Solve truncated H5 files migration related bugs

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.
https://utdallas.box.com/s/djgkj4sf930e84lw6oy09qow8vqkshz3

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