Open brindakv opened 7 months ago
Currently, make-mmcif.py
is not part of the python-ihm
Python Package. It can be got from the python-ihm
repository:
git clone https://github.com/ihmwg/python-ihm.git
The make-mmcif.py
file is on the python-ihm/util
directory.
If you have versions preference, please go to https://github.com/informatics-isi-edu/protein-database/blob/master/scripts/ubuntu/www/deploy.sh#L81-L93 and specify them. So far, there was never a problem by using the latest version of them.
The *.yml
files are now present in the py-rcsb_db_v0.86.tar.gz
file, and those are the ones used. In case an update occurs to them, how should we get them? A new *.tar.gz
file? Or a different way?
Regarding CifCheck
, it was built only once as described at https://github.com/informatics-isi-edu/protein-database/blob/master/scripts/ubuntu/www/deploy.sh#L105-L113 and the binary code was comitted into the protein-database
repository. It was working on all the new Fedora versions as well as now on Ubuntu. So far, no problem was reported by using only the very first build of CifCheck
.
from https://github.com/informatics-isi-edu/protein-database/issues/163#issuecomment-2010307830 by @svoinea
- On
production
, the script is/root/ihm_validation_checkout.sh
. The checkout is for the tag20240315
:Each time you want to apply a new tag, set its value in the
/root/ihm_validation_checkout.sh
script and run it.
- On
dev
, we have the daily script/etc/cron.daily/dev-update
. The checkout forIHMValidation
is for the latestdev_2.0
:Each time you want to apply an update, run manually the script
/etc/cron.daily/dev-update
. Or if want a specific tag, replaceorigin/dev_2.0
by the tag value, and then run the script.The generated log file is
/root/pdb-cron-hourly-update.log
.
IHMCIF
python-ihm
python-ihm
is used in the PDB-Dev backend submission workflow and in validation report generation.python-ihm
gets updated when new kinds of entries are deposited, e.g., branched polymers.python-ihm
make-mmcif.py
is part of the python-ihm packagedev
andproduction
IHMValidation
dev
and tagged version onproduction
py-rcsb_db
Hosted by @aozalevsky at https://salilab.org/~arthur/ihmv/packages/py-rcsb_db_v0.86.tar.gz
Also contains two
yml
config filesUsed to convert mmCIF to JSON in the workflow
Package will be updated offline by @brindakv and will be tagged
Use tagged version on both
dev
andproduction
Different config JSON files that depend on
IHMCIF
andpy-rcsb_db
tables.json
depends on the full JSON schema inpy-rcsb_db
vocab_ucode.json
depends on IHMCIF and PDBx/mmCIF data items that are ucodeorder_by.json
has to be updated for tables with composite primary keyscpp-dict-pack (@svoinea to update how this software is deployed)
cpp-dict-pack
software is stablesdb
file is provided by @brindakvMolstar
Used for visualization
https://github.com/informatics-isi-edu/protein-database/tree/master/scripts/molstar
py-mmcif
Used for
testGetUcode.py