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/__init__.py#L120 from: https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_table_manager.py#L88 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 <p...@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.sora...@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 <p...@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 >>> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> >> >>
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