def test_cleanup_index_all(app, load_default_data, identifiers, mocker):
index = app.config.get('ELASTICSEARCH_INDEX')
m = mocker.patch('fixes.cleanup_index.cleanup_index_batch')
# Should be no calls made at first as there is only one version of all submissions
cleanup_index_all(index=index, synchronous=True)
m.assert_not_called()
m.reset_mock()
# Create a new version for ins1283842
new_submission = HEPSubmission(publication_recid=1,
inspire_id=identifiers[0]["inspire_id"],
version=2,
overall_status='finished')
db.session.add(new_submission)
db.session.commit()
# New id should be 3
assert (new_submission.id == 3)
# Cleanup should now clean up id 1
cleanup_index_all(index=index, synchronous=True)
m.assert_called_once_with([1], index)
m.reset_mock()
# Create more new versions
new_submission1 = HEPSubmission(publication_recid=1,
inspire_id=identifiers[0]["inspire_id"],
version=3,
overall_status='finished')
db.session.add(new_submission1)
new_submission2 = HEPSubmission(publication_recid=1,
inspire_id=identifiers[0]["inspire_id"],
version=4,
overall_status='todo')
db.session.add(new_submission2)
new_submission3 = HEPSubmission(publication_recid=16,
inspire_id=identifiers[1]["inspire_id"],
version=2,
overall_status='finished')
db.session.add(new_submission3)
db.session.commit()
assert (new_submission1.id == 4)
assert (new_submission2.id == 5)
assert (new_submission3.id == 6)
# Cleanup should now clean up ids 1, 2 and 3 (ie versions lower than the highest finished version)
cleanup_index_all(index=index, synchronous=True)
m.assert_called_once_with([1, 2, 3], index)
m.reset_mock()
# Check batch size works
cleanup_index_all(index=index, batch=2, synchronous=True)
m.assert_has_calls([call([1, 2], index), call([3], index)])
m.reset_mock()
cleanup_index_all(index=index, batch=1, synchronous=True)
m.assert_has_calls([call([1], index), call([2], index), call([3], index)])
def test_status_reset_error(app, mocker, caplog):
"""
Test that an error is logged if something goes wrong in the status reset
:return:
"""
caplog.set_level(logging.ERROR)
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='processing',
version=1)
db.session.add(hepsubmission)
db.session.commit()
assert (hepsubmission.overall_status == 'processing')
mocker.patch('hepdata.modules.records.api.process_zip_archive',
side_effect=Exception("Something went wrong"))
mocker.patch('hepdata.modules.records.api.cleanup_submission',
side_effect=Exception("Could not clean up the submission"))
zip_file = os.path.join(base_dir, 'test_data/TestHEPSubmission.zip')
process_saved_file(zip_file, 12345, 1, '', 'todo')
# After initial failure, overall_status has not been able to be reset
assert (hepsubmission.overall_status == 'processing')
assert (len(caplog.records) == 1)
assert (caplog.records[0].levelname == "ERROR")
assert (caplog.records[0].msg ==
"Exception while cleaning up: Could not clean up the submission")
def test_submission_too_big(app, mocker):
"""
Test the right thing happens when the submission data is too big
:return:
"""
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='todo',
version=1)
db.session.add(hepsubmission)
db.session.commit()
# Patch the app config to reduce the max upload size
mocker.patch.dict('flask.current_app.config', {'CONVERT_MAX_SIZE': 1000})
test_directory = os.path.join(base_dir, 'test_data/test_submission')
errors = process_submission_directory(
test_directory, os.path.join(test_directory, 'submission.yaml'), 12345)
assert ('Archive' in errors)
assert (len(errors['Archive']) == 1)
assert (errors['Archive'][0]['level'] == 'error')
assert (errors['Archive'][0]['message'].startswith(
"Archive is too big for conversion to other formats."))
