"Merging tabular data tables with non-matching columns is not allowed"
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
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
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:
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:
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 <mailto: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
___________________________________________________________ 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/
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
___________________________________________________________ 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/
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
___________________________________________________________ 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/
Hi Peter vH, I wonder if adding columns is not supported - because some tools would define the table without the extra column? You might have to define a new data table instead (with largely the same content). But to be clear, I am not an expert in this area of Galaxy. However, it does seem the IUC could lay out some *.loc file best practises for tool authors. There is currently a TODO entry here: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xm... Peter C. On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden <pvh@sanbi.ac.za> wrote:
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
Yes that was my conclusion, thanks Peter. As a result I switched to a new table named (shapeit2_ref) and a new tool name (data_manager_shapeit2_reference) and from planemo side upload seemed to succeed but the tool is in an error state. I resorted to manually editing the tool-data table. Data managers are a bit of an ugly duckling part of Galaxy - not receiving as much love as other kinds of tools. Peter On Tue, 18 Sep 2018 at 14:22 Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Peter vH,
I wonder if adding columns is not supported - because some tools would define the table without the extra column? You might have to define a new data table instead (with largely the same content). But to be clear, I am not an expert in this area of Galaxy.
However, it does seem the IUC could lay out some *.loc file best practises for tool authors. There is currently a TODO entry here:
https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xm...
Peter C.
On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden <pvh@sanbi.ac.za> wrote:
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
participants (3)
-
Nicola Soranzo -
Peter Cock -
Peter van Heusden