HumanCellAtlas/dcp-cli issues and pull requests

#529 - [Snyk] Security upgrade setuptools from 40.5.0 to 70.0.0

Pull Request - State: open - Opened by Fab-T 7 months ago

#528 - [Snyk] Security upgrade zipp from 3.15.0 to 3.19.1

Pull Request - State: open - Opened by Bento007 8 months ago

#527 - [Snyk] Security upgrade setuptools from 40.5.0 to 65.5.1

Pull Request - State: open - Opened by Fab-T 12 months ago

#526 - Deprecate repository

Pull Request - State: closed - Opened by amarjandu almost 4 years ago - 2 comments

#525 - [Snyk] Security upgrade rsa from 4.5 to 4.7

Pull Request - State: open - Opened by sbeara about 4 years ago

#524 - Unable to login due to headers

Issue - State: open - Opened by amarjandu almost 5 years ago - 1 comment
Labels: BUG, orange

#523 - create sub-directories when downloading files with !

Pull Request - State: open - Opened by amarjandu almost 5 years ago - 1 comment
Labels: orange

#522 - Remove dss-prod from testing

Pull Request - State: closed - Opened by amarjandu almost 5 years ago - 2 comments
Labels: orange

#521 - Fall back to copying when os.link raises error

Pull Request - State: closed - Opened by chmreid almost 5 years ago - 6 comments
Labels: orange

#520 - Add symbolic links as alternative to hard links

Issue - State: open - Opened by hannes-ucsc almost 5 years ago - 1 comment
Labels: orange

#519 - Hard-link creation fails when downloading to NFS mounts

Issue - State: closed - Opened by fangpingmu almost 5 years ago - 5 comments
Labels: BUG, orange, no demo

#518 - Develop script to restore the zarr directory structure following download

Issue - State: closed - Opened by theathorn almost 5 years ago - 4 comments
Labels: BUG, orange

#517 - Close file handlers after use

Pull Request - State: closed - Opened by GPelayo almost 5 years ago - 1 comment

#516 - Order of arguments matters for `hca dss download-manifest`

Issue - State: closed - Opened by chmreid about 5 years ago - 7 comments
Labels: BUG, orange

#515 - Create subdirectories with `hca dss download-manifest --layout bundle`

Issue - State: open - Opened by jessebrennan about 5 years ago - 1 comment
Labels: ENH, orange

#514 - Set version for gitdb2, a secondary dependency of Trufflehog

Pull Request - State: closed - Opened by achave11-ucsc about 5 years ago - 1 comment
Labels: orange

#513 - Close file handlers after use

Pull Request - State: closed - Opened by GPelayo about 5 years ago - 2 comments
Labels: demoed, orange

#512 - commit reordering attempt

Pull Request - State: closed - Opened by GPelayo about 5 years ago - 1 comment

#511 - pin docutils in requirements.txt

Pull Request - State: closed - Opened by amarjandu about 5 years ago - 2 comments
Labels: BUG

#510 - Pen testing build infrastructure

Pull Request - State: closed - Opened by GPelayo about 5 years ago - 2 comments
Labels: demoed, orange

#509 - Test Travis when creating PR from forked repo against parent repo

Pull Request - State: closed - Opened by GPelayo about 5 years ago
Labels: demoed, orange

#508 - Pen-test build infrastructure

Issue - State: closed - Opened by hannes-ucsc about 5 years ago
Labels: demoed, orange

#507 - Version numbers are inconsistent

Issue - State: closed - Opened by chmreid about 5 years ago - 1 comment

#506 - Close file handlers after use

Pull Request - State: closed - Opened by GPelayo about 5 years ago - 1 comment
Labels: orange

#505 - Upload breaks if too many files (100+?)

Issue - State: closed - Opened by GPelayo about 5 years ago
Labels: demoed, orange

#504 - Remove references to query service

Pull Request - State: closed - Opened by MDunitz about 5 years ago - 1 comment

#503 - [easy] Fix readme.rst links to API/CLI examples

Pull Request - State: open - Opened by chmreid about 5 years ago - 1 comment

#502 - Allow a user to specify file uuids in "upload()".

Pull Request - State: closed - Opened by DailyDreaming about 5 years ago - 2 comments

#501 - login command says "address already in use" but does not provide useful information

Issue - State: open - Opened by chmreid about 5 years ago - 1 comment

#500 - post_search.iterate() iterator does not terminate cleanly

Issue - State: open - Opened by chmreid about 5 years ago
Labels: BUG

#499 - Allow user-specified bundle uuid for upload().

Pull Request - State: closed - Opened by DailyDreaming about 5 years ago - 2 comments

#498 - Add `httpie` as dev requirement (#495)

Pull Request - State: closed - Opened by jessebrennan about 5 years ago - 1 comment

#497 - hca dss refresh-swagger no longer exists.

