Question: Data managers tool: the content of data table disappear after restart Galaxy
0
gravatar for yliu41
8 months ago by
yliu4150
yliu4150 wrote:

Hi there,

I am developing a data managers tool to add trained data. The tool works and can create a entry to the data table every time it runs. However, after I restart Galaxy instance, the entries in the data table are gone.

I am wondering if we need to fetch the data again after restart the system? Otherwise, how can I fix this?

Thank you very much!

Best, Yating

galaxy • 253 views
ADD COMMENTlink modified 8 months ago by y.hoogstrate460 • written 8 months ago by yliu4150
2
gravatar for y.hoogstrate
8 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

Galaxy makes clones of these loc files for each revision of each installed tool and does not write content always to the loc file directly in ./tool-data. In older versions of Galaxy it was possible to find all corresponding loc files via the web interface but this has disappeared some time ago. Anyway, you can find the loc files as follows:

cd galaxy ; find tool-data -name all_fasta.loc cd galaxy ; wc -l $( find tool-data -name "*.loc" )

That will show you all *.loc files (not .sample, but those that are actively used) and the number of lines in those files.

When I do the following:

~/src/galaxy (dev)✭ ᐅ wc -l $( find tool-data -name "*.loc" ) | grep star_index2
23 tool-data/127.0.0.1/repos/iuc/rgrnastar/5d734e53a0d0/rnastar_index2.loc
25 tool-data/127.0.0.1/repos/iuc/data_manager_star_index_builder/c6bec9468b26/rnastar_index2.loc
23 tool-data/rnastar_index2.loc

There are 2 files with 23 lines and one with 25. This means that there are two entries in the one located at tool-data/127.0.0.1/repos/iuc/data_manager_star_index_builder/c6bec9468b26/rnastar_index2.loc

Youri

ADD COMMENTlink modified 8 months ago • written 8 months ago by y.hoogstrate460
1

Thank you for the information! I found why it happened. After I searched for all *loc file, I found there was no loc file in data_manager tool directory. I deleted and reinstalled the data manager tool. It created a loc file in its directory and everything works. I used testtoolshed to test the tool, and I just clicked on "update shed status" every time I changed the tool. I guess it is not enough to get all the updates.

ADD REPLYlink written 8 months ago by yliu4150
0
gravatar for y.hoogstrate
8 months ago by
y.hoogstrate460
Netherlands
y.hoogstrate460 wrote:

This does not sound like normal Galaxy behaviour. Did you test this in planemo or in a Galaxy instance? Galaxy usually writes to flat LOC files and as far as I know there is no mechanism that automatically reverts or resets. Is the name of the loc file not used by others tools maybe? Does your file system do some strange backups?

ADD COMMENTlink written 8 months ago by y.hoogstrate460

I tested the tool (https://testtoolshed.g2.bx.psu.edu/repository?repository_id=a09497a087b272fe&changeset_revision=c5f8cd66db69) in a Galaxy virtual machine instance. The loc file is only used for one tool (https://toolshed.g2.bx.psu.edu/repository?repository_id=05cfe76518348625&changeset_revision=6618d16f276c). After I ran the data manager tool, I can see an new entry in Tool Data Table Entries through Galaxy admin interface. However, the loc file in tool-data/ directory did not have any entries, which means Galaxy did not write to the loc file. Is it supposed to write to the loc file? Thank you!

ADD REPLYlink written 8 months ago by yliu4150
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