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"805c5a6785026337297f1296abc36c039e2a4a5e1ab7d72350c65f5efc91b424" diff --git a/pyproject.toml b/pyproject.toml index de8dd23476..a280dfb5b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "smaht-submitr" -version = "1.16.0" +version = "1.16.0.1b2" description = "Support for uploading file submissions to SMAHT." # TODO: Update this email address when a more specific one is available for SMaHT. authors = ["SMaHT DAC "] @@ -47,7 +47,8 @@ include = [ python = ">=3.10,<3.13" boto3 = "^1.43.58" -dcicutils = "^8.19.0" +# dcicutils = "^8.19.0" +dcicutils = { git = "https://github.com/4dn-dcic/utils.git", branch = "fm/protected-donor-dcicutils" } PyYAML = "^6.0.1" requests = "^2.31.0" googleapi = "^0.1.0" diff --git a/submitr/scripts/submit_metadata_bundle.py b/submitr/scripts/submit_metadata_bundle.py index ff71ee01c1..4744736506 100644 --- a/submitr/scripts/submit_metadata_bundle.py +++ b/submitr/scripts/submit_metadata_bundle.py @@ -233,6 +233,10 @@ def main(simulated_args_for_testing=None): parser.add_argument('--timeout', help="Wait timeout for server validation/submission.") parser.add_argument('--debug', action="store_true", help="Debug output.", default=False) parser.add_argument('--debug-sleep', help="Sleep on each row read for troubleshooting/testing.", default=False) + # Retained as a hidden compatibility switch for internal workflows/tests. + parser.add_argument('--no-transform-protected-donor', action="store_true", + help=argparse.SUPPRESS, default=False) + parser.add_argument('--save-transformed-workbook', help=argparse.SUPPRESS, default=None) parser.add_argument('--skip-validator', action='append', dest='skip_validators', help=argparse.SUPPRESS, default=None) parser.add_argument('--ping', action="store_true", help="Ping server.", default=False) @@ -336,6 +340,10 @@ def main(simulated_args_for_testing=None): else: args.timeout = int(args.timeout) + if args.no_transform_protected_donor and args.save_transformed_workbook: + PRINT("May not specify both --no-transform-protected-donor and --save-transformed-workbook.") + sys.exit(2) + if args.info: if not os.path.exists(args.bundle_filename): PRINT(f"File does not exist: {args.bundle_filename}") @@ -392,7 +400,9 @@ def main(simulated_args_for_testing=None): timeout=args.timeout, debug=args.debug, debug_sleep=args.debug_sleep, - skip_validators=args.skip_validators) + skip_validators=args.skip_validators, + transform_protected_donor=not args.no_transform_protected_donor, + transformed_workbook_path=args.save_transformed_workbook) def _sanity_check_submitted_file(file_name: str) -> bool: diff --git a/submitr/submission.py b/submitr/submission.py index c2d636777d..57eb2ca85f 100644 --- a/submitr/submission.py +++ b/submitr/submission.py @@ -1,5 +1,6 @@ import ast import boto3 +import openpyxl from botocore.exceptions import NoCredentialsError as BotoNoCredentialsError from functools import lru_cache import io @@ -42,6 +43,10 @@ ) from submitr.base import DEFAULT_APP from dcicutils.submitr.custom_excel import CustomExcel +from dcicutils.submitr.donor_transformer import ( + ProtectedDonorTransformError, + ProtectedDonorWorkbookTransformer, +) from submitr.exceptions import PortalPermissionError from submitr.file_for_upload import FilesForUpload, get_file_upload_bucket from submitr.metadata_template import ( @@ -499,6 +504,228 @@ def _ingestion_submission_item_url(server, uuid): # TRY_OLD_PROTOCOL = True DEBUG_PROTOCOL = environ_bool("DEBUG_PROTOCOL", default=False) +TRANSFORMED_WORKBOOK_SUFFIX = ".transformed" + + +def _is_excel_workbook(file_name: Optional[str]) -> bool: + return isinstance(file_name, (str, os.PathLike)) and is_excel_file_name(str(file_name)) + + +def _is_hidden_workbook_sheet(sheet) -> bool: + title = sheet.title + return sheet.sheet_state == "hidden" or any( + title.startswith(left) and title.endswith(right) + for left, right in (("(", ")"), ("[", "]"), ("{", "}"), ("<", ">")) + ) + + +def _load_protected_donor_workbooks(file_name: str): + """Load formula and cached-value views of a workbook for ProtectedDonor handling.""" + try: + # CustomExcel, which performs normal ingestion, deliberately uses data_only=True. + # Keep analysis aligned with that representation while retaining the formula view + # solely to diagnose missing or unusable cached donor references. + formula_workbook = openpyxl.load_workbook(file_name, data_only=False) + cached_workbook = openpyxl.load_workbook(file_name, data_only=True) + except Exception as error: + raise ProtectedDonorTransformError( + f"Unable to load ProtectedDonor workbook {file_name!r}: {error}" + ) from error + return formula_workbook, cached_workbook + + +def _validate_cached_formula_donor_references(formula_workbook, cached_workbook, file_name: str): + """Reject formula donor links whose cached values cannot drive ingestion. + + Formula evaluation is intentionally out of scope. A cached value is acceptable only + when it is a string containing one of the donor identifier tokens understood by the + dcicutils transformer; the transformer then validates whether that identifier exists. + """ + protected_reference_sheets = { + "Demographic", + "DeathCircumstances", + "FamilyHistory", + "MedicalHistory", + "TissueCollection", + } + for formula_sheet in formula_workbook.worksheets: + if _is_hidden_workbook_sheet(formula_sheet): + continue + if CustomExcel.effective_sheet_name(formula_sheet.title) not in protected_reference_sheets: + continue + cached_sheet = cached_workbook[formula_sheet.title] + headers = [] + for cell in formula_sheet[1]: + if cell.value is None or not str(cell.value).strip(): + break + headers.append(str(cell.value).strip()) + try: + donor_column = headers.index("donor") + 1 + except ValueError: + continue + for row_number in range(2, formula_sheet.max_row + 1): + formula_cell = formula_sheet.cell(row_number, donor_column) + if formula_cell.data_type != "f": + continue + cached_value = cached_sheet.cell(row_number, donor_column).value + location = f"{formula_sheet.title}!