Update data model to support latest IHMCIF updates (consistent with CifCheck sdb file)

[brindakv]

See https://github.com/ihmwg/IHMCIF/pull/104 for details

• [x] Add _struct.pdbx_structure_determination_methodology and the corresponding vocab table
• [x] Add ihm_ordered_model
• [x] Add Crosslinking-MS data to the vocab table of _ihm_dataset_list.data_type
• [x] Add modeling to the vocab table of _ihm_dataset_group.application
• [x] Add PDH and DMTMM to the vocab table of _ihm_cross_link_list.linker_type
• [x] Add ProteomeXchange to the vocab table of ihm_dataset_related_db_reference_db_name
• [x] Add ihm_multi_state_scheme, ihm_multi_state_scheme_connectivity, ihm_kinetic_rate
• [x] Add ihm_relaxation_time, ihm_relaxation_time_multi_state_scheme
• [x] Add _ihm_ensemble_info.model_group_superimposed_flag and the corresponding enumerations to Vocab
• [x] Update Data Dictionary and Supported Dictionary for version information
• [x] Update _audit_conform.dict_location and _audit_conform.dict_name values in the database
• [x] Update tables.json file based on the new JSON schema (@svoinea)
• [x] Update vocab_ucode.json file based on the new IHMCIF and PDBx/mmCIF dictionaries (@svoinea)
• [x] Update order_by.json file manually for including new tables that have composite primary keys (e.g., ihm_ordered_model) in system generated mmCIF file (@svoinea)
• [x] Update sdb file v1.26 (mmcif_ihm-v1.26.sdb) for CifCheck in the backend pipeline
• [x] Update python-ihm v1.3 to support all new model updates at ingest and in validation
• [x] Update py-rcsb_db v0.88 and the json-full-db-ihm_dev_full-col-ihm_dev_full.json JSON schema to support all new model updates at ingest and export
• [x] Update IHMValidation v1.2 to support all new model updates (@aozalevsky)

SDB file can be moved to v1.26 to support _database_2.database_id = PDB-Dev (https://github.com/informatics-isi-edu/protein-database/issues/208 and https://github.com/informatics-isi-edu/protein-database/issues/231) and ermrest can catch up later when this issue if fully addressed. It is backward compatible.

[aozalevsky]

@svoinea @brindakv new py-rscb_db is available at https://salilab.org/~arthur/ihmv/packages/py-rcsb_db_v0.88.tar.gz

[aozalevsky]

@brindakv i've updated v1.2 reports with Crosslinking-MS data and tested compatibility with the current stack on dev. You can proceed with testing.

[svoinea]

@aozalevsky On the Ubuntu dev instance, in the /etc/cron.daily/dev-update file, the line is:

    "python_ihm_validation 48c8415"

Update the commit number each time you need and then run /etc/cron.daily/dev-update.

[aozalevsky]

@svoinea awesome, thanks!

[aozalevsky]

@svoinea @brindakv, the update has worked. the only comment is that the cron.daily updates are executed at 6:25 Pacific Time:

Sep 11 06:25:01 docker-pdbdev-validation-o3558551 CRON[83276]: (root) CMD (test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.daily ))

# Example of job definition:
# .---------------- minute (0 - 59)
# |  .------------- hour (0 - 23)
# |  |  .---------- day of month (1 - 31)
# |  |  |  .------- month (1 - 12) OR jan,feb,mar,apr ...
# |  |  |  |  .---- day of week (0 - 6) (Sunday=0 or 7) OR sun,mon,tue,wed,thu,fri,sat
# |  |  |  |  |
# *  *  *  *  * user-name command to be executed
17 *    * * *   root    cd / && run-parts --report /etc/cron.hourly
25 6    * * *   root    test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.daily )
47 6    * * 7   root    test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.weekly )
52 6    1 * *   root    test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.monthly )
#
0  5    * * *   root    unattended-upgrade

This looks like a bit too late for an "overnight" update, especially if Brinda and Monica start testing things early on Eastern time.

[svoinea]

@aozalevsky Each time you update the commit number of the python_ihm_validation, run manually the /etc/cron.daily/dev-update script. In that way, it becomes independent of the overnight update.