From c9ea043919834d00610d34e8dbe39ea00b8dba53 Mon Sep 17 00:00:00 2001 From: ozgury Date: Thu, 21 Nov 2024 22:38:28 +0000 Subject: [PATCH] refactor: upload submission refactor and create study utility method --- .../submission/submission_download.py | 6 +- .../commands/submission/submission_upload.py | 74 +- .../provider/ftp/default_ftp_client.py | 27 +- .../provider/submission_model.py | 8 + .../provider/submission_repository.py | 258 ++++++- poetry.lock | 683 +++++++++--------- .../provider/test_submission_provider.py | 25 +- 7 files changed, 671 insertions(+), 410 deletions(-) diff --git a/metabolights_utils/commands/submission/submission_download.py b/metabolights_utils/commands/submission/submission_download.py index 5676ad8..d35e9bd 100644 --- a/metabolights_utils/commands/submission/submission_download.py +++ b/metabolights_utils/commands/submission/submission_download.py @@ -65,7 +65,7 @@ def submission_download( study_id: MetaboLights study accession number (MTBLSxxxx). - files (optional): files will be donwloaded. If not specified, downloads all ISA metadata files. + files (optional): files will be downloaded. If not specified, downloads all ISA metadata files. """ study_id = study_id.upper().strip() client = MetabolightsSubmissionRepository( @@ -83,7 +83,3 @@ def submission_download( click.echo(f"Download submission study {study_id} on {study_path} status:") for item in result.actions: click.echo(f" {result.actions[item]}\t{item}") - - -if __name__ == "__main__": - submission_download(["MTBLS5397"]) diff --git a/metabolights_utils/commands/submission/submission_upload.py b/metabolights_utils/commands/submission/submission_upload.py index 7870ccc..316d387 100644 --- a/metabolights_utils/commands/submission/submission_upload.py +++ b/metabolights_utils/commands/submission/submission_upload.py @@ -1,4 +1,4 @@ -from typing import Union +from typing import List, Union import click @@ -40,24 +40,30 @@ default=definitions.default_local_submission_credentials_file_path, help="Path to store cache files of study submission file indices, study models, etc.", ) +@click.option( + "--user_api_token", + "-a", + help="MetaboLights user API token.", +) @click.argument("study_id") @click.argument("metadata_files", required=False) def submission_upload( study_id: str = "", - metadata_files: str = "", + metadata_files: Union[List[str], None] = None, use_only_local: bool = False, local_path: Union[None, str] = None, local_cache_path: Union[None, str] = None, rest_api_base_url: Union[None, str] = None, override_remote_files: bool = False, credentials_file_path: str = "", + user_api_token: Union[str, None] = None, ): """ - Uploads local metadata files to private FTP and start sync task to update study folder. + Uploads local files to private FTP and start sync task to update study folder. - study_id: MetaboLights study accession number (MTBLSxxxx). + study_id: MetaboLights study accession number / submission id (MTBLSxxxx or REQXXXX). - files (optional): files will be donwloaded. If not specified, downloads all ISA metadata files. + files (optional): files will be downloaded. If not specified, downloads all ISA metadata files. """ study_id = study_id.upper().strip() client = MetabolightsSubmissionRepository( @@ -66,26 +72,66 @@ def submission_upload( rest_api_base_url=rest_api_base_url, credentials_file_path=credentials_file_path, ) + ftp_details, error = client.get_ftp_upload_details( + study_id=study_id, + user_api_token=user_api_token, + rest_api_base_url=rest_api_base_url, + ) + if not ftp_details: + click.echo(f"Upload private ftp details for {study_id}: Failed {str(error)}") + exit(1) success, message = client.upload_metadata_files( study_id=study_id, override_remote_files=override_remote_files, - metadata_files=None, + metadata_files=metadata_files, + ftp_server_url=ftp_details.ftp_host, + ftp_username=ftp_details.ftp_user, + ftp_password=ftp_details.ftp_password, + user_api_token=user_api_token, ) if