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galaxy.tools.verify package

Module of utilities for verifying test results.

galaxy.tools.verify.verify(item_label, output_content, attributes, filename=None, get_filename=None, keep_outputs_dir=None, verify_extra_files=None)[source]

Verify the content of a test output using test definitions described by attributes.

Throw an informative assertion error if any of these tests fail.

galaxy.tools.verify.make_temp_fname(fname=None)[source]

Safe temp name - preserve the file extension for tools that interpret it.

galaxy.tools.verify.files_diff(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences.

galaxy.tools.verify.files_re_match(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences using re.match.

galaxy.tools.verify.files_re_match_multiline(file1, file2, attributes=None)[source]

Check the contents of 2 files for differences using re.match in multiline mode.

galaxy.tools.verify.files_contains(file1, file2, attributes=None)[source]

Check the contents of file2 for substrings found in file1, on a per-line basis.

Submodules

galaxy.tools.verify.test_data module

class galaxy.tools.verify.test_data.TestDataResolver(env_var='GALAXY_TEST_FILE_DIR', environ={'JENKINS_HOME': '/var/lib/jenkins', 'BUILD_CAUSE': 'UPSTREAMTRIGGER', 'JOB_BASE_NAME': 'PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01', 'PYTHON': 'System-CPython-2.7', 'HUDSON_URL': 'https://jenkins.galaxyproject.org/', 'BUILD_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/', 'GIT_PREVIOUS_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'BUILD_TAG': 'jenkins-galaxy-sphinx-by-branch-PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01-3485', 'XDG_SESSION_TYPE': 'tty', 'HUDSON_SERVER_COOKIE': 'f442d5996560f01b', 'JENKINS_URL': 'https://jenkins.galaxyproject.org/', 'LOGNAME': 'jenkins', 'USER': 'jenkins', 'WORKSPACE': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01', 'HOME': '/home/jenkins', 'PATH': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv/bin:/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv/bin:/usr/local/bin:/usr/bin:/bin:/usr/games', 'PS1': '(.venv)(.venv)$ ', 'JOB_NAME': 'galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01', 'MAKEFLAGS': 'w', 'LANG': 'en_US.UTF-8', 'RUN_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/display/redirect', 'VIRTUAL_ENV': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv', 'SHELL': '/bin/sh', 'GIT_PREVIOUS_SUCCESSFUL_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'HUDSON_HOME': '/var/lib/jenkins', 'NODE_LABELS': 'doc_builder n11.galaxyproject.org psu_node', 'MFLAGS': '-w', 'ROOT_BUILD_CAUSE': 'TIMERTRIGGER', 'XDG_SESSION_CLASS': 'user', 'BUILD_ID': '3485', 'BUILD_NUMBER': '3485', 'XDG_RUNTIME_DIR': '/run/user/1000', 'HUDSON_COOKIE': '380cc1fc-1ed0-4967-bfa6-89ddc33058c3', 'JOB_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/', 'GIT_URL': 'https://github.com/galaxyproject/galaxy/', 'GIT_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'RUN_CHANGES_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/display/redirect?page=changes', 'ROOT_BUILD_CAUSE_TIMERTRIGGER': 'true', 'XDG_SESSION_ID': '1184', 'AWS_ACCESS_KEY_ID': 'AKIAYX7HSEMC7DKPIMU7', 'BUILD_CAUSE_UPSTREAMTRIGGER': 'true', 'JOB_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/display/redirect', 'WORKSPACE_TMP': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01@tmp', 'SSH_CLIENT': '172.18.2.43 46836 22', 'EXECUTOR_NUMBER': '0', 'NODE_NAME': 'n11.galaxyproject.org', 'MAKELEVEL': '2', 'PWD': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01', 'JENKINS_SERVER_COOKIE': 'f442d5996560f01b', 'BUILD_DISPLAY_NAME': '#3485', 'AWS_SECRET_ACCESS_KEY': 'L+6N5EfuLyZB/84Hv0vAun6h9DXcn0pLcePGuSV9', 'MAIL': '/var/mail/jenkins', 'SSH_CONNECTION': '172.18.2.43 46836 172.18.2.51 22', 'TARGET_GIT_BRANCH': 'release_18.01', 'GIT_BRANCH': 'origin/dev'})[source]

