{ "info": { "author": "Colby T. Ford", "author_email": "colby@tuple.xyz", "bugtrack_url": null, "classifiers": [ "License :: Other/Proprietary License", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# ahab - Library \ud83e\udd91\nLibrary for interacting with _ahab_-based cloud API and Kubernetes systems\n\n

Tuple, LLC

\n

tuple.xyz/solutions/ahab/

\n\n## Installation\n```bash\n## Python library from PyPI using pip\npip install ahab-lib\n\n## CLI using pipx\npipx install git+https://github.com/tuplexyz/ahab-lib.git\n```\n\n## Environment Variables\nThis library can use environment variables to avoid passing sensitive information in code.\nThe following environment variables are used by this library:\n- `AHAB_API_URL` - The URL for the _ahab_ cloud API\n- `AHAB_API_KEY` - Your API key for the _ahab_ cloud API\n\nYou can retrieve these values using the following [Azure CLI](https://learn.microsoft.com/en-us/cli/azure/install-azure-cli) commands:\n\n```bash\n## On Unix\nexport AHAB_API_URL=https://$(az functionapp show --name func-ahab-dev-eastus-001 --resource-group rg-ahab-dev-eastus-001 --query defaultHostName -o tsv)\nexport AHAB_API_KEY=$(az functionapp keys list --name func-ahab-dev-eastus-001 --resource-group rg-ahab-dev-eastus-001 --query functionKeys -o tsv)\n\n## On Windows\nset AHAB_API_URL=https://$(az functionapp show --name func-ahab-dev-eastus-001 --resource-group rg-ahab-dev-eastus-001 --query defaultHostName -o tsv)\nset AHAB_API_KEY=$(az functionapp keys list --name func-ahab-dev-eastus-001 --resource-group rg-ahab-dev-eastus-001 --query functionKeys -o tsv)\n```\n...changing the `--name` and `--resource-group` values to the names of your Function App and Resource Group, respectively.\n\n\n## CLI Usage\n\n### Submit Job\n```bash\npython3 ahab.py job submit --body='{\"job_type\": \"rnaseq\", \"metadata\": {\"project\": \"project_001\", \"sample\": \"sample_001\"}, \"inputs\": {\"references\": \"/mnt/datalake/reference/rnaseq_1\", \"fastq_1\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.fastq.gz\", \"fastq_2\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_2.fastq.gz\"}}'\n```\n\n### Get Job\n```bash\npython3 ahab.py job get --job_type=rnaseq\n```\n\n### Update Job\n```bash\npython3 ahab.py job update --id=fb273f3b-9665-4f9d-978c-9f6cb9f1cc19 --status=COMPLETE --body='{\"outputs\": {\"bam\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.bam\", \"bai\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.bam.bai\"}}'\n```\n\n## Python Usage\n\n### Load in the library and get API information\n```python\nfrom ahab.job import get_job, submit_job, update_job\nimport os, json\n\napi_base_url = os.environ.get('AHAB_API_URL', '')\napi_key = os.environ.get('AHAB_API_KEY', '')\n```\n\n### Submit Job\n```python\nbody = {\n \"job_type\": \"rnaseq\",\n \"metadata\": {\n \"project\": \"project_001\",\n \"sample\": \"sample_001\"\n },\n \"inputs\": {\n \"references\": \"/mnt/datalake/reference/rnaseq_1\",\n \"fastq_1\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.fastq.gz\",\n \"fastq_2\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_2.fastq.gz\"\n }\n}\n\nresponse = submit_job(body = body, api_base_url = api_base_url, api_key = api_key)\n\n# {'message': 'Job created successfully.', 'id': 'fb273f3b-9665-4f9d-978c-9f6cb9f1cc19', 'job_type': 'rnaseq'}\n\n```\n\n### Get Job\n```python\njob = get_job(job_type='rnaseq', api_base_url = api_base_url, api_key = api_key)\n\n# {'id': 'fb273f3b-9665-4f9d-978c-9f6cb9f1cc19', 'job_type': 'rnaseq', 'current_status': 'STARTED', 'status_history': {'2024-04-29T17:10:18.552843': 'PENDING', '2024-04-29T17:11:15.582001': 'STARTED'}, 'metadata': {'project': 'project_001', 'sample': 'sample_001'}, 'inputs': {'references': '/mnt/datalake/reference/rnaseq_1', 'fastq_1': '/mnt/datalake/project_001/sample_001/rnaseq/file_1.fastq.gz', 'fastq_2': '/mnt/datalake/project_001/sample_001/rnaseq/file_2.fastq.gz'}}\n\n```\n\n### Update Job\n```python\nbody = {\n \"outputs\": {\n \"bam\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.bam\",\n \"bai\": \"/mnt/datalake/project_001/sample_001/rnaseq/file_1.bam.bai\"\n }\n}\n\nresponse = update_job(id = 'fb273f3b-9665-4f9d-978c-9f6cb9f1cc19', status = \"COMPLETE\", body = body, api_base_url = api_base_url, api_key = api_key)\n\n# {'message': 'Job updated successfully.', 'id': 'fb273f3b-9665-4f9d-978c-9f6cb9f1cc19', 'status': 'COMPLETE'}\n```\n GNU GENERAL PUBLIC LICENSE\n Version 3, 29 June 2007\n\n Copyright (C) 2007 Free Software Foundation, Inc. \n Everyone is permitted to copy and distribute verbatim copies\n of this license document, but changing it is not allowed.\n\n Preamble\n\n The GNU General Public License is a free, copyleft license for\nsoftware and other kinds of works.\n\n The licenses for most software and other practical works are designed\nto take away your freedom to share and change the works. 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You may not convey a covered\nwork if you are a party to an arrangement with a third party that is\nin the business of distributing software, under which you make payment\nto the third party based on the extent of your activity of conveying\nthe work, and under which the third party grants, to any of the\nparties who would receive the covered work from you, a discriminatory\npatent license (a) in connection with copies of the covered work\nconveyed by you (or copies made from those copies), or (b) primarily\nfor and in connection with specific products or compilations that\ncontain the covered work, unless you entered into that arrangement,\nor that patent license was granted, prior to 28 March 2007.\n\n Nothing in this License shall be construed as excluding or limiting\nany implied license or other defenses to infringement that may\notherwise be available to you under applicable patent law.\n\n 12. No Surrender of Others' Freedom.