欧洲X射线自由电子激光设施元数据目录Web应用的Python客户端，可在https://in.xfel.eu/metadata找到。
项目描述
MyMdC是为欧洲X射线自由电子激光设施数据管理设计的Web应用。
此库（metadata_client）是欧洲X射线自由电子激光设施元数据目录Web应用（myMdC）公开的RESTful API的客户端 - myMdC (https://in.xfel.eu/metadata)。
仓库
依赖关系
oauthlib (https://pypi.python.org/pypi/oauthlib)
requests (https://github.com/psf/requests)
requests-oauthlib (https://github.com/requests/requests-oauthlib)
oauth2_xfel_client (https://git.xfel.eu/ITDM/oauth2_xfel_client)
安装
Python项目
安装需求，如果之前从未执行过
1.1. 对于OS X发行版
1.1.1. Homebrew brew install python3 1.1.2 Port sudo port install python36 sudo port select --set python3 python36 sudo port install py36-pip sudo port select --set pip pip361.2. 对于Linux发行版
sudo apt-get update sudo apt-get install python3.9
在Python环境中使metadata_client库可用
2.1. 通过pip安装它
# Use venv python3.10 -m venv .venv source .venv/bin/activate # Install dependencies from local wheels files pip install . --no-index --find-links ./external_dependencies/ # Install dependencies from the pypi pip install . # Force re-installation of packages pip install . --ignore-installed安装它将在当前Python安装的site-packages文件夹下放置两个文件夹
metadata_client 包含源代码；
metadata_client-4.1.0.dist-info/ 包含Wheels配置文件。
要识别Python site-packages文件夹，请运行
python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"
用法
要使用此项目，您需要导入它
from metadata_client import MetadataClient
连接到MdC（元数据目录）
from metadata_client import MetadataClient # Necessary configuration variables to establish a connection # Go to https://in.xfel.eu/metadata/oauth/applications to make a token for # the metadata catalogue. user_id = '201ed15ff071a63e76cb0b91a1ab17b36d5f92d24b6df4497aa646e39c46a324' user_secret = 'a8ae80f5e96531f19bf2d2b6102f5a537196aca44a673ad36533310e07529757' user_email = 'luis.maia@xfel.eu' # metadata_web_app_url = 'https://in.xfel.eu/metadata' token_url = 'https://in.xfel.eu/metadata/oauth/token' refresh_url = 'https://in.xfel.eu/metadata/oauth/token' auth_url = 'https://in.xfel.eu/metadata/oauth/authorize' scope = '' base_api_url = 'https://in.xfel.eu/metadata/api/' # Generate the connection (example with minimum parameter options) client_conn = MetadataClient(client_id=user_id, client_secret=user_secret, user_email=user_email, token_url=token_url, refresh_url=refresh_url, auth_url=auth_url, scope=scope, base_api_url=base_api_url) # Generate the connection (example with all parameter options) client_conn = MetadataClient(client_id=user_id, client_secret=user_secret, user_email=user_email, token_url=token_url, refresh_url=refresh_url, auth_url=auth_url, scope=scope, base_api_url=base_api_url, session_token=None, max_retries=3, timeout=12, ssl_verify=True)与MyMdC（元数据目录）的交互
2.1 示例数据组类型
all_group_types = client_conn.get_all_data_group_types() all_group_types # >>> {'success': True, # 'pagination': {'Date': 'Tue, 10 May 2022 22:48:14 GMT', 'X-Total-Pages': '1', 'X-Count-Per-Page': '100', 'X-Current-Page': '1', 'X-Total-Count': '6'}, # 'data': [{'description': '', 'identifier': 'RAW', 'name': 'Raw', 'flg_available': True, 'id': 1}, # {'description': '', 'identifier': 'CAL', 'name': 'Calibration', 'flg_available': True, 'id': 2}, # {'description': '', 'identifier': 'PROC', 'name': 'Processed', 'flg_available': True, 'id': 3}, # {'description': '', 'identifier': 'REDU', 'name': 'Reduced', 'flg_available': True, 'id': 4}, # {'description': '', 'identifier': 'SIM', 'name': 'Simulation', 'flg_available': True, 'id': 5}, # {'description': '', 'identifier': 'UNK', 'name': 'Unknown', 'flg_available': True, 'id': 6}], # 'app_info': {}, # 'info': 'Got data_group_type successfully'} all_group_types['success'] # >>> True all_group_types['pagination'] # >>> {'Date': 'Wed, 11 May 2022 09:55:34 GMT', 'X-Total-Pages': '1', 'X-Count-Per-Page': '100', 'X-Current-Page': '1', 'X-Total-Count': '6'} all_group_types['data'][0] # >>> {'description': '', 'identifier': 'RAW', 'name': 'Raw', 'flg_available': True, 'id': 1} all_group_types['data'][0]['name'] # >>> 'Raw'2.2 示例仪器