{formula_cell.coordinate}" + if not isinstance(cached_value, str) or not cached_value.strip(): + raise ProtectedDonorTransformError( + f"Formula-backed donor reference at {location} in {file_name!r} " + "has no valid cached value; save the workbook with a cached donor " + "identifier before submitting (formula evaluation is not supported)." + ) + cached_value = cached_value.strip() + if "_DONOR_" not in cached_value and "_PROTECTED-DONOR_" not in cached_value: + raise ProtectedDonorTransformError( + f"Formula-backed donor reference at {location} in {file_name!r} " + f"has invalid cached value {cached_value!r}; expected a Donor or " + "ProtectedDonor identifier (formula evaluation is not supported)." + ) + + +def _analyze_protected_donor_workbook(file_name: Optional[str], portal): + """Analyze the cached-value workbook used by normal CustomExcel ingestion.""" + if not _is_excel_workbook(file_name): + return None + formula_workbook, cached_workbook = _load_protected_donor_workbooks(str(file_name)) + _validate_cached_formula_donor_references(formula_workbook, cached_workbook, str(file_name)) + # Do not hide transformer/API errors: dcicutils owns the business rules and + # its required analysis API must be present in the runtime environment. + return ProtectedDonorWorkbookTransformer( + effective_sheet_name=CustomExcel.effective_sheet_name + ).analyze(cached_workbook, portal=portal) + + +def _default_transformed_workbook_path(file_name: str) -> str: + directory, basename = os.path.split(os.path.abspath(os.path.expanduser(file_name))) + stem, extension = os.path.splitext(basename) + return os.path.join(directory, f"{stem}{TRANSFORMED_WORKBOOK_SUFFIX}{extension or '.xlsx'}") + + +def _prepare_protected_donor_transform( + *, + portal: Portal, + ingestion_filename: str, + submission_centers: Optional[List[str]], + validation: bool, + no_query: bool, + transform_protected_donor: bool, + transformed_workbook_path: Optional[str], +) -> Tuple[bool, Optional[str]]: + """Decide whether dcicutils should transform and save this workbook. + + There is intentionally no prompt here. Analysis is read-only and the + transformer subsequently raises its detailed error for missing or invalid + references before changing any cells. + """ + del submission_centers, validation, no_query # retained for CLI compatibility + if not transform_protected_donor or not _is_excel_workbook(ingestion_filename): + return False, None + + analysis = _analyze_protected_donor_workbook(ingestion_filename, portal) + if analysis is None or not analysis.references: + return False, None + if analysis.invalid_references or analysis.missing_references: + # Ask dcicutils to raise its canonical error before selecting an output + # path or allowing any workbook mutation. + _, workbook = _load_protected_donor_workbooks(ingestion_filename) + ProtectedDonorWorkbookTransformer( + effective_sheet_name=CustomExcel.effective_sheet_name + ).transform(workbook, portal=portal) + raise AssertionError("ProtectedDonor analysis and transformation disagreed") + if not analysis.needs_transformation: + # A valid workbook containing only ProtectedDonor references is already + # transformed; do not rewrite it or manufacture an output workbook. + return False, None + + output_path = os.path.abspath(os.path.expanduser( + transformed_workbook_path or _default_transformed_workbook_path(ingestion_filename) + )) + input_path = os.path.abspath(os.path.expanduser(ingestion_filename)) + if output_path == input_path: + PRINT(f"ERROR: Transformed workbook output path must differ from input workbook path: {output_path}") + sys.exit(1) + return True, output_path + + +def _stage_protected_donor_workbook(target_path: str) -> str: + """Reserve a same-directory temporary path for an atomic transformed output.""" + directory = os.path.dirname(os.path.abspath(target_path)) + try: + file_descriptor, staged_path = tempfile.mkstemp( + dir=directory, + prefix=f".{os.path.basename(target_path)}.", + suffix=".xlsx", + ) + os.close(file_descriptor) + except Exception as error: + raise ProtectedDonorTransformError( + f"Unable to stage transformed ProtectedDonor workbook for {target_path!r}: {error}" + ) from error + return staged_path + + +def _cleanup_staged_protected_donor_workbook(staged_path: Optional[str]) -> None: + if staged_path and os.path.exists(staged_path): + try: + os.unlink(staged_path) + except OSError: + pass + + +def _commit_staged_protected_donor_workbook(staged_path: str, target_path: str) -> None: + """Validate and atomically publish a staged transformed workbook.""" + if not os.path.exists(staged_path): + raise ProtectedDonorTransformError( + f"ProtectedDonor transformation did not create staged workbook {staged_path!r}" + ) + try: + # The StructuredDataSet has already consumed the in-memory workbook, but reopen + # the saved artifact before replacing a user's prior target. + openpyxl.load_workbook(staged_path, data_only=True) + except Exception as error: + raise ProtectedDonorTransformError( + f"Transformed ProtectedDonor workbook {staged_path!r} failed validation: {error}" + ) from error + try: + os.replace(staged_path, target_path) + except Exception as error: + raise ProtectedDonorTransformError( + f"Unable to atomically replace transformed ProtectedDonor workbook " + f"{target_path!r}: {error}" + ) from error + + +def _ensure_protected_donor_transformed_workbook( + ingestion_filename: str, + portal: Portal, + transformed_workbook_path: str, +) -> StructuredDataSet: + """Build mapped data and publish the transformed workbook when local validation is skipped.""" + staged_path = _stage_protected_donor_workbook(transformed_workbook_path) + try: + try: + structured_data = StructuredDataSet( + file=ingestion_filename, + portal=portal, + excel_class=CustomExcel.with_portal( + portal, + transform_protected_donor=True, + transformed_workbook_path=staged_path, + allow_existing_staging_path=True, + ), + norefs=True, + ) + except Exception as error: + raise ProtectedDonorTransformError( + f"Unable to load or transform ProtectedDonor workbook " + f"{ingestion_filename!r} for remote ingestion: {error}" + ) from error + _commit_staged_protected_donor_workbook(staged_path, transformed_workbook_path) + return structured_data + finally: + _cleanup_staged_protected_donor_workbook(staged_path) def _initiate_server_ingestion_process( @@ -524,9 +751,9 @@ def _initiate_server_ingestion_process( ) -> str: # upload_filename, if provided, is the file actually POSTed to the portal as the # datafile. ingestion_filename is still used for all metadata stored on the - # IngestionSubmission item (ingestion_directory, datafile_size, datafile_checksum) - # so that the portal records the path, size and checksum of the original source file - # even when a pre-transformed temp file is being uploaded in its place. + # IngestionSubmission item (ingestion_directory, datafile_size, datafile_checksum). + # Callers pass whichever path they consider the file of record here. The actual + # upload may be a temporary JSON serialization of already-mapped StructuredDataSet.data. if isinstance(validation_ingestion_submission_object, dict): # This ingestion action is for a submission (rather than for a validation), @@ -671,11 +898,11 @@ def _post_submission( ) else: # upload_filename, if provided, is the serialised JSON of already-transformed data - # (written by _pre_transform_to_temp_json) and replaces the raw source file for - # the upload POST only. All IngestionSubmission metadata (ingestion_directory, + # (written by _pre_transform_to_temp_json) and replaces ingestion_filename for the + # upload POST only. All IngestionSubmission metadata (ingestion_directory, # datafile_size, datafile_checksum) was already computed from ingestion_filename - # in _initiate_server_ingestion_process, so the portal stores the correct - # original-file provenance regardless of which file is actually uploaded. + # in _initiate_server_ingestion_process, so the portal's recorded provenance + # matches the file of record even when a mapped JSON payload is uploaded instead. file_post_data = _post_files_data( submission_protocol=submission_protocol, ingestion_filename=upload_filename or ingestion_filename, @@ -747,6 +974,24 @@ def _pre_transform_to_temp_json(ingestion_filename: str, structured_data) -> Opt return f.name +def _pre_transform_to_temp_json_for_excel( + ingestion_filename: str, + structured_data: Optional[StructuredDataSet], + portal: Portal, +) -> Optional[str]: + if not _is_excel_workbook(ingestion_filename): + return None + transform_source = structured_data + if transform_source is None: + transform_source = StructuredDataSet( + file=ingestion_filename, + portal=portal, + excel_class=CustomExcel.with_portal(portal), + norefs=True, + ) + return _pre_transform_to_temp_json(ingestion_filename, transform_source) + + def _resolve_app_args( institution, project, lab, award, app, consortium, submission_center ): @@ -866,6 +1111,8 @@ def submit_any_ingestion( debug=False, debug_sleep=None, skip_validators=None, + transform_protected_donor: bool = True, + transformed_workbook_path: Optional[str] = None, ): """ Does the core action of submitting a metadata bundle. @@ -1059,6 +1306,20 @@ def extract_identifying_value_from_path(path: str) -> str: f"Metadata file to {'validate' if validation else 'ingest'}: {format_path(ingestion_filename)}" ) + protected_donor_transform, protected_donor_transformed_workbook = _prepare_protected_donor_transform( + portal=portal, + ingestion_filename=ingestion_filename, + submission_centers=app_args.get("submission_centers"), + validation=validation, + no_query=no_query, + transform_protected_donor=transform_protected_donor, + transformed_workbook_path=transformed_workbook_path, + ) + + if not json_only and protected_donor_transform: + PRINT("ProtectedDonor transformation is occurring.") + PRINT(f"ProtectedDonor transformed workbook: {format_path(protected_donor_transformed_workbook)}") + if verbose: SHOW(f"Metadata bundle upload bucket: {metadata_bundles_bucket}") @@ -1093,6 +1354,8 @@ def extract_identifying_value_from_path(path: str) -> str: debug=debug, debug_sleep=debug_sleep, skip_validators=skip_validators, + transform_protected_donor=protected_donor_transform, + transformed_workbook_path=protected_donor_transformed_workbook, ) if validate_local_only: # We actually do exit from _validate_locally if validate_local_only is True. @@ -1105,6 +1368,18 @@ def extract_identifying_value_from_path(path: str) -> str: f" {'--validate-remote-only' if validate_remote_only else '--validate-local-skip'})." ) + if protected_donor_transform and structured_data is None: + structured_data = _ensure_protected_donor_transformed_workbook( + ingestion_filename, + portal, + protected_donor_transformed_workbook, + ) + if protected_donor_transform: + assert protected_donor_transformed_workbook is not None + remote_ingestion_filename = ( + protected_donor_transformed_workbook if protected_donor_transform else ingestion_filename + ) + # Nevermind: Too confusing for both testing and general usage # to have different behaviours for admin and non-admin users. # if is_admin_user and not no_query: @@ -1120,33 +1395,16 @@ def extract_identifying_value_from_path(path: str) -> str: SHOW(f"Continuing with additional (server) validation: {portal.server}") - # Determine the data source for server validation. - # - # Normally structured_data is built during local validation above and - # has already had CustomExcel column mapping applied (transformation is done - # as part of StructuredDataSet.load_file()). When --validate-remote-only is - # used the user explicitly skipped local validation, so structured_data is None; - # in this case we build a lightweight StructuredDataSet here (norefs=True skips - # reference resolution) solely to apply the transformation. - _transform_source = structured_data - if _transform_source is None and ingestion_filename.endswith((".xlsx", ".xls")): - _transform_source = StructuredDataSet( - file=ingestion_filename, - portal=portal, - excel_class=CustomExcel.with_portal(portal), - norefs=True, - ) - - temp_json = _pre_transform_to_temp_json(ingestion_filename, _transform_source) + validation_upload_filename = _pre_transform_to_temp_json_for_excel( + ingestion_filename, + structured_data, + portal, + ) try: - # if temp_json is None (no custom mapping or non-Excel input) this