def test_old_submission_yaml(app, admin_idx):
"""
Test we can validate against the old submission schema (for use when importing)
:return:
"""
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='todo',
version=1)
db.session.add(hepsubmission)
db.session.commit()
directory = os.path.join(base_dir, 'test_data/test_v0_submission')
# This should fail against current schema
errors = process_submission_directory(
directory, os.path.join(directory, 'submission.yaml'), 12345)
assert ('submission.yaml' in errors)
assert (len(errors['submission.yaml']) == 1)
assert (errors['submission.yaml'][0]['level'] == 'error')
assert (errors['submission.yaml'][0]['message'].decode().startswith(
"Invalid value (in GeV) for cmenergies: 1.383-1.481"))
# Use old schema - should now work
errors = process_submission_directory(directory,
os.path.join(directory,
'submission.yaml'),
12345,
old_submission_schema=True)
assert (errors == {})
def create_new_version(recid, user, notify_uploader=True, uploader_message=None):
hepsubmission = get_latest_hepsubmission(publication_recid=recid)
if hepsubmission.overall_status == 'finished':
# Reopen the submission to allow for revisions,
# by creating a new HEPSubmission object.
_rev_hepsubmission = HEPSubmission(publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=hepsubmission.coordinator,
version=hepsubmission.version + 1)
db.session.add(_rev_hepsubmission)
db.session.commit()
if notify_uploader:
uploaders = SubmissionParticipant.query.filter_by(
role='uploader', publication_recid=recid, status='primary'
)
record_information = get_record_by_id(recid)
for uploader in uploaders:
send_cookie_email(uploader,
record_information,
message=uploader_message,
version=_rev_hepsubmission.version)
return jsonify({'success': True, 'version': _rev_hepsubmission.version})
else:
return jsonify({"message": f"Rec id {recid} is not finished so cannot create a new version"}), 400
def process_payload(recid, file, redirect_url, synchronous=False):
"""Process an uploaded file
:param recid: int
The id of the record to update
:param file: file
The file to process
:param redirect_url: string
Redirect URL to record, for use if the upload fails or in synchronous mode
:param synchronous: bool
Whether to process asynchronously via celery (default) or immediately (only recommended for tests)
:return: JSONResponse either containing 'url' (for success cases) or
'message' (for error cases, which will give a 400 error).
"""
if file and (allowed_file(file.filename)):
file_path = save_zip_file(file, recid)
hepsubmission = get_latest_hepsubmission(publication_recid=recid)
if hepsubmission.overall_status == 'finished':
# If it is finished and we receive an update,
# then we need to reopen the submission to allow for revisions,
# by creating a new HEPSubmission object.
_rev_hepsubmission = HEPSubmission(
publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=hepsubmission.coordinator,
version=hepsubmission.version + 1)
db.session.add(_rev_hepsubmission)
hepsubmission = _rev_hepsubmission
previous_status = hepsubmission.overall_status
hepsubmission.overall_status = 'sandbox_processing' if previous_status == 'sandbox' else 'processing'
db.session.add(hepsubmission)
db.session.commit()
if synchronous:
process_saved_file(file_path, recid, current_user.get_id(),
redirect_url, previous_status)
else:
process_saved_file.delay(file_path, recid, current_user.get_id(),
redirect_url, previous_status)
flash(
'File saved. You will receive an email when the file has been processed.',
'info')
return jsonify({'url': redirect_url.format(recid)})
else:
return jsonify({
"message":
"You must upload a .zip, .tar, .tar.gz or .tgz file" +
" (or a .oldhepdata or single .yaml or .yaml.gz file)."
}), 400
def _create_new_versions(version, expected_range):
# Create new HEPSubmission and DataSubmissions for ins1283842
new_hep_submission = HEPSubmission(
publication_recid=1,
inspire_id=identifiers[0]["inspire_id"],
version=version,
overall_status='finished')
db.session.add(new_hep_submission)
db.session.commit()
new_data_submissions = []
for i in range(5):
new_data_submission = DataSubmission(publication_recid=1,
associated_recid=1,
version=version)
db.session.add(new_data_submission)
new_data_submissions.append(new_data_submission)
db.session.commit()
assert [x.id for x in new_data_submissions] == expected_range
def get_or_create_hepsubmission(recid, coordinator=1, status="todo"):
"""
Gets of creates a new HEPSubmission record
:param recid: the publication record id
:param coordinator: the user id of the user who owns this record
:param status: e.g. todo, finished.
