{"id":20930683,"url":"https://github.com/intermine/intermine-ws-python","last_synced_at":"2025-10-25T15:38:44.518Z","repository":{"id":817450,"uuid":"14398732","full_name":"intermine/intermine-ws-python","owner":"intermine","description":"InterMine Client library in Python","archived":false,"fork":false,"pushed_at":"2023-05-17T08:23:30.000Z","size":2334,"stargazers_count":7,"open_issues_count":17,"forks_count":34,"subscribers_count":9,"default_branch":"dev","last_synced_at":"2025-05-13T19:32:40.212Z","etag":null,"topics":["bioinformatics","genomics","python"],"latest_commit_sha":null,"homepage":"http://www.intermine.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/intermine.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-BSD","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2013-11-14T15:23:12.000Z","updated_at":"2023-12-26T14:17:00.000Z","dependencies_parsed_at":"2024-11-18T21:40:57.874Z","dependency_job_id":"a6046492-942a-4214-880d-1048d3ae5cde","html_url":"https://github.com/intermine/intermine-ws-python","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/intermine/intermine-ws-python","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-ws-python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-ws-python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-ws-python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-ws-python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/intermine","download_url":"https://codeload.github.com/intermine/intermine-ws-python/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fintermine-ws-python/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280979468,"owners_count":26423964,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-25T02:00:06.499Z","response_time":81,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","genomics","python"],"created_at":"2024-11-18T21:35:38.170Z","updated_at":"2025-10-25T15:38:44.481Z","avatar_url":"https://github.com/intermine.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"The InterMine Python Webservice Client\n=====================================\n\n\n[![Build Status][badge]][ci] \n![Version](http://img.shields.io/badge/version-1.12.0-blue.svg?style=flat)\n[![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/intermine/intermine/blob/master/LICENSE) \n[![Research software impact](http://depsy.org/api/package/pypi/intermine/badge.svg)](http://depsy.org/package/python/intermine)\n\n[![Conda](https://anaconda.org/intermine/intermine/badges/installer/conda.svg)](https://anaconda.org/bioconda/intermine)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/intermine/badges/version.svg)](https://anaconda.org/bioconda/intermine)\n[![Downloads](https://anaconda.org/bioconda/intermine/badges/downloads.svg)](https://anaconda.org/bioconda/intermine)\n\n\nAn implementation of a webservice client \nfor InterMine webservices, written in Python\n\nWho should use this software?\n-----------------------------\n\nThis software is intended for people who make \nuse of InterMine datawarehouses (ie. Biologists)\nand who want a quicker, more automated way \nto perform queries. Some examples of sites that\nare powered by InterMine software, and thus offer\na compatible webservice API, are:\n\n  * [FlyMine](https://www.flymine.org)\n  * [MouseMine](http://www.mousemine.org)\n  * [YeastMine](http://yeastmine.yeastgenome.org)\n  * [ZebrafishMine](http://zebrafishmine.org)\n  * [RatMine](http://ratmine.mcw.edu/ratmine/begin.do)\n  * [TargetMine](http://targetmine.mizuguchilab.org/)\n  * [ThaleMine](https://apps.araport.org/thalemine)\n  * [PhytoMine](https://phytozome.jgi.doe.gov/phytomine)\n\nSee the [InterMine registry](http://registry.intermine.org/) for the full list of available InterMines.\n\nQueries here refer to database queries over the \nintegrated datawarehouse. Instead of using \nSQL, InterMine services use a flexible and \npowerful sub-set of database query language\nto enable wide-ranging and arbitrary queries.\n\nRequirements\n------------\nThis package is compatible with both Python 2.7 and 3.x. We plan to drop 2.7 support next year.\n\nDownloading:\n------------\n\nThe easiest way to install is to use pip:\n\n```\n  pip install intermine\n```\n\nThe client is also available via [bioconda](https://anaconda.org/bioconda/intermine).\n\nRunning the Tests:\n------------------\n\nIf you would like to run the test suite against a local mock server, you can do so by executing\nthe following command: (from the source directory)\n\n```\n  python setup.py test\n```\n\nIf you want to run the suite against a live server (e.g. as deployed by the testmodel/setup.sh in \nthe InterMine distribution, then you can run:\n\n```\n  python setup.py livetest\n```\n\nBy default this will use the location http://localhost:8080/intermine-demo/service.  If you want\nit to use a different service, set the service URL in the TESTMODEL_URL shell environment variable.