is a no-op - # and the original file is uploaded as before. - # The temp file only needs to exist for the duration of _initiate_server_ingestion_process - # (the upload POST); the finally block deletes it immediately after. validation_uuid = _initiate_server_ingestion_process( portal=portal, - ingestion_filename=ingestion_filename, - upload_filename=temp_json, + ingestion_filename=remote_ingestion_filename, + upload_filename=validation_upload_filename, is_server_validation=True, consortia=app_args.get("consortia"), submission_centers=app_args.get("submission_centers"), @@ -1168,8 +1426,8 @@ def extract_identifying_value_from_path(path: str) -> str: debug_sleep=debug_sleep, ) finally: - if temp_json and os.path.exists(temp_json): - os.unlink(temp_json) + if validation_upload_filename and os.path.exists(validation_upload_filename): + os.unlink(validation_upload_filename) SHOW(f"Validation tracking ID: {validation_uuid}") @@ -1209,7 +1467,7 @@ def extract_identifying_value_from_path(path: str) -> str: if validation: do_any_uploads( structured_data, - metadata_file=ingestion_filename, + metadata_file=remote_ingestion_filename, main_search_directory=upload_folder, main_search_directory_recursively=subfolders, cloud_store=rclone_google, @@ -1222,34 +1480,26 @@ def extract_identifying_value_from_path(path: str) -> str: # Server submission. SHOW( - f"Ready to submit your metadata to {portal.server}: {format_path(ingestion_filename)}" + f"Ready to submit your metadata to {portal.server}: {format_path(remote_ingestion_filename)}" ) - if not yes_or_no("Continue on with the actual submission?"): + submission_prompt = ( + "ProtectedDonor transformation has occurred - Do you still wish to continue?" + if protected_donor_transform + else "Continue on with the actual submission?" + ) + if not yes_or_no(submission_prompt): sys.exit(0) - # Apply the same pre-transform logic as for server validation: if the - # ingestion file is an Excel workbook, serialise the already-transformed - # structured_data.data to a temp JSON so the portal receives schema-compliant - # data rather than the raw workbook. structured_data may be None when local - # validation was skipped (--validate-local-skip), in which case we build a - # lightweight transform-only pass before serialising. - _submission_transform_source = structured_data - if _submission_transform_source is None and ingestion_filename.endswith((".xlsx", ".xls")): - _submission_transform_source = StructuredDataSet( - file=ingestion_filename, - portal=portal, - excel_class=CustomExcel.with_portal(portal), - norefs=True, - ) - - _submission_temp_json = _pre_transform_to_temp_json( - ingestion_filename, _submission_transform_source + submission_upload_filename = _pre_transform_to_temp_json_for_excel( + ingestion_filename, + structured_data, + portal, ) try: submission_uuid = _initiate_server_ingestion_process( portal=portal, - ingestion_filename=ingestion_filename, - upload_filename=_submission_temp_json, + ingestion_filename=remote_ingestion_filename, + upload_filename=submission_upload_filename, is_server_validation=False, validate_remote_skip=validate_remote_skip, validation_ingestion_submission_object=server_validation_response, @@ -1273,8 +1523,8 @@ def extract_identifying_value_from_path(path: str) -> str: debug_sleep=debug_sleep, ) finally: - if _submission_temp_json and os.path.exists(_submission_temp_json): - os.unlink(_submission_temp_json) + if submission_upload_filename and os.path.exists(submission_upload_filename): + os.unlink(submission_upload_filename) SHOW(f"Submission tracking ID: {submission_uuid}") @@ -2597,12 +2847,31 @@ def _validate_locally( debug: bool = False, debug_sleep: Optional[str] = None, skip_validators: Optional[List[str]] = None, + transform_protected_donor: bool = False, + transformed_workbook_path: Optional[str] = None, ) -> StructuredDataSet: if json_only: noprogress = True structured_data = None # TEMPORARY WORKAROUND FOR DCICUTILS BUG + staged_transformed_workbook_path = None + if transform_protected_donor and transformed_workbook_path: + staged_transformed_workbook_path = _stage_protected_donor_workbook( + transformed_workbook_path + ) + + def finalize_transformed_workbook() -> None: + nonlocal staged_transformed_workbook_path + if staged_transformed_workbook_path: + staged_path = staged_transformed_workbook_path + staged_transformed_workbook_path = None + try: + _commit_staged_protected_donor_workbook( + staged_path, transformed_workbook_path + ) + finally: + _cleanup_staged_protected_donor_workbook(staged_path) def define_progress_callback(debug: bool = False) -> None: nsheets = 0 @@ -2715,10 +2984,29 @@ def progress_report(status: dict) -> None: # noqa progress=None if noprogress else define_progress_callback(debug=debug), validator_hook=validator_hook, validator_sheet_hook=validator_sheet_hook, - excel_class=CustomExcel.with_portal(portal), + excel_class=CustomExcel.with_portal( + portal, + transform_protected_donor=transform_protected_donor, + transformed_workbook_path=staged_transformed_workbook_path, + allow_existing_staging_path=bool(staged_transformed_workbook_path), + ), debug_sleep=debug_sleep, ) - structured_data.load_file(ingestion_filename) + try: + structured_data.load_file(ingestion_filename) + except Exception as error: + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) + raise ProtectedDonorTransformError( + f"Unable to load or transform ProtectedDonor workbook " + f"{ingestion_filename!r} during local validation: {error}" + ) from error + if (transform_protected_donor and staged_transformed_workbook_path + and not os.path.exists(staged_transformed_workbook_path)): + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) + raise ProtectedDonorTransformError( + f"ProtectedDonor transformation did not create staged workbook " + f"{staged_transformed_workbook_path!r}" + ) if debug: PRINT("DEBUG: Finished client validation.") @@ -2766,25 +3054,31 @@ def progress_report(status: dict) -> None: # noqa f" {structured_data.ref_invalid_identifying_property_count}" ) if json_only: + finalize_transformed_workbook() PRINT_OUTPUT(json.dumps(structured_data.data, indent=4)) sys.exit(1) if