:return: the newly created HEPSubmission object
"""
hepsubmission = HEPSubmission.query.filter_by(publication_recid=recid).first()
if hepsubmission is None:
hepsubmission = HEPSubmission(publication_recid=recid,
coordinator=coordinator,
overall_status=status)
db.session.add(hepsubmission)
db.session.commit()
return hepsubmission
def test_find_submission_data_file_path(app):
data_dir = app.config['CFG_DATADIR']
expected_file_name = 'HEPData-987654321-v2-yaml.zip'
old_file_path = data_dir + '/987654321/' + expected_file_name
new_file_path = data_dir + '/8a/987654321/' + expected_file_name
# /8a/987654321/
if os.path.exists(new_file_path):
os.remove(new_file_path)
# No new format file found, so should return old directory
submission = HEPSubmission(publication_recid=987654321, version=2)
assert (find_submission_data_file_path(submission) == old_file_path)
# Create new file
os.makedirs(data_dir + '/8a/987654321/', exist_ok=True)
f = open(new_file_path, 'w')
f.close()
assert (find_submission_data_file_path(submission) == new_file_path)
def test_duplicate_table_names(app):
"""
Test that an error is returned for a submission.yaml file with duplicate table names.
"""
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='todo',
version=1)
db.session.add(hepsubmission)
db.session.commit()
directory = os.path.join(base_dir, 'test_data/test_duplicate_table_names')
errors = process_submission_directory(
directory, os.path.join(directory, 'submission.yaml'), 12345)
assert ('submission.yaml' in errors)
assert (len(errors['submission.yaml']) == 2)
for error in errors['submission.yaml']:
assert (error['level'] == 'error')
assert (error['message'].startswith("Duplicate table with name"))
def test_status_reset(app, mocker):
"""
Test that the status is reset if something unexpected goes wrong
:return:
"""
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='processing',
version=1)
db.session.add(hepsubmission)
db.session.commit()
assert (hepsubmission.overall_status == 'processing')
mocker.patch('hepdata.modules.records.api.process_zip_archive',
side_effect=Exception("Something went wrong"))
zip_file = os.path.join(base_dir, 'test_data/TestHEPSubmission.zip')
process_saved_file(zip_file, 12345, 1, '', 'todo')
# After initial failure, overall_status should be reset to 'todo'
assert (hepsubmission.overall_status == 'todo')
def test_invalid_data_yaml(app, admin_idx):
"""
Test the right thing happens when a data yaml file is invalid
:return:
"""
base_dir = os.path.dirname(os.path.realpath(__file__))
hepsubmission = HEPSubmission(publication_recid=12345,
overall_status='todo',
version=1)
db.session.add(hepsubmission)
db.session.commit()
directory = os.path.join(base_dir, 'test_data/test_invalid_data_file')
errors = process_submission_directory(
directory, os.path.join(directory, 'submission.yaml'), 12345)
assert ('data1.yaml' in errors)
assert (len(errors['data1.yaml']) == 1)
assert (errors['data1.yaml'][0]['level'] == 'error')
assert (errors['data1.yaml'][0]['message'].startswith(
"There was a problem parsing the file"))
def process_submission_directory(basepath,
submission_file_path,
recid,
update=False,
*args,
**kwargs):
"""
Goes through an entire submission directory and processes the
files within to create DataSubmissions
with the files and related material attached as DataResources.
:param basepath:
:param submission_file_path:
:param recid:
:return:
"""
added_file_names = []
errors = {}
if submission_file_path is not None:
submission_file = open(submission_file_path, 'r')
submission_file_validator = SubmissionFileValidator()
is_valid_submission_file = submission_file_validator.validate(
file_path=submission_file_path)
data_file_validator = DataFileValidator()
if is_valid_submission_file:
try:
submission_processed = yaml.load_all(submission_file,
Loader=yaml.CSafeLoader)
except:
submission_processed = yaml.safe_load_all(submission_file)
# process file, extracting contents, and linking
# the data record with the parent publication
hepsubmission = get_latest_hepsubmission(publication_recid=recid)
if hepsubmission is None:
HEPSubmission(publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=kwargs.get('user_id') if 'user_id'
in kwargs else int(current_user.get_id()),
version=hepsubmission.version + 1)