\n\n If conditions are imposed on you (whether by court order, agreement or\notherwise) that contradict the conditions of this License, they do not\nexcuse you from the conditions of this License. If you cannot convey a\ncovered work so as to satisfy simultaneously your obligations under this\nLicense and any other pertinent obligations, then as a consequence you may\nnot convey it at all. For example, if you agree to terms that obligate you\nto collect a royalty for further conveying from those to whom you convey\nthe Program, the only way you could satisfy both those terms and this\nLicense would be to refrain entirely from conveying the Program.\n\n 13. Use with the GNU Affero General Public License.\n\n Notwithstanding any other provision of this License, you have\npermission to link or combine any covered work with a work licensed\nunder version 3 of the GNU Affero General Public License into a single\ncombined work, and to convey the resulting work. The terms of this\nLicense will continue to apply to the part which is the covered work,\nbut the special requirements of the GNU Affero General Public License,\nsection 13, concerning interaction through a network will apply to the\ncombination as such.\n\n 14. Revised Versions of this License.\n\n The Free Software Foundation may publish revised and/or new versions of\nthe GNU General Public License from time to time. Such new versions will\nbe similar in spirit to the present version, but may differ in detail to\naddress new problems or concerns.\n\n Each version is given a distinguishing version number. If the\nProgram specifies that a certain numbered version of the GNU General\nPublic License \"or any later version\" applies to it, you have the\noption of following the terms and conditions either of that numbered\nversion or of any later version published by the Free Software\nFoundation. If the Program does not specify a version number of the\nGNU General Public License, you may choose any version ever published\nby the Free Software Foundation.\n\n If the Program specifies that a proxy can decide which future\nversions of the GNU General Public License can be used, that proxy's\npublic statement of acceptance of a version permanently authorizes you\nto choose that version for the Program.\n\n Later license versions may give you additional or different\npermissions. However, no additional obligations are imposed on any\nauthor or copyright holder as a result of your choosing to follow a\nlater version.\n\n 15. Disclaimer of Warranty.\n\n THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY\nAPPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT\nHOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT WARRANTY\nOF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,\nTHE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\nPURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM\nIS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\nALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n\n 16. 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Interpretation of Sections 15 and 16.\n\n If the disclaimer of warranty and limitation of liability provided\nabove cannot be given local legal effect according to their terms,\nreviewing courts shall apply local law that most closely approximates\nan absolute waiver of all civil liability in connection with the\nProgram, unless a warranty or assumption of liability accompanies a\ncopy of the Program in return for a fee.\n\n END OF TERMS AND CONDITIONS\n\n How to Apply These Terms to Your New Programs\n\n If you develop a new program, and you want it to be of the greatest\npossible use to the public, the best way to achieve this is to make it\nfree software which everyone can redistribute and change under these terms.\n\n To do so, attach the following notices to the program. It is safest\nto attach them to the start of each source file to most effectively\nstate the exclusion of warranty; and each file should have at least\nthe \"copyright\" line and a pointer to where the full notice is found.\n\n \n Copyright (C) \n\n This program is free software: you can redistribute it and/or modify\n it under the terms of the GNU General Public License as published by\n the Free Software Foundation, either version 3 of the License, or\n (at your option) any later version.\n\n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU General Public License for more details.\n\n You should have received a copy of the GNU General Public License\n along with this program. If not, see .\n\nAlso add information on how to contact you by electronic and paper mail.\n\n If the program does terminal interaction, make it output a short\nnotice like this when it starts in an interactive mode:\n\n Copyright (C) \n This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.\n This is free software, and you are welcome to redistribute it\n under certain conditions; type `show c' for details.\n\nThe hypothetical commands `show w' and `show c' should show the appropriate\nparts of the General Public License. Of course, your program's commands\nmight be different; for a GUI interface, you would use an \"about box\".\n\n You should also get your employer (if you work as a programmer) or school,\nif any, to sign a \"copyright disclaimer\" for the program, if necessary.\nFor more information on this, and how to apply and follow the GNU GPL, see\n.\n\n The GNU General Public License does not permit incorporating your program\ninto proprietary programs. If your program is a subroutine library, you\nmay consider it more useful to permit linking proprietary applications with\nthe library. If this is what you want to do, use the GNU Lesser General\nPublic License instead of this License. But first, please read\n.\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": null, "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "dynamic": null, "home_page": "https://tuple.xyz/solutions/ahab", "keywords": "ahab, bioinformatics, genomics, computational biology, data science, machine learning, ai, Kubernetes, cloud, pipelines", "license": "Copyright 2024, Tuple, LLC. 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