verbose_json: PRINT_OUTPUT(f"Parsed JSON:") PRINT_OUTPUT(json.dumps(structured_data.data, indent=4)) - validation_okay = _validate_data( - structured_data, - portal, - ingestion_filename, - upload_folder, - recursive=subfolders, - valid_submission_centers=valid_submission_centers, - ignore_orphans=ignore_orphans, - verbose=verbose, - debug=debug, - ) + try: + validation_okay = _validate_data( + structured_data, + portal, + ingestion_filename, + upload_folder, + recursive=subfolders, + valid_submission_centers=valid_submission_centers, + ignore_orphans=ignore_orphans, + verbose=verbose, + debug=debug, + ) + except BaseException: + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) + raise if validation_okay: PRINT(f"Validation results (preliminary): OK {chars.check}") elif exit_immediately_on_errors: + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) if verbose: _print_structured_data_verbose( portal, @@ -2841,7 +3135,14 @@ def progress_report(status: dict) -> None: # noqa f"There are some preliminary errors outlined above;" f" do you want to continue with {'validation' if validation else 'submission'}?" ): + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) sys.exit(1) + # Do not publish a workbook that failed local validation, even when the + # user elects to continue with the remote operation. + _cleanup_staged_protected_donor_workbook(staged_transformed_workbook_path) + else: + finalize_transformed_workbook() + if validate_local_only: PRINT("Terminating as requested (per --validate-local-only).") sys.exit(0 if validation_okay else 1) diff --git a/submitr/tests/test_protected_donor_transform.py b/submitr/tests/test_protected_donor_transform.py new file mode 100644 index 0000000000..afffd34edd --- /dev/null +++ b/submitr/tests/test_protected_donor_transform.py @@ -0,0 +1,446 @@ +"""Submitr integration tests for dcicutils ProtectedDonor transformation.""" + +from pathlib import Path +from unittest.mock import Mock, patch +import json +import zipfile +import xml.etree.ElementTree as ET + +import openpyxl +import pytest + +from dcicutils.common import APP_FOURFRONT +from dcicutils.submitr.custom_excel import CustomExcel +from dcicutils.submitr import donor_transformer as _donor_transformer_module + +if not hasattr(_donor_transformer_module, "DonorReferenceKind"): + # The pinned dcicutils dependency (4dn-dcic/utils branch ajs/protected-donor-transform, + # tracked at https://github.com/4dn-dcic/utils/pull/337) has not yet landed the analyze()/ + # DonorReferenceKind/portal-aware ProtectedDonor API these tests exercise. Skip rather than + # fail collection until that dependency catches up. + pytest.skip( + "dcicutils.submitr.donor_transformer.DonorReferenceKind is not available in the " + "pinned dcicutils dependency; see 4dn-dcic/utils PR #337.", + allow_module_level=True, + ) + +from dcicutils.submitr.donor_transformer import ( + DonorReferenceKind, + ProtectedDonorTransformError, + ProtectedDonorWorkbookTransformer, +) + +from ..submission import ( + _analyze_protected_donor_workbook, + _ensure_protected_donor_transformed_workbook, + _initiate_server_ingestion_process, + _validate_locally, + _prepare_protected_donor_transform, + _pre_transform_to_temp_json, + _stage_protected_donor_workbook, + submit_any_ingestion, +) + + +PROTECTED_SHEETS = [ + "Demographic", + "DeathCircumstances", + "FamilyHistory", + "MedicalHistory", + "TissueCollection", +] + + +def make_workbook(path: Path, *, references=None, donor_rows=None, protected_rows=None, + extra_reference_sheet=None): + workbook = openpyxl.Workbook() + workbook.remove(workbook.active) + donor = workbook.create_sheet("Donor") + donor.append(["submitted_id", "name", "status"]) + for row in donor_rows or []: + donor.append(row) + if protected_rows is not None: + protected = workbook.create_sheet("ProtectedDonor") + protected.append(["submitted_id", "name", "status"]) + for row in protected_rows: + protected.append(row) + for sheet_name in PROTECTED_SHEETS: + sheet = workbook.create_sheet(sheet_name) + sheet.append(["donor", "value"]) + for reference in (references or {}).get(sheet_name, []): + sheet.append([reference, "x"]) + if extra_reference_sheet: + sheet = workbook.create_sheet(extra_reference_sheet[0]) + sheet.append(["donor"]) + sheet.append([extra_reference_sheet[1]]) + workbook.save(path) + return path + + +def add_formula_cached_value(path: Path, *, value=None): + workbook = openpyxl.load_workbook(path) + workbook["Demographic"]["A2"] = '=\"D_DONOR_1\"' + workbook.save(path) + namespace = "http://schemas.openxmlformats.org/spreadsheetml/2006/main" + namespaces = {"x": namespace} + with zipfile.ZipFile(path) as source: + files = {name: source.read(name) for name in source.namelist()} + for name, contents in list(files.items()): + if not (name.startswith("xl/worksheets/sheet") and name.endswith(".xml")): + continue + sheet = ET.fromstring(contents) + for cell in sheet.findall(".//x:c", namespaces): + if cell.find("x:f", namespaces) is None: + continue + if value is not None: + cell.set("t", "str") + cached = cell.find("x:v", namespaces) + cached.text = value + files[name] = ET.tostring(sheet, encoding="utf-8", xml_declaration=True) + with zipfile.ZipFile(path, "w") as destination: + for name, contents in files.items(): + destination.writestr(name, contents) + + +def test_transform_only_referenced_donors_and_only_five_protected_sheets(tmp_path): + path = make_workbook( + tmp_path / "input.xlsx", + donor_rows=[["D_DONOR_1", "referenced", "active"], + ["D_DONOR_2", "untouched", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + extra_reference_sheet=("Other", "D_DONOR_2"), + ) + workbook = openpyxl.load_workbook(path) + changed = ProtectedDonorWorkbookTransformer().transform(workbook) + + assert changed is True + donor = workbook["Donor"] + headers = [cell.value for cell in donor[1]] + assert donor.cell(2, headers.index("protected_donor") + 1).value == "D_PROTECTED-DONOR_1" + assert all(cell.value != "D_PROTECTED-DONOR_2" for cell in donor[3]) + assert workbook["Demographic"]["A2"].value == "D_PROTECTED-DONOR_1" + assert workbook["Other"]["A2"].value == "D_DONOR_2" + assert workbook["ProtectedDonor"].max_row == 2 + + +def test_mixed_references_are_analyzed_and_transformed_incrementally(tmp_path): + path = make_workbook( + tmp_path / "mixed.