# On a new upload, we reset the flag to notify reviewers
hepsubmission.reviewers_notified = False
# if it is finished and we receive an update,
# then we need to reopen the submission to allow for revisions.
if hepsubmission.overall_status == 'finished' and not update:
# we create a new HEPSubmission object
_rev_hepsubmission = HEPSubmission(
publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=hepsubmission.coordinator,
version=hepsubmission.version + 1)
db.session.add(_rev_hepsubmission)
hepsubmission = _rev_hepsubmission
reserve_doi_for_hepsubmission(hepsubmission, update)
for yaml_document in submission_processed:
if 'record_ids' in yaml_document or 'comment' in yaml_document or 'modifications' in yaml_document:
# comments are only present in the general submission
# information document.
process_general_submission_info(basepath, yaml_document,
recid)
else:
existing_datasubmission_query = DataSubmission.query \
.filter_by(name=encode_string(yaml_document["name"]),
publication_recid=recid,
version=hepsubmission.version)
added_file_names.append(yaml_document["name"])
if existing_datasubmission_query.count() == 0:
datasubmission = DataSubmission(
publication_recid=recid,
name=encode_string(yaml_document["name"]),
description=encode_string(
yaml_document["description"]),
version=hepsubmission.version)
else:
datasubmission = existing_datasubmission_query.one()
datasubmission.description = encode_string(
yaml_document["description"])
db.session.add(datasubmission)
main_file_path = os.path.join(basepath,
yaml_document["data_file"])
if data_file_validator.validate(file_path=main_file_path):
process_data_file(recid, hepsubmission.version,
basepath, yaml_document,
datasubmission, main_file_path)
else:
errors = process_validation_errors_for_display(
data_file_validator.get_messages())
data_file_validator.clear_messages()
cleanup_submission(recid, hepsubmission.version, added_file_names)
db.session.commit()
if len(errors) is 0:
package_submission(basepath, recid, hepsubmission)
reserve_dois_for_data_submissions(recid, hepsubmission.version)
admin_indexer = AdminIndexer()
admin_indexer.index_submission(hepsubmission)
else:
errors = process_validation_errors_for_display(
submission_file_validator.get_messages())
submission_file_validator.clear_messages()
data_file_validator.clear_messages()
else:
# return an error
errors = {
"submission.yaml": [{
"level":
"error",
"message":
"No submission.yaml file found in submission."
}]
}
return errors
# we return all the errors collectively.
# This makes more sense that returning errors as
# soon as problems are found on one file.
return errors
def process_submission_directory(basepath,
submission_file_path,
recid,
update=False,
*args,
**kwargs):
"""
Goes through an entire submission directory and processes the
files within to create DataSubmissions
with the files and related material attached as DataResources.
:param basepath:
:param submission_file_path:
:param recid:
:param update:
:return:
"""
added_file_names = []
errors = {}
if submission_file_path is not None:
submission_file_validator = SubmissionFileValidator()
is_valid_submission_file = submission_file_validator.validate(
file_path=submission_file_path)
if is_valid_submission_file:
submission_file = open(submission_file_path, 'r')
submission_processed = yaml.load_all(submission_file,
Loader=Loader)
# process file, extracting contents, and linking
# the data record with the parent publication
hepsubmission = get_latest_hepsubmission(publication_recid=recid)
if hepsubmission is None:
HEPSubmission(publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=kwargs.get('user_id') if 'user_id'
in kwargs else int(current_user.get_id()),
version=hepsubmission.version + 1)
# On a new upload, we reset the flag to notify reviewers
hepsubmission.reviewers_notified = False
# if it is finished and we receive an update,
# then we need to reopen the submission to allow for revisions.
if hepsubmission.overall_status == 'finished' and not update:
# we create a new HEPSubmission object
_rev_hepsubmission = HEPSubmission(
publication_recid=recid,
overall_status='todo',
inspire_id=hepsubmission.inspire_id,
coordinator=hepsubmission.coordinator,
version=hepsubmission.version + 1)
db.session.add(_rev_hepsubmission)
hepsubmission = _rev_hepsubmission
reserve_doi_for_hepsubmission(hepsubmission, update)
no_general_submission_info = True
data_file_validator = DataFileValidator()
# Delete all data records associated with this submission.
# Fixes problems with ordering where the table names are changed between uploads.
# See https://github.com/HEPData/hepdata/issues/112
# Side effect that reviews will be deleted between uploads.
cleanup_submission(recid, hepsubmission.version, added_file_names)
for yaml_document_index, yaml_document in enumerate(
submission_processed):
if not yaml_document:
continue
# Check for presence of local files given as additional_resources.
if 'additional_resources' in yaml_document:
for resource in yaml_document['additional_resources']:
location = os.path.join(basepath, resource['location'])
if not resource['location'].startswith(
('http', '/resource/')):
if not os.path.isfile(location):
errors[resource['location']] = [{
"level":
"error",
"message":
"Missing 'additional_resources' file from uploaded archive."
