Dear
galaxy users,
here at European Institute of Oncology we're deploying a brand
new galaxy install, but facing problems with history
(re)importing.
We have configured a galaxy running on one node where users took a
"sneek peek" on features while developing a real deployment on nfs
and cluster integration. Now I have to migrate histories to new
galaxy install, I'm doing that on behalf my users because we
choose to integrate with an apache proxy that does reverse
proxying and ldap authentication.
Yesterday I produced four tar.gz for a user, placed on a temporary
webserver and then proceeded with reimport on new instance: two
where reimported, two not.
All those files are relatively small (from 1MB to 13MB), and no
clues from galaxy debug log:
SUCCESSFUL ONE:
galaxy.jobs DEBUG 2013-12-18 13:29:32,718 (354) Working directory
for job is:
/srv/galaxy/galaxy-dist/database/job_working_directory/000/354
galaxy.jobs.handler DEBUG 2013-12-18 13:29:32,738 (354)
Dispatching to local runner
galaxy.jobs DEBUG 2013-12-18 13:29:32,826 (354) Persisting job
destination (destination id: local)
galaxy.jobs.handler INFO 2013-12-18 13:29:32,864 (354) Job
dispatched
galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:33,151 (354)
executing: export GALAXY_SLOTS="1"; python
/srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
http://debian.ieo.eu/drosano/dalia-37.tar.gz
/srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url
galaxy.jobs DEBUG 2013-12-18 13:29:33,326 (354) Persisting job
destination (destination id: local)
galaxy.jobs.runners.local DEBUG 2013-12-18 13:29:34,451 execution
finished: export GALAXY_SLOTS="1"; python
/srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
http://debian.ieo.eu/drosano/dalia-37.tar.gz
/srv/galaxy/galaxy-dist/database/tmp/tmpLAAF5z --url
galaxy.jobs DEBUG 2013-12-18 13:29:34,644 job 354 ended
galaxy.datatypes.metadata DEBUG 2013-12-18 13:29:34,644 Cleaning
up external metadata files
UNSUCCESSFUL ONE:
galaxy.jobs DEBUG 2013-12-18 13:30:42,824 (392) Working directory
for job is:
/srv/galaxy/galaxy-dist/database/job_working_directory/000/392
galaxy.jobs.handler DEBUG 2013-12-18 13:30:42,844 (392)
Dispatching to local runner
galaxy.jobs DEBUG 2013-12-18 13:30:42,934 (392) Persisting job
destination (destination id: local)
galaxy.jobs.handler INFO 2013-12-18 13:30:42,963 (392) Job
dispatched
galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:43,236 (392)
executing: export GALAXY_SLOTS="1"; python
/srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
http://debian.ieo.eu/drosano/dalia-138.tar.gz
/srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url
galaxy.jobs DEBUG 2013-12-18 13:30:43,400 (392) Persisting job
destination (destination id: local)
galaxy.jobs.runners.local DEBUG 2013-12-18 13:30:47,524 execution
finished: export GALAXY_SLOTS="1"; python
/srv/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
http://debian.ieo.eu/drosano/dalia-138.tar.gz
/srv/galaxy/galaxy-dist/database/tmp/tmpH8buNE --url
galaxy.jobs DEBUG 2013-12-18 13:30:47,711 job 392 ended
galaxy.datatypes.metadata DEBUG 2013-12-18 13:30:47,712 Cleaning
up external metadata files
sorry for line wraps, I also attached logs.
I cloned your repository on my development machine to try to
recreate/debug this issue but unfortunately this time I'm unable
to import successfully any history (plain galaxy instance, sqlite,
no ext user, no job_conf, either default and stable branches).
I'm attaching the new galaxy instance universe_wsgi.ini and
job_conf.xml, as you can see they are pretty straight-forward.
What I'm asking to you : which is the correct way for debugging
this sort of things ? No luck putting some debugging code in
* lib/galaxy/tools/actions/history_imp_exp.py
* lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
maybe I'm missing something ...
also, I'd like to contribute some patch on a couple of minor
glitches I found, but I'll write to -dev list for that
Thank you, and thanks for this great tool :) ciao
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