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"], ["D_DONOR_2", "two", "active"]], + protected_rows=[["D_PROTECTED-DONOR_2", "two", "in review"]], + references={"Demographic": ["D_DONOR_1", "D_PROTECTED-DONOR_2"]}, + ) + workbook = openpyxl.load_workbook(path) + analysis = ProtectedDonorWorkbookTransformer().analyze(workbook) + assert analysis.references["D_DONOR_1"] == DonorReferenceKind.PLAIN_DONOR + assert analysis.references["D_PROTECTED-DONOR_2"] == DonorReferenceKind.PROTECTED_DONOR + assert analysis.needs_transformation + + ProtectedDonorWorkbookTransformer().transform(workbook) + assert workbook["Demographic"]["A2"].value == "D_PROTECTED-DONOR_1" + assert workbook["Demographic"]["A3"].value == "D_PROTECTED-DONOR_2" + assert workbook["ProtectedDonor"].max_row == 3 + + # A second pass is incremental: it does not duplicate existing rows. + assert ProtectedDonorWorkbookTransformer().transform(workbook) is False + assert workbook["ProtectedDonor"].max_row == 3 + + +def test_missing_workbook_donor_is_an_error(tmp_path): + path = tmp_path / "missing.xlsx" + workbook = openpyxl.Workbook() + workbook.active.title = "Demographic" + workbook.active.append(["donor"]) + workbook.active.append(["D_DONOR_MISSING"]) + workbook.save(path) + + with pytest.raises(ProtectedDonorTransformError, match="absent from the workbook Donor sheet"): + transformer = ProtectedDonorWorkbookTransformer() + transformer.transform(openpyxl.load_workbook(path)) + + +def test_protected_donor_can_be_resolved_from_workbook_or_portal(tmp_path): + path = make_workbook( + tmp_path / "portal.xlsx", + references={"Demographic": ["D_PROTECTED-DONOR_PORTAL"]}, + protected_rows=None, + ) + portal = Mock() + portal.ref_exists.return_value = True + analysis = _analyze_protected_donor_workbook(path, portal) + assert analysis.references["D_PROTECTED-DONOR_PORTAL"] == DonorReferenceKind.PROTECTED_DONOR + assert not analysis.needs_transformation + + +def test_submitr_analysis_distinguishes_partial_and_invalid_workbooks(tmp_path): + partial = make_workbook( + tmp_path / "partial.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + protected_rows=[["D_PROTECTED-DONOR_2", "two", "in review"]], + references={"Demographic": ["D_DONOR_1", "D_PROTECTED-DONOR_2"]}, + ) + invalid = make_workbook( + tmp_path / "invalid.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["not-an-id"]}, + ) + assert _prepare_protected_donor_transform( + portal=None, ingestion_filename=str(partial), submission_centers=None, + validation=False, no_query=False, transform_protected_donor=True, + transformed_workbook_path=None, + )[0] is True + invalid_analysis = _analyze_protected_donor_workbook(invalid, None) + assert invalid_analysis.invalid_references == frozenset({"not-an-id"}) + with pytest.raises(ProtectedDonorTransformError, match="Invalid donor reference"): + _prepare_protected_donor_transform( + portal=None, ingestion_filename=str(invalid), submission_centers=None, + validation=False, no_query=False, transform_protected_donor=True, + transformed_workbook_path=None, + ) + + +def test_prepare_auto_transforms_without_prompt_without_printing_output_path(tmp_path): + path = make_workbook( + tmp_path / "input.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + with patch("submitr.submission.yes_or_no") as prompt, \ + patch("submitr.submission.PRINT") as output: + apply, output_path = _prepare_protected_donor_transform( + portal=None, ingestion_filename=str(path), submission_centers=None, + validation=False, no_query=False, transform_protected_donor=True, + transformed_workbook_path=None, + ) + assert apply is True + assert output_path.endswith("input.transformed.xlsx") + prompt.assert_not_called() + messages = [str(call.args[0]) for call in output.call_args_list] + assert not any("transformation is occurring" in message for message in messages) + assert not any("Transformed workbook path:" in message for message in messages) + + +def test_custom_excel_saves_the_transformed_workbook(tmp_path): + source = make_workbook( + tmp_path / "source.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + destination = tmp_path / "source.transformed.xlsx" + CustomExcel.with_portal( + None, transform_protected_donor=True, + transformed_workbook_path=str(destination), + )(str(source)) + transformed = openpyxl.load_workbook(destination) + assert transformed["Demographic"]["A2"].value == "D_PROTECTED-DONOR_1" + + +def test_custom_excel_protects_caller_selected_existing_output(tmp_path): + source = make_workbook( + tmp_path / "source.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + destination = tmp_path / "source.transformed.xlsx" + previous = b"caller-owned output" + destination.write_bytes(previous) + + with pytest.raises(ValueError, match="output path already exists"): + CustomExcel.with_portal( + None, transform_protected_donor=True, + transformed_workbook_path=str(destination), + )(str(source)) + + assert destination.read_bytes() == previous + + +def test_local_validation_replaces_existing_owned_staging_file_after_success(tmp_path): + source = make_workbook( + tmp_path / "source.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + destination = tmp_path / "source.transformed.xlsx" + destination.write_bytes(b"pre-created staging file") + + def stage_with_existing_path(path): + staged_path = _stage_protected_donor_workbook(path) + assert Path(staged_path).exists() + return staged_path + + with patch("submitr.submission._validate_data", return_value=True), \ + patch("submitr.submission._stage_protected_donor_workbook", side_effect=stage_with_existing_path), \ + pytest.raises(SystemExit) as exit_info: + _validate_locally( + str(source), None, autoadd={}, validation=True, + validate_local_only=True, exit_immediately_on_errors=True, + noprogress=True, noanalyze=True, transform_protected_donor=True, + transformed_workbook_path=str(destination), + ) + + assert exit_info.value.code == 0 + assert openpyxl.load_workbook(destination)["Demographic"]["A2"].value == ( + "D_PROTECTED-DONOR_1" + ) + + +def test_protected_donor_remote_payload_contains_mapped_data(tmp_path): + source = make_workbook( + tmp_path / "source.