Index

Symbols

--anon modos command line option --auth-url modos-remote-login command line option --base-uri modos-publish command line option --client-id modos-remote-login command line option --config modos-update command line option --debug modos command line option --element modos-add command line option --endpoint modos command line option --files modos-show command line option --force modos-remove command line option modos-update command line option --from-file modos-add command line option modos-create command line option --meta modos-create command line option --output-format modos-publish command line option --parent modos-add command line option --passphrase modos-c4gh-decrypt command line option modos-c4gh-encrypt command line option --public-key modos-c4gh-encrypt command line option --query modos-codes-search command line option --region modos-remote-stream command line option --secret-key modos-c4gh-decrypt command line option modos-c4gh-encrypt command line option --source-file modos-add command line option

--target modos-remote-download command line option modos-remote-upload command line option --top modos-codes-search command line option --version modos command line option --zarr modos-show command line option -a modos-remote-login command line option -c modos-remote-login command line option modos-update command line option -e modos-add command line option -f modos-add command line option modos-create command line option modos-remove command line option modos-show command line option modos-update command line option -m modos-create command line option -p modos-add command line option modos-c4gh-encrypt command line option -pw modos-c4gh-decrypt command line option modos-c4gh-encrypt command line option -q modos-codes-search command line option -r modos-remote-stream command line option -s modos-add command line option modos-c4gh-decrypt command line option modos-c4gh-encrypt command line option -t modos-codes-search command line option modos-remote-download command line option modos-remote-upload command line option -z modos-show command line option

_

__call__() (modos.remote.BearerAuth method) __class_vars__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __iter__() (modos.genomics.htsget._HtsgetBlockIter method) __next__() (modos.genomics.htsget._HtsgetBlockIter method) __post_init__() (modos.genomics.region.Region method) __private_attributes__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_complete__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_computed_fields__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_core_schema__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_custom_init__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_decorators__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_extra__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_fields__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_fields_set__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_generic_metadata__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute)

__pydantic_parent_namespace__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_post_init__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_private__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_root_model__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_serializer__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __pydantic_validator__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __signature__ (modos.remote.Permissions attribute) (modos.remote.S3Key attribute) (modos.remote.S3KeySpec attribute) __str__() (modos.remote.Permissions method) (modos.storage.S3Path method) __truediv__() (modos.storage.S3Path method) __version__ (in module modos) _add_any_element() (modos.api.MODO method) _blocks (modos.genomics.htsget._HtsgetBlockIter attribute) _consume_block() (modos.genomics.htsget._HtsgetBlockIter method) _expires_at (modos.remote.JWT attribute) _HtsgetBlockIter (class in modos.genomics.htsget) _iterator (modos.genomics.htsget.HtsgetStream attribute) _leftover (modos.genomics.htsget.HtsgetStream attribute) _path (modos.storage.LocalStorage attribute) (modos.storage.S3Storage attribute) _s3_pattern (modos.storage.S3Path attribute) _set_metadata() (modos.helpers.schema.DataElement method) _source (modos.genomics.htsget._HtsgetBlockIter attribute) _update_checksum() (modos.helpers.schema.DataElement method)

A

access_key_id (modos.remote.S3Key attribute) access_token (modos.remote.JWT attribute) add_data() (in module modos.storage) add_element() (modos.api.MODO method) add_file() (modos.helpers.schema.DataElement method) add_metadata_group() (in module modos.storage) add_suffix() (in module modos.genomics.formats)

arrays (modos.io.ExtractedMetadata attribute) ASSAY (modos.helpers.enums.ElementType attribute) (modos.helpers.enums.UserElementType attribute) (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) attrs_to_graph() (in module modos.rdf) auth (modos.remote.EndpointManager property)

B

BAM (modos.genomics.formats.GenomicFileSuffix attribute) BCF (modos.genomics.formats.GenomicFileSuffix attribute) BearerAuth (class in modos.remote)

bucket (modos.genomics.refget.RefgetStorage attribute) (modos.remote.S3KeySpec attribute) (modos.storage.S3Path property) build_htsget_url() (in module modos.genomics.htsget)

C

calculate_checksums() (in module modos.genomics.refget) checksum() (modos.api.MODO method) chrom (modos.genomics.region.Region attribute) chunk_size (modos.genomics.htsget._HtsgetBlockIter attribute) class_from_name() (in module modos.helpers.schema) Code (class in modos.codes)

