Index

_

__init__() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) (gene.etl.base.Base method) (gene.etl.ensembl.Ensembl method) (gene.etl.hgnc.HGNC method) (gene.etl.merge.Merge method) (gene.etl.ncbi.NCBI method) (gene.query.QueryHandler method)

A

AbstractDatabase (class in gene.database.database) add_location() (gene.etl.vrs_locations.sequence_location.SequenceLocation method) add_merged_record() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) add_record() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

add_source_metadata() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) ALIAS (gene.schemas.MatchType attribute) aliases (gene.schemas.BaseGene attribute) associated_with (gene.schemas.BaseGene attribute) ASSOCIATED_WITH (gene.schemas.MatchType attribute) AwsEnvName (class in gene.database.database)

B

Base (class in gene.etl.base)

BaseGene (class in gene.schemas)

C

check_schema_initialized() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) check_tables_populated() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) ChromosomeLocation (class in gene.etl.vrs_locations.chromosome_location) close_connection() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

complete_write_transaction() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) concept_id (gene.schemas.BaseGene attribute) CONCEPT_ID (gene.schemas.MatchType attribute) confirm_aws_db_use() (in module gene.database.database) create_db() (in module gene.database.database) create_merged_concepts() (gene.etl.merge.Merge method)

D

DatabaseException DatabaseInitializationException DatabaseReadException DatabaseWriteException delete_normalized_concepts() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

delete_source() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) DEVELOPMENT (gene.database.database.AwsEnvName attribute) drop_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) DynamoDbDatabase (class in gene.database.dynamodb)

E

Ensembl (class in gene.etl.ensembl) ENSEMBL (gene.schemas.SourcePriority attribute)

export_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

F

FUZZY_MATCH (gene.schemas.MatchType attribute)

G

gene.database.database module gene_type (gene.schemas.BaseGene attribute) get_aliases() (gene.etl.vrs_locations.sequence_location.SequenceLocation method) get_all_concept_ids() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_all_records() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_location() (gene.etl.vrs_locations.chromosome_location.ChromosomeLocation method) get_record_by_id() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

get_refs_by_type() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_seqrepo() (gene.etl.base.Base method) (gene.etl.ensembl.Ensembl method) (gene.etl.hgnc.HGNC method) (gene.etl.ncbi.NCBI method) get_source_metadata() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

H

HGNC (class in gene.etl.hgnc) (gene.schemas.SourcePriority attribute)

I

initialize_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

InvalidParameterException

L

label (gene.schemas.BaseGene attribute) list_tables() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

load_from_remote() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) location_annotations (gene.schemas.BaseGene attribute) locations (gene.schemas.BaseGene attribute)

M

MatchType (class in gene.schemas) Merge (class in gene.etl.merge)

module gene.database.database

N

NCBI (class in gene.etl.ncbi) (gene.schemas.SourcePriority attribute)

NO_MATCH (gene.schemas.MatchType attribute) normalize() (gene.query.QueryHandler method) normalize_unmerged() (gene.query.QueryHandler method)

P

perform_etl() (gene.etl.base.Base method) (gene.etl.ensembl.Ensembl method) (gene.etl.hgnc.HGNC method) (gene.etl.ncbi.NCBI method)

PostgresDatabase (class in gene.database.postgresql) PREV_SYMBOL (gene.schemas.MatchType attribute) previous_symbols (gene.schemas.BaseGene attribute) PRODUCTION (gene.database.database.AwsEnvName attribute)

Q

QueryHandler (class in gene.query)

S

search() (gene.query.QueryHandler method) SequenceLocation (class in gene.etl.vrs_locations.sequence_location) set_interval_range() (gene.etl.vrs_locations.chromosome_location.ChromosomeLocation method) SourcePriority (class in gene.schemas)

STAGING (gene.database.database.AwsEnvName attribute) strand (gene.schemas.BaseGene attribute) symbol (gene.schemas.BaseGene attribute) SYMBOL (gene.schemas.MatchType attribute) symbol_status (gene.schemas.BaseGene attribute)

U

update_merge_ref() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method)

X

XREF (gene.schemas.MatchType attribute)

xrefs (gene.schemas.BaseGene attribute)