`phystool.physql.metadata`

Module Contents

`stats`
`consolidate`	Wrapper function around `create_sql_database()” that prints a minimalistic progress bar in the terminal
`create_sql_database`	Create the SQL database by analysing all “.tex” and related “.json” files
`filter_pdb_files`	Returns a list of PDBFile that match search criteria
`filter_pdb_files_by_uuids`
`update_pdb_file`
`remove_pdb_files`	Remove all files related to the PDBFiles. If the database is managed by git, the files can be recovered. The PDBRecords are also deleted.
`create_new_tag`
`update_tags`	Update the tags, both in the SQL database and in the .json file

phystool.physql.metadata.stats() → dict[str, str | int | Sequence[str] | dict[str, list[str]]]

phystool.physql.metadata.consolidate() → None: Wrapper function around `create_sql_database()” that prints a minimalistic progress bar in the terminal

phystool.physql.metadata.create_sql_database() → Iterator[tuple[int, int, str]]: Create the SQL database by analysing all “.tex” and related “.json” files

phystool.physql.metadata.filter_pdb_files(query: str, uuid_bit: str, pdb_types: set[str], selected_tags: phystool.tags.Tags, excluded_tags: phystool.tags.Tags) → list[phystool.pdbfile.PDBFile]

Returns a list of PDBFile that match search criteria

Paramètres:

query – string that should appear in the “.tex” file
uuid_bit – string that should match part of a uuid
pdb_type_set – restrain search only to those file types
selected_tags – restrain search to the PDBFiles tagged with any of the selected_tags
excluded_tags – exclude PDBFiles tagged with any of the excluded_tags

phystool.physql.metadata.filter_pdb_files_by_uuids(uuids: list[uuid.UUID]) → list[phystool.pdbfile.PDBFile]

phystool.physql.metadata.remove_pdb_files(uuids: list[uuid.UUID]) → None: Remove all files related to the PDBFiles. If the database is managed by git, the files can be recovered. The PDBRecords are also deleted.

phystool.physql.metadata.create_new_tag(category_name: str, tag_name: str) → None

phystool.physql.metadata.update_tags(pdb_file: phystool.pdbfile.PDBFile, session: sqlalchemy.orm.session.Session, to_remove_ids: set[int], to_add_ids: set[int]) → None: Update the tags, both in the SQL database and in the .json file