diff --git a/.gitignore b/.gitignore index 68bc17f..409d158 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +*.DS_Store +*.vscode +.idea # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] @@ -27,8 +30,6 @@ share/python-wheels/ MANIFEST # PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec @@ -83,31 +84,7 @@ profile_default/ ipython_config.py # pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -#pdm.lock -# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it -# in version control. -# https://pdm.fming.dev/#use-with-ide -.pdm.toml +.python-version # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm __pypackages__/ @@ -152,9 +129,4 @@ dmypy.json # Cython debug symbols cython_debug/ -# PyCharm -# JetBrains specific template is maintained in a separate JetBrains.gitignore that can -# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore -# and can be added to the global gitignore or merged into this file. For a more nuclear -# option (not recommended) you can uncomment the following to ignore the entire idea folder. -#.idea/ +# pytest output diff --git a/README.md b/README.md index 48c8aa6..1356911 100644 --- a/README.md +++ b/README.md @@ -1 +1,40 @@ -# heal-platform-sdk \ No newline at end of file +# heal-platform-sdk + +The HEAL Platform Software Development Kit (SDK) for Python provides classes and functions for handling HEAL specific tasks. + +### qdr_downloads + +The qdr_downloads module include a retriever function for downloading files from Syracuse QDR. + +This is intended to be called by gen3sdk [external download functions](https://github.com/uc-cdis/gen3sdk-python/blob/master/gen3/tools/download/external_file_download.py). It is also possible to write a wrapper script for the qdr download functions. + +### Run tests + +``` +poetry run pytest -vv tests +``` + +### Pip install for using heal-platform-sdk + +Until the `heal-platform-sdk` is available on PyPI, any local pip installs should directly +reference the git repo. + +As an example, `pip install` can be called from the command line for getting +the master branch of the `heal-platform-sdk`, + +``` +pip install -e git+ssh://git@github.com/uc-cdis/heal-platform-sdk.git#egg=heal +``` + +or a particular branch, eg, + +``` +pip install -e git+ssh://git@github.com/uc-cdis/heal-platform-sdk.git@feat/add-syracuse-qdr-retriever#egg=heal +``` + +The specification can also be listed in requirements.txt file +(with, say, a tag specification of 0.1.0) + +``` +-e git+ssh://git@github.com/uc-cdis/heal-platform-sdk.git@0.1.0#egg=heal +``` diff --git a/heal/__init__.py b/heal/__init__.py new file mode 100644 index 0000000..8d0fd2b --- /dev/null +++ b/heal/__init__.py @@ -0,0 +1,4 @@ +from cdislogging import get_logger + +LOG_FORMAT = "[%(asctime)s][%(levelname)7s] %(message)s" +logging = get_logger("__name__", format=LOG_FORMAT, log_level="info") diff --git a/heal/qdr_downloads.py b/heal/qdr_downloads.py new file mode 100644 index 0000000..a6e980d --- /dev/null +++ b/heal/qdr_downloads.py @@ -0,0 +1,314 @@ +""" +This module includes an external file retriever function intended to be called +by the external_files_download module in the Gen3-SDK. + +The retriever function sends requests to the Syracuse QDR API for downloading studies or files. + +The QDR documentation describes how to download studies +https://guides.dataverse.org/en/latest/api/dataaccess.html#basic-download-by-dataset + +and how to download files +https://guides.dataverse.org/en/latest/api/dataaccess.html#basic-file-access + +In order to get an API token from the WTS server, users should have already +sent a request to +/oauth2/authorization_url?idp=externaldata-keycloak +and logged in to QDR after the redirect. + +The WTS-SERVER is a Gen3 commons that has been configured to return +tokens for the 'idp' specified in the external_file_metadata. +""" + +import os + +from pathlib import Path +import requests +from typing import Dict, List, Tuple +from urllib.parse import unquote +import zipfile + +from cdislogging import get_logger +from gen3.auth import Gen3Auth +from gen3.tools.download.drs_download import DownloadStatus, wts_get_token + +logger = get_logger("__name__", log_level="debug") + + +def get_syracuse_qdr_files( + wts_hostname: str, auth, file_metadata_list: List, download_path: str = "." +) -> Dict: + """ + Retrieves external data from the Syracuse QDR. + + Args: + wts_hostname (str): hostname for commons with wts + auth (Gen3Auth): auth for commons with wts + file_metadata_list (List of Dict): list of studies or files + download_path (str): path to download files and unpack + + Returns: + Dict of download status + """ + if not Path(download_path).exists(): + logger.critical(f"Download path does not exist: {download_path}") + return None + + completed = {} + logger.debug(f"Input file metadata list={file_metadata_list}") + + for file_metadata in file_metadata_list: + id = get_id(file_metadata) + if id == None: + logger.warning( + f"Could not find 'study_id' or 'file_id' in metadata {file_metadata}" + ) + continue + logger.info(f"ID = {id}") + completed[id] = DownloadStatus(filename=id, status="pending") + + download_url = get_download_url_for_qdr(file_metadata) + if download_url == None: + logger.critical(f"Could not get download_url for {id}") + completed[id].status = "invalid url" + continue + + idp_access_token = get_idp_access_token(wts_hostname, auth, file_metadata) + request_headers = get_request_headers(idp_access_token) + if "X-Dataverse-key" not in request_headers: + logger.critical("WARNING Request headers do not include 'X-Dataverse-key'.") + + logger.debug(f"Request headers = {request_headers}") + + logger.debug(f"Ready to send request to download_url: GET {download_url}") + downloaded_file = download_from_url( + qdr_url=download_url, + headers=request_headers, + download_path=download_path, + ) + if downloaded_file == None: + completed[id].status = "failed" + continue + + if downloaded_file.endswith("zip"): + # unpack if download is zip file + try: + logger.debug(f"Ready to unpack {downloaded_file}.") + unpackage_object(filepath=downloaded_file) + except Exception as e: + logger.critical(f"{id} had an issue while being unpackaged: {e}") + completed[id].status = "failed" + + completed[id].status = "downloaded" + # remove the zip file + Path(downloaded_file).unlink() + else: + completed[id].status = "downloaded" + + if completed == {}: + return None + return completed + + +def download_from_url( + qdr_url: str, + headers=None, + download_path: str = ".", +) -> str: + """ + Retrieve data file (study_id or file_id) from url. + Save the file based on the filename in the Content-Disposition response header. + + Args: + qdr_url (str): url for QDR API + headers (Dict): request headers + download_path (str): path for saving downloaded zip file + + Returns: + path to downloaded and renamed file. + """ + try: + response = requests.get(url=qdr_url, headers=headers, stream=True) + response.raise_for_status() + except requests.exceptions.Timeout: + logger.critical( + f"Was unable to get the download url: {qdr_url}. Timeout Error." + ) + return None + except requests.exceptions.HTTPError as exc: + logger.critical(f"HTTPError in download {exc}") + return None + except requests.exceptions.ConnectionError as exc: + logger.critical(f"ConnectionError in download {exc}") + return None + except Exception as exc: + logger.critical(f"Error in download {exc}") + return None + logger.debug(f"Status code={response.status_code}") + downloaded_file_name = get_filename_from_headers(response.headers) + if downloaded_file_name == None: + downloaded_file_name = qdr_url.split("/")[-1] + logger.info(f"Using file name from id in url {downloaded_file_name}") + + if downloaded_file_name.endswith( + "zip" + ) and not "application/zip" in response.headers.get("Content-Type"): + logger.critical("Response headers do not show zipfile content-type") + + total_downloaded = 0 + block_size = 8092 # 8K blocks might want to tune this. + download_filename = f"{download_path}/{downloaded_file_name}" + try: + logger.info(f"Saving download as {download_filename}") + with open(download_filename, "wb") as file: + for data in response.iter_content(block_size): + total_downloaded += len(data) + file.write(data) + except IOError as ex: + logger.critical(f"IOError opening {download_filename} for writing: {ex}") + return None + + if total_downloaded == 0: + logger.critical(f"content-length is 0 and it should not be") + return None + logger.debug(f"Download size = {total_downloaded}") + + return download_filename + + +def