add API endpoint to create TS repository #2

martenson · 2015-02-23T22:55:21Z

This PR introduces new endpoint at the Tool Shed
you can POST {toolshed_url}/api/repository

{
"name": "new_repo_17",
"synopsis": "new_synopsis",
"description": "this is some repository",
"type": "unrestricted",
"remote_repository_url": "https://github.com/galaxyproject/tools-devteam",
"homepage_url": "https://github.com/galaxyproject/",
"category_ids[]": [ "adb5f5c93f827949", "529fd61ab1c6cc36" ]
}

and you will receive:

{
"deleted": false,
"deprecated": false,
"description": "new_synopsis",
"homepage_url": "https://github.com/galaxyproject/",
"id": "8cf91205f2f737f4",
"long_description": "this is some repository",
"model_class": "Repository",
"name": "new_repo_17",
"owner": "qqqqqq",
"private": false,
"remote_repository_url": "https://github.com/galaxyproject/tools-devteam",
"times_downloaded": 0,
"type": "unrestricted",
"user_id": "adb5f5c93f827949"
}

add API endpoint to create TS repository

dannon · 2015-02-26T20:38:16Z

This is an automated message. Thanks for your contribution, a Trello card to track this issue has been created. Apply this patch for testing.

hexylena · 2015-02-27T02:21:40Z

Thanks @martenson. @jmchilton I'm assuming code for this will need to be added to bioblend for it can be used in planemo?

jmchilton · 2015-02-27T02:25:38Z

Good plan! I don't know if I can get to it before the release (there are a lot of bugs left) - but ping after please if I forget - or PR's to bioblend welcome :).

hexylena · 2015-02-27T02:27:20Z

Ok, I'll have some time tomorrow for making those PRs, I'll see what I can get done. It's significantly of interest to me to automate that portion.

bgruening · 2015-02-27T07:43:55Z

How should we handle this in shed.yml? Simply adding

synopsis
description
type: one out of three?
remote_repository_url
homepage_url
category_ids []

Category list will fail silently if the category does not exists?

hexylena · 2015-02-27T13:59:58Z

I was going to use category titles rather than IDs and yes, print a warning
if the category doesn't exist.

Will need to add code to handle updating that information if it gets
changed over time

fre. 27. feb. 2015, 07.43 skrev Björn Grüning [email protected]:

How should we handle this in shed.yml? Simply adding

synopsis

description

type: one out of three?

remote_repository_url

homepage_url

category_ids []

Category list will fail silently if the category does not exists?

—
Reply to this email directly or view it on GitHub
#2 (comment).

hexylena · 2015-03-02T13:32:03Z

@martenson which parameters are required? name/synopsis/description?

bgruening · 2015-03-02T13:34:17Z

afaik, description is not required ...

hexylena · 2015-03-02T13:35:30Z

@martenson @bgruening never mind...it's documented in the docstring. Thanks @martenson!

Develop

Updates to take advantage of galaxyproject#229 infrastructure

Add a library_data input test case and small fix.

add some trello card links to release notes

update

Tweak a few indentations to avoid kicking toplevel parameters into se…

Merge Reports_homepage against latest dev.

Collect error messages (which fixes the current travis build), some other cleanup for sanity.

Remove trailing whitespace

Remove deprecated datatype stuff

Adjustments to sanitize_whitelist reloading.

A few more tweaks to tours

A first pass on the "admin" UI related section

Minor tweaks to i18n work

More general safe_walk function, handles symlinks loops

Conditional galaxycloudrunner

Release 19.01 updates

Fix test tool label and tool xsd

Use a base URI set in config for Custos Authnz backend.

get latest from dev

Release 19.09

fix crash when no input selected

1. Remove `item` instance attribute: it's not used and is meaningless. 2. Make user and item parameters in the constructor required: a rating cannot exist without a rater or the item being rated. 3. For the same reason as in #2, make the `set_item()` method private and only call it from the constructor. 4. Simplify mapping test: just use the constructor.

