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Overhaul link checker #3092

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a0f2ebc
Add linkinator
dannon Apr 23, 2025
f14455a
Remove broken-link-checker
dannon Apr 23, 2025
1174625
Rewrite check-links to use linkinator
dannon Apr 23, 2025
caff22e
Refine link checking to focus on local links and exclude external URLs
dannon Apr 23, 2025
392182d
Fix link checking excluding external links
dannon Apr 23, 2025
f860ea8
Test localhost availability in action?
dannon Apr 23, 2025
1fc3147
Fix an old galaxy-blast link to verify checker.
dannon Apr 23, 2025
0ebbb43
Fix broken links in blog
dannon May 4, 2025
1f56db6
Fix broken links in events
dannon May 4, 2025
5abd665
Fix broken links in news
dannon May 4, 2025
8e9c5a3
Fix remaining broken links
dannon May 4, 2025
155326f
More broken link fixes
dannon May 6, 2025
a068c5c
Merge branch 'master' into overhaul-link-checker
dannon May 15, 2025
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110 changes: 55 additions & 55 deletions content/archive/dev-news-briefs/2014-04-14/index.md
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Expand Up @@ -67,11 +67,11 @@ date: 2014-04-14
<br />
# Visualizations

1. Framework turning https://trello.com/c/kdhJ1Dit
1. Framework turning [https://trello.com/c/kdhJ1Dit](https://trello.com/c/kdhJ1Dit)
1. *Trackster*:

* View complete read/feature across tile boundaries, in all tiles https://trello.com/c[/Q03dC1](/archive/dev-news-briefs/2014-04-14/Q03dC1/)QC
* Better handling of deep coverage regions in read tracks https://trello.com/c/TxxzqWNx
* View complete read/feature across tile boundaries, in all tiles [https://trello.com/c/Q03dC1QC](https://trello.com/c/Q03dC1QC)
* Better handling of deep coverage regions in read tracks [https://trello.com/c/TxxzqWNx](https://trello.com/c/TxxzqWNx)

<table>
<tr>
Expand All @@ -88,7 +88,7 @@ date: 2014-04-14
<br />
# Workflows

1. Prep for dataset collections: Refactor out common logic for running workflows across controllers https://trello.com/c/pdGNjllH
1. Prep for dataset collections: Refactor out common logic for running workflows across controllers [https://trello.com/c/pdGNjllH](https://trello.com/c/pdGNjllH)

<br />
# UI
Expand All @@ -98,65 +98,65 @@ date: 2014-04-14
* Located at the top of the history pane
* Ability to select: all, none, or check individual datasets
* Actions: Hide, Unhide, Delete, Undelete, Permanently delete (Purge)
* https://wiki.galaxyproject.org/Learn/ManagingDatasets#Searching_Datasets
* [https://wiki.galaxyproject.org/Learn/ManagingDatasets#Searching_Datasets](https://wiki.galaxyproject.org/Learn/ManagingDatasets#Searching_Datasets)
* Additional actions pending review/implementation
* https://trello.com/c/8gLGPzxV, https://trello.com/c/mq1m6X5M,

1. When multiple tool versions installed, default to the latest version https://trello.com/c/zRBZ9nvD
1. Better handling when one of many versions of a tool repo is uninstalled https://trello.com/c[/BmdG2201](/archive/dev-news-briefs/2014-04-14/BmdG2201/)
1. Unify the places where histories are shown and used: UI view and in core code https://trello.com/c/7cN0nmKH
1. Configure workflow menu, improve buttons and styling https://trello.com/c/xFzp3lt6
1. Handle disabled `sessionStorage/localStorage` more gracefully in the history pane https://trello.com/c/V2VCxzmx
1. Remove `BaseView` from base-mvc https://trello.com/c/xUV4qvIc
1. Do not serve non-HTML content that may contain `JavaScript` in such a way that web browsers execute it https://trello.com/c/G67ELiMI
1. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomed https://trello.com/c/d3muKvqr
1. Wiki page on how to compile the css. https://wiki.galaxyproject.org/Develop/CSS https://trello.com/c/gLI6hUjN
* [https://trello.com/c/8gLGPzxV](https://trello.com/c/8gLGPzxV), [https://trello.com/c/mq1m6X5M](https://trello.com/c/mq1m6X5M),

1. When multiple tool versions installed, default to the latest version [https://trello.com/c/zRBZ9nvD](https://trello.com/c/zRBZ9nvD)
1. Better handling when one of many versions of a tool repo is uninstalled [https://trello.com/c/BmdG2201](https://trello.com/c/BmdG2201)
1. Unify the places where histories are shown and used: UI view and in core code [https://trello.com/c/7cN0nmKH](https://trello.com/c/7cN0nmKH)
1. Configure workflow menu, improve buttons and styling [https://trello.com/c/xFzp3lt6](https://trello.com/c/xFzp3lt6)
1. Handle disabled `sessionStorage/localStorage` more gracefully in the history pane [https://trello.com/c/V2VCxzmx](https://trello.com/c/V2VCxzmx)
1. Remove `BaseView` from base-mvc [https://trello.com/c/xUV4qvIc](https://trello.com/c/xUV4qvIc)
1. Do not serve non-HTML content that may contain `JavaScript` in such a way that web browsers execute it [https://trello.com/c/G67ELiMI](https://trello.com/c/G67ELiMI)
1. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomed [https://trello.com/c/d3muKvqr](https://trello.com/c/d3muKvqr)
1. Wiki page on how to compile the css. [https://wiki.galaxyproject.org/Develop/CSS](https://wiki.galaxyproject.org/Develop/CSS) [https://trello.com/c/gLI6hUjN](https://trello.com/c/gLI6hUjN)

<br />
# API

1. New functions:

* Make histories importable and/or published via the API is now implemented (sharing with individual users a pending feature update) https://trello.com/c/Bcsadi1q
* History export/import https://trello.com/c/qhu1KdWU
* Ability to extract workflow from a history to workflows https://trello.com/c/ZTehdMZH
* Make histories importable and/or published via the API is now implemented (sharing with individual users a pending feature update) [https://trello.com/c/Bcsadi1q](https://trello.com/c/Bcsadi1q)
* History export/import [https://trello.com/c/qhu1KdWU](https://trello.com/c/qhu1KdWU)
* Ability to extract workflow from a history to workflows [https://trello.com/c/ZTehdMZH](https://trello.com/c/ZTehdMZH)

1. Improved history payload and returned error consistency https://trello.com/c/fWC7WgQf
1. Check `ftype` attribute (if defined) on test output datasets https://trello.com/c/hFFlM4gY
1. Published histories contents now fully accessible (no permissions issue) https://trello.com/c/KME3ZRRY
1. Correct exception formats used in history & HDA https://trello.com/c/bS9wY4Ri
1. Improved history payload and returned error consistency [https://trello.com/c/fWC7WgQf](https://trello.com/c/fWC7WgQf)
1. Check `ftype` attribute (if defined) on test output datasets [https://trello.com/c/hFFlM4gY](https://trello.com/c/hFFlM4gY)
1. Published histories contents now fully accessible (no permissions issue) [https://trello.com/c/KME3ZRRY](https://trello.com/c/KME3ZRRY)
1. Correct exception formats used in history & HDA [https://trello.com/c/bS9wY4Ri](https://trello.com/c/bS9wY4Ri)

<br />
# Core

1. Admin:

* History view, allow importing purged datasets https://trello.com/c/tbhpQdMF
* User list, show 'activated' and 'create_time' columns https://trello.com/c[/C6Mh](/archive/dev-news-briefs/2014-04-14/C6Mh/)EHWo
* Setting user quota at zero is now permitted (no `ZeroDivisionError`) https://trello.com/c/38NoBtlL
* Admin user now has permissions to copy datasets from any history to a library https://trello.com/c/Ed91qIUC
* Improvements to 'Impersonate User' implementation https://trello.com/c/lny2me4u
* History view, allow importing purged datasets [https://trello.com/c/tbhpQdMF](https://trello.com/c/tbhpQdMF)
* User list, show 'activated' and 'create_time' columns https://trello.com/c/C6MhEHWo
* Setting user quota at zero is now permitted (no `ZeroDivisionError`) [https://trello.com/c/38NoBtlL](https://trello.com/c/38NoBtlL)
* Admin user now has permissions to copy datasets from any history to a library [https://trello.com/c/Ed91qIUC](https://trello.com/c/Ed91qIUC)
* Improvements to 'Impersonate User' implementation [https://trello.com/c/lny2me4u](https://trello.com/c/lny2me4u)

1. Config:

* Rename `tool-data/shared/ucsc/ucsc_build_sites.txt` to `ucsc_build_sites.txt.sample` https://trello.com/c/FTbvqDMd
* Rename `tool-data/shared/ucsc/ucsc_build_sites.txt` to `ucsc_build_sites.txt.sample` [https://trello.com/c/FTbvqDMd](https://trello.com/c/FTbvqDMd)

1. Jobs:

* Prevent 'unicode' strings being sent to pbs library as hostname https://trello.com/c/NlFXYDta
* Fix Torque CLI runner to recognize complete ('C') state as 'ok' https://trello.com/c/vSO52k17
* Are now cancelled if a running history item is deleted (via API). https://trello.com/c/PDmUdtbw
* Prevent 'unicode' strings being sent to pbs library as hostname [https://trello.com/c/NlFXYDta](https://trello.com/c/NlFXYDta)
* Fix Torque CLI runner to recognize complete ('C') state as 'ok' [https://trello.com/c/vSO52k17](https://trello.com/c/vSO52k17)
* Are now cancelled if a running history item is deleted (via API). [https://trello.com/c/PDmUdtbw](https://trello.com/c/PDmUdtbw)

