def test_loading_paths_traversal(app, db, es_clear, subjects_service):
dir_ = Path(__file__).parent
fixtures = PrioritizedVocabulariesFixtures(system_identity,
dir_ / "app_data",
dir_ / "data",
"vocabularies.yaml",
delay=False)
fixtures.load()
# app_data/vocabularies/resource_types.yaml only has image resource types
with pytest.raises(PIDDoesNotExistError):
vocabulary_service.read(
('resourcetypes', 'publication-annotationcollection'),
system_identity)
# languages are found
item = vocabulary_service.read(('languages', 'aae'), system_identity)
assert item.id == "aae"
# Only subjects from app_data/ are loaded
item = subjects_service.read("https://id.nlm.nih.gov/mesh/D000001",
system_identity)
assert item.id == "https://id.nlm.nih.gov/mesh/D000001"
# - subjects in extension but from already loaded scheme are not loaded
with pytest.raises(PIDDoesNotExistError):
subjects_service.read("https://id.nlm.nih.gov/mesh/D000015",
system_identity)
# - subjects in extension from not already loaded scheme are loaded
item = subjects_service.read(
"https://id.loc.gov/authorities/subjects/sh85118623", system_identity)
assert item.id == "https://id.loc.gov/authorities/subjects/sh85118623"
def get_programme_activity_from_record(
identity: Identity,
record: Record,
programme_vocabulary: str = "geowptypes") -> Union[None, Dict]:
"""Retrieve the GEO Work Programme activity metadata associated with the record.
Args:
identity (flask_principal.Identity): User identity
record (invenio_records.Record): Record API Object from where the GEO Work Programme activity must be
extracted.
programme_vocabulary (str): Vocabulary used to search the programme metadata.
Returns:
Union[None, Dict]: None or the GEO Work Programme metadata (as dict).
"""
result = None
# extracting the geo work programme activity metadata
activity_id = py_.get(record, "metadata.geo_work_programme_activity.id",
None)
if activity_id:
result = vocabulary_service.read(
identity, (programme_vocabulary, activity_id)).to_dict()
return result
def test_loading_paths_traversal(app, db):
dir_ = Path(__file__).parent
fixtures = PrioritizedVocabulariesFixtures(system_identity,
dir_ / "app_data",
dir_ / "data",
"vocabularies.yaml",
delay=False)
fixtures.load()
# app_data/vocabularies/resource_types.yaml only has image resource types
with pytest.raises(PIDDoesNotExistError):
vocabulary_service.read(
('resourcetypes', 'publication-annotationcollection'),
system_identity)
# languages are found
item = vocabulary_service.read(('languages', 'aae'), system_identity)
assert item.id == "aae"
# Only subjects A from app_data/ are loaded
item = vocabulary_service.read(('subjects', 'A-D000008'), system_identity)
assert item.id == "A-D000008"
with pytest.raises(PIDDoesNotExistError):
vocabulary_service.read(('subjects', 'A-D000015'), system_identity)
# subjects B from an extension are loaded
item = vocabulary_service.read(('subjects', 'B-D000008'), system_identity)
assert item.id == "B-D000008"
def test_load_languages(app, db, es_clear):
id_ = 'languages'
languages = GenericVocabularyEntry(
Path(__file__).parent / "data", id_, {
"pid-type": "lng",
"data-file": "vocabularies/languages.yaml"
})
languages.load(system_identity, delay=False)
item = vocabulary_service.read((id_, 'aae'), system_identity)
assert item.id == "aae"
def test_loading_paths_traversal(app, db):
dir_ = Path(__file__).parent
vocabularies = VocabulariesFixture(
system_identity,
[dir_ / "app_data", dir_ / "data"],
"vocabularies.yaml"
)
vocabularies.load()
# app_data/vocabularies/resource_types.yaml only has image resource types
with pytest.raises(PIDDoesNotExistError):
vocabulary_service.read(
('resource_types', 'publication-annotationcollection'),
system_identity
)
# languages are found
item = vocabulary_service.read(
('languages', 'aae'), system_identity)
item_dict = item.to_dict()
assert item_dict["id"] == "aae"
def test_load_languages(app, db, vocabularies):
id_ = 'languages'
filepath = Path(__file__).parent / "data/vocabularies/languages.yaml"
vocabularies.create_vocabulary_type(
id_,
{
"pid-type": "lng",
"data-file": filepath
},
)
vocabularies.load_datafile(id_, filepath, delay=False)
item = vocabulary_service.read((id_, 'aae'), system_identity)
assert item.id == "aae"
def test_load_languages(app, db, vocabularies):
vocabularies.load_vocabulary(
'languages',
{
"pid-type": "lng",
"data-file": (
Path(__file__).parent / "data/vocabularies/languages.yaml"
)
},
delay=False
)
item = vocabulary_service.read(
('languages', 'aae'), system_identity)
item_dict = item.to_dict()
assert item_dict["id"] == "aae"
def test_load_resource_types(app, db, es_clear):
id_ = 'resourcetypes'
resource_types = GenericVocabularyEntry(
Path(__file__).parent / "data",
id_,
{
"pid-type": "rsrct",
"data-file": "vocabularies/resource_types.yaml"
},
)
resource_types.load(system_identity, delay=False)
item = vocabulary_service.read((id_, 'publication-annotationcollection'),
system_identity)
item_dict = item.to_dict()
assert item_dict["id"] == "publication-annotationcollection"
assert item_dict["props"]["datacite_general"] == "Collection"
def test_load_resource_types(app, db, vocabularies):
id_ = 'resourcetypes'
filepath = Path(__file__).parent / "data/vocabularies/resource_types.yaml"
vocabularies.create_vocabulary_type(
id_,
{
"pid-type": "rsrct",
"data-file": filepath
},
)
vocabularies.load_datafile(id_, filepath, delay=False)
item = vocabulary_service.read((id_, 'publication-annotationcollection'),
system_identity)
item_dict = item.to_dict()
assert item_dict["id"] == "publication-annotationcollection"
assert item_dict["props"]["datacite_general"] == "Collection"
def test_load_resource_types(app, db, vocabularies):
vocabularies.load_vocabulary(
'resource_types',
{
"pid-type": "rsrct",
"data-file": (
Path(__file__).parent / "data/vocabularies/resource_types.yaml"
)
},
delay=False
)
item = vocabulary_service.read(
('resource_types', 'publication-annotationcollection'),
system_identity
)
item_dict = item.to_dict()
assert item_dict["id"] == "publication-annotationcollection"
assert item_dict["props"]["datacite_general"] == "Collection"
def update_license(license_dict):
"""Update the stored vocabulary with the new icon."""
try:
echo(f"Updating license: {license_dict['id']}... ", nl=False)
license_ = vocabulary_svc.read(
system_identity, ("licenses", license_dict["id"]))._obj
# NOTE: we don't use the service update method here because we
# want to evade validation errors, and the migration guide tells
# the users to completely rebuild the search indices anyway
# and we pop the '$schema' because it might be outdated and is
# a constant field anyway
license_["icon"] = license_dict["icon"]
license_.pop("$schema", None)
license_.commit()
secho("OK", fg="green")
except Exception as e:
secho("Error", fg="red")
return f"Error updating license '{license_dict['id']}': {e}"
return None
def _read_resource_type(self, id_):
"""Retrieve resource type record using service."""
return vocabulary_service.read(('resource_types', id_),
system_identity)._record
def _read_resource_type(self, id_):
"""Retrieve resource type record using service."""
rec = vocabulary_service.read(system_identity, ("resourcetypes", id_))
return rec._record