get_download_url_for_qdr(file_metadata: Dict) -> str: + """ + Get the download url for Syracuse QDR. + + Args: + file_metadata (Dict) + + Returns: + url, None if there are errors + """ + base_url = "https://data.qdr.syr.edu/api/access" + + if "study_id" in file_metadata: + url = f"{base_url}/dataset/:persistentId/?persistentId={file_metadata.get('study_id')}" + elif "file_id" in file_metadata: + url = f"{base_url}/datafile/{file_metadata.get('file_id')}" + else: + url = None + + return url + + +def get_filename_from_headers(headers: Dict) -> str: + """ + Parse and decode downloaded file name from response headers + + Args: + headers (dict): response headers + + Returns: + file name as string + """ + try: + file_name = None + content_response = headers.get("Content-Disposition").split(";") + for part in content_response: + # look for UTF-8 encoded file name + if part.strip().startswith("filename*="): + file_name = part.split("=", 1)[1].strip() + if file_name.lower().startswith("utf-8''"): + file_name = file_name[7:] + file_name = unquote(file_name) + break + elif part.strip().startswith("filename="): + file_name = part.split("=", 1)[1].strip().strip('"') + break + if file_name == None: + logger.info("Could not parse file name from headers") + + except Exception as e: + logger.warning("Could not get file name from headers") + + return file_name + + +def get_idp_access_token(wts_hostname: str, auth: Gen3Auth, file_metadata: Dict) -> str: + """Get an access token for QDR using a Gen3 commons WTS""" + try: + logger.debug("Ready to get auth token") + wts_access_token = auth.get_access_token() + logger.debug("Ready to get idp token") + idp = file_metadata.get("external_oidc_idp") + idp_access_token = wts_get_token( + hostname=wts_hostname, idp=idp, access_token=wts_access_token + ) + except Exception as e: + logger.critical(f"Could not get token: {e}") + return None + + return idp_access_token + + +def get_request_headers(idp_access_token: str) -> Dict: + """ + Generate the request headers. + + Args: + idp_access_token (str): QDR token is included in X-Dataverse-key header + file_metadata (Dict) + + Returns: + Dictionary of request headers + """ + headers = {} + if idp_access_token: + headers["X-Dataverse-key"] = idp_access_token + + return headers + + +def get_id(file_metadata: Dict) -> str: + """ + Parse out the object id from the metadata. + + Args: + file_metadata (Dict) + + Returns: + string + """ + id_types = ["study_id", "file_id"] + for id_type in id_types: + if id_type in file_metadata: + return file_metadata.get(id_type) + + return None + + +def is_valid_qdr_file_metadata(file_metadata: Dict) -> bool: + """ + Check that the file_metadata has the required keys: + 'study_id' or 'file_id'. + + Args: + file_metadata (Dict) + + Returns: + True if valid file_metadata object. + """ + if not isinstance(file_metadata, dict): + logger.critical(f"Invalid metadata - item is not a dict: {file_metadata}") + return False + if "study_id" not in file_metadata and "file_id" not in file_metadata: + logger.critical(f"Invalid metadata - missing required QDR keys {file_metadata}") + return False + if "study_id" in file_metadata and "file_id" in file_metadata: + logger.critical( + f"Invalid metadata - item has both 'study_id' and 'file_id': {file_metadata}" + ) + return False + return True + + +def unpackage_object(filepath: str): + """Unpackage the downloaded zip file""" + with zipfile.ZipFile(filepath, "r") as package: + 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mode 100644 index 0000000..1b5943b --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,32 @@ +[tool.poetry] +name = "heal" +version = "0.1.0" +description = "HEAL Platform SDK" +authors = ["Center for Translational Data Science at the University of Chicago "] +license = "Apache-2.0" +packages = [ + { include = "heal" }, +] + +[tool.poetry.dependencies] +python = "^3.9" +cdislogging = "^1.1.0" +gen3 = "^4.22.4" +requests = "*" + +[tool.poetry.dev-dependencies] +pytest = "^6.0.0" +pytest-cov = "*" +requests-mock = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = "-vv" +pythonpath = "heal" +testpaths = [ + "tests", +] diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/ci_commands_script.sh b/tests/ci_commands_script.sh new file mode 100644 index 0000000..c75ea89 --- /dev/null +++ b/tests/ci_commands_script.