def do_import(self, workbook: IngestWorkbook, is_update, project_uuid=None, update_project=False,
worksheet_titles: List[str] = None):
registry = _ImportRegistry(self.template_mgr)
if worksheet_titles:
importable_worksheets = workbook.select_importable_worksheets(worksheet_titles)
else:
importable_worksheets = workbook.importable_worksheets()
workbook_errors = self.validate_worksheets(is_update, importable_worksheets)
importable_worksheets = [ws for ws in importable_worksheets]
for worksheet in importable_worksheets:
try:
self._import_worksheet(project_uuid, registry, update_project, workbook_errors, worksheet)
except Exception as e:
workbook_errors.append(
{"location": f'sheet={worksheet.title}', "type": e.__class__.__name__, "detail": str(e)})
if not registry.has_project() and not project_uuid:
e = NoProjectFound()
workbook_errors.append({"location": "File", "type": e.__class__.__name__, "detail": str(e)})
if project_uuid and update_project and not registry.has_project():
workbook_errors.append({"location": "File", "type": "NoProjectWorksheet",
"detail": "The option to update the project was specified but there is no project "
"worksheet found."})
if project_uuid and not registry.has_project():
registry.add_project_reference(project_uuid)
self._import_modules(registry, workbook_errors)
return registry.flatten(), workbook_errors
def test_importable_worksheets(self):
# given:
importable_names = ['Organ From Donor', 'Cell Suspension', 'Project']
workbook = create_test_workbook(*importable_names)
workbook.create_sheet('Schemas')
# and:
ingest_workbook = IngestWorkbook(workbook)
# when:
actual_worksheets = ingest_workbook.importable_worksheets()
# then:
actual_titles = [ingest_worksheet.title for ingest_worksheet in actual_worksheets]
self.assertEqual(importable_names, actual_titles)
def do_import(self, workbook: IngestWorkbook, project_uuid=None):
registry = _ImportRegistry()
for worksheet in workbook.importable_worksheets():
metadata_entities = self.worksheet_importer.do_import(worksheet)
module_field_name = worksheet.get_module_field_name()
for entity in metadata_entities:
if worksheet.is_module_tab():
entity.retain_content_fields(module_field_name)
registry.add_module(entity)
else:
registry.add_submittable(entity)
if registry.has_project():
registry.import_modules()
else:
raise NoProjectFound()
return registry.flatten()
def do_import(self, workbook: IngestWorkbook, project_uuid=None):
spreadsheet_json = {}
self.import_or_reference_project(project_uuid, spreadsheet_json,
workbook)
for worksheet in workbook.importable_worksheets():
concrete_entity = self.template_mgr.get_concrete_entity_of_tab(
worksheet.title)
domain_entity = self.template_mgr.get_domain_entity(
concrete_entity)
entities_dict = self.worksheet_importer.do_import(
worksheet, self.template_mgr)
if spreadsheet_json.get(domain_entity) is None:
spreadsheet_json[domain_entity] = {}
spreadsheet_json[domain_entity].update(entities_dict)
return spreadsheet_json
def test_importable_worksheets(self):
# given:
workbook = Workbook()
# and:
importable_names = ['Organ From Donor', 'Cell Suspension']
expected_worksheets = [
workbook.create_sheet(name) for name in importable_names
]
workbook.create_sheet('Schemas')
# and:
default_worksheet = workbook.get_sheet_by_name('Sheet')
workbook.remove_sheet(default_worksheet)
# and:
ingest_workbook = IngestWorkbook(workbook)
# when:
actual_worksheets = ingest_workbook.importable_worksheets()
# then:
self.assertEqual(expected_worksheets, actual_worksheets)
