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  1. The Virtual Brain
  2. TVB-2925

Solve truncated H5 files migration related bugs



    • Bug
    • Status: Resolved
    • Major
    • Resolution: Fixed
    • 2.2.1
    • 2.2.2
    • TVB Framework
    • None
    • VBC Sprint 12
    • 8.2 Pipeline Integration


      Here is the mail sent by Dr. Christopher S. Simmons:

      From: Simmons, Christopher <Christopher.Simmons@UTDallas.edu>
      Sent: Monday, April 19, 2021 6:17:58 PM
      To: Solodkin, Ana Josefa; WOODMAN Michael
      Cc: Wang, Yile
      Subject: problems with tvb1 -> tvb2 migration

      Hey Marmaduke,

      Sorry for contacting you directly. If there is a better person I should
      contact or a better way to ask questions about TVB, please let me know.

      On Friday, I was doing the migration from 1.5.8 to 2.2.1 using the
      instructions on the website.

      I stopped the TVB web service, removed the old TVB_Distribution
      directory, replaced it with the new TVB_Distribution and restarted the
      web service. As expected, it started migrating the h5 files from the
      old format to the new format, but it errored out.

      There are 47 h5 output files that are only 48 bytes and it looks like
      the TVB migration scripts expect them to be at least 2048. I don't know
      why these files are truncated or what caused it. I assume the
      simulation might not have been set up correctly or it was started and
      stopped or something equivalent for those subset of runs.

      Because the migration wasn't working, and it left the TVB install in a
      partially migrated state and thus unable to run, I restore the DB
      backup (postgresql) and restored the TVB 1 data and TVB_Distribution
      and tried to restart TVB1. I am now getting this error.

      File "/home/tvbadmin/TVB_Distribution/tvb_data/lib/python2.7/site-
      packages/sqlalchemy/engine/default.py", line 470, in do_execute
      cursor.execute(statement, parameters)
      sqlalchemy.exc.ProgrammingError: (psycopg2.ProgrammingError) no schema
      has been selected to create in
      LINE 2: CREATE TABLE migrate_version (
      [SQL: '\nCREATE TABLE migrate_version (\n\trepository_id VARCHAR(250)
      NOT NULL, \n\trepository_path TEXT, \n\tversion INTEGER, \n\tPRIMARY
      KEY (repository_id)\n)\n\n']
      [tvbadmin@europa bin]$

      Attached below is the full error.

      Also here is a link to a gzip'd tarball.

      The tarball has the SQL dump, the TVB configuration file, and the TVB
      data and TVB_Distribution directory from TVB 1.5.8.

      Any suggestions on how we should proceed? Right now, the migration wont

      Gliffy Diagrams




              robert.vincze Robert Francisc Vincze
              robert.vincze Robert Francisc Vincze
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