gene.database.dynamodb#

Provide DynamoDB client.

class gene.database.dynamodb.DynamoDbDatabase(db_url=None, **db_args)[source]#

Database class employing DynamoDB.

__init__(db_url=None, **db_args)[source]#

Initialize Database class.

Parameters:

db_url (str) – URL endpoint for DynamoDB source

Keyword Arguments:

region_name: AWS region (defaults to “us-east-2”)

Raises:

DatabaseInitializationException – if initial setup fails

add_merged_record(record)[source]#

Add merged record to database.

Parameters:: record (dict) – merged record to add
Return type:: None

add_record(record, src_name)[source]#

Add new record to database.

Parameters:

record (Dict) – record to upload
src_name (SourceName) – name of source for record

Return type:

None

add_source_metadata(src_name, metadata)[source]#

Add new source metadata entry.

Parameters:

src_name (SourceName) – name of source
data – known source attributes

Raises:

DatabaseWriteException – if write fails

Return type:

None

check_schema_initialized()[source]#

Check if database schema is properly initialized.

Return type:: bool
Returns:: True if DB appears to be fully initialized, False otherwise

check_tables_populated()[source]#

Perform rudimentary checks to see if tables are populated.

Emphasis is on rudimentary – if some rogueish element has deleted half of the gene aliases, this method won’t pick it up. It just wants to see if a few critical tables have at least a small number of records.

Return type:: bool
Returns:: True if queries successful, false if DB appears empty

close_connection()[source]#

Perform any manual connection closure procedures if necessary.

Return type:: None

complete_write_transaction()[source]#

Conclude transaction or batch writing if relevant.

Return type:: None

delete_normalized_concepts()[source]#

Remove merged records from the database. Use when performing a new update of normalized data.

Raises:

DatabaseReadException – if DB client requires separate read calls and encounters a failure in the process
DatabaseWriteException – if deletion call fails

Return type:

None

delete_source(src_name)[source]#

Delete all data for a source. Use when updating source data.

Parameters:

src_name (SourceName) – name of source to delete

Raises:

DatabaseReadException – if DB client requires separate read calls and encounters a failure in the process
DatabaseWriteException – if deletion call fails

Return type:

None

drop_db()[source]#

Delete all tables from database. Requires manual confirmation.

Raises:: DatabaseWriteException – if called in a protected setting with confirmation silenced.
Return type:: None

export_db(output_directory)[source]#

Dump DB to specified location.

Parameters:: output_directory (Path) – path to directory to save DB dump in
Return type:: None
Returns:: Nothing, but saves dump to gzip file named gene_norm_<date and time>.ndjson.gz
Raises:: ValueError – if output directory isn’t a directory or doesn’t exist

get_all_concept_ids()[source]#

Retrieve concept IDs for use in generating normalized records.

Return type:: set[str]
Returns:: List of concept IDs as strings.

get_all_records(record_type)[source]#

Retrieve all source or normalized records. Either return all source records, or all records that qualify as “normalized” (i.e., merged groups + source records that are otherwise ungrouped).

For example,

>>> from gene.database import create_db
>>> from gene.schemas import RecordType
>>> db = create_db()
>>> for record in db.get_all_records(RecordType.MERGER):
>>>     pass  # do something

Parameters:: record_type (RecordType) – type of result to return
Return type:: Generator[dict, None, None]
Returns:: Generator that lazily provides records as they are retrieved

get_record_by_id(concept_id, case_sensitive=True, merge=False)[source]#

Fetch record corresponding to provided concept ID

Parameters:

concept_id (str) – concept ID for gene record
case_sensitive (bool) – if true, performs exact lookup, which is more efficient. Otherwise, performs filter operation, which doesn’t require correct casing.
merge (bool) – if true, look for merged record; look for identity record otherwise.

Return type:

Optional[dict]

Returns:

complete gene record, if match is found; None otherwise

get_refs_by_type(search_term, ref_type)[source]#

Retrieve concept IDs for records matching the user’s query. Other methods are responsible for actually retrieving full records.

Parameters:

search_term (str) – string to match against
ref_type (RefType) – type of match to look for.

Return type:

list[str]

Returns:

list of associated concept IDs. Empty if lookup fails.

get_source_metadata(src_name)[source]#

Get license, versioning, data lookup, etc information for a source.

Parameters:: src_name (str | SourceName) – name of the source to get data for
Return type:: dict

initialize_db()[source]#

Create gene_normalizer table if not already created.

Return type:: None

list_tables()[source]#

Return names of tables in database.

Return type:: list[str]
Returns:: Table names in DynamoDB

load_from_remote(url=None)[source]#

Load DB from remote dump. Not available for DynamoDB database backend.

Parameters:: url (Optional[str]) – remote location to retrieve gzipped dump file from
Return type:: None

update_merge_ref(concept_id, merge_ref)[source]#

Update the merged record reference of an individual record to a new value.

Parameters:

concept_id (str) – record to update
merge_ref (Any) – new ref value

Raises:

DatabaseWriteException – if attempting to update non-existent record

Return type:

None