Upload1 tool error

1

I am uploading tabular data files (Sailfish output) from my computer to my single-user galaxy-local instance (v20.05, Linux Mint20, python3.6, postgresql 12, nginx). The following error code was recorded in the galaxy.log.

127.0.0.1 - - [03/Aug/2020:14:06:46 -0700] “POST /api/uploads HTTP/1.1” 200 - “http://localhost:8080/” “Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:79.0) Gecko/20100101 Firefox/79.0”
[pid: 3630|app: 0|req: 1/20] 127.0.0.1 () {48 vars in 882 bytes} [Mon Aug 3 14:06:46 2020] POST /api/uploads => generated 26 bytes in 155 msecs (HTTP/1.1 200) 3 headers in 139 bytes (40 switches on core 1)
galaxy.tools INFO 2020-08-03 14:06:46,877 [p:3623,w:7,m:0] [uWSGIWorker7Core2] Validated and populated state for tool request (15.074 ms)
galaxy.tools.actions.upload DEBUG 2020-08-03 14:06:46,986 [p:3623,w:7,m:0] [uWSGIWorker7Core2] Persisted uploads (0.026 ms)
galaxy.tools ERROR 2020-08-03 14:06:47,010 [p:3623,w:7,m:0] [uWSGIWorker7Core2] Exception caught while attempting to execute tool with id ‘upload1’:
Traceback (most recent call last):
File “/home/wgerthoffer/galaxy/.venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py”, line 1248, in _execute_context cursor, statement, parameters, context
File “/home/wgerthoffer/galaxy/.venv/lib/python3.6/site-packages/sqlalchemy/engine/default.py”, line 590, in do_execute cursor.execute(statement, parameters)
psycopg2.errors.DataCorrupted: could not read block 4 in file “base/16385/16560”: read only 0 of 8192 bytes

Troubleshooting so far:

  1. The files are not corrupt. They upload to usegalaxy.org and the data are intact.
  2. Read up on psycopg2 and tried updating the package using synaptic pkg manager
  3. Verified postgresql was running and had a role defined and database set up for wgerthoffer (my user name)
  4. Searched Galaxy help forums for similar errors and found none that offered an explanation or solution.

I am an end user cell and molecular biologist analyzing RNA-seq datasets. I have set up galaxy-local instances (v19 and v20.05) previously on the same computer running Ubuntu 18.04 and Linux Mint20. but I cannot upload the most recent installation does not allow uploading my local files to a history, or to shared data. I could use some expert admin input on the nature of the error and possible solutions.
Thanks in advance, Bill Gerthoffer

2

This is a new error for me - one thing to verify, does the filesystem on which your database resides (I believe this would be /var/lib/postgresql on Mint) have adequate space? Can you check the PostgreSQL error logs (/var/log/postgresql) and other system logs in /var/log for anything suspicious?

3

Thanks for the suggestions. The database is in my Home directory on a drive with 4.9Tb free space, so no issues there. I checked the PostgreSQL log after reproducing the error state. Here is the entry:

2020-08-04 00:04:33.897 PDT [22259] wgerthoffer@wgerthoffer STATEMENT: INSERT INTO dataset (create_time, update_time, state, deleted, purged, purgable, object_store_id, external_filename, _extra_files_path, created_from_basename, file_size, total_size, uuid) VALUES (‘2020-08-04T07:04:33.896212’::timestamp, ‘2020-08-04T07:04:33.896224’::timestamp, ‘new’, false, false, true, NULL, NULL, NULL, NULL, NULL, NULL, ‘564ab42820144dd8b40a75b39172c683’) RETURNING dataset.id
2020-08-04 08:48:54.634 PDT [32557] wgerthoffer@wgerthoffer ERROR: could not read block 4 in file “base/16385/16560”: read only 0 of 8192 bytes

4

No elegant solution to the upload1 tool error. Installing a new instance of Galaxy v20.01, postgresql 12 and nginx running in Linux Mint20 fixed things. Case closed.