1. Remove id parameter from constructor (this is created by the db). 2. Remove `item` instance attribute: it's not used and is meaningless. 3. Make user and item parameters in the constructor required: a rating cannot exist without a rater or the item being rated. 4. For the same reason as in #2, make the `set_item()` method private and only call it from the constructor. 5. Simplify mapping test: just use the constructor.

Reason: late evaluation of arguments causes errors in mypy; also this seems to be the more common (as per SA docs) and more readable method compared to lambdas. Downside #1: a typo in the string value won't be caught by lint tools. Downside #2: if there's a sufficiently complex statement, it will be hard to read if it's all on one line; primaryjoin = "and_(HistoryDatasetAssociation.history_id == History.id, not_(HistoryDatasetAssociation.deleted), HistoryDatasetAssociation.visible)" splitting across lines will require surrounding each line with quotes: primaryjoin = ( "and_(" "HistoryDatasetAssociation.history_id == History.id," "not_(HistoryDatasetAssociation.deleted)," "HistoryDatasetAssociation.visible," ")" ) Still, I think it's better than the alternative (lambda + multiple type-ignores after each line: primaryjoin = lambda( and_( HistoryDatasetAssociation.history_id == History.id, # type:ignore[has-type, arg-type] not_(HistoryDatasetAssociation.deleted), # type:ignore[has-type, arg-type] HistoryDatasetAssociation.visible, # type:ignore[has-type, arg-type] ) )

add API endpoint to create TS repository

dafa844

jmchilton added a commit that referenced this pull request Feb 25, 2015

Merge pull request #2 from martenson/ts-api-create-repo

e75ad46

add API endpoint to create TS repository

jmchilton merged commit e75ad46 into galaxyproject:dev Feb 25, 2015

jmchilton mentioned this pull request Feb 27, 2015

Add Endpoint for Tool Shed Repository Creation galaxyproject/bioblend#116

Closed

martenson deleted the ts-api-create-repo branch March 5, 2015 21:38

This was referenced Mar 17, 2015

Fixes #116 galaxyproject/bioblend#124

Merged

Automate pushing to TTS/MTS galaxyproject/tools-iuc#73

Closed

Missing brackets in API url parameter galaxyproject/bioblend#128

Merged

Expose category list in show call for repositories #29

Merged

hexylena referenced this pull request in hexylena/galaxy May 6, 2015

Merge pull request #2 from erasche/develop

1599644

Develop

jmchilton referenced this pull request in jmchilton/galaxy May 11, 2015

Merge pull request #2 from erasche/rstudio2

67e7dcf

Updates to take advantage of galaxyproject#229 infrastructure

guerler added a commit that referenced this pull request May 13, 2015

Merge pull request #2 from jmchilton/library_data

5ec0bf2

Add a library_data input test case and small fix.

natefoo referenced this pull request in natefoo/galaxy May 13, 2015

Merge pull request #2 from martenson/patch-1

660e9a7

add some trello card links to release notes

jmchilton pushed a commit that referenced this pull request Jul 2, 2015

Merge pull request #2 from galaxyproject/dev

7b06d5a

update

carlfeberhard added a commit that referenced this pull request Jul 23, 2015

Merge pull request #2 from dannon/pephate

05a15c8

Tweak a few indentations to avoid kicking toplevel parameters into se…

dannon referenced this pull request in dannon/galaxy Jul 29, 2015

Merge pull request #2 from jmchilton/Reports_homepage

739dddb

Merge Reports_homepage against latest dev.

blankenberg added a commit that referenced this pull request Aug 25, 2015

Merge pull request #2 from dannon/recurse-toolshed-changeset

dde800b

Collect error messages (which fixes the current travis build), some other cleanup for sanity.