Issue - State: open - Opened by DailyDreaming about 5 years ago

#496 - DSS: Verbose URLS

Issue - State: closed - Opened by amarjandu about 5 years ago - 1 comment

#495 - Release script fails part way through

Issue - State: closed - Opened by jessebrennan about 5 years ago - 4 comments
Labels: BUG, orange, added_to_sprint

#494 - Rename bundle.json to bundle_manifest.json

Issue - State: open - Opened by hannes-ucsc over 5 years ago - 1 comment
Labels: orange

#493 - Auth error.

Issue - State: open - Opened by DailyDreaming over 5 years ago

#492 - DSS Subscriptions: Callback Url

Pull Request - State: closed - Opened by amarjandu over 5 years ago - 1 comment

#491 - Fix some progress bar tests failing silently

Pull Request - State: closed - Opened by natanlao over 5 years ago - 2 comments
Labels: added_to_sprint

#490 - test_swagger_client_refresh is flaky

Issue - State: open - Opened by jessebrennan over 5 years ago

#489 - Rearrange new tutorials pages in sphinx documentation

Pull Request - State: closed - Opened by chmreid over 5 years ago

#488 - Add a checkout sync operation.

Issue - State: closed - Opened by DailyDreaming over 5 years ago

#487 - Refresh jwt using dcplib.

Issue - State: open - Opened by DailyDreaming over 5 years ago

#486 - Fix dss download docstring to use correct flags

Pull Request - State: closed - Opened by chmreid over 5 years ago - 1 comment

#485 - dss download-manifest throws exceptions on duplicate files

Issue - State: closed - Opened by chmreid over 5 years ago - 5 comments
Labels: BUG, demoed, orange

#484 - Update version number to revert #476

Pull Request - State: closed - Opened by chmreid over 5 years ago - 1 comment

#483 - Fix import dependencies

Pull Request - State: closed - Opened by DailyDreaming over 5 years ago - 2 comments

#482 - Fix import dependencies.

Pull Request - State: closed - Opened by DailyDreaming over 5 years ago - 3 comments

#481 - Downloading resources are wasted if threads are downloading the same file

Issue - State: open - Opened by jessebrennan over 5 years ago
Labels: orange

#480 - Change flags starting with - to start with --

Pull Request - State: closed - Opened by chmreid over 5 years ago - 1 comment

#479 - Fix sub-command description indentation in sphinx docs

Pull Request - State: closed - Opened by chmreid over 5 years ago - 1 comment

#478 - Autopagination hangs in staging and prod.

Issue - State: open - Opened by DailyDreaming over 5 years ago - 2 comments

#477 - Fix duplicate download (#450)

Pull Request - State: closed - Opened by jessebrennan over 5 years ago - 4 comments

#476 - Fix version numbering

Pull Request - State: closed - Opened by chmreid over 5 years ago - 7 comments

#475 - Incorrect version number behavior

Issue - State: closed - Opened by chmreid over 5 years ago

#474 - Make user choose download layout

Issue - State: open - Opened by theathorn over 5 years ago
Labels: orange

#473 - Logging messages with weird `.hca` paths are confusing to users

Issue - State: closed - Opened by jessebrennan over 5 years ago - 1 comment

#472 - Add API/CLI tutorial pages to Sphinx documentation

Pull Request - State: closed - Opened by chmreid over 5 years ago - 8 comments

#471 - remove api version from method_name

Pull Request - State: closed - Opened by amarjandu over 5 years ago - 4 comments

#468 - Wrap CLI functionality as an R library.

Issue - State: open - Opened by DailyDreaming over 5 years ago - 1 comment

#467 - Pagination error in get_bundles_all

Issue - State: closed - Opened by kislyuk over 5 years ago - 2 comments

#465 - auto pagination

Pull Request - State: closed - Opened by amarjandu over 5 years ago - 5 comments

#461 - Inline Support for Pagination

Issue - State: closed - Opened by amarjandu over 5 years ago

#460 - Fix documentation - remove extra periods between paragraphs

Pull Request - State: closed - Opened by chmreid over 5 years ago - 7 comments

#459 - update required python version to 3.5+

Pull Request - State: closed - Opened by mshadbolt over 5 years ago - 1 comment

#458 - Use proper configurations for csv reading/writing (#449)

Pull Request - State: closed - Opened by jessebrennan over 5 years ago - 3 comments

#455 - Work around link limit with manifest download (#427)

Pull Request - State: closed - Opened by jessebrennan over 5 years ago - 2 comments

#454 - Prettify the contents of bundle.json

Pull Request - State: closed - Opened by GPelayo over 5 years ago - 2 comments

#453 - Download-manifest reverts to copying if it can no longer link

Issue - State: open - Opened by jessebrennan over 5 years ago
Labels: orange

#452 - Help string is out of date for `hca dss download`

Issue - State: closed - Opened by jessebrennan over 5 years ago
Labels: BUG, orange

#450 - download-manifest downloads fastq files twice for analysed projects?