\n\nInstallation:\n-------------\n\nOnce downloaded, you can install the module with the command (from the source directory):\n\n```\n  python setup.py install\n```\n\nFurther documentation:\n----------------------\n\nWe have detailed tutorials:\n\n* https://github.com/intermine/intermine-ws-python-docs/\n\nExtensive documentation is available by using the \"pydoc\" command, eg:\n\n```\n  pydoc intermine.query.Query\n```\n\nAlso see:\n\n* Documentation on PyPi: http://packages.python.org/intermine/\n\nBefore Making PRs:\n-------------------------------\nPlease run autopep8 on your files so your code will follow the pep8 conventions. Do it as follows:\n\n```\n  autopep8 \u003cfilenames\u003e --in-place\n```\n\nFor example:\n\n```\n  autopep8 file1.py file2.py  --in-place\n```\n\n\n\nChanges:\n--------\n\n    1.13.00   Added get_template_by_user method\n\t\t\t  Added property view_types to the template\n    1.12.00   Added organism to list upload\n              Support for Python 3.7\n              Added getVersion for registry mines\n              Added display method for list object\n              Added get_anonymous_token method for service object\n              Make registry getMines print all when no organism is given\n              Added dataframe method for query object\n    1.11.00   Added Query Manager\n    1.10.00   Added registry features\n    1.09.09   Add Python 3 support\n    1.09.06   Dual license under BSD as well as LGPL\n    1.07.00   Provide ListManagers as context managers, where users need to create\n              temporary lists and clean up after themselves.\n              Added ID resolution.\n    1.05.00   Allowed constraints to be added on root paths implicitly, eg:\n              q.where('LOOKUP', 'eve') or q.where('IN', 'My List')\n    1.01.00   Added widget listing requests.\n    1.00.00   Added widget enrichment requests.\n    0.99.08   Added simpler constraint definition with kwargs.\n    0.99.07   Fixed bugs with lazy reference fetching handling empty collections and null references.\n    0.99.06   Fixed bug whereby constraint codes in xml were being ignored when queries were deserialised.\n    0.99.05   Allow template parameters of the form 'A = \"zen\"', where only the value is being replaced.\n    0.99.04   Merged 'list.to_query and 'list.to_attribute_query' in response to the changes in list upload behaviour.\n    0.99.03   Allow query construction from Columns with \"where\" and \"filter\"\n              Allow list and query objects as the value in an add_constraint call with \"IN\" and \"NOT IN\" operators.\n              Ensure lists and queries share the same overloading\n    0.99.02   Allow sort-orders which are not in the view but are on selected classes\n    0.99.01   Better representation of multiple sort-orders.\n    0.99.00   Fixed bug with subclasses not being included in clones \n              Added support for new json format for ws versions \u003e= 8.\n    0.98.16   Fixed bug with XML parsing and subclasses where the subclass is mentioned in the first view.\n              better result format documentation and tests\n              added len() to results iterators\n              added ability to parse xml from the service object (see new_query())\n              improved service.select() - now accepts plain class names which work equally well for results and lists\n              Allowed lists to be generated from queries with unambiguous selected classes.\n              Fixed questionable constraint parsing bug which lead to failed template parsing\n    0.98.15   Added lazy-reference fetching for result objects, and list-tagging support\n    0.98.14   Added status property to list objects\n    0.98.13   Added query column summary support\n\n[badge]: https://travis-ci.org/intermine/intermine-ws-python.svg?branch=dev\n[ci]: https://travis-ci.org/intermine/intermine-ws-python\n\nCopyright and Licence\n------------------------\n\nCopyright (C) 2002-2018 InterMine\n\nAll code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license\n\nPlease cite\n------------------------\n\n**InterMine: extensive web services for modern biology.**\u003cbr/\u003e\n\n*Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stěpán R, Sullivan J, Micklem G.*\u003cbr/\u003e\n\n[Nucleic Acids Res. 2014 Jul;42(Web Server issue):W468-72](https://academic.oup.com/nar/article/42/W1/W468/2435235)\n\n[![doi](http://img.shields.io/badge/doi-10.1093/nar/gku301-blue.svg?style=flat)](https://doi.org/10.1093/nar/gku301) \n[![pubmed](http://img.shields.io/badge/pubmed-24753429-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/24753429)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fintermine-ws-python","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fintermine%2Fintermine-ws-python","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fintermine-ws-python/lists"}