hexylena pushed a commit that referenced this pull request Oct 14, 2015

Merge pull request #2 from erasche/whitespace-fix-827

e54df2e

Remove trailing whitespace

jennaj mentioned this pull request Nov 5, 2015

Enhancements for Custom Builds form #1034

Open

jmchilton pushed a commit that referenced this pull request Dec 3, 2015

Merge pull request #2 from jmchilton/triples_2

4c13c92

Remove deprecated datatype stuff

nsoranzo added a commit that referenced this pull request Dec 10, 2015

Merge pull request #2 from dannon/release_15.10_config

2835aea

Adjustments to sanitize_whitelist reloading.

dannon pushed a commit that referenced this pull request Oct 26, 2017

Merge pull request #2 from dannon/selten_dev

32ffcaf

A few more tweaks to tours

dannon pushed a commit that referenced this pull request Dec 22, 2017

Merge pull request #2 from yvanlebras/patch-4

c828fa4

A first pass on the "admin" UI related section

dannon pushed a commit that referenced this pull request Feb 7, 2018

Merge pull request #2 from dannon/i18n

c3bb285

Minor tweaks to i18n work

martenson pushed a commit that referenced this pull request Mar 2, 2018

Merge pull request #2 from natefoo/bwlang-import_dirs_check_whitelist

a017470

More general safe_walk function, handles symlinks loops

jmchilton pushed a commit that referenced this pull request Jan 18, 2019

Merge pull request #2 from dannon/conditional_galaxycloudrunner

76ac198

Conditional galaxycloudrunner

ThanKarab referenced this pull request in madgik/galaxy Mar 6, 2019

Merge pull request #2 from galaxyproject/release_19.01

b7f454f

Release 19.01 updates

martenson pushed a commit that referenced this pull request Mar 7, 2019

Merge pull request #2 from mvdbeek/fmareuil-dev

b8c5ee3

Fix test tool label and tool xsd

afgane pushed a commit that referenced this pull request Apr 8, 2019

Merge pull request #2 from VJalili/patch-5

5ed8d11

Use a base URI set in config for Custos Authnz backend.

dannon pushed a commit that referenced this pull request May 14, 2019

Merge pull request #2 from galaxyproject/dev

38a04f1

get latest from dev

almahmoud referenced this pull request in almahmoud/galaxy Oct 10, 2019

Merge pull request #2 from galaxyproject/release_19.09

dd45125

Release 19.09

martenson mentioned this pull request Apr 28, 2020

Sort Tool Search Result by ranking #9579

Merged

mvdbeek pushed a commit that referenced this pull request Sep 22, 2020

Merge pull request #2 from abretaud/fix_nofile

ed9f5a5

fix crash when no input selected

hmenager mentioned this pull request Oct 29, 2020

Replace tool panel sections with EDAM #10587

Closed

kjetilkl mentioned this pull request Dec 17, 2020

History options menu webhook kjetilkl/galaxy#1

Open

bgruening pushed a commit that referenced this pull request Jul 5, 2022

QIIME 2: Strip properties from semantic types (#2)

38b1bfc

mvdbeek mentioned this pull request Nov 29, 2023

dataset.file_name removal breaks exisiting tools #17098

Closed

mvdbeek pushed a commit that referenced this pull request Nov 25, 2024

Suppress mypy error (#2)

48d88ea

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

add API endpoint to create TS repository #2

add API endpoint to create TS repository #2

martenson commented Feb 23, 2015

dannon commented Feb 26, 2015

hexylena commented Feb 27, 2015

jmchilton commented Feb 27, 2015

hexylena commented Feb 27, 2015

bgruening commented Feb 27, 2015

hexylena commented Feb 27, 2015

hexylena commented Mar 2, 2015

bgruening commented Mar 2, 2015

hexylena commented Mar 2, 2015

add API endpoint to create TS repository #2

add API endpoint to create TS repository #2

Conversation

martenson commented Feb 23, 2015

dannon commented Feb 26, 2015

hexylena commented Feb 27, 2015

jmchilton commented Feb 27, 2015

hexylena commented Feb 27, 2015

bgruening commented Feb 27, 2015

hexylena commented Feb 27, 2015

hexylena commented Mar 2, 2015

bgruening commented Mar 2, 2015

hexylena commented Mar 2, 2015