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +# run tests +poetry run pytest -vv --cov=heal --cov-report xml tests \ No newline at end of file diff --git a/tests/test_qdr_download.py b/tests/test_qdr_download.py new file mode 100644 index 0000000..16cdd77 --- /dev/null +++ b/tests/test_qdr_download.py @@ -0,0 +1,477 @@ +import os +from pathlib import Path +import requests +from typing import Dict, List, Tuple +from unittest import mock + +import pytest +import requests_mock +from unittest.mock import MagicMock + +from gen3.tools.download.drs_download import DownloadStatus, wts_get_token +from heal.qdr_downloads import ( + download_from_url, + get_download_url_for_qdr, + get_filename_from_headers, + get_id, + get_idp_access_token, + get_request_headers, + get_syracuse_qdr_files, + is_valid_qdr_file_metadata, +) + + +@pytest.fixture(scope="session") +def download_dir(tmpdir_factory): + path = tmpdir_factory.mktemp("qdr_download_dir") + return path + + +@pytest.fixture +def wts_hostname(): + return "test.commons.io" + + +@pytest.mark.parametrize( + "file_metadata", + [ + ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "study_id": "QDR_study_01", + } + ), + ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "file_id": "QDR_file_02", + } + ), + ], +) +def test_is_valid_qdr_file_metadata(file_metadata: Dict): + assert is_valid_qdr_file_metadata(file_metadata) == True + + +def test_is_valid_qdr_file_metadata_failed(): + # missing keys + file_metadata = ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "description": "missing study_id or file_id", + }, + ) + assert is_valid_qdr_file_metadata(file_metadata) == False + + # has both study_id and file_id keys + file_metadata = ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "file_id": "QDR_file_02", + "study_id": "QDR_file_02", + }, + ) + assert is_valid_qdr_file_metadata(file_metadata) == False + + # not a dict + file_metadata = ("file_metadata_is_not_a_dict",) + assert is_valid_qdr_file_metadata(file_metadata) == False + + +@pytest.mark.parametrize( + "file_metadata, expected", + [ + ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "study_id": "QDR_study_01", + }, + "QDR_study_01", + ), + ( + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "file_id": "QDR_file_02", + }, + "QDR_file_02", + ), + ], +) +def test_get_id(file_metadata: Dict, expected: str): + assert get_id(file_metadata) == expected + + +def test_get_id_bad_input(): + # missing study_id and file_id + file_metadata = { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + } + assert get_id(file_metadata) == None + + +def test_get_idp_access_token(wts_hostname): + test_idp = "extermal-keycloak" + file_metadata = { + "external_oidc_idp": test_idp, + "file_retriever": "QDR", + "study_id": "QDR_study_01", + } + returned_idp_token = "some-idp-token" + mock_auth = MagicMock() + mock_auth.get_access_token.return_value = "some_token" + with requests_mock.Mocker() as m: + m.get( + f"https://{wts_hostname}/wts/token/?idp={test_idp}", + json={"token": returned_idp_token}, + ) + with mock.patch( + "gen3.tools.download.drs_download.wts_get_token" + ) as wts_get_token: + wts_get_token.return_value = returned_idp_token + assert ( + get_idp_access_token( + wts_hostname=wts_hostname, + auth=mock_auth, + file_metadata=file_metadata, + ) + == returned_idp_token + ) + + +def test_get_request_headers_for_study_or_file(): + mock_idp_token = "some-idp-token" + + # idp_token is present - just the X-Dataverse-key + expected_headers = {"X-Dataverse-key": mock_idp_token} + assert get_request_headers(idp_access_token=mock_idp_token) == expected_headers + + # missing idp token - empty headers + assert get_request_headers(idp_access_token=None) == {} + + +@pytest.mark.parametrize( + "file_metadata, expected", + [ + ( + { + "study_id": "QDR_study_01", + }, + "https://data.qdr.syr.edu/api/access/dataset/:persistentId/?persistentId=QDR_study_01", + ), + ( + { + "file_id": "QDR_file_02", + }, + "https://data.qdr.syr.edu/api/access/datafile/QDR_file_02", + ), + ], +) +def test_get_download_url_for_qdr(file_metadata: Dict, expected: str): + assert get_download_url_for_qdr(file_metadata) == expected + + +def test_get_download_url_for_qdr_failed(): + # missing