CodeMatcher (class in modos.codes) compute_checksum() (in module modos.helpers.schema) connect_s3() (in module modos.storage) contains() (modos.genomics.region.Region method) CRAM (modos.genomics.formats.GenomicFileSuffix attribute) create_sequence_id() (in module modos.genomics.cram)

D

DATA_ENTITY (modos.helpers.enums.ElementType attribute) (modos.helpers.enums.UserElementType attribute) (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) DataElement (class in modos.helpers.schema)

decrypt() (modos.api.MODO method) (modos.helpers.schema.DataElement method) decrypt_file() (in module modos.genomics.c4gh) default() (modos.remote.Permissions class method) dict_to_instance() (in module modos.helpers.schema) download() (modos.api.MODO method)

E

ELEMENT_ID modos-remove command line option modos-show command line option ELEMENT_TYPE modos-add command line option elements (modos.io.ExtractedMetadata attribute) ElementType (class in modos.helpers.enums) (class in modos.helpers.schema) empty() (modos.storage.Storage method) encrypt() (modos.api.MODO method) (modos.helpers.schema.DataElement method) encrypt_file() (in module modos.genomics.c4gh) end (modos.genomics.region.Region attribute) endpoint (modos.api.MODO attribute), [1] (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute) (modos.storage.S3Storage attribute)

EndpointManager (class in modos.remote) enrich_metadata() (modos.api.MODO method) exists() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) expiration (modos.remote.S3KeySpec attribute) expires_at (modos.remote.JWT property) ext2loader (in module modos.io) extract_metadata() (in module modos.genomics.cram) (in module modos.io) (in module modos.metabolomics.mztab) extract_tables() (in module modos.metabolomics.mztab) ExtractedMetadata (class in modos.io)

F

FASTA (modos.genomics.formats.GenomicFileSuffix attribute) FASTQ (modos.genomics.formats.GenomicFileSuffix attribute) FILE_PATH modos-remote-stream command line option find_codes() (modos.codes.CodeMatcher method) (modos.codes.LocalCodeMatcher method) (modos.codes.RemoteCodeMatcher method) from_cache() (modos.remote.JWT class method) from_file() (modos.api.MODO class method) from_htsget_query() (modos.genomics.region.Region class method) from_model_name() (modos.helpers.enums.ElementType class method) (modos.helpers.schema.ElementType class method)

from_object() (modos.helpers.enums.ElementType class method) (modos.helpers.enums.UserElementType class method) (modos.helpers.schema.ElementType class method) (modos.helpers.schema.UserElementType class method) from_path() (modos.genomics.formats.GenomicFileSuffix class method) from_pysam() (modos.genomics.region.Region class method) from_ucsc() (modos.genomics.region.Region class method) from_url() (modos.genomics.htsget.HtsgetConnection class method) fs (modos.genomics.refget.RefgetStorage attribute) fuzon (modos.remote.EndpointManager property) fuzzy_complete() (in module modos.prompt)

G

GenomicFileSuffix (class in modos.genomics.formats) get_assay() (in module modos.metabolomics.mztab) get_cache_dir() (in module modos.remote) get_cache_path() (modos.remote.JWT static method) get_completions() (modos.prompt.SlotCodeCompleter method) get_enum_values() (in module modos.helpers.schema) get_haspart_property() (in module modos.helpers.schema) get_index() (in module modos.genomics.formats) get_index_suffix() (modos.genomics.formats.GenomicFileSuffix method) get_keys() (in module modos.genomics.c4gh) get_loader() (in module modos.io) get_metadata_from_remote() (in module modos.remote)

get_s3_path() (in module modos.remote) get_samples() (in module modos.metabolomics.mztab) get_secret_key() (in module modos.genomics.c4gh) get_session() (in module modos.remote) get_slot_matcher() (in module modos.codes) get_slot_matchers() (in module modos.codes) get_slot_range() (in module modos.helpers.schema) get_slots() (in module modos.helpers.schema) get_target_class() (modos.helpers.enums.ElementType method) (modos.helpers.enums.UserElementType method) (modos.helpers.schema.ElementType method) (modos.helpers.schema.UserElementType method)

H

host (modos.genomics.htsget.HtsgetConnection attribute) htsget (modos.remote.EndpointManager property)

HtsgetConnection (class in modos.genomics.htsget) HtsgetStream (class in modos.genomics.htsget)

