Notable changes introduced in modos releases are documented in this file
- (deploy) switch from minio to garage as S3 storage service (#183)
- (cli) oauth device code flow support (#183)
- (api) do not consolidate on read operations (#173)
- (api) auto-attach assays to MODO (#176)
- (server) explicit error message on missing bucket (#165)- vcf streaming to pysam (#180)
- (tutorials) fix obsolete api parameters (#168)
- (tutorials) add advanced yaml example (#172)
- (cli) codes for sample processing (#178)
- (cli) pass s3 credentials via env (#179)
- (fuzon) cli fallback without autocomplete (#164)- schema upgrade (#177)
- (deploy) drop depends_on.required for compat with older compose (#156)
- (deploy) nonroot container users (#157)
- (deploy) addgroup -> groupadd for debian-based images
- (deploy) caddy with https support (#160)- compatibility with air-gapped deployments (#154)
- (cli) syntax when reading passphrase from file (#140)
- (storage) transfer metadata (#148)
- (api) sequential encryption (#138)
- pin typer AND click versions for compatibility
- add encryption and upload sections (#136)
- (api) update data path (#118)
- (deps) remove misplaced pyfuzon import
- (server) api compatibility for /meta and /get (#126)
- (readme) fix gha badge url (#132)
- (tuto) document modos enrich subcommand- add file format design notes (#111)
- (cli) update prompts for removal of missing config elements (#123)
- (deploy) setup refget service (#121)- logger (#130)
- local crypt4gh encryption (#127)
- (deploy) htsget networking (#102)
- (htsget) minio connection
- (readme) fix example sparql query
- (tuto) fix mztab example
- (cli) consistent path options (#105)
- (cli, api) show only target element (#98)- support terminology codes (#106)
- mztab support (#107)
- (rdf) inject schema:identifier (#99)
- (tutorial) update remote and genomics (#97)
- (rdf) schema.org prefix (#96)
- (api) add type hints, fix doctests
- (api) MODO.metadata extracts own attributes
- (api) update changed values in update_element (#83)
- (cli) duplicated prompt for id
- (cli) drop zarr group creation on modo create
- (compose) network syntax
- (compose) volume mounts + listening address
- (compose) env vars to specify buckets and policies
- (compose) disconnect s3 volume from modo-server (accessed via net)
- (cram) add slicing logic
- (cram) coords -> region
- (deploy) disable body size limit in nginx (#42)
- (deploy) disable max body size in nginx
- (docker) missing dep in client dockerfile
- (introspection) support inheritance in get_slots
- (io) rm unneeded id_ -> id
- (minio) add env variables for auth
- (minio) expose console port locally
- (nginx) define rewrite rules for s3+htsget
- (rdf) handle path->uri conversion for data_path
- (server) pin dependencies
- (server) safer bucket replacement
- (server) safer bucket replacement
- (server) make exact_match match exactly
- (server) pin htsget version + bump msrv (#49)
- (server) reload minio filesystem on server queries (#62)- schema syntax
- drop unused query
- visit nodes recursively when extracting metadata
- path handling on modo creation
- cli display of modo show
- rm unused linkml-owl helper+undeclared linkml dep
- add missing --data-file option
- set filename using metadata when copying into digital object
- validate types of has_part relationship in MODO.add
- handle root path when adding data
- allow flexible number of elements in yaml
- change path in example config.yaml
- use schema model to build modo from yaml
- directly cast schema models
- add check for list
- propagate function name change
- minor fix in example yaml id
- add check for existing before adding element to modo
- missing typing import
- create unique sequence ids from extracted metadata
- standardize metadata extraction
- extract reference from list
- remote metadata streaming
- add group level to extract_metadata in line with the new structure
- adapt tests to zarr path as id
- prevent failing for non existing keys in whitelist
- define existing paths in test yaml
- use relative path to enrich metadata
- rename whitelist, simplify conditions
- set full id for has_part attributes when build from yaml
- adapt has_part ids to full id when build from yaml
- consistent naming
- include metadata from all modos
- wildcard use in fstring
- adapt env var name
- name mismatch in slice_remote_cram
- mutable args (#52)
- auto upload cram index (#64)
- Add
direnvtooling and ignore - Add
pyrightlsp - format bug in feature-request.yml
- consistent ids (#70)
- client-side region-filter on htsget streams (#71)
- (cli) shorten command descriptions
- (compose) mount -> volume for minio
- (deploy) add deployment instructions and docs
- (deploy) update readme with nginx setup
- (deploy) document configuration with .env file
- (readme) add usage+development guidelines
- (readme) refresh api description
- (readme) add credits (#55)
- (readme) styling + update examples (#80)
- (readme) fix api example
- (typo) deploy/README.md
- (typo) deploy/README.md- add initial README.md
- add implementation details to README.md
- add status to readme
- add license
- add NOTE in get_slot_range about class-independence
- mention class-independence in get_slot_range docstring
- docstring for MODO.update_element
- sphinx website with API reference (#32)
- Add some documentation for using
nix - format markdown documents (#66)
- (api) basic metadata extraction
- (api) update existing elements
- (api) allow passing zarr archive to MODO constructor
- (cli) implement create command
- (cli) add write commands for metadata+data
- (cli) add support for multi-choice prompt
- (cli) allow skipping slot prompts
- (cli) stream command (#87)
- (cli) update modo from yaml file (#89)
- (cli, api) remove modo (#76)
- (cram) region parsing func
- (cram) slice local files
- (deploy) add nginx service in compose
- (deploy) htsget over s3 (#26)
- (docker) version as build arg + metadata label
- (helpers) allow enum from model object
- (introspection) add getter methods, cache schema views
- (io) helper functions for loading instances
- (makefile) docker build recipe
- (meta) add custom rdf converter
- (nginx) placeholder config
- (s3) allow virtual-host-style buckets (#75)
- (server) extend client dockerfile
- (server) list modos and gather metadata[wip]
- (server) sort matches by similarity- add draft rdf metadata schema
- add taxid in schema
- add pkg skeleton
- add helper functions to inspect schema
- add zarr mgmt funcs to modo.storage
- list samples in archive via API
- add remove command
- allow adding reference genomes
- relevant metadata from cram file
- first version to build full obj from yaml
- extend cli create
- server deployment (#12)
- update build_modo_from_file for new structure
- use zarr path as id, check for unique
- fail early for duplicated id in build_modo_from_file
- repeat prompt for invalid inputs (non unique ids)
- copy files into modo when building from yaml
- request server endpoints
- Add get?query to modo server
- enable instantiation of remote modo
- add a function to handle both cram and vcf/bcf BytesIO buffers.
- add helper function to determine the file format. needed for generalized save/stream_genomics methods, and possibly for oter methods/functions as well
- add a function to handle both cram and vcf/bcf BytesIO buffers.
- add a function to handle both cram and vcf/bcf BytesIO buffers.
- Add development setup for Nix shell
- Enable
nixdevelopment - auto update last_update_date attr (#73)
- htsget client (#78)
- streamline remote options (#90)