On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Peter, I've added comments to each of these issues in bitbucket, and have pated them inline below as well.
On Jun 16, 2011, at 5:03 AM, Peter Cock wrote:
Hi all,
I just tried updating one of my tools on the new hg based Galaxy Tool Shed and ran into some issues. I guess I'm the first person to try this...
First of all, there is no clear "update" action like there used to me. Could that be restored please? https://bitbucket.org/galaxy/galaxy-central/issue/585/hg-tool-shed-lacks-upd...
The requested functionality is currently possible using normal mercurial features ( clone -> make changes to the cloned repo -> commit changes to the cloned repo -> push changes to the tool shed repo ).
Right, but not everyone wants to use hg for this.
It is also currently possible to upload a new tarball to any "upload point" (position) in the tool shed repository by selecting the upload point in the built-in repository file browser. - The hierarchy that the uploaded tarball contains will be added to that upload point in the tool shed repository. - Any files in the uploaded tarball that do not currently exist in the tool shed repository will be added. - Any files that exist in the hierarchy of the uploaded tarball that also exist in the same location of the hierarchy of the repository relative to the upload point will be replaced in the repository.
Yes, I tried that and its broken (bug 586 below).
It is on my list to: Delete any files that do not exist in the uploaded tarball's hierarchy but that do existin the same position of the tool shed repository's hierarchy relative to the upload point. This feature will require clear documented communication to the user, which I've not yet had a chance to do, but will soon.
That would be a change from "upload files" to "replace all the files", in line with the missing update tool functionality (#585). To me mixing these two is quite strange.
I tried using the "upload files to repository" option, and picked my tarball. I did not pick a location since I wanted the tar ball unpacked at the repository root, but this isn't what happened: https://bitbucket.org/galaxy/galaxy-central/issue/586/hg-tool-shed-upload-fi...
Peter, I believe this is a duplicate of # 584, correct?
Not really, 584 is about deleting files via the web interface. Perhaps you regard 585 (missing tool update) and 586 (broken upload at root) as the same basic issue?
Finally, it seems there is currently no delete files action, so I can't fix this (delete the misplaced files) via the web interface. https://bitbucket.org/galaxy/galaxy-central/issue/584/cant-delete-files-in-n...
You can currently delete specific files by cloning the repository, making any changes you want (including deleting), and committing and pushing the changes using mercurial's command line.
Again, I'd prefer not to have to do this.
I've added it to my list to provide a feature allowing a user to select a specific file in the repository (hopefully using the built-in file browser) and deleting the file in some way that doesn't require mercurial's command line, but in the meantime, use the above existing feature.
Are you expecting tool authors to work primarily at the hg level?
You didn't answer that one ;) Peter