I

init_zarr() (in module modos.storage) instance_to_graph() (in module modos.helpers.schema) is_encrypted() (in module modos.genomics.formats) is_expired (modos.remote.JWT property) is_full_id() (in module modos.helpers.schema)

is_fuzon_available() (in module modos.prompt) is_genomic (modos.helpers.schema.DataElement property) is_remote (modos.api.MODO property) is_s3_path() (in module modos.remote) is_uri() (in module modos.helpers.schema)

J

JWT (class in modos.remote)

K

key (modos.storage.S3Path property)

kms (modos.remote.EndpointManager property) knowledge_graph() (modos.api.MODO method)

L

label (modos.codes.Code attribute) list() (modos.remote.EndpointManager method) (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) list_arrays() (modos.api.MODO method) list_files() (modos.api.MODO method) list_formats() (modos.genomics.formats.GenomicFileSuffix class method)

list_remote_items() (in module modos.remote) list_remote_modos() (in module modos.storage) list_samples() (modos.api.MODO method) list_zarr_items() (in module modos.storage) load_mztab() (in module modos.metabolomics.mztab) load_prefixmap() (in module modos.helpers.schema) load_schema() (in module modos.helpers.schema) LocalCodeMatcher (class in modos.codes) LocalStorage (class in modos.storage)

M

MAGIC_NUMBER (in module modos.genomics.formats) matcher (modos.prompt.SlotCodeCompleter attribute) metadata (modos.api.MODO property) model (modos.helpers.schema.DataElement attribute) MODO (class in modos.api) modos module modos (modos.remote.EndpointManager attribute) modos command line option --anon --debug --endpoint --version modos-add command line option --element --from-file --parent --source-file -e -f -p -s ELEMENT_TYPE OBJECT_PATH modos-c4gh-decrypt command line option --passphrase --secret-key -pw -s OBJECT_PATH modos-c4gh-encrypt command line option --passphrase --public-key --secret-key -p -pw -s OBJECT_PATH modos-codes-search command line option --query --top -q -t SLOT modos-create command line option --from-file --meta -f -m OBJECT_PATH modos-enrich command line option OBJECT_PATH modos-publish command line option --base-uri --output-format OBJECT_PATH modos-remote-download command line option --target -t OBJECT_PATH modos-remote-login command line option --auth-url --client-id -a -c modos-remote-stream command line option --region -r FILE_PATH OBJECT_PATH modos-remote-upload command line option --target -t OBJECT_PATH modos-remove command line option --force -f ELEMENT_ID OBJECT_PATH

modos-show command line option --files --zarr -f -z ELEMENT_ID OBJECT_PATH modos-update command line option --config --force -c -f OBJECT_PATH modos.api module modos.codes module modos.genomics module modos.genomics.c4gh module modos.genomics.cram module modos.genomics.formats module modos.genomics.htsget module modos.genomics.refget module modos.genomics.region module modos.helpers module modos.helpers.enums module modos.helpers.schema module modos.io module modos.logging module modos.metabolomics module modos.metabolomics.mztab module modos.prompt module modos.rdf module modos.remote module modos.storage module module modos modos.api modos.codes modos.genomics modos.genomics.c4gh modos.genomics.cram modos.genomics.formats modos.genomics.htsget modos.genomics.refget modos.genomics.region modos.helpers modos.helpers.enums modos.helpers.schema modos.io modos.logging modos.metabolomics modos.metabolomics.mztab modos.prompt modos.rdf modos.remote modos.storage move() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) move_file() (modos.helpers.schema.DataElement method)

N

name (modos.remote.S3KeySpec attribute)

O

OBJECT_PATH modos-add command line option modos-c4gh-decrypt command line option modos-c4gh-encrypt command line option modos-create command line option modos-enrich command line option modos-publish command line option modos-remote-download command line option modos-remote-stream command line option modos-remote-upload command line option modos-remove command line option modos-show command line option modos-update command line option

open() (modos.genomics.htsget.HtsgetConnection method) (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) overlaps() (modos.genomics.region.Region method) owner (modos.remote.Permissions attribute)

P

parse_attributes() (in module modos.io) parse_htsget_url() (in module modos.genomics.htsget) parse_instance() (in module modos.io) parse_multiple_instances() (in module modos.io) path (modos.api.MODO property) (modos.genomics.htsget.HtsgetConnection attribute) (modos.storage.LocalStorage property) (modos.storage.S3Storage property) (modos.storage.Storage property)