Issue - State: closed - Opened by mshadbolt over 5 years ago - 6 comments
Labels: BUG, demoed, orange

#449 - _.csv.Error when using hca dss download-manifest

Issue - State: closed - Opened by mshadbolt over 5 years ago - 4 comments
Labels: BUG, orange, no demo

#446 - Refresh session token when the jwt expires.

Pull Request - State: closed - Opened by DailyDreaming over 5 years ago - 5 comments

#445 - --no-data not working for dss download-manifest command

Issue - State: closed - Opened by NoopDog over 5 years ago - 5 comments
Labels: BUG, orange, invalid

#444 - Format bundle.json

Issue - State: closed - Opened by jessebrennan over 5 years ago
Labels: demoed, orange

#443 - Issues with Readthedocs documentation

Issue - State: closed - Opened by chmreid over 5 years ago - 2 comments

#439 - Create HCA Login

Issue - State: open - Opened by Bento007 over 5 years ago - 5 comments

#427 - Reached link limit when downloading a large amount of bundles (140000+)

Issue - State: closed - Opened by GPelayo over 5 years ago - 3 comments
Labels: BUG, demoed, orange

#425 - Make `--layout=bundle` the default

Issue - State: closed - Opened by hannes-ucsc over 5 years ago - 11 comments
Labels: orange, needs info

#424 - Added API/CLI example sphinx pages

Pull Request - State: closed - Opened by jeffrey856 over 5 years ago - 7 comments

#417 - Add Fusillade API client

Pull Request - State: closed - Opened by Bento007 over 5 years ago - 7 comments

#405 - Eagerly initiate checkout when downloading bundles

Issue - State: open - Opened by hannes-ucsc over 5 years ago

#397 - Clarify resulting location of files from download command

Issue - State: open - Opened by kozbo over 5 years ago - 1 comment
Labels: orange

#394 - Add an option to delete the cache when download completes.

Pull Request - State: open - Opened by DailyDreaming over 5 years ago - 5 comments

#391 - hca dss put-bundle --files argument error

Issue - State: open - Opened by jeffrey856 over 5 years ago - 3 comments
Labels: BUG

#390 - dss download size prioritization

Issue - State: open - Opened by amarjandu over 5 years ago - 1 comment

#362 - DSS API Testing and Tutorials

Issue - State: closed - Opened by DailyDreaming over 5 years ago - 1 comment
Labels: Epic

#357 - Force user to choose download directory

Issue - State: open - Opened by DailyDreaming over 5 years ago - 4 comments
Labels: ENH, orange

#356 - Manifest download does not support downloading files not associated with a bundle

Issue - State: open - Opened by natanlao over 5 years ago - 2 comments
Labels: ENH

#355 - Download manifest improvements

Issue - State: open - Opened by theathorn over 5 years ago
Labels: Epic, orange

#353 - [easy] Choose an unused port when logging in.

Pull Request - State: open - Opened by DailyDreaming over 5 years ago - 1 comment

#350 - Test Refactor for Windows

Issue - State: closed - Opened by amarjandu over 5 years ago - 1 comment
Labels: demoed, orange

#348 - README doesn't describe tool that adds command line options from the code

Issue - State: open - Opened by diekhans almost 6 years ago - 2 comments

#238 - Generate full metadata.tsv upon completed manifest download

Issue - State: open - Opened by hannes-ucsc about 6 years ago - 3 comments
Labels: ENH, orange

#237 - Implement per-project+sample directory layout for manifest downloads

Issue - State: open - Opened by hannes-ucsc about 6 years ago - 2 comments
Labels: ENH, orange

#230 - [WIP] Manifest download improvements

Pull Request - State: closed - Opened by hannes-ucsc about 6 years ago - 2 comments

#202 - Improve thread safety of SwaggerClient

Pull Request - State: open - Opened by mckinsel over 6 years ago - 7 comments

#198 - CLI help lists unusable parameters on post-search

Issue - State: open - Opened by kozbo over 6 years ago - 1 comment
Labels: BUG

#191 - Don't retry if endpoint hostname does not resolve

Issue - State: open - Opened by hannes-ucsc over 6 years ago - 4 comments
Labels: BUG

#130 - Adjust default client timeouts

Pull Request - State: closed - Opened by hannes-ucsc over 6 years ago - 1 comment

GitHub / HumanCellAtlas/dcp-cli issues and pull requests