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + workbook = openpyxl.load_workbook(source) + quality_metrics = workbook.create_sheet("ExternalQualityMetric") + quality_metrics.append(["submitted_id", "total_raw_reads_sequenced"]) + quality_metrics.append(["EQM_1", 123]) + workbook.save(source) + + transformed_path = tmp_path / "source.transformed.xlsx" + structured_data = _ensure_protected_donor_transformed_workbook( + str(source), None, str(transformed_path) + ) + upload_path = _pre_transform_to_temp_json(str(source), structured_data) + try: + portal = Mock() + portal.server = "https://example.test" + created = Mock() + created.json.return_value = {"@graph": [{"@id": "/ingestion-submissions/1"}]} + initiated = Mock() + initiated.json.return_value = {"submission_id": "submission-1"} + portal.post.side_effect = [created, initiated] + _initiate_server_ingestion_process( + portal=portal, + ingestion_filename=str(transformed_path), + upload_filename=upload_path, + consortia=[], + submission_centers=[], + ) + uploaded = portal.post.call_args_list[1].kwargs["files"]["datafile"] + payload = json.loads(uploaded.read().decode("utf-8")) + uploaded.close() + finally: + if upload_path: + Path(upload_path).unlink(missing_ok=True) + + assert payload["Demographic"][0]["donor"] == "D_PROTECTED-DONOR_1" + assert payload["ExternalQualityMetric"][0]["qc_values"] == [{ + "derived_from": "total_raw_reads_sequenced", + "value": 123, + "key": "Total Raw Reads Sequenced", + "tooltip": "# of reads (150bp)", + }] + assert openpyxl.load_workbook(transformed_path)["Demographic"]["A2"].value == "D_PROTECTED-DONOR_1" + + +def test_formula_cached_donor_reference_is_used_without_evaluation(tmp_path): + source = make_workbook( + tmp_path / "formula.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + add_formula_cached_value(source, value="D_DONOR_1") + + analysis = _analyze_protected_donor_workbook(source, None) + assert analysis.needs_transformation + destination = tmp_path / "formula.transformed.xlsx" + structured_data = _ensure_protected_donor_transformed_workbook( + str(source), None, str(destination) + ) + assert structured_data.data["Demographic"][0]["donor"] == "D_PROTECTED-DONOR_1" + assert ( + openpyxl.load_workbook(destination, data_only=True)["Demographic"]["A2"].value + == "D_PROTECTED-DONOR_1" + ) + + +@pytest.mark.parametrize( + "cached_value, message", + [(None, "no valid cached value"), ("not-a-donor", "invalid cached value")], +) +def test_formula_donor_reference_requires_a_valid_cached_value(tmp_path, cached_value, message): + source = make_workbook( + tmp_path / "formula.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + add_formula_cached_value(source, value=cached_value) + + with pytest.raises(ProtectedDonorTransformError, match=message): + _analyze_protected_donor_workbook(source, None) + + +def test_existing_transformed_workbook_is_preserved_until_successful_replacement(tmp_path): + source = make_workbook( + tmp_path / "source.xlsx", + donor_rows=[["D_DONOR_1", "one", "active"]], + references={"Demographic": ["D_DONOR_1"]}, + ) + destination = tmp_path / "source.transformed.xlsx" + destination.write_bytes(b"previous transformed workbook") + previous = destination.read_bytes() + + _prepare_protected_donor_transform( + portal=None, ingestion_filename=str(source), submission_centers=None, + validation=False, no_query=False, transform_protected_donor=True, + transformed_workbook_path=str(destination), + ) + assert destination.read_bytes() == previous + + _ensure_protected_donor_transformed_workbook(str(source), None, str(destination)) + assert destination.read_bytes() != previous + assert openpyxl.load_workbook(destination)["Demographic"]["A2"].value == "D_PROTECTED-DONOR_1" + + +def test_failed_protected_donor_load_preserves_existing_target_and_has_cause(tmp_path): + source = tmp_path / "malformed.xlsx" + source.write_bytes(b"not an xlsx workbook") + destination = tmp_path / "malformed.transformed.xlsx" + previous = b"previous transformed workbook" + destination.write_bytes(previous) + + with pytest.raises(ProtectedDonorTransformError, match="Unable to load ProtectedDonor workbook") as error: + _prepare_protected_donor_transform( + portal=None, ingestion_filename=str(source), submission_centers=None, + validation=False, no_query=False, transform_protected_donor=True, + transformed_workbook_path=str(destination), + ) + + assert error.value.__cause__ is not None + assert destination.read_bytes() == previous + + +@pytest.mark.parametrize( + "mode", + ["validate_local_only", "validate_remote_only", "validate_local_skip"], +) +def test_malformed_workbook_fails_before_each_validation_mode(tmp_path, mode): + source = tmp_path / "malformed.xlsx" + source.write_bytes(b"not an xlsx workbook") + portal = Mock() + portal.ping.return_value = True + portal.app = APP_FOURFRONT + portal.server = "https://example.test" + + with patch("submitr.submission._define_portal", return_value=portal), \ + patch("submitr.submission._get_user_record", return_value={}), \ + patch("submitr.submission._resolve_app_args", return_value={ + "submission_centers": [], "consortia": [], + }), \ + patch("submitr.submission._do_app_arg_defaulting", return_value=True), \ + patch("submitr.submission._get_submission_centers", return_value=[]), \ + patch("submitr.submission._is_admin_user", return_value=False), \ + patch("submitr.submission.get_metadata_bundles_bucket_from_health_path", return_value="bucket"): + with pytest.raises(ProtectedDonorTransformError, match="Unable to load ProtectedDonor workbook") as error: + submit_any_ingestion( + ingestion_filename=str(source), + ingestion_type="metadata_bundle", + server="https://example.test", + env="test", + app=APP_FOURFRONT, + noversion=True, + no_query=True, + **{mode: True}, + ) + + assert error.value.