file_ids or study_id + file_metadata = {} + assert get_download_url_for_qdr(file_metadata) == None + + +def test_get_filename_from_headers(): + # zip file for study_id + mock_zip_file_name = "test.zip" + mock_response_headers = { + "Content-Type": "application/zip", + "Content-Disposition": f"application; filename={mock_zip_file_name}", + } + assert get_filename_from_headers(mock_response_headers) == mock_zip_file_name + + # utf-8 encoded file name for file_id + mock_file_name = "test.pdf" + mock_response_headers = { + "Content-Type": "application/pdf", + "Content-Disposition": f"application; filename*=UTF-8''{mock_file_name}", + } + assert get_filename_from_headers(mock_response_headers) == mock_file_name + + +def test_get_filename_from_headers_invalid(): + mock_response_headers = { + "Content-Type": "application/pdf", + "Content-Disposition": f"application; filename", + } + assert get_filename_from_headers(mock_response_headers) == None + + +def test_download_from_url(download_dir): + request_headers = {"X-Dataverse-key": "some-idp-token"} + mock_data = "foo" + + with requests_mock.Mocker() as m: + # get study_id + mock_zip_file_name = "dataverse_files.zip" + qdr_url = "https://data.qdr.test.edu/api/access/:persistentId/?persistentId=QDR_study_01" + valid_response_headers = { + "Content-Type": "application/zip", + "Content-Disposition": f"application; filename={mock_zip_file_name}", + } + m.get( + qdr_url, headers=valid_response_headers, content=bytes(mock_data, "utf-8") + ) + download_filename = download_from_url( + qdr_url=qdr_url, + headers=request_headers, + download_path=download_dir, + ) + assert download_filename == f"{download_dir}/{mock_zip_file_name}" + assert os.path.exists(download_filename) + with open(download_filename, "r") as f: + assert f.read() == mock_data + + # get file_id + mock_file_id = "123456" + mock_filename = "some_file.pdf" + valid_response_headers = { + "Content-Type": "application/pdf", + "Content-Disposition": f"application; filename*=UTF-8''{mock_filename}", + } + qdr_url = f"https://data.qdr.test.edu/api/access/datafile/{mock_file_id}" + m.get( + qdr_url, headers=valid_response_headers, content=bytes(mock_data, "utf-8") + ) + + download_filename = download_from_url( + qdr_url=qdr_url, + headers=request_headers, + download_path=download_dir, + ) + # filename is from response headers, not file_id + assert download_filename == f"{download_dir}/{mock_filename}" + assert os.path.exists(download_filename) + with open(download_filename, "r") as f: + assert f.read() == mock_data + + # cannot get downloaded file name from header - fall back to file id + response_headers = { + "Content-Disposition": "application; ", + } + m.get(qdr_url, headers=response_headers, content=bytes(mock_data, "utf-8")) + + download_filename = download_from_url( + qdr_url=qdr_url, + headers=request_headers, + download_path=download_dir, + ) + # filename is from file_id + assert download_filename != f"{download_dir}/{mock_filename}" + assert download_filename == f"{download_dir}/{mock_file_id}" + assert os.path.exists(download_filename) + with open(download_filename, "r") as f: + assert f.read() == mock_data + + +def test_download_from_url_failures(download_dir): + request_headers = {"X-Dataverse-key": "some-idp-token"} + valid_response_headers = {"Content-Type": "application/zip"} + mock_data = "foo" + mock_zip_file_name = "dataverse_files.zip" + download_filename = f"{download_dir}/dataverse_files.zip" + if os.path.exists(download_filename): + Path(download_filename).unlink() + + # bad url + downloaded_file = download_from_url( + qdr_url="https://bad_url", + headers=request_headers, + download_path=download_dir, + ) + assert downloaded_file == None + assert not os.path.exists(download_filename) + + with requests_mock.Mocker() as m: + valid_response_headers = { + "Content-Type": "application/zip", + "Content-Disposition": f"application; filename={mock_zip_file_name}", + } + + # bad download path + qdr_url = "https://data.qdr.test.edu/api/access/datafiles/some_id" + m.get( + qdr_url, headers=valid_response_headers, content=bytes(mock_data, "utf-8") + ) + + download_file = download_from_url( + qdr_url=qdr_url, + headers=request_headers, + download_path="/path/does/not/exist", + ) + assert download_file == None + assert not os.path.exists(download_filename) + + # zero size response + m.get(qdr_url, headers=valid_response_headers, content=bytes()) + download_file = download_from_url( + qdr_url=qdr_url, + headers=request_headers, + download_path=download_dir, + ) + assert download_file == None + assert (os.path.getsize(download_filename)) == 0 + Path(download_filename).unlink() + + +def test_get_syracuse_qdr_files(wts_hostname, download_dir): + test_idp = "test-external-idp" + test_data = "foo" + + # valid input and successful download + test_file_id = "some_id" + file_metadata_list = [ + { + "external_oidc_idp": test_idp, + "file_retriever": "QDR", + "file_id": test_file_id, + }, + ] + expected_status = { + test_file_id: DownloadStatus(filename=test_file_id, status="downloaded") + } + + returned_idp_token = "some-idp-token" + mock_auth = MagicMock() + mock_auth.get_access_token.return_value = "some_token" + valid_response_headers = {"Content-Type": "application/pdf"} + with requests_mock.Mocker() as m, mock.patch( + "gen3.tools.download.drs_download.wts_get_token" + ) as wts_get_token: + m.get( + f"https://{wts_hostname}/wts/token/?idp={test_idp}", + json={"token": returned_idp_token}, + ) + m.get( + f"https://data.qdr.syr.edu/api/access/datafile/{test_file_id}", + headers=valid_response_headers, + content=bytes(test_data, "utf-8"), + ) + wts_get_token.return_value = "some-idp-token" + result = get_syracuse_qdr_files( + wts_hostname=wts_hostname, + auth=mock_auth, + file_metadata_list=file_metadata_list, + download_path=download_dir, + ) + assert result == expected_status + + +@pytest.mark.parametrize( + "file_metadata_list", + [ + ({"not": "a list"},), + (["not", "dict", "items"],), + ( + [ + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "missing": "file_id key", + } + ], + ), + ], +) +def test_get_syracuse_qdr_files_bad_input( + wts_hostname, download_dir, file_metadata_list +): + mock_auth = MagicMock() + mock_auth.get_access_token.return_value = "some_token" + + result = get_syracuse_qdr_files( + wts_hostname=wts_hostname, + auth=mock_auth, + file_metadata_list=file_metadata_list, + download_path=download_dir, + ) + assert result == None + + +def test_get_syracuse_qdr_files_no_url(wts_hostname, download_dir): + test_file_id = "some_id" + file_metadata_list = [ + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "file_id": test_file_id, + }, + ] + expected_status_invalid_url = { + test_file_id: DownloadStatus(filename=test_file_id, status="invalid url") + } + mock_auth = MagicMock() + mock_auth.get_access_token.return_value = "some_token" + with mock.patch( + "heal.qdr_downloads.get_download_url_for_qdr" + ) as mock_get_download_url_for_qdr: + # failed get_download_url + mock_get_download_url_for_qdr.return_value = None + + result = get_syracuse_qdr_files( + wts_hostname=wts_hostname, + auth=mock_auth, + file_metadata_list=file_metadata_list, + download_path=download_dir, + ) + assert result == expected_status_invalid_url + + +def test_get_syracuse_qdr_files_failed_download(wts_hostname, download_dir): + idp = "test-external-idp" + test_data = "foo" + + # valid input + test_file_id = "some_id" + file_metadata_list = [ + { + "external_oidc_idp": "test-external-idp", + "file_retriever": "QDR", + "file_id": test_file_id, + }, + ] + expected_status = { + test_file_id: DownloadStatus(filename=test_file_id, status="failed") + } + + returned_idp_token = "some-idp-token" + mock_auth = MagicMock() + mock_auth.get_access_token.return_value = "some_token" + valid_response_headers = {"Content-Type": "application/zip"} + with requests_mock.Mocker() as m, mock.patch( + "gen3.tools.download.drs_download.wts_get_token" + ) as wts_get_token: + m.get( + f"https://{wts_hostname}/wts/token/?idp={idp}", + json={"token": returned_idp_token}, + ) + m.get( + "https://data.qdr.syr.edu/api/access/datafile/{test_file_id}", + headers=valid_response_headers, + content=bytes(test_data, "utf-8"), + ) + with mock.patch( + "heal.qdr_downloads.download_from_url" + ) as mock_download_from_url: + # failed download + mock_download_from_url.return_value = None + + result = get_syracuse_qdr_files( + wts_hostname=wts_hostname, + auth=mock_auth, + file_metadata_list=file_metadata_list, + download_path=download_dir, + ) + assert result == expected_status