Permissions (class in modos.remote) permissions (modos.remote.S3KeySpec attribute) prefixes (modos.remote.S3KeySpec attribute) prompt (modos.prompt.SlotPrompter attribute) prompt_for_slot() (modos.prompt.SlotPrompter method) prompt_for_slots() (modos.prompt.SlotPrompter method) put() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method)

Q

query() (modos.api.MODO method)

R

read (modos.remote.Permissions attribute) read_pysam() (in module modos.genomics.formats) readable() (modos.genomics.htsget.HtsgetStream method) readinto() (modos.genomics.htsget.HtsgetStream method) REFERENCE_GENOME (modos.helpers.enums.ElementType attribute) (modos.helpers.enums.UserElementType attribute) (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) REFERENCE_SEQUENCE (modos.helpers.enums.ElementType attribute) (modos.helpers.schema.ElementType attribute) refget (modos.remote.EndpointManager property) RefgetStorage (class in modos.genomics.refget)

refresh() (modos.remote.JWT method) Region (class in modos.genomics.region) region (modos.genomics.htsget.HtsgetConnection attribute) (modos.remote.S3KeySpec attribute) RemoteCodeMatcher (class in modos.codes) remove() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) remove_element() (modos.api.MODO method) remove_file() (modos.helpers.schema.DataElement method) remove_object() (modos.api.MODO method) remove_suffix() (in module modos.genomics.formats)

S

s3 (modos.remote.EndpointManager property) s3_url_parts() (modos.storage.S3Path method) S3Key (class in modos.remote) S3KeySpec (class in modos.remote) S3Path (class in modos.storage) S3Storage (class in modos.storage) SAM (modos.genomics.formats.GenomicFileSuffix attribute) SAMPLE (modos.helpers.enums.ElementType attribute) (modos.helpers.enums.UserElementType attribute) (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) SCHEMA_PATH (in module modos.helpers.schema) secret_access_key (modos.remote.S3Key attribute) services (modos.remote.EndpointManager attribute) session (modos.remote.EndpointManager property) set_data_path() (in module modos.helpers.schema) set_haspart_relationship() (in module modos.helpers.schema)

setup_logging() (in module modos.logging) show_contents() (modos.api.MODO method) SLOT modos-codes-search command line option slot (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute) SLOT_TERMINOLOGIES (in module modos.codes) SlotCodeCompleter (class in modos.prompt) SlotPrompter (class in modos.prompt) spec (modos.remote.S3Key attribute) start (modos.genomics.region.Region attribute) Storage (class in modos.storage) storage (modos.api.MODO attribute) (modos.helpers.schema.DataElement attribute) store (modos.storage.S3Storage attribute) stream_genomics() (modos.api.MODO method)

T

ticket (modos.genomics.htsget.HtsgetConnection property) timeout (modos.genomics.htsget._HtsgetBlockIter attribute) to_cache() (modos.remote.JWT method) to_file() (modos.genomics.htsget.HtsgetConnection method) to_htsget_endpoint() (modos.genomics.formats.GenomicFileSuffix method) to_htsget_query() (modos.genomics.region.Region method)

to_pysam() (modos.genomics.htsget.HtsgetConnection method) to_tuple() (modos.genomics.region.Region method) top (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute) transfer() (modos.storage.Storage method)

U

update_date() (modos.api.MODO method) update_element() (modos.api.MODO method) update_file() (modos.helpers.schema.DataElement method) update_haspart_id() (in module modos.helpers.schema) update_metadata_from_model() (in module modos.helpers.schema) upload() (modos.api.MODO method) upload_fasta() (modos.genomics.refget.RefgetStorage method)

upload_seq() (modos.genomics.refget.RefgetStorage method) upload_to_s3() (in module modos.genomics.refget) uri (modos.codes.Code attribute) url (modos.genomics.htsget.HtsgetConnection property) (modos.storage.S3Path attribute) UserElementType (class in modos.helpers.enums) (class in modos.helpers.schema)

V

valid_paths() (modos.remote.S3Key method)

validate_cram_files() (in module modos.genomics.cram) VCF (modos.genomics.formats.GenomicFileSuffix attribute)

W

write (modos.remote.Permissions attribute)

Z

zarr (modos.api.MODO property) (modos.storage.LocalStorage property) (modos.storage.S3Storage property) (modos.storage.Storage property)

ZARR_ROOT (in module modos.storage) zarr_store (modos.storage.S3Storage attribute)