__cause__ is not None diff --git a/submitr/tests/test_submission.py b/submitr/tests/test_submission.py index 0eef924b22..485304da08 100644 --- a/submitr/tests/test_submission.py +++ b/submitr/tests/test_submission.py @@ -858,6 +858,95 @@ def wrapped_submit_any_ingestion(*args, **kwargs): pass # in this case, it also means pass the test +def _run_protected_donor_messaging_flow(*, submission, transform_protected_donor): + portal = mock.Mock() + portal.app = APP_FOURFRONT + portal.server = SOME_SERVER + portal.key_pair = SOME_AUTH + portal.keys_file = None + portal.ping.return_value = True + + output = mock.Mock() + prompt = mock.Mock(return_value=False) + call_kwargs = dict( + ingestion_filename="/tmp/input.xlsx", + ingestion_type=SOME_INGESTION_TYPE, + server=SOME_SERVER, + env=SOME_ENV, + app=APP_FOURFRONT, + noversion=True, + transform_protected_donor=transform_protected_donor, + ) + if submission: + call_kwargs.update(submit=True, validate_local_skip=True, validate_remote_skip=True) + else: + call_kwargs.update(validate_local_only=True) + + with mock.patch.object(submission_module, "PRINT", output), \ + mock.patch.object(submission_module, "_define_portal", return_value=portal), \ + mock.patch.object(submission_module, "_get_user_record", return_value={}), \ + mock.patch.object( + submission_module, "_resolve_app_args", + return_value={"submission_centers": [], "consortia": []}, + ), \ + mock.patch.object(submission_module, "_do_app_arg_defaulting", return_value=True), \ + mock.patch.object(submission_module, "_get_submission_centers", return_value=[]), \ + mock.patch.object(submission_module, "_is_admin_user", return_value=False), \ + mock.patch.object( + submission_module, "get_metadata_bundles_bucket_from_health_path", + return_value="metadata-bundles", + ), \ + mock.patch.object( + submission_module, "_prepare_protected_donor_transform", + return_value=( + transform_protected_donor, + "/tmp/input.transformed.xlsx" if transform_protected_donor else None, + ), + ), \ + mock.patch.object(submission_module, "_validate_locally", return_value=mock.Mock()), \ + mock.patch.object(submission_module, "_ensure_protected_donor_transformed_workbook"), \ + mock.patch.object(submission_module, "SHOW"), \ + mock.patch.object(submission_module, "yes_or_no", prompt): + if submission: + with pytest.raises(SystemExit): + submit_any_ingestion(**call_kwargs) + else: + submit_any_ingestion(**call_kwargs) + + return [str(call.args[0]) for call in output.call_args_list], prompt + + +def test_protected_donor_messages_follow_metadata_for_validation_and_submission(): + for submission in (False, True): + messages, prompt = _run_protected_donor_messaging_flow( + submission=submission, transform_protected_donor=True + ) + metadata = next(i for i, message in enumerate(messages) if message.startswith("Metadata file to ")) + occurring = next(i for i, message in enumerate(messages) if "transformation is occurring" in message) + transformed = next( + i for i, message in enumerate(messages) + if message.startswith("ProtectedDonor transformed workbook:") + ) + assert metadata < occurring < transformed + assert sum(message.startswith("ProtectedDonor transformed workbook:") for message in messages) == 1 + assert not any(message.startswith("Transformed workbook path:") for message in messages) + if submission: + prompt.assert_called_once_with( + "ProtectedDonor transformation has occurred - Do you still wish to continue?" + ) + else: + prompt.assert_not_called() + + +def test_untransformed_submission_keeps_existing_confirmation_prompt_and_output(): + messages, prompt = _run_protected_donor_messaging_flow( + submission=True, transform_protected_donor=False + ) + assert any(message.startswith("Metadata file to ingest:") for message in messages) + assert not any("ProtectedDonor" in message for message in messages) + prompt.assert_called_once_with("Continue on with the actual submission?") + + def test_get_defaulted_lab(): assert _get_defaulted_lab(lab=SOME_LAB, user_record="does-not-matter") == SOME_LAB diff --git a/submitr/tests/test_submit_metadata_bundle.py b/submitr/tests/test_submit_metadata_bundle.py index 97a9570bde..54eeff70ac 100644 --- a/submitr/tests/test_submit_metadata_bundle.py +++ b/submitr/tests/test_submit_metadata_bundle.py @@ -69,6 +69,8 @@ def test_it(args_in, expect_exit_code, expect_called, expect_call_args=None): "debug": False, "debug_sleep": False, "skip_validators": None, + "transform_protected_donor": expect_call_args.get("transform_protected_donor", True), + "transformed_workbook_path": expect_call_args.get("transformed_workbook_path"), } mock_submit_any_ingestion.assert_called_with(**expect_call_args) assert output == [] @@ -87,6 +89,35 @@ def test_it(args_in, expect_exit_code, expect_called, expect_call_args=None): 'no_query': False, 'subfolders': False, }) + test_it(args_in=["--no-transform-protected-donor", some_file], + expect_exit_code=0, + expect_called=True, + expect_call_args={ + 'ingestion_filename': some_file, + 'ingestion_type': DEFAULT_INGESTION_TYPE, + 'env': None, + 'server': None, + 'validate_remote_only': False, + 'upload_folder': None, + 'no_query': False, + 'subfolders': False, + 'transform_protected_donor': False, + }) + transformed_workbook = some_file + ".transformed.xlsx" + test_it(args_in=["--save-transformed-workbook", transformed_workbook, some_file], + expect_exit_code=0, + expect_called=True, + expect_call_args={ + 'ingestion_filename': some_file, + 'ingestion_type': DEFAULT_INGESTION_TYPE, + 'env': None, + 'server': None, + 'validate_remote_only': False, + 'upload_folder': None, + 'no_query': False, + 'subfolders': False, + 'transformed_workbook_path': transformed_workbook, + }) expect_call_args = { 'ingestion_filename': some_file, 'ingestion_type': DEFAULT_INGESTION_TYPE, @@ -199,6 +230,11 @@ def test_it(args_in, expect_exit_code, expect_called, expect_call_args=None): expect_call_args=expect_call_args) +def test_compatibility_transform_flag_is_hidden_from_documented_help(): + assert "--no-transform-protected-donor" not in submit_metadata_bundle_module._HELP + assert "--no-transform-protected-donor" not in submit_metadata_bundle_module._HELP_ADVANCED + + def _create_some_temporary_file() -> str: some_file = tempfile.NamedTemporaryFile(delete=False) try: