{ "info": { "author": "Andrii Iudin", "author_email": "andrii@ebi.ac.uk, andrii.iudin@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.7" ], "description": "================\nEMPIAR depositor\n================\n\n.. image:: https://badge.fury.io/py/empiar-depositor.svg\n :target: https://badge.fury.io/py/empiar-depositor\n\n.. image:: https://travis-ci.org/emdb-empiar/empiar-depositor.svg?branch=dev\n :target: https://travis-ci.org/emdb-empiar/empiar-depositor\n\n.. image:: https://coveralls.io/repos/github/emdb-empiar/empiar-depositor/badge.svg?branch=dev\n :target: https://coveralls.io/github/emdb-empiar/empiar-depositor?branch=dev\n\nCommand line tool for depositing data into `Electron Microscopy Public Image Archive\n`_.\n\nHow to use\n----------\n\nPlease follow these steps:\n\n1. Create a JSON file according to the structure provided in the `example `_.\n\n2. Download and install `ascp tool `_ and/or install globus-cli (supported version 1.7.0) with\n\n .. code:: bash\n\n pip install globus-cli==1.7.0\n\n Globus can be used as a separate upload option or as a fallback if Aspera fails.\n\n3. Set the environmental variable for EMPIAR transfer password to the one that EMPIAR team has provided you with. Please note that this is not the API token from 1) and is a separate password from the one that you create when registering EMPIAR user.\n\n - On Linux and Mac OS X execute\n\n .. code:: bash\n\n export EMPIAR_TRANSFER_PASS=\n\n - On Windows execute\n\n .. code:: batch\n\n set EMPIAR_TRANSFER_PASS=\n\n4. Run the script as:\n\n .. code:: bash\n\n empiar-depositor [-h] [-a ASCP] [-g GLOBUS] [-f] [-e ENTRY_THUMBNAIL] [-r ENTRY_ID ENTRY_DIR] [-i] [-v] EMPIAR_TOKEN JSON_INPUT DATA\n\nPositional arguments:\n+++++++++++++++++++++\n\n``EMPIAR_TOKEN``\n~~~~~~~~~~~~~~~~\nEMPIAR API token. Contact EMPIAR team to obtain it.\n\n``JSON_INPUT``\n~~~~~~~~~~~~~~\nThe location of the JSON with EMPIAR deposition information.\n\n``DATA``\n~~~~~~~~\nThe location of the data that you would like to upload to EMPIAR. It should contain directories that correspond to the image set directories specified in the JSON file.\n\nOptional arguments:\n+++++++++++++++++++\n\n``-h, --help``\n~~~~~~~~~~~~~~\nShow help message and exit\n\n``-a ASCP, --ascp ASCP``\n~~~~~~~~~~~~~~~~~~~~~~~~\nThe location of the ascp executable. By default it is installed in ~/.aspera/connect/bin directory on Linux machines, in ~/Applications/Aspera\\\\ Connect.app/Contents/Resources directory on Macs and in C:\\\\Users\\\\\\\\AppData\\\\Local\\\\Programs\\\\Aspera\\\\Aspera Connect\\\\bin on Windows.\n\n``-g GLOBUS, --globus GLOBUS``\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nUse Globus if Aspera is not specified or Aspera transfer fails. Requirement: globus-cli installed and an endpoint created. Specify your unique user identifier (UUID) as the input parameter.\n\n``-f, --globus-force-login``\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nForce login to Globus. Login even if the globus-cli already has valid login credentials. Any existing credentials will be removed from local storage and globally revoked.\n\n``-e ENTRY_THUMBNAIL, --entry-thumbnail ENTRY_THUMBNAIL``\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nThumbnail image that will represent your deposition on EMPIAR pages. Minimum size is 400 x 400, preferred format is png. If none is provided, then the image from the related EMDB entry will be used.\n\n``-r ENTRY_ID ENTRY_DIR, --resume ENTRY_ID ENTRY_DIR``\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nResume Aspera upload or re-deposit an entry. The entry has to be successfully created as specifying EMPIAR entry ID and entry directory is required. All entry metadata will be replaced with the one provided in the JSON file. Aspera transfer will continue from where it stopped.