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Wiki to hub link update. #3754

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merged 16 commits into from Apr 28, 2017

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@dannon
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commented Mar 14, 2017

Unfortunately there are quite a few of these. I updated a couple and pretty much immediately ran into a missing page, so I'm going to add those as I hit them.

As mentioned in one of the commits, this logic needs to be consolidated in a lot of places.

This may be WIP for a while.

@dannon dannon added the status/WIP label Mar 14, 2017

@dannon dannon added this to the 17.05 milestone Mar 14, 2017

@dannon dannon changed the title Wiki to hub Wiki to hub link update. Mar 14, 2017

@nsoranzo nsoranzo added the kind/bug label Mar 14, 2017

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commented Mar 14, 2017

doc/source/ also has a bunch of them.

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commented Mar 14, 2017

Yep, there are quite a few. I'm grepping through incrementally.

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commented Mar 15, 2017

Redirects are in place so I believe we do not need to commit to a big cleanup.

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commented Mar 15, 2017

I agree that because of the redirects it's not particularly important to get this out the door right away, but we should still update URLs where they are incorrect (or, let's say, can be improved to be more accurate as the current URL), and I'll do so in this PR.

Merge pull request #16 from bgruening/wf_link
/learn/advanced-workflow/variables-edit

@martenson martenson changed the title Wiki to hub link update. [WIP] Wiki to hub link update. Apr 19, 2017

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commented Apr 26, 2017

@dannon If you fix the merge conflict and remove the WIP label, I'll review and eventually merge this.

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commented Apr 26, 2017

@nsoranzo Yep. Going to make one quick pass over it when we're off the call and will take it out of WIP today.

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commented Apr 26, 2017

(back in WIP for a sec -- merge looks like it had an issue)

edit: fixed with 0dd75e6

@dannon dannon added status/review and removed status/WIP labels Apr 26, 2017

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commented Apr 26, 2017

I suppose the qunit build failure is legit?

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commented Apr 26, 2017

@nsoranzo Yep, could be, I'll look at it.

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commented Apr 26, 2017

Yep, just need to update a test case, one sec.

@dannon dannon changed the title [WIP] Wiki to hub link update. Wiki to hub link update. Apr 26, 2017

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commented Apr 26, 2017

Thanks, I thought that was the case. Let's do the other tests too when Jenkins is back.

CITATION Outdated
@@ -16,7 +16,7 @@ following publications:
a platform for interactive large-scale genome analysis."
Genome Research. 2005 Oct; 15(10):1451-5.

See also: http://wiki.galaxyproject.org/CitingGalaxy
See also: http://galaxyproject.org/citing-galaxy

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@@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({
'</table>',
'<div class="empty-folder-message" style="display:none;">',
'This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up',
' please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
' please consult the <a href="https://galaxyproject.org/admin/data-libraries/library-security" target="_blank">library security wikipage</a>',

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@@ -151,7 +151,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
type : 'text',
value : '',
ignore : '',
help : 'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
help : 'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables-edit/">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'

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# The URL linked by the "Search" link in the "Help" menu.
#search_url = http://galaxyproject.org/search/usegalaxy/
#search_url = http://galaxyproject.org/search/

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# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
# These library upload options are described in much more detail in the Galaxy
# Community Hub:
# https://galaxyproject.org/admin/data-libraries/uploading-library-files

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[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ],
[_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ],
[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://galaxyproject.org/tool-shed" ), "_blank" ],
[_('Support'), app.config.get( "support_url", "https://galaxyproject.org/support" ), "_blank" ],
[_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ],

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@@ -33,7 +33,7 @@ def get_message_for_no_shed_tool_config():
message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
message += '<toolbox tool_path="../shed_tools">). For details, see the "Installation of Galaxy tool shed repository tools into a local '
message += 'Galaxy instance" section of the Galaxy tool shed wiki at http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#'
message += 'Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
message += 'Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance.'

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dannon Apr 28, 2017

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@nsoranzo This one's not quite right -- given the context it looks like it should just link to the base page.

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nsoranzo Apr 28, 2017

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@nsoranzo This one's not quite right -- given the context it looks like it should just link to the base page.

Agreed.

@@ -51,11 +51,11 @@
repository tools may include code that produces malicious behavior, so be aware of what you are installing.
</p>
<p>
If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/Support" target="_blank">Galaxy support</a>,
If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/support" target="_blank">Galaxy support</a>,

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@nsoranzo What's wrong with this one?

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Argh, nevermind :)

@@ -104,7 +104,7 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
<h4>Sample tracking</h4>
<ul>
<li>
Please see the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySampleTracking" target="_blank">sample tracking tutorial</a>.
Please see the <a href="https://galaxyproject.org/admin/data-libraries/library-sample-tracking" target="_blank">sample tracking tutorial</a>.

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@@ -115,13 +115,13 @@
if qa_url:
menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ]
menu_options.extend( [
[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ],
[_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ],
[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://galaxyproject.org/tool-shed" ), "_blank" ],

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dannon added some commits Apr 28, 2017

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Thanks @dannon for bearing with me, there are still 2 small partially-fixed tweaks, I'll fix them, resolve the merge conflicts locally and merge.

@@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({
'</table>',
'<div class="empty-folder-message" style="display:none;">',
'This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up',
' please consult the <a href="https://galaxyproject.org/admin/data-libraries/library-security" target="_blank">library security wikipage</a>',
' please consult the <a href="https://galaxyproject.org/admin/data-libraries/#permissions" target="_blank">library security wikipage</a>',

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@@ -895,7 +895,7 @@ use_interactive = True

# These library upload options are described in much more detail in the Galaxy
# Community Hub:
# https://galaxyproject.org/admin/data-libraries/uploading-library-files
# https://galaxyproject.org/admin/data-libraries/

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commented Apr 28, 2017

@nsoranzo Sounds good, thanks! Always feel free to just PR against my branches or whatever, too, if that's easier.

@nsoranzo nsoranzo merged commit f074013 into galaxyproject:dev Apr 28, 2017

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