planemo shed_update failing, Connection aborted, BadStatusLine

[peterjc]

I've not updated anything on the (Test) ToolShed for a while, so I don't know when this changed but:

$ uname
Darwin
$ planemo --version
planemo, version 0.33.0.dev0
$ planemo shed_update -t testtoolshed ~/repositories/galaxy_blast/tools/blast2go/ -m "v0.0.11 Fix parameter help text which was not being displayed"
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git rev-parse HEAD
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git diff --quiet
Could not update blast2go
('Connection aborted.', BadStatusLine("''",))
Repository metadata updated successfully for repository blast2go.
Failed to update a repository.

The blank status line is odd...

[bgruening]

Can you try planemo 0.32.0? I have seen this a few time but not always. ping @martenson; similar to what I have reported.

[peterjc]

Thanks @bgruening - sadly no change:

$ planemo --version
planemo, version 0.32.0
$ planemo shed_update -t testtoolshed ~/repositories/galaxy_blast/tools/blast2go/ -m "v0.0.11 Fix parameter help text which was not being displayed"
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git rev-parse HEAD
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git diff --quiet
Could not update blast2go
('Connection aborted.', BadStatusLine("''",))
Repository metadata updated successfully for repository blast2go.
Failed to update a repository.

[peterjc]

Note that this example is with matching credentials, peterjc and https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go - no complications about a different owner vs write permissions.

[peterjc]

Updates still broken with Planemo 0.35.0.dev0 (on Mac),

$ planemo --version
planemo, version 0.35.0.dev0

Same example where I own the repo:

$ planemo shed_update -t testtoolshed ~/repositories/galaxy_blast/tools/blast2go/ -m "v0.0.11 Fix parameter help text which was not being displayed"
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git rev-parse HEAD
cd '/Volumes/Hitachi-3TB-mirrored/repositories/galaxy_blast/tools/blast2go' && git diff --quiet
Could not update blast2go
('Connection aborted.', BadStatusLine("''",))
Repository metadata updated successfully for repository blast2go.
Failed to update a repository.

Example where I should have permissions:

$ planemo shed_update -t testtoolshed -m "Polishing GMAP wrappers v3.0.1" tools/gmap/
cd '/Volumes/Hitachi-3TB-mirrored/repositories/tools-iuc/tools/gmap' && git rev-parse HEAD
cd '/Volumes/Hitachi-3TB-mirrored/repositories/tools-iuc/tools/gmap' && git diff --quiet
Could not update gmap
('Connection aborted.', BadStatusLine("''",))
Repository metadata updated successfully for repository gmap.
Failed to update a repository.

@martenson is this a Tool Shed issue?

[remimarenco]

@peterjc Hi Peter, I have the same issue here. Did you find a workaround?

[peterjc]

Thanks @remimarenco - It is reassuring to know this isn't something unique to my machine.

My only workaround is using planemo shed_upload --tar_only to make the tar-ball, and manually uploading that to the Tool Shed via my browser.

[remimarenco]

Ok thanks! Working with the team to try to solve this issue.

[bebatut]

Hi,

I have the same issue on my computer. @remimarenco Did you find a way to solve this issue?

Thanks,

Bérénice

[jmchilton]

I assumed this meant the tool shed was down or something - I'm not sure what could cause this error. I guess I'd like to see the tool shed logs corresponding to such an upload attempt.

[bebatut]

What is strange is that I am trying with the TTS (which is not down). And I am having this issue several times at different time point since the end of last week...

[martenson]

I think we narrowed this down to permission issues. If you have authority to make changes on the repo, that does not mean you can upload a new version - you can only change the metadata. You have to be the administrator of such repo - either through your group or through your role directly.

[peterjc]

So is planemo failing to capture a permissions error message, or is the Tool Shed giving an ambiguous failure?

[martenson]

If I recall correctly it was a bit of both maybe Planemo taking more blame. Did adding you as member of the IUC group fix this for you @bebatut ?