Handle collections of entries

[brindakv]

Extend the model to accommodate collection of entries belonging to a project or investigation.

[brindakv]

ihm_entry_collection data category has the following data items (populated in the entry mmCIF file and supplementary collection file)

    _ihm_entry_collection.id (text) --> enter by curator
    _ihm_entry_collection.name (text)
    _ihm_entry_collection.details (text)

ihm_entry_collection_mapping data category with the following data items (populated in the entry mmCIF file and the supplementary collection file)

    _ihm_entry_collection_mapping.entry_id (text)
    _ihm_entry_collection_mapping.collection_id (text)

Refer to https://docs.google.com/document/d/1lVgJIMEdmlQ7VKV_ZtshFhmvDVRS1HncsUOkItr_nyI/edit# for rules regarding foreign key naming convention (combo1 vs combo2).

mmCIF generation process (System Generated mmCIF file) needs to be reviewed to make sure new tables are included in the mmCIF file generation process.

ACL: Users should not be able to provide this information during deposition. Users should not be able to populate both tables above. Curators should add this information during processing. Users should be able to see the contents of the table for entries that they create.

[hongsudt]

here is a list of action items:

The first list should be done shortly to accommodate the 35 entries that need to be released soon:

• [x] extend model for "PDB"."_ihm_entry_collection" table to have all three columns (text) -- @brindakv -- done on dev
  • unique(id) -- _ihm_entry_collection_id_key
• [x] extend model for "PDB"."_ihm_entry_collection_mapping" table -- @brindakv -- done on dev
  • unique(entry_id, collection_id) -- _ihm_entry_collection_mapping_primary_key or _ihm_entry_collection_mapping_entry_id_collection_id_key --> decided to go with primary_key for consistency. unique(id)? -- ihm_entry_collection_mapping_id_key (BV: This has been removed to make (entry_id, collection_id) as the composite primary key)
  • fkey from entry_id to "PDB".entry(id) -- _ihm_entry_collection_mapping_entry_id_fkey (no need for combo since there is only 1 fkey that refers to entry).
  • fkey from collection_id to "PDB"._ihm_entry_collection(id) -- _ihm_entry_collection_mapping_id_fkey
• [x] update ACL to be the same as entry_related_tables (submitters can only modify during a certain workflow stags) -- @hongsudt or @svoinea (BV: ACL is described above. Users have no edit access at any point in the workflow. This is completely managed by curator.)
• [x] set annotations for both tables: ihm_entry_collection and ihm_entry_collection_mapping
  • use source syntax to traverse foreign keys
• [x] update mmcif generation script to output these additional 2 tables -- @svoinea
  • value of _ihm_entry_collection_mapping.entry_id should be
  • mmcif generation should handle these tables similar to pdbx_audit_revision tables as in #73 but these tables are in ermrest unlike pdbx_audit_revision
  • These tables can follow the pdbx_audit_revision tables in the mmcif file

The second list is to make the mmCIF generation more robust

• [ ] outline the current config needed to generate mmCIF -- @svoinea
• [ ] identify the metadata that should be omitted in user-submitted mmCIF files -- @brindakv @monica81567
  • group collection: _ihm_entry_collection, _ihm_entry_collection_mapping
  • accession code/revision related: xxx
  • [ ] reorganize the mmCIF generation -- @svoinea
  • [ ] Comment for entry table needs to be added (in the model)

[brindakv]

Need to consider incorporating Accession_Code in addition to or instead of entry_id in the ihm_entry_collection_mapping table.