{"id":34701894,"url":"https://github.com/hubmapconsortium/hubmap-clt","last_synced_at":"2026-05-26T03:34:54.634Z","repository":{"id":39853066,"uuid":"447300329","full_name":"hubmapconsortium/hubmap-clt","owner":"hubmapconsortium","description":"The HuBMAP Command Line Transfer application","archived":false,"fork":false,"pushed_at":"2023-04-07T17:33:45.000Z","size":32,"stargazers_count":0,"open_issues_count":6,"forks_count":0,"subscribers_count":11,"default_branch":"main","last_synced_at":"2024-04-14T03:54:46.529Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/hubmapconsortium.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-01-12T16:58:03.000Z","updated_at":"2022-02-04T18:34:10.000Z","dependencies_parsed_at":"2022-09-13T04:15:44.986Z","dependency_job_id":null,"html_url":"https://github.com/hubmapconsortium/hubmap-clt","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/hubmapconsortium/hubmap-clt","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhubmap-clt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhubmap-clt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhubmap-clt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhubmap-clt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/hubmapconsortium","download_url":"https://codeload.github.com/hubmapconsortium/hubmap-clt/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/hubmapconsortium%2Fhubmap-clt/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33503230,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T03:12:49.672Z","status":"ssl_error","status_checked_at":"2026-05-26T03:12:47.976Z","response_time":63,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2025-12-24T22:53:12.162Z","updated_at":"2026-05-26T03:34:54.629Z","avatar_url":"https://github.com/hubmapconsortium.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hubmap-clt\n\n## This Repo has moved to the [x-atlas-consortia/clt](https://github.com/x-atlas-consortia/clt) repository.  This repository is no longer maintained.\n\n---\n\nA command line interface to download multiple files and directories from the Globus file transfer service.\n\n### Overview\n\nThe HuBMAP Command-Line Transfer uses the Globus cli to transfer files from a manifest file. This file contains the ID (UUID or HuBMAP ID) and the path to the specific file or directory to be downloaded. \n\n### Installing  and Using hubmap-clt\n\nThe HuBMAP Command-Line Transfer requires a local Globus Connect Personal Endpoint to be connected. The user must have an account with Globus and be logged into both the local endpoint as well as the Globus command line interface. Hubmap-clt is available through PyPi and can be installed with:\n\n```bash\npip3 hubmap-clt\n```\n\nhubmap-clt requirements can be found [here](requirements.txt)\n\nConsult \u003ca href=\"https://software.docs.hubmapconsortium.org/\"\u003eInstalling hubmap-clt\u003c/a\u003e and Consult \u003ca href=\"https://software.docs.hubmapconsortium.org/\"\u003eUsing hubmap-clt\u003c/a\u003e for full documentation on getting started with hubmap-clt as we as information on the required Globus software. \n\n### Building and Publishing hubmap-clt\n\n\u003ca href=\"https://pypi.org/project/setuptools/\"\u003eSetupTools\u003c/a\u003e and \u003ca href=\"https://pypi.org/project/wheel/\"\u003eWheel\u003c/a\u003e is required to build the clt distribution. \u003ca href=\"https://pypi.org/project/twine/\"\u003eTwine\u003c/a\u003e is required to publish to Pypi\n\nBuild the distribution directory with: \n\n```bash\npython3 setup.py sdist bdist_wheel\n```\n\nfrom within the hubmap-clt project directory\n\nTo publish, from inside the project directory, run:\n\n```bash\ntwine upload dist/*\n```\n\nA prompt to enter login information to the hubmap Pypi account will appear\n\n### Files\n\nThis code contains:\n\n**\\_\\_main\\_\\_.py**: Contains the implementation of the command-line interface as well as the logic for the clt.\n\nInside of **\\_\\_main\\_\\_.py** are the following classes:\n\n* whoami: Informs the user if they are logged into Globus\n* login: Initiates a Globus login using the default web browser\n* transfer: Sets up a transfer into the user's downloads file. Accepts a single required argument. This argument is the name of a manifest file which contains information on the files to be downloaded\n* batch_transfer: Calls globus batch transfer for each source collection represented in the manifest file. \n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fhubmap-clt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhubmapconsortium%2Fhubmap-clt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhubmapconsortium%2Fhubmap-clt/lists"}