1. LWR:

* Several updates including communication via message queue, more planned https://trello.com/c/6DcXqXNt
* Introduce and extend along with `ComputeEnvironment`, to eliminate string based path rewriting https://trello.com/c/dL0poowc
* Several updates including communication via message queue, more planned [https://trello.com/c/6DcXqXNt](https://trello.com/c/6DcXqXNt)
* Introduce and extend along with `ComputeEnvironment`, to eliminate string based path rewriting [https://trello.com/c/dL0poowc](https://trello.com/c/dL0poowc)

1. Eggs:

* Guppy 0.1.9+ https://trello.com/c/zeSnHEav
* Boto 2.25 to facilitate launching into VPC https://trello.com/c/QXfJQhlS
* PyYAML 3.10 to be used initially with `Cloudlaunch` for parsing `persistent_data yaml` https://trello.com/c/JMZkqBtH
* Guppy 0.1.9+ [https://trello.com/c/zeSnHEav](https://trello.com/c/zeSnHEav)
* Boto 2.25 to facilitate launching into VPC [https://trello.com/c/QXfJQhlS](https://trello.com/c/QXfJQhlS)
* PyYAML 3.10 to be used initially with `Cloudlaunch` for parsing `persistent_data yaml` [https://trello.com/c/JMZkqBtH](https://trello.com/c/JMZkqBtH)

<br />
# Pull Requests Merged
Expand All @@ -166,16 +166,16 @@ Thanks to our Galaxy community contributors!
1. 309 - Job module for API (list and inspect jobs). Kyle Ellrott. https://trello.com/c/s2Gk6QlH
1. 312 - Remove unused imports and unused variables. Fix spacing. Nicola Soranzo. https://trello.com/c/iWaf1ak4
1. 316 - Fixing non-string parameter selection for job searches. Kyle Ellrott. https://trello.com/c/ZXZ9lEkN
1. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo. https://trello.com/c[/JaC2](/archive/dev-news-briefs/2014-04-14/JaC2/)EBM8
1. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo. https://trello.com/c/JaC2EBM8
1. 318 - Adding deleted field to 'to_dict' and search selection of Workflows. Kyle Ellrott. https://trello.com/c/lv9q67nF
1. 315 - Allow jobs to be filtered by tool_id and history_id as well as by state. The tool_id is compared with the like operator. James Johnson https://trello.com/c/dvLvPUmK
1. 322 - Added "ignore lines starting with specific characters" to group tool. Clayton Turner. https://trello.com/c/j6TP6M7m
1. 323 - API methods to access Workflow Usage. Kyle Ellrott. https://trello.com/c[/UetzHj64](/archive/dev-news-briefs/2014-04-14/UetzHj64/)
1. 323 - API methods to access Workflow Usage. Kyle Ellrott. https://trello.com/c/UetzHj64
1. 325 - Use `placeholder` instead of `value` in html5 - editor.mako. Trevor Wennblom. https://trello.com/c/PIZAXsOS
1. 326 - Specify third-party cookies must not be blocked - repository.py. Trevor Wennblom. https://trello.com/c/XsAUr6wl
1. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom. https://trello.com/c[/WtWdxP2n](/archive/dev-news-briefs/2014-04-14/WtWdxP2n/)
1. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom. https://trello.com/c/WtWdxP2n
1. 341 - Workflows API enhancements (pull request #337 corrected). Nicola Soranzo and Simone Leo. https://trello.com/c/zizGdqy1
1. 338 - Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). Kyle Ellrott https://trello.com/c[/BrOscq](/archive/dev-news-briefs/2014-04-14/BrOscq/)TJ
1. 338 - Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). Kyle Ellrott https://trello.com/c/BrOscqTJ
1. 339 - Strip trailing slashes in tool IDs. Björn Grüning. https://trello.com/c/bpKNn66u
1. 334 - Optional Input Datasets Not Compatible with Parallelism Tag. Michael Li https://trello.com/c/WMgr8Xx0 https://trello.com/c/Muw6fd8h
1. 346 - Tool panel label bug correction. Nicola Soranzo. https://trello.com/c/8NpgYM3U
Expand All @@ -184,35 +184,35 @@ Thanks to our Galaxy community contributors!

