.objects(upload_id=upload_id).first()
+ assert upload_proc.published
+
+ entries = get_upload_entries_metadata(upload)
+ assert_upload_files(upload_id, entries, files.PublicUploadFiles)
+ assert_search_upload(entries, additional_keys=['atoms', 'dft.system'])
+
def test_post_from_oasis_admin(self, api, non_empty_uploaded, other_test_user_auth, test_user, no_warn):
url = '/uploads/?%s' % urlencode(dict(
local_path=non_empty_uploaded[1], oasis_upload_id='oasis_upload_id',
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index e435f09ec447bb802a02acb361b78a3ffb05eda2..1edf034a82ee4b8627d84bae75ae48751443e30d 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -53,10 +53,10 @@ def uploaded_id_with_warning(raw_files) -> Generator[Tuple[str, str], None, None
yield example_upload_id, example_file
-def run_processing(uploaded: Tuple[str, str], test_user) -> Upload:
+def run_processing(uploaded: Tuple[str, str], test_user, **kwargs) -> Upload:
uploaded_id, uploaded_path = uploaded
upload = Upload.create(
- upload_id=uploaded_id, user=test_user, upload_path=uploaded_path)
+ upload_id=uploaded_id, user=test_user, upload_path=uploaded_path, **kwargs)
upload.upload_time = datetime.utcnow()
assert upload.tasks_status == 'RUNNING'
@@ -165,6 +165,16 @@ def test_publish(non_empty_processed: Upload, no_warn, internal_example_user_met
assert_processing(Upload.get(processed.upload_id, include_published=True), published=True)
+def test_publish_directly(non_empty_uploaded, test_user, proc_infra, no_warn, monkeypatch):
+ processed = run_processing(non_empty_uploaded, test_user, publish_directly=True)
+
+ with processed.entries_metadata() as entries:
+ assert_upload_files(processed.upload_id, entries, PublicUploadFiles, published=True)
+ assert_search_upload(entries, [], published=True)
+
+ assert_processing(Upload.get(processed.upload_id, include_published=True), published=True)
+
+
def test_republish(non_empty_processed: Upload, no_warn, internal_example_user_metadata, monkeypatch):
processed = non_empty_processed
processed.compress_and_set_metadata(internal_example_user_metadata)