all_xfel_instruments = client_conn.get_all_xfel_instruments() >>> for instrument in all_xfel_instruments['data']: ... print('id = {0} | name = {1}'.format(instrument['id'], instrument['name'])) ... # id = -1 | name = test-instrument # id = 1 | name = SPB/SFX SASE1 # id = 2 | name = FXE SASE1 # id = 3 | name = SQS SASE3 # id = 4 | name = SCS SASE3 # id = 5 | name = MID SASE2 # id = 6 | name = HED SASE2 # id = 7 | name = Hera South Detector Test Stand # id = 8 | name = SASE1 Test Stand # id = 9 | name = SASE2 Test Stand # id = 10 | name = SASE3 Test Stand all_xfel_instruments = client_conn.get_all_xfel_instruments(page=1, page_size=1) all_xfel_instruments # >>> {'success': True, # 'info': 'Got instrument successfully', # 'app_info': {}, # 'pagination': {'Date': 'Wed, 11 May 2022 09:57:45 GMT', 'X-Total-Pages': '21', 'X-Count-Per-Page': '1', 'X-Current-Page': '1', 'X-Total-Count': '21'}, # 'data': [{'id': 1, 'name': 'SPB/SFX SASE1', 'identifier': 'SPB', 'url': 'https://www.xfel.eu/facility/instruments/spb_sfx', 'instrument_leader_id': 230, 'deputy_instrument_leader_id': 1018, 'facility_id': 1, 'instrument_type_id': 2, 'repository_id': 103, 'topic_id': 1, 'dsg_host': None, 'system_user': None, 'flg_online_resource': True, 'online_script': 'make_online', 'flg_available': True, 'description': 'The Single Particles, Clusters, and Biomolecules & Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is primarily concerned with three-dimensional diffractive imaging, and three-dimensional structure determination, of micrometre-scale and smaller objects, at atomic or near-atomic¿resolution.', 'doi': None, 'techniques': [{'id': 250, 'identifier': 'PaNET01168', 'name': 'serial femtosecond crystallography', 'url': 'http://purl.org/pan-science/PaNET/PaNET01168', 'flg_available': True, 'description': None}, {'id': 259, 'identifier': 'PaNET01188', 'name': 'small angle x-ray scattering', 'url': 'http://purl.org/pan-science/PaNET/PaNET01188', 'flg_available': True, 'description': None}, {'id': 364, 'identifier': 'PaNET01101', 'name': 'x-ray powder diffraction', 'url': 'http://purl.org/pan-science/PaNET/PaNET01101', 'flg_available': True, 'description': None}, {'id': 28, 'identifier': 'PaNET01174', 'name': 'coherent diffraction imaging', 'url': 'http://purl.org/pan-science/PaNET/PaNET01174', 'flg_available': True, 'description': None}]}]}2.3 获取仪器活动提案
active_proposal = client_conn.get_active_proposal_by_instrument(1)2.4 注册运行副本
# (e.g. proposal_number == 1234) # (e.g. proposal_number == 12) # (e.g. repository_identifier == 'XFEL_GPFS_OFFLINE_RAW_CC') resp = client_conn.register_run_replica( proposal_number, run_number, repository_identifier ) # resp = {'success': True, # 'info': 'Run replica registered successfully', # 'pagination': {'Date': 'Tue, 10 May 2022 22:48:14 GMT', 'X-Total-Pages': '1', 'X-Count-Per-Page': '100', 'X-Current-Page': '1', 'X-Total-Count': '6'}, # 'data': {'experiment_id': '-1', # 'sample_id': '-1', # 'run_id': '1588', # 'data_group_id': '777'}, # 'app_info': {}}2.5 注销运行副本
# (e.g. proposal_number == 1234) # (e.g. proposal_number == 12) # (e.g. repository_identifier == 'XFEL_GPFS_OFFLINE_RAW_CC') resp = client_conn.unregister_run_replica( proposal_number, run_number, repository_identifier ) # resp = {'success': True, # 'info': 'Run replica unregistered successfully', # 'pagination': {'Date': 'Tue, 10 May 2022 22:48:14 GMT', 'X-Total-Pages': '1', 'X-Count-Per-Page': '100', 'X-Current-Page': '1', 'X-Total-Count': '6'}, # 'data': {'data_group_id': '-1', # 'repository_id': '1', # 'flg_available': 'false'}, # 'app_info': {}}2.6 获取提案的运行
# (e.g. proposal_number == 1234) # (e.g. page == 1 | Default == 1) # (e.g. page_size == 5 | Default == 100 | Limit: 500) resp = client_conn.get_proposal_runs(proposal_number, page=1, page_size=5) # RESPONSE example # # resp = {'info': 'Got proposal successfully', # 'success': True, # 'pagination': {'Date': 'Tue, 10 May 2022 22:48:14 GMT', # 'X-Total-Pages': '1', # 'X-Count-Per-Page': '100', # 'X-Current-Page': '1', # 'X-Total-Count': '6'}, # 'data': { # 'proposal': { # 'id': -1, # 'number': 0, # 'title': 'Proposal Title 001' # }, # 'runs': [ # { # 'id': -1, # 'run_number': 1, # 'flg_status': 1, # 'flg_run_quality': -1, # 'size': null, # 'num_files': 0, # 'repositories': { # 'XFEL_TESTS_REPO': { # 'name": 'XFEL Tests Repository', # 'mount_point': '/webstorage/XFEL', # 'data_groups': 1 # } # } # } # ] # }, # 'app_info': {}}
2.7 获取提案的样本
# (e.g. proposal_number == 1234)
# (e.g. page == 1 | Default == 1)
# (e.g. page_size == 50 | Default == 100 | Limit: 500)
resp = client_conn.get_proposal_samples(proposal_number, page=1, page_size=50)
#
# RESPONSE example
#
# resp = {'info': 'Got sample successfully',
# 'success': True,
# 'pagination': {'Date': 'Tue, 10 May 2022 22:48:14 GMT',
# 'X-Total-Pages': '1',
# 'X-Count-Per-Page': '100',
# 'X-Current-Page': '1',
# 'X-Total-Count': '6'},
# 'data': [{'id': -1,
# 'name': 'TestSample DO NOT DELETE!',
# 'proposal_id': -1,
# 'sample_type_id': 1,
# 'flg_available': True,
# 'url': '',
# 'description': ''}],
# 'app_info': {}}
有关更多示例，请参阅tests/文件夹。
开发和测试
在开发过程中，提交更改之前，请验证以下内容：
所有测试都继续成功通过（验证运行 pytest）
# Go to the source code directory cd metadata_client # Use venv python3.10 -m venv .venv source .venv/bin/activate # Upgrade package and all its required packages pip install . -U --upgrade-strategy eager # Install test dependencies pip install '.[test]' -U --upgrade-strategy eager # Run all tests using pytest pytest metadata_client/tests # When running all tests against the standard http application OAUTHLIB_INSECURE_TRANSPORT=1 pytest metadata_client/tests # Run all tests and get information about coverage for all files inside metadata_client package pytest --cov metadata_client/tests --cov-report term-missing
代码继续遵守pycodestyle代码约定（验证运行 pycodestyle）
pycodestyle . pycodestyle . --exclude venv
要生成依赖项的所有wheels文件，请执行
# Generate Wheels to itself and dependencies pip wheel --wheel-dir=./external_dependencies . pip wheel --wheel-dir=./external_dependencies --find-links=./external_dependencies .
请确保在external_dependencies文件夹中有所需的依赖项版本，因为目前在setup.py中未设置任何版本。
在https://pypi.ac.cn上注册库
要注册此Python库，需要以下步骤
# Install twine python -m pip install --upgrade twine # Generates source distribution (.tar.gz) and wheel (.whl) files in the dist/ folder python setup.py sdist python setup.py bdist_wheel # Upload new version .egg and .whl files twine upload dist/* # In case a test is necessary, it is possible to test it against test.pypi.org twine upload --repository-url https://test.pypi.org/legacy/ dist/* --verbose
下载文件
下载适用于您的平台的文件。如果您不确定选择哪个，请了解更多关于安装包的信息。
源分布
metadata_client-4.1.0.tar.gz (68.2 kB 查看哈希)
构建分布
metadata_client-4.1.0-py3-none-any.whl (124.9 kB 查看哈希)