success: click.echo(f"Upload private study {study_id} metadata files: Success") click.echo(message) - + else: + click.echo(f"Upload private study {study_id} metadata files: Failed {message}") + exit(1) + success, message = client.upload_data_files( + study_id=study_id, + local_path=local_path, + remote_folder_directory=ftp_details.ftp_folder, + ftp_server_url=ftp_details.ftp_host, + ftp_username=ftp_details.ftp_user, + ftp_password=ftp_details.ftp_password, + ) + if success: + click.echo(f"Upload private study {study_id} data files: Success") + click.echo(message) + click.echo(f"Sync private FTP metadata files for {study_id}.") success, error = client.sync_private_ftp_metadata_files( - study_id=study_id, pool_period=10, retry=10 + study_id=study_id, pool_period=10, retry=10, user_api_token=user_api_token ) if success: - click.echo(f"Sync private study {study_id} folder: Success") + click.echo(f"Success: Sync private FTP metadata files for {study_id}.") + click.echo(f"Sync private FTP data files for {study_id}.") + success, error = client.sync_private_ftp_data_files( + study_id=study_id, + pool_period=10, + retry=10, + user_api_token=user_api_token, + ) + if success: + click.echo( + f"Sync private study date files for {study_id} folder: Success" + ) + else: + click.echo( + f"Failure: Sync private study metadata files for {study_id}: {error}" + ) + else: - click.echo(f"Failure: Sync private study {study_id} folder: {error}") + click.echo( + f"Failure: Sync private study metadata files for {study_id}. {error}" + ) else: click.echo(f"Upload private study {study_id}: {message}") - - -if __name__ == "__main__": - submission_upload(["MTBLS5397"]) diff --git a/metabolights_utils/provider/ftp/default_ftp_client.py b/metabolights_utils/provider/ftp/default_ftp_client.py index 542349b..4989cf6 100644 --- a/metabolights_utils/provider/ftp/default_ftp_client.py +++ b/metabolights_utils/provider/ftp/default_ftp_client.py @@ -23,7 +23,9 @@ def __init__( password: Union[str, None] = None, ) -> None: self.ftp_server_url = ftp_server_url - self.remote_repository_root_directory = remote_repository_root_directory.replace("\\","").rstrip("/") + self.remote_repository_root_directory = ( + remote_repository_root_directory.replace("\\", "").rstrip("/") + ) self.local_storage_root_path = local_storage_root_path self.username = username if username else "" self.password = password if password else "" @@ -75,7 +77,7 @@ def list_directory( directory: Union[str, None] = None, search_pattern: Union[str, None] = None, ) -> FtpFolderContent: - directory = directory.replace("\\", '/').strip("/") if directory else "" + directory = directory.replace("\\", "/").strip("/") if directory else "" root_dir = self.remote_repository_root_directory remote_directory = f"{root_dir}/{directory}" @@ -118,8 +120,11 @@ def upload_files( with open(file_path, "rb") as file: self.ftp.storbinary(f"STOR {filename}", file) + return True, "" except Exception as ex: - logger.error("FTP directory %s upload error: %s", remote_directory, str(ex)) + message = f"FTP directory {remote_directory} upload error: {str(ex)}" + logger.error(message) + return False, message finally: self.quit() @@ -161,7 +166,9 @@ def download_file( remote_directory = f"{remote_root_dir}/{relative_file_path}".replace("\\", "/") relative_parent_path = os.path.dirname(relative_file_path) - remote_parent_directory = os.path.dirname(os.path.join(remote_root_dir, relative_file_path)) + remote_parent_directory = os.path.dirname( + os.path.join(remote_root_dir, relative_file_path) + ) remote_parent_directory = remote_parent_directory.replace("\\", "/") logger.debug("List files within %s on FTP server ", relative_parent_path) result = self.list_directory(relative_parent_path, search_pattern=filename) @@ -219,9 +226,11 @@ def download_file( for item in local_file_list: if item not in listed_folders and item not in listed_files: item_path: str = os.path.join(target_path, item) - relative_item_path = item_path.replace( - f"{local_path}", "" - ).strip("/").strip("\\") + relative_item_path = ( + item_path.replace(f"{local_path}", "") + .strip("/") + .strip("\\") + ) if keep_local_files and item in keep_local_files: actions[relative_item_path] = "SKIPPED" logger.debug( @@ -243,7 +252,9 @@ def download_file( response.local_folders.append(relative_file_path) for collection in (result.folders, result.files): for entry in collection: - new_relative_file_path = join_path(relative_file_path, entry).replace("\\", "/") + new_relative_file_path = join_path( + relative_file_path, entry + ).replace("\\", "/") self.download_file( relative_file_path=new_relative_file_path, local_path=local_path, diff --git a/metabolights_utils/provider/submission_model.py b/metabolights_utils/provider/submission_model.py index 366d6f6..f9b2c1a 100644 --- a/metabolights_utils/provider/submission_model.py +++ b/metabolights_utils/provider/submission_model.py @@ -199,3 +199,11 @@ class PolicyResultResponse(WorkerTaskStatus): description="This field contains task id of the task.", ), ] = PolicySummaryResult() + + +class FtpUploadDetails(BaseModel): + study_id: str + ftp_folder: str + ftp_host: str + ftp_user: str + ftp_password: str diff --git a/metabolights_utils/provider/submission_repository.py b/metabolights_utils/provider/submission_repository.py index 2cd5bf0..ed34a71 100644 --- a/metabolights_utils/provider/submission_repository.py +++ b/metabolights_utils/provider/submission_repository.py @@ -1,9 +1,10 @@ import datetime +import glob import io import json import os import time -from typing import List, Tuple, Union +from typing import List, Literal, Tuple, Union import httpx @@ -41,9 +42,8 @@ ) from metabolights_utils.provider.submission_model import ( APIResponse, - PolicyMessage, + FtpUploadDetails, PolicyResultResponse, - PolicySummaryResult, ValidationMessage, ValidationReport, ValidationResponse, @@ -196,21 +196,23 @@ def upload_metadata_files( study_id, remote_folder_directory: Union[str, None] = None, local_path: Union[str, None] = None, - credentials_file_path: Union[str, None] = None, ftp_server_url: Union[str, None] = None, metadata_files: Union[List[str], None] = None, override_remote_files: bool = False, + ftp_username: Union[str, None] = None, + ftp_password: Union[str, None] = None, + user_api_token: Union[str, None] = None, ) -> Tuple[bool, str]: if not local_path: local_path = self.local_storage_root_path local_path = join_path(local_path) - if not credentials_file_path: - credentials_file_path = self.credentials_file_path - credentials_file_path = join_path(credentials_file_path) + if not ftp_server_url: ftp_server_url = self.ftp_server_url - response, errors = self.list_isa_metadata_files(study_id=study_id) + response, errors = self.list_isa_metadata_files( + study_id=study_id, user_api_token=user_api_token + ) if not response: return False, "Errors while listing metadata files." if not remote_folder_directory: @@ -257,24 +259,66 @@ def upload_metadata_files( False, "There is no metadata file to upload or local metadata files are up-to-date.", ) - username, password, error = self.get_ftp_credentials() - if not error: - ftp_client = DefaultFtpClient( - local_storage_root_path=local_path, - ftp_server_url=ftp_server_url, - remote_repository_root_directory="", - username=username, - password=password, + if not ftp_password or not ftp_username: + ftp_username, ftp_password, error = self.get_ftp_credentials() + + ftp_client = DefaultFtpClient( + local_storage_root_path=local_path, + ftp_server_url=ftp_server_url, + remote_repository_root_directory="", + username=ftp_username, + password=ftp_password, + ) + input_files = [os.path.join(study_path, x) for x in new_requested_files] + try: + success, message = ftp_client.upload_files( + remote_folder_directory, input_files ) - input_files = [os.path.join(study_path, x) for x in