Bases: object

__init__(env_var='GALAXY_TEST_FILE_DIR', environ={'JENKINS_HOME': '/var/lib/jenkins', 'BUILD_CAUSE': 'UPSTREAMTRIGGER', 'JOB_BASE_NAME': 'PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01', 'PYTHON': 'System-CPython-2.7', 'HUDSON_URL': 'https://jenkins.galaxyproject.org/', 'BUILD_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/', 'GIT_PREVIOUS_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'BUILD_TAG': 'jenkins-galaxy-sphinx-by-branch-PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01-3485', 'XDG_SESSION_TYPE': 'tty', 'HUDSON_SERVER_COOKIE': 'f442d5996560f01b', 'JENKINS_URL': 'https://jenkins.galaxyproject.org/', 'LOGNAME': 'jenkins', 'USER': 'jenkins', 'WORKSPACE': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01', 'HOME': '/home/jenkins', 'PATH': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv/bin:/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv/bin:/usr/local/bin:/usr/bin:/bin:/usr/games', 'PS1': '(.venv)(.venv)$ ', 'JOB_NAME': 'galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01', 'MAKEFLAGS': 'w', 'LANG': 'en_US.UTF-8', 'RUN_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/display/redirect', 'VIRTUAL_ENV': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01/.venv', 'SHELL': '/bin/sh', 'GIT_PREVIOUS_SUCCESSFUL_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'HUDSON_HOME': '/var/lib/jenkins', 'NODE_LABELS': 'doc_builder n11.galaxyproject.org psu_node', 'MFLAGS': '-w', 'ROOT_BUILD_CAUSE': 'TIMERTRIGGER', 'XDG_SESSION_CLASS': 'user', 'BUILD_ID': '3485', 'BUILD_NUMBER': '3485', 'XDG_RUNTIME_DIR': '/run/user/1000', 'HUDSON_COOKIE': '380cc1fc-1ed0-4967-bfa6-89ddc33058c3', 'JOB_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/', 'GIT_URL': 'https://github.com/galaxyproject/galaxy/', 'GIT_COMMIT': '6ac956b57c753caef7f28ed3dbfdbd498f0858fe', 'RUN_CHANGES_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/3485/display/redirect?page=changes', 'ROOT_BUILD_CAUSE_TIMERTRIGGER': 'true', 'XDG_SESSION_ID': '1184', 'AWS_ACCESS_KEY_ID': 'AKIAYX7HSEMC7DKPIMU7', 'BUILD_CAUSE_UPSTREAMTRIGGER': 'true', 'JOB_DISPLAY_URL': 'https://jenkins.galaxyproject.org/job/galaxy-sphinx-by-branch/PYTHON=System-CPython-2.7, TARGET_GIT_BRANCH=release_18.01/display/redirect', 'WORKSPACE_TMP': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01@tmp', 'SSH_CLIENT': '172.18.2.43 46836 22', 'EXECUTOR_NUMBER': '0', 'NODE_NAME': 'n11.galaxyproject.org', 'MAKELEVEL': '2', 'PWD': '/var/jenkins/workspace/galaxy-sphinx-by-branch/PYTHON/System-CPython-2.7/TARGET_GIT_BRANCH/release_18.01', 'JENKINS_SERVER_COOKIE': 'f442d5996560f01b', 'BUILD_DISPLAY_NAME': '#3485', 'AWS_SECRET_ACCESS_KEY': 'L+6N5EfuLyZB/84Hv0vAun6h9DXcn0pLcePGuSV9', 'MAIL': '/var/mail/jenkins', 'SSH_CONNECTION': '172.18.2.43 46836 172.18.2.51 22', 'TARGET_GIT_BRANCH': 'release_18.01', 'GIT_BRANCH': 'origin/dev'})[source]
get_filename(name)[source]
galaxy.tools.verify.test_data.build_resolver(uri, environ)[source]
class galaxy.tools.verify.test_data.FileDataResolver(file_dir)[source]

Bases: object

__init__(file_dir)[source]
exists(filename)[source]
path(filename)[source]
class galaxy.tools.verify.test_data.GitDataResolver(repository, environ)[source]

Bases: galaxy.tools.verify.test_data.FileDataResolver

__init__(repository, environ)[source]
exists(filename)[source]
update_repository()[source]
execute(cmd)[source]