\n\n``-i, --ignore-certificate``\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nActivate this flag to skip the verification of SSL certificate.\n\n``-v, --version``\n~~~~~~~~~~~~~~~~~\nShow program's version number and exit\n\nExamples:\n+++++++++\n\n.. code:: bash\n\n empiar-depositor -a ~/Applications/Aspera\\ Connect.app/Contents/Resources/ascp 0123456789 ~/Documents/empiar_deposition_1.json ~/Downloads/micrographs\n\n.. code:: bash\n\n empiar-depositor -r 10 ABC123 -e ~/Downloads/dep_thumb.png 0123456789 -g 01234567-89a-bcde-fghi-jklmnopqrstu ~/Documents/empiar_deposition_1.json ~/Downloads/micrographs", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "", "keywords": "EMPIAR,deposition,microscopy", "license": "Apache License", "maintainer": "", "maintainer_email": "", "name": "empiar-depositor", "package_url": "https://pypi.org/project/empiar-depositor/", "platform": "", "project_url": "https://pypi.org/project/empiar-depositor/", "project_urls": null, "release_url": "https://pypi.org/project/empiar-depositor/1.6b8/", "requires_dist": null, "requires_python": "", "summary": "Script for depositing the data into EMPIAR using EMPIAR API", "version": "1.6b8" }, "last_serial": 4430759, "releases": { "1.4b1": [ { "comment_text": "", "digests": { "md5": "dfa9fe26d7d510e5149381b70e404b89", "sha256": "b3956dd0147247050c0632626033331667497492ac1a749b7c075c514bf7b5ed" }, "downloads": -1, "filename": "empiar_depositor-1.4b1-py2-none-any.whl", "has_sig": false, "md5_digest": "dfa9fe26d7d510e5149381b70e404b89", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 12461, "upload_time": "2018-03-21T16:48:51", "url": "https://files.pythonhosted.org/packages/6e/5a/7405436d2e9e9093cc45988f5918c304df46d8a506fe5bb92a804fd43ff2/empiar_depositor-1.4b1-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3530177678f6caaa35a1ba8e0d0747be", "sha256": "c34f27434e61b718fa7f9e8f2fa9da1527481213a5c5da0192ce57b3a01a84d8" }, "downloads": -1, "filename": "empiar_depositor-1.4b1.tar.gz", "has_sig": false, "md5_digest": "3530177678f6caaa35a1ba8e0d0747be", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7416, "upload_time": "2018-03-21T16:48:52", "url": "https://files.pythonhosted.org/packages/70/e0/d2c797511104831add40b509de77833a790dfb099e50b542ca8abcb87f61/empiar_depositor-1.4b1.tar.gz" } ], "1.5b1": [ { "comment_text": "", "digests": { "md5": "329107e910ee6dd5626a39a6a74ab759", "sha256": "9e9aaf44ef61bbbda778362c0c9ac317504f69730c6ab8431bd1efc3ddb228f4" }, "downloads": -1, "filename": "empiar_depositor-1.5b1-py2-none-any.whl", "has_sig": false, "md5_digest": "329107e910ee6dd5626a39a6a74ab759", "packagetype": "bdist_wheel", "python_version": "py2", "requires_python": null, "size": 13151, "upload_time": "2018-03-28T14:34:18", "url": "https://files.pythonhosted.org/packages/fe/67/da60f2db9c88a0d821ab811d235251663c50d323233af5a72f5f99e56df6/empiar_depositor-1.5b1-py2-none-any.whl" }, { "comment_text": "", "digests": { "md5": "c990ea89422545811353ea321605a2cd", "sha256": "42a69c682927acc018f45c5b99e879c9a16cef9245d2ca51dda39fa5a80f2709" }, "downloads": -1, "filename": "empiar_depositor-1.5b1.tar.gz", "has_sig": false, "md5_digest": "c990ea89422545811353ea321605a2cd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7917, "upload_time": "2018-03-28T14:34:18", "url": "https://files.pythonhosted.org/packages/3c/0a/8b12f26b9ab1c28a6ead99eb5229a478610eca37cce8341787979b61a6ff/empiar_depositor-1.5b1.tar.gz" } ], "1.6b3": [ { "comment_text": "", "digests": { "md5": "0cc8eec0eccde46d6fec0c4b534dbb1b", "sha256": "a9629c59806fd16d0b06c119212479908fef0f3c95723111e87fda6557fad8fe" }, "downloads": -1, "filename": "empiar-depositor-1.6b3.tar.gz", "has_sig": false, "md5_digest": "0cc8eec0eccde46d6fec0c4b534dbb1b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8471, "upload_time": "2018-05-31T11:46:54", "url": "https://files.pythonhosted.org/packages/e1/43/ee30ae6040df5d973f224aa86621cbd786c0a4f5aa062b21bf81b0c483e2/empiar-depositor-1.6b3.tar.gz" } ], "1.6b4": [ { "comment_text": "", "digests": { "md5": "a4640cc4f13e958f8cf326aed8dcbec3", "sha256": "e94d67371f53ac629126aeaf3905caa8fa8c5a42258552ccee4a4f67fe0f59e9" }, "downloads": -1, "filename": "empiar_depositor-1.6b4-py3-none-any.whl", "has_sig": false, "md5_digest": "a4640cc4f13e958f8cf326aed8dcbec3", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 12134, "upload_time": "2018-08-13T15:48:55", "url": "https://files.pythonhosted.org/packages/65/7c/2bb2ef7717c12fce3b5864478b279cad0b8feca0ab6afec9c647da781cf4/empiar_depositor-1.6b4-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "e7eb075b33e7b5a3f4c53b00ff1e119b", "sha256": "f91fac57c0c732501fac9963aa41201d08480a84babffe5ec07ec1e8f44a7c7a" }, "downloads": -1, "filename": "empiar-depositor-1.6b4.tar.gz", "has_sig": false, "md5_digest": "e7eb075b33e7b5a3f4c53b00ff1e119b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7727, "upload_time": "2018-08-13T15:48:56", "url": "https://files.pythonhosted.org/packages/6c/bb/c8459f25956170e8acf4ec9686e0dd002a50a45c10ba57b0e7ff69499c60/empiar-depositor-1.6b4.tar.gz" } ], "1.6b5": [ { "comment_text": "", "digests": { "md5": "79f4dac7fd354a8b69558a99a1cb541c", "sha256": "d2ad03f716a40a8b1e12ad63802969abb980e686acfd691ead4c1e9a11eb6059" }, "downloads": -1, "filename": "empiar_depositor-1.6b5-py3-none-any.whl", "has_sig": false, "md5_digest": "79f4dac7fd354a8b69558a99a1cb541c", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 12168, "upload_time": "2018-08-14T10:27:37", "url": "https://files.pythonhosted.org/packages/19/06/3868d2ae12fa632ac9afd47ef67cdd195f802b747f00ff32908365ad2c99/empiar_depositor-1.6b5-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "c354078adfcb5412cb335618604934d4", "sha256": "0c59e57ccfebb4f001ba2fc7d275a1e8fdeab4ace5a8dc75c5f6b26214d147f0" }, "downloads": -1, "filename": "empiar-depositor-1.6b5.tar.gz", "has_sig": false, "md5_digest": "c354078adfcb5412cb335618604934d4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 7765, "upload_time": "2018-08-14T10:27:38", "url": "https://files.pythonhosted.org/packages/79/9a/5308f46f59e992bf8b57faee456472020e157362f5955fe2c74220cf3b6b/empiar-depositor-1.6b5.tar.gz" } ], "1.6b7": [ { "comment_text": "", "digests": { "md5": "65f5dcd81558764e6113960a15dbcc1c", "sha256": "e23f4b83979097b0b1f8021c5074e91a38760bafd06acbb75d3024ab6c474abb" }, "downloads": -1, "filename": "empiar-depositor-1.6b7.tar.gz", "has_sig": false, "md5_digest": "65f5dcd81558764e6113960a15dbcc1c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 13145, "upload_time": "2018-10-23T09:22:51", "url": "https://files.pythonhosted.org/packages/5e/a8/af6b7bb6cef0269027f3c3754a2398cc58a68451656d0e1fea33f3227a27/empiar-depositor-1.6b7.tar.gz" } ], "1.6b8": [ { "comment_text": "", "digests": { "md5": "d2178894bb76db6ea2df65e44b6699dc", "sha256": "c4ef3a4272f52e6875f30cd42db0d60375bf17bb243ee508998cb6f6c478724d" }, "downloads": -1, "filename": "empiar-depositor-1.6b8.tar.gz", "has_sig": false, "md5_digest": "d2178894bb76db6ea2df65e44b6699dc", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 13209, "upload_time": "2018-10-30T09:17:36", "url": "https://files.pythonhosted.org/packages/3f/71/99a2e70faed5c51d2ce8be4f42bee80bee2da14fc9fd06c6148a76020096/empiar-depositor-1.6b8.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "d2178894bb76db6ea2df65e44b6699dc", "sha256": "c4ef3a4272f52e6875f30cd42db0d60375bf17bb243ee508998cb6f6c478724d" }, "downloads": -1, "filename": "empiar-depositor-1.6b8.tar.gz", "has_sig": false, "md5_digest": "d2178894bb76db6ea2df65e44b6699dc", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 13209, "upload_time": "2018-10-30T09:17:36", "url": "https://files.pythonhosted.org/packages/3f/71/99a2e70faed5c51d2ce8be4f42bee80bee2da14fc9fd06c6148a76020096/empiar-depositor-1.6b8.tar.gz" } ] }