new_requested_files] - try: - ftp_client.upload_files(remote_folder_directory, input_files) + if success: + return success, "Uploaded Files: " + ", ".join(new_requested_files) + else: + return success, message + except Exception as ex: + return False, str(ex) - return True, "Uploaded Files: " + ", ".join(new_requested_files) - except Exception as ex: - return False, str(ex) - else: - return False, error + def upload_data_files( + self, + study_id, + local_path: Union[str, None] = None, + remote_folder_directory: Union[str, None] = None, + ftp_server_url: Union[str, None] = None, + ftp_username: Union[str, None] = None, + ftp_password: Union[str, None] = None, + ) -> Tuple[bool, str]: + if not local_path: + local_path = self.local_storage_root_path + local_study_path = join_path(local_path, study_id) + if not ftp_server_url: + ftp_server_url = self.ftp_server_url + + study_path = os.path.realpath(local_study_path) + if not os.path.exists(study_path): + return False, f"Study path does not exist: {study_path}" + + files = glob.iglob(f"{study_path}/**/*", recursive=True) + + input_files = [ + x for x in files if not is_metadata_filename_pattern(os.path.basename(x)) + ] + + # username, password, error = self.get_ftp_credentials() + ftp_client = DefaultFtpClient( + local_storage_root_path=local_path, + ftp_server_url=ftp_server_url, + remote_repository_root_directory="", + username=ftp_username, + password=ftp_password, + ) + try: + ftp_client.upload_files(remote_folder_directory, input_files) + return True, "Uploaded Files: " + ", ".join(input_files) + except Exception as ex: + return False, str(ex) def check_api_response(self, api_name, response): if not response: @@ -289,6 +333,45 @@ def check_api_response(self, api_name, response): f"Failure of {api_name} {code}: {text}", ) + def get_ftp_upload_details( + self, + study_id, + rest_api_base_url: Union[str, None] = None, + user_api_token: Union[str, None] = None, + timeout: int = 5, + ) -> Tuple[Union[None, FtpUploadDetails], str]: + + headers = {} + if not user_api_token: + user_api_token, error = self.get_api_token() + if not user_api_token: + return None, error + sub_path = f"/studies/{study_id}/upload-info" + headers["User-Token"] = user_api_token + + api_name = "get private ftp upload details" + rest_api_base_url = ( + rest_api_base_url if rest_api_base_url else self.rest_api_base_url + ) + try: + url = f"{rest_api_base_url.rstrip('/')}/{sub_path.lstrip('/')}" + parameters = {} + response = httpx.get( + url=url, + timeout=timeout, + headers=headers, + params=parameters, + ) + success, error = self.check_api_response(api_name, response) + if not success: + return None, error + + data = json.loads(response.text) + details = FtpUploadDetails.model_validate(data, from_attributes=True) + return details, "" + except Exception as ex: + return None, f"Validation task start failure: {str(ex)}." + def validate_study( self, study_id, @@ -431,7 +514,9 @@ def validate_study_v2( pool_period: int = 5, retry: int = 20, timeout: int = 30, - api_token: str = None, + validation_api_base_url: Union[None, str] = None, + rest_api_base_url: Union[None, str] = None, + api_token: Union[None, str] = None, ): sub_path = f"/study-model/validation" @@ -457,8 +542,12 @@ def validate_study_v2( api_header, error = self.get_api_token() api_name = "validation v2 get jwt token" jwt_token = None + rest_api_base_url = ( + rest_api_base_url if rest_api_base_url else self.rest_api_base_url + ) + try: - url = f"{self.rest_api_base_url.rstrip('/')}/{auth_sub_path.lstrip('/')}" + url = f"{rest_api_base_url.rstrip('/')}/{auth_sub_path.lstrip('/')}" parameters = {} response = httpx.post( url=url, @@ -488,8 +577,13 @@ def validate_study_v2( headers["Authorization"] = f"Bearer {jwt_token}" task_id = None api_name = "validation v2 task start" + validation_api_base_url = ( + validation_api_base_url + if validation_api_base_url + else self.validation_api_base_url + ) try: - url = f"{self.validation_api_base_url.rstrip('/')}/{sub_path.lstrip('/')}" + url = f"{validation_api_base_url.rstrip('/')}/{sub_path.lstrip('/')}" parameters = {} response = httpx.post( url=url, @@ -554,19 +648,58 @@ def validate_study_v2( return True, task_status_response.content.task_id def sync_private_ftp_metadata_files( - self, study_id: str, pool_period: int = 10, retry: int = 10, timeout: int = 10 + self, + study_id: str, + pool_period: int = 10, + retry: int = 10, + timeout: int = 10, + user_api_token: Union[None, str] = None, + ): + return self.sync_from_private_ftp( + study_id, + "metadata", + pool_period, + retry, + timeout, + user_api_token=user_api_token, + ) + + def sync_private_ftp_data_files( + self, + study_id: str, + pool_period: int = 10, + retry: int = 1000, + timeout: int = 10, + user_api_token: Union[None, str] = None, + ): + return self.sync_from_private_ftp( + study_id, "data", pool_period, retry, timeout, user_api_token=user_api_token + ) + + def sync_from_private_ftp( + self, + study_id: str, + sync_type: Literal["metadata", "data"] = "metadata", + pool_period: int = 10, + retry: int = 10, + timeout: int = 10, + user_api_token: Union[None, str] = None, ): sub_path = f"/studies/{study_id}/study-folders/rsync-task" - api_header, error = self.get_api_token() + if not user_api_token: + user_api_token, error = self.get_api_token() headers = {} - if api_header: - headers["User-Token"] = api_header + if user_api_token: + headers["User-Token"] = user_api_token else: return None, error headers["Dry-Run"] = "false" - headers["Sync-Type"] = "metadata" + headers["Sync-Type"] = sync_type headers["Source-Staging-Area"] = "private-ftp" - headers["Target-Staging-Area"] = "rw-study" + if sync_type == "metadata": + headers["Target-Staging-Area"] = "rw-study" + else: + headers["Target-Staging-Area"] = "readonly-study" url = f"{self.rest_api_base_url.rstrip('/')}/{sub_path.lstrip('/')}" parameters = {} @@ -601,8 +734,44 @@ def sync_private_ftp_metadata_files( return True, status elif "FAIL" in status: return False, status + return False, "No result" + else: + return False, "Response does not have a task id" else: - return False, response.text if response else None + return ( + (False, response.text) + if response + else (False, f"Response code: {str(response.status_code)}") + ) + + def create_submission( + self, + user_api_token: Union[None, str] = None, + timeout: int = 30, + ) -> Tuple[Union[None, str], Union[None, str]]: + if not user_api_token: + user_api_token, error = self.get_api_token() + headers = {} + if user_api_token: + headers["User-Token"] = user_api_token + else: + return None, error + + sub_path = f"/studies/create" + url = f"{self.rest_api_base_url.rstrip('/')}/{sub_path.lstrip('/')}" + + try: + response = httpx.get(url=url, timeout=timeout, headers=headers, params={}) + if response and response.status_code in (200, 201): + data = json.loads(response.text) + if "new_study" in data: + return data["new_study"], "" + + return None, "Invalid response." + else: + return None, response.text if response else "Invalid response." + except Exception as ex: + return None, str(ex) def create_assay( self, @@ -825,10 +994,14 @@ def download_submission_metadata_files( return response def list_isa_metadata_files( - self, study_id: str + self, + study_id: str, + user_api_token: Union[str, None] = None, ) -> Tuple[Union[StudyResponse, None], Union[None, str]]: - response, error = self.list_study_directory(study_id=study_id) + response, error = self.list_study_directory( + study_id=study_id, user_api_token=user_api_token + ) if response: response.study = [ x for x in response.study if is_metadata_filename_pattern(x.file) @@ -901,13 +1074,18 @@ def get_ftp_credentials(self): return (result.user_name, result.password, None) def list_study_directory( - self, study_id: str, subdirectory: Union[str, None] = None, timeout=None + self, + study_id: str, + subdirectory: Union[str, None] = None, + timeout=None, + user_api_token: Union[str, None] = None, ) -> Tuple[Union[None, StudyResponse], Union[None, str]]: study_id = study_id.upper().strip("/") if study_id else "" - api_header, error = self.get_api_token() + if not user_api_token: + user_api_token, error = self.get_api_token() headers = {} - if api_header: - headers["User-Token"] = api_header + if user_api_token: + headers["User-Token"] = user_api_token else: return None, error diff --git a/poetry.lock b/poetry.lock index f95bb46..eb4d540 100644 --- a/poetry.lock +++ b/poetry.lock @@ -16,13 +16,13 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} [[package]] name = "anyio" -version = "4.5.0" +version = "4.5.2" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.5.0-py3-none-any.whl", hash = "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"}, - {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"}, + {file = "anyio-4.5.2-py3-none-any.whl", hash = "sha256:c011ee36bc1e8ba40e5a81cb9df91925c218fe9b778554e0b56a21e1b5d4716f"}, + {file = "anyio-4.5.2.tar.gz", hash = "sha256:23009af4ed04ce05991845451e11ef02fc7c5ed29179ac9a420e5ad0ac7ddc5b"}, ] [package.dependencies] @@ -33,7 +33,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"] trio = ["trio (>=0.26.1)"] [[package]] @@ -560,37 +560,37 @@ toml = ["tomli"] [[package]] name = "debugpy" -version = "1.8.7" +version = "1.8.9" description = "An implementation of the Debug Adapter Protocol for Python" optional = false python-versions = ">=3.8" files = [ - 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a/tests/metabolights_utils/provider/test_submission_provider.py +++ b/tests/metabolights_utils/provider/test_submission_provider.py @@ -445,7 +445,8 @@ class HttpxResponse(BaseModel): return_value=HttpxResponse( status_code=201, text=open( - "tests/test-data/rest-api-test-data/validation_task_started_response.json", encoding="utf-8" + "tests/test-data/rest-api-test-data/validation_task_started_response.json", + encoding="utf-8", ).read(), ), ) @@ -455,13 +456,15 @@ class HttpxResponse(BaseModel): HttpxResponse( status_code=200, text=open( - "tests/test-data/rest-api-test-data/validation_task_success_response.json", encoding="utf-8" + "tests/test-data/rest-api-test-data/validation_task_success_response.json", + encoding="utf-8", ).read(), ), HttpxResponse( status_code=200, text=open( - "tests/test-data/rest-api-test-data/validation_report.json", encoding="utf-8" + "tests/test-data/rest-api-test-data/validation_report.json", + encoding="utf-8", ).read(), ), ], @@ -469,9 +472,7 @@ class HttpxResponse(BaseModel): repository, credentials = submission_repository - validation_file_path = ( - f"test-temp/mtbls_unit_test_validation_{random.randint(1000000, 9999999)}_tmp.json" - ) + validation_file_path = f"test-temp/mtbls_unit_test_validation_{random.randint(1000000, 9999999)}_tmp.json" try: success, message = repository.validate_study( study_id=study_id, @@ -484,7 +485,11 @@ class HttpxResponse(BaseModel): @pytest.mark.parametrize("study_id", ["MTBLS1"]) -def test_private_ftp_sync_01(mocker: MockerFixture, submission_repository, study_id): +def test_private_ftp_sync_01( + mocker: MockerFixture, + submission_repository: Tuple[MetabolightsSubmissionRepository, Dict[str, Any]], + study_id, +): """ Test private ftp sync (without error) """ @@ -501,7 +506,8 @@ class HttpxResponse(BaseModel): get_response = HttpxResponse( status_code=201, text=open( - "tests/test-data/rest-api-test-data/ftp_sync_task_started_response.json", encoding="utf-8" + "tests/test-data/rest-api-test-data/ftp_sync_task_started_response.json", + encoding="utf-8", ).read(), ) mocker.patch( @@ -514,7 +520,8 @@ class HttpxResponse(BaseModel): return_value=HttpxResponse( status_code=200, text=open( - "tests/test-data/rest-api-test-data/ftp_sync_task_success_response.json", encoding="utf-8" + "tests/test-data/rest-api-test-data/ftp_sync_task_success_response.json", + encoding="utf-8", ).read(), ), )