# Fixes

1. Fix issue with tool panel display when the tool_conf.xml has only a single entry https://trello.com/c/6nJIhOdJ
1. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panel https://trello.com/c/SlNI79mR
1. Fix Published Page's JS error https://trello.com/c/yGw1DwwM
1. Fix error in Babel egg utf-8, OSX 10.7 https://trello.com/c/PUdh6SWw
1. Fix failures when using unicode in History name editable_text fields https://trello.com/c/MTdotrHR
1. Fix tool form image display for toolshed installed tools https://trello.com/c/5G6jlB4B
1. Fix to improve link format in user activation emails https://trello.com/c/JALX9DL3
1. Fix problem with rerun of tools having `DataToolParameter` set as optional https://trello.com/c/pzHcSGzK
1. Fix bug in Tool Panel when installing repositories https://trello.com/c[/AiUefff](/archive/dev-news-briefs/2014-04-14/AiUefff/)C
1. Fix issue with tool panel display when the tool_conf.xml has only a single entry [https://trello.com/c/6nJIhOdJ](https://trello.com/c/6nJIhOdJ)
1. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panel [https://trello.com/c/SlNI79mR](https://trello.com/c/SlNI79mR)
1. Fix Published Page's JS error [https://trello.com/c/yGw1DwwM](https://trello.com/c/yGw1DwwM)
1. Fix error in Babel egg utf-8, OSX 10.7 [https://trello.com/c/PUdh6SWw](https://trello.com/c/PUdh6SWw)
1. Fix failures when using unicode in History name editable_text fields [https://trello.com/c/MTdotrHR](https://trello.com/c/MTdotrHR)
1. Fix tool form image display for toolshed installed tools [https://trello.com/c/5G6jlB4B](https://trello.com/c/5G6jlB4B)
1. Fix to improve link format in user activation emails [https://trello.com/c/JALX9DL3](https://trello.com/c/JALX9DL3)
1. Fix problem with rerun of tools having `DataToolParameter` set as optional [https://trello.com/c/pzHcSGzK](https://trello.com/c/pzHcSGzK)
1. Fix bug in Tool Panel when installing repositories [https://trello.com/c/AiUefffC](https://trello.com/c/AiUefffC)

<br />
# Tool Shed

**[Tool Shed](/toolshed/)**
## Documentation

1. Reorganization of the Tool Shed wiki is underway! See current changes https://wiki.galaxyproject.org[/ToolShed](/archive/dev-news-briefs/2014-04-14/ToolShed/) and what is next up https://trello.com/c/Gg0jnll7
1. Data Manager documentation specific to toolshed http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository https://trello.com/c/OPOakK4w
1. Reorganization of the Tool Shed wiki is underway! See current changes [https://wiki.galaxyproject.org/ToolShed](https://wiki.galaxyproject.org/ToolShed) and what is next up [https://trello.com/c/Gg0jnll7](https://trello.com/c/Gg0jnll7)
1. Data Manager documentation specific to toolshed [http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository](http://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool_shed_repository) [https://trello.com/c/OPOakK4w](https://trello.com/c/OPOakK4w)

## Repositories

1. New Tool Shed categories https://trello.com/c/niCdaARH
1. New Tool Shed categories [https://trello.com/c/niCdaARH](https://trello.com/c/niCdaARH)

* Genome-Wide Association Study
* Imaging
* RNA

1. Add support for the new repository type: Repository suite definition https://trello.com/c/sxXMmfLs
1. Enhancements for updating a repository https://trello.com/c/c4Y9t7db
1. Add support for the new repository type: Repository suite definition [https://trello.com/c/sxXMmfLs](https://trello.com/c/sxXMmfLs)
1. Enhancements for updating a repository [https://trello.com/c/c4Y9t7db](https://trello.com/c/c4Y9t7db)

* Will now trigger the install of new dependencies
* Handles newly defined repository dependencies included in updates to installed repositories
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2 changes: 1 addition & 1 deletion content/blog/2022-01-14-users-guide-to-contribution-ross/index.md
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Expand Up @@ -24,7 +24,7 @@ Whatever motivates individuals, in addition to the satisfaction of contributing

### Where to start?

Galaxy is a complicated project, with many moving parts. At first, it can be hard to figure out how it all works, or where your specific skill set and interests might fit. One person's view of the *big picture* in terms of Galaxy's impact on open scientific computing can be found [here](../2022-01-16-open-scientific-computing-ross).
Galaxy is a complicated project, with many moving parts. At first, it can be hard to figure out how it all works, or where your specific skill set and interests might fit. One person's view of the *big picture* in terms of Galaxy's impact on open scientific computing can be found [here](/blog/2022-01-16-open-scientific-computing-ross).

Two main activity areas can be distinguished, ***technical*** and ***community***. The distinction is only useful for organising things, because active two way interchange and overlap are always needed to keep all the different activities coordinated. There are a number of contributors who work in both areas, to ensure good communication and integration.

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