}]
elif '/' in resource['location']:
errors[resource['location']] = [{
"level":
"error",
"message":
"Location of 'additional_resources' file should not contain '/'."
}]
if not yaml_document_index and 'name' not in yaml_document:
no_general_submission_info = False
process_general_submission_info(basepath, yaml_document,
recid)
elif not all(k in yaml_document
for k in ('name', 'description', 'keywords',
'data_file')):
errors["submission.yaml"] = [{
"level":
"error",
"message":
"YAML document with index {} ".format(
yaml_document_index) +
"missing one or more required keys (name, description, keywords, data_file)."
}]
else:
existing_datasubmission_query = DataSubmission.query \
.filter_by(name=encode_string(yaml_document["name"]),
publication_recid=recid,
version=hepsubmission.version)
added_file_names.append(yaml_document["name"])
try:
if existing_datasubmission_query.count() == 0:
datasubmission = DataSubmission(
publication_recid=recid,
name=encode_string(yaml_document["name"]),
description=encode_string(
yaml_document["description"]),
version=hepsubmission.version)
else:
datasubmission = existing_datasubmission_query.one(
)
datasubmission.description = encode_string(
yaml_document["description"])
db.session.add(datasubmission)
except SQLAlchemyError as sqlex:
errors[yaml_document["data_file"]] = [{
"level":
"error",
"message":
str(sqlex)
}]
db.session.rollback()
continue
main_file_path = os.path.join(basepath,
yaml_document["data_file"])
data, ex = _eos_fix_read_data(main_file_path)
if not data or data is None or ex is not None:
errors[yaml_document["data_file"]] = \
[{"level": "error", "message": "There was a problem parsing the file.\n" + str(ex)}]
elif '/' in yaml_document["data_file"]:
errors[yaml_document["data_file"]] = \
[{"level": "error", "message": "Name of data_file should not contain '/'.\n"}]
else:
if data_file_validator.validate(
file_path=main_file_path, data=data):
try:
process_data_file(recid, hepsubmission.version,
basepath, yaml_document,
datasubmission,
main_file_path)
except SQLAlchemyError as sqlex:
errors[yaml_document["data_file"]] = [{
"level":
"error",
"message":
"There was a problem processing the file.\n"
+ str(sqlex)
}]
db.session.rollback()
else:
errors = process_validation_errors_for_display(
data_file_validator.get_messages())
data_file_validator.clear_messages()
if yaml_document["data_file"] not in errors:
# Check that the length of the 'values' list is consistent
# for each of the independent_variables and dependent_variables.
indep_count = [
len(indep['values'])
for indep in data['independent_variables']
]
dep_count = [
len(dep['values'])
for dep in data['dependent_variables']
]
if len(set(indep_count + dep_count)
) > 1: # if more than one unique count
errors.setdefault(
yaml_document["data_file"], []
).append({
"level":
"error",
"message":
"Inconsistent length of 'values' list:\n" +
"independent_variables{}, dependent_variables{}"
.format(str(indep_count), str(dep_count))
})
submission_file.close()
if no_general_submission_info:
hepsubmission.last_updated = datetime.now()
db.session.add(hepsubmission)
db.session.commit()
# The line below is commented out since it does not preserve the order of tables.
# Delete all tables above instead: side effect of deleting reviews between uploads.
#cleanup_submission(recid, hepsubmission.version, added_file_names)
db.session.commit()
if len(errors) is 0:
errors = package_submission(basepath, recid, hepsubmission)
reserve_dois_for_data_submissions(
publication_recid=recid, version=hepsubmission.version)
admin_indexer = AdminIndexer()
admin_indexer.index_submission(hepsubmission)
else: # delete all tables if errors
cleanup_submission(recid, hepsubmission.version, {})
else:
errors = process_validation_errors_for_display(
submission_file_validator.get_messages())
submission_file_validator.clear_messages()
else:
# return an error
errors = {
"submission.yaml": [{
"level":
"error",
"message":
"No submission.yaml file found in submission."
}]
}
return errors
# we return all the errors collectively.
# This makes more sense that returning errors as
# soon as problems are found on one file.
return errors