{ "info": { "author": "Chris Cotter", "author_email": "cotter@uga.edu", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: MIT License", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# Python port of the iRODS icommands.\n---\n## Install\n```bash\npip3 install --user pyicmd\n```\n\n## Usage\n```bash\nusage: pyicmd [--host HOST] [--port PORT] [--user USER] [--passwd PASSWD]\n [--zone ZONE] [--version]\n [cmd]\n\n Python port of the iRODS icommands.\n\n Supports irods_environment.json file created by iinit. File can be at its\n default location ('~/.irods/irods_environment.json') or set via the\n IRODS_ENVIRONMENT_FILE variable.\n\n If user is set via the command line irods_environment.json is ignored\n and given (or default) command line arguments are used to open the session.\n\n\npositional arguments:\n cmd The icommand to run:\n rm [file(s)] Remove the files listed from the iRODS server\n ls [path] List the files and folders at the given path\n put [loc] [file(s)] Copy file(s) and folder(s) from the local computer to [loc] on the server\n get [files(s)] [loc] Copy file(s) and folder(s) from the server to [loc] on the local computer\n test Test the connection to the iRODS server.\n To learn more about a function, type pyicmd [cmd] -h\n\n\noptional arguments:\n --host HOST Address of iRODS server\n --port PORT iRODS server port\n --user USER iRODS username\n --passwd PASSWD iRODS user password\n --zone ZONE iRODS zone\n --version show programs version number and exit\n```\n\n## Speed Test\nBy default, icommands uses multi-threading for uploads greater than ~35MB. pyicmd does not currently support multiple threaded uploads, causing it to be slower for large files.\n![Speed Test](assets/UploadTimes.png)\n\n# Contributing\n----\n## Testing\nTests for the functional.py API are written in pytest format and can be run\nwith\n\n```bash\nmake test\n```\n\nTests require a valid iRODS server and configured irods_environment.json file created by iinit. [This iRODS docker container](https://github.com/mjstealey/irods-provider-postgres) was used to run the tests.\n\n## Code Standard\nCode should follow [Python's PEP8 style guide](https://www.python.org/dev/peps/pep-0008/). All contributions should pass standard pylint tests. 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