Question: upload file format is data - type not recognized in galaxy
1
gravatar for pavel.fibich
7 months ago by
pavel.fibich10
pavel.fibich10 wrote:

Hello,

do you have any idea why my galaxy 16.07 stop recognizing uploaded files and format of uploaded files is set to the format 'data'?

After using older version of database backup, galaxy stop recognizing format of uploaded files (e.g. fasta, fastqc) and everything is set to format 'data'. Uploaded files are OK, I have tested them on other public galaxy servers, where they were recognized well. Before changing database (after the technical problems with the server), recognizing of the files were OK. Even in debugging level I do not see any errors or problems in the log (I have compared logs before changing database with new ones, and there are no differences). From the investigating upload.py, I think something happen with galaxy.datatypes.registry (settings and code of galaxy were not changed). Do you have any ideas? I cannot switch the database back and changing file format in Edit attributes is annoying.

Best, Pavel

upload galaxy • 227 views
ADD COMMENTlink modified 6 months ago • written 7 months ago by pavel.fibich10

This is a guess - but it sounds like there is a conflict between the database backup (you didn't state which release that was from) and the new 16.07 release it was added to. Were they both based off of 16.07?

https://docs.galaxyproject.org/en/master/releases/

ADD REPLYlink modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson24k

Backup database was one release before 16.07. Now, I have upgraded galaxy to 17.05, and it does not help. Before that I tried to run galaxy with empty database and tried to upload file, again it does not help, format of uploaded file was not recognized.

ADD REPLYlink written 7 months ago by pavel.fibich10

First, you should create an instance that is from the same release as your database backup, swap it in, and make sure things are working. From there you can upgrade Galaxy. Be sure to note any special upgrade instructions in the release notes for all releases between then and now.

This should resolve the datatype of data being assigned. It is no longer used.

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson24k
0
gravatar for pavel.fibich
6 months ago by
pavel.fibich10
pavel.fibich10 wrote:

I got the solution by debugging upload.py. Problem was in the environmental file, where was the command for changing directory. So running upload.py (that is run after the applying environmental settings, that included cd command) did not find galaxy.json, that is not specified in the absolute path. Removing cd command solved the problem.

Thank you for all your suggestions.

ADD COMMENTlink written 6 months ago by pavel.fibich10
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