A bit more tracing leads me to suspect that what is happening is that a merge is being called here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/data/__ini... from: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_ta... i.e. the toolshed maintains an in-memory copy of tool-data tables and if the list of columns in an incoming tool-data table is not the same as the in-memory version the error I saw happens. Which leaves me with the question: how is one meant to update the column list of a tool data table? Peter On Mon, 17 Sep 2018 at 13:23 Peter van Heusden <pvh@sanbi.ac.za> wrote:
Thanks - which is probably because of the previous failures with `shed_update` - which relate back to the topic of my original email. I suspect that failure from `planemo shed_update` has led to this "not installable" state. And I don't know how to solve the problem from `shed_update` which *looks* like it is coming from a clash between previous and current definitions of the tool-data table.
Peter
On Mon, 17 Sep 2018 at 12:58 Nicola Soranzo <nicola.soranzo@gmail.com> wrote:
Hi Peter, if you open the page for data_manager_shapeit_reference in the test ToolShed you will see that revision 5 and 6 are not installable, they both have "*This revision can be installed:* False" . If you instead select revision 3 it is installable.
Cheers, Nicola
On 17/09/18 11:51, Peter van Heusden wrote:
I'm following up on my previous email. I somehow managed to get `planemo shed_update` to work but now I seem to have an inconsistent view of the Test toolshed. This is how it looks from the Admin panel of my Galaxy server:
[image: https://files.gitter.im/galaxyproject/Lobby/k2qH/image.png] Notice that it shows 3 installable revisions for the data manager, last updated 13th of September. And this is how it looks from the Test toolshed website:
[image: https://files.gitter.im/galaxyproject/Lobby/ymY9/image.png]
Notice that it has 6 installabale revisions for the data manager. Is my Galaxy server perhaps caching something?
Peter
On Sat, 15 Sep 2018 at 09:57 Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there
I'm working on a data manager to keep track of the reference data collection used by the SHAPEIT2 tool. I had to add a column to the data manager but when I try and do a `planemo shed_update` I get the error:
Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse file tool_data_table_conf.xml.sample: Merging tabular data tables with non matching columns is not allowed: shapeit_ref:{'path': 2, 'reference_prefix': 3, 'name': 1, 'value': 0, 'map_prefix': 4} != shapeit_ref:{'name': 1, 'value': 0, 'sample_prefix': 5, 'path': 2, 'reference_prefix': 3, 'map_prefix': 4}"}
This is for data_manager_shapeit_reference in testtoolshed, which is on github at
https://github.com/pvanheus/data_manager_shapeit_reference
As far as I can tell the columns do accord. Is there any way to see which files are being merged to help try and debug this error?
Thanks! Peter
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