Migrate session to new ADIT-NMR platform

“Joint” ADIT-NMR to “BMRB-only” ADIT-NMR

It is possible to just copy an old session to the new server. However, there is a chance that the dictionary used to create the old session is not compatible with the software/dictionary currently on the new server, and the session will crash when authors try to deposit it. It is safer to instead bootstrap a brand new session from a “preview” header file.

Old ADIT-NMR sessions directories are archived on walleye:/joint-adit-sessions. As of the time of this writing it is also NFS-mounted on stingray:/joint-adit-sessions.

You will need a session restart ID, of course. Session directory has the same name as restart ID, in there

  1. check for lockFlagFileBmrb and/or loclFlagFilePdb. If present, the session has been submitted and they're better off starting from an “author view” file.
  2. Copy Table-db.odb file from the session directory to somewhere temporary and run
    /bmrb/linux/bin/obj2cif Table-db.odb Table-db.cif

1. Check Table-db.cif file:

  • the person requesting it should be in Contact_persons or Entry_author or Citation_author tables, otherwise you'll need to figure out if they're authorized to see the entry.
  • If this is a structure deposition: Entry_interview.PDB_deposition is a yes and/or there's a coordinate file in the session's upload subdirectory: we cannot migrate a structure deposition. We can, however, migrate the NMR side of it.

2. Create header file.

Unfortunately Table-db.cif cannot be read into a new ADIT-NMR session. It needs to be post-processed into NMR-STAR. The simple way to do it is copy the session to a programmers platform (because programmers platforms are configured to not send e-mails) and use ADIT-NMR's “generate preview file” button.

You may need to spin up the appropriate VM first, if it isn't running:

ssh root@squid
virsh start VM_NAME

where VM_NAME is either

  • adit-alpha : “BMRB-only” platform, file generation should work but may fail due to dictionary/software incompatibility, or
  • deposit-prog : “joint” platform, file generation is less likely to fail due to dictionary/software incompatibility (but it's still possible).

(adit@adit-alpha has no password so anyone can ssh in, adit@deposit-prog has a password and it's written on a yellow sticky on the right side of Dimitri's monitors.)

  1. As adit on adit-alpha:
    1. create a session directory, e.g. /adit/www/adit/sessions/bmrb-adit/temptemp,
    2. cd to it
    3. run
      nc -l 1234 | tar -xvf -
  2. On stingray or waleye:
    1. cd to session directory you want to migrate and
    2. run
      tar -cvf - . | nc adit-alpha 1234
  3. Once the copy is done,
    1. continue session temptemp
    2. hit the preview button up top
    3. type in your e-mail address and click on generate preview

Processing will take a little time and then the file bmrPREVIEW.nmrif.post.nmrstr will appear in the session directory on adit-alpha.

If it fails and dumps core, try copying the new dictionary file into the session directory first

cp /adit/adit/config/bmrb-adit/dict.cif .
rm dict.odb 

Then try generating preview again.

3. Create new session

You can leave this to the authors and just send them all the files and the link to the instructions: http://deposit.bmrb.wisc.edu/bmrb-adit/bootstrap.shtml

To create a session for them:

  1. take everything from the upload directory of the original session and upload it into the new one. Use the Upload_data table in bmrPREVIEW.nmrif.post.nmrstr to figure out which file contains what.
  2. Upload bmrPREVIEW.nmrif.post.nmrstr last as “other kinds of data” file.
  3. Hit continue deposition.
  4. If you want to be really nice, edit each data section and select the name of appropriate uploaded file.

At this point you've migrated everything you could to the new platform.

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