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feat: initial api aligned with smoc-schema #3

Merged
merged 46 commits into from
Jan 17, 2024
Merged

feat: initial api aligned with smoc-schema #3

merged 46 commits into from
Jan 17, 2024

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cmdoret
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@cmdoret cmdoret commented Jan 8, 2024 •
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Initial design relying on the smoc-schema. It provides the modo package, which exposes a python API and command line interface to create, edit and read multi-omics digital objects.

cmdoret added 24 commits December 22, 2023 13:39
@cmdoret
chore: add schema repository to deps
a5acae9
@cmdoret
placeholder cli
cc01817
@cmdoret
feat(cli): implement create command
ebd56a0
@cmdoret
refactor(models): drop unused models module
594d54c
@cmdoret
feat: add helper functions to inspect schema
db187f5
@cmdoret
feat(io): helper functions for loading instances
5601aa3
@cmdoret
chore: register cli entrypoint in pyproject.toml
7d243e0
@cmdoret
feat(introspection): add getter methods, cache schema views
8fffbde
@cmdoret
feat(meta): add custom rdf converter
e580fc8
@cmdoret
refactor: mv helpers to helpers module
b592bc9
@cmdoret
feat: add zarr mgmt funcs to modo.storage
7981535
@cmdoret
refactor(api): use zarr for metadata in public API
08bd263
@cmdoret
feat(cli): add write commands for metadata+data
fccb04a
@cmdoret
fix: visit nodes recursively when extracting metadata
c583c50
@cmdoret
update test data to use zarr
5a962fc
@cmdoret
feat: list samples in archive via API
5ad3816
@cmdoret
fix: path handling on modo creation
59ee99a
@cmdoret
test: update expected results
c533393
@cmdoret
chore: update default prefix
f8ca08c
@cmdoret
fix: cli display of modo show
5620dd9
@cmdoret
refactor: use slot inheritance to identify correct has_part property
0de79a8
@cmdoret
test(introspection): doctests for getting has_prop subprops
fcffc30
@cmdoret
refactor(introspection): simpler logic
91bd61b
@cmdoret
feat: add remove command
e3b24ce
@cmdoret cmdoret changed the title Feat/schema feat: initial api aligned with smoc-schema Jan 8, 2024
almutlue
almutlue reviewed Jan 10, 2024
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@almutlue almutlue left a comment

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Very minor comments. Looks like a very good prototype version.

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cmdoret added 17 commits January 10, 2024 20:02
@cmdoret
feat(cli): add support for multi-choice prompt
176abbc
@cmdoret
refactor(introspection): drop unused get_class function
64263f4
@cmdoret
refactor(introspection): drop unused get_class_uri function
585c427
@cmdoret
docs: add NOTE in get_slot_range about class-independence
f56a2d8
@cmdoret
docs: mention class-independence in get_slot_range docstring
1346174
@cmdoret
fix(rdf): handle path->uri conversion for data_path
35b2249
@cmdoret
fix(introspection): support inheritance in get_slots
7819bf6
@cmdoret
chore(dep): update smoc-schema git ref
30f6706
@cmdoret
fix(cli): duplicated prompt for id
6de54b1
@cmdoret
feat(cli): allow skipping slot prompts
799c4a3
@cmdoret
fix: set filename using metadata when copying into digital object
2c8e652
@cmdoret
fix: validate types of has_part relationship in MODO.add
283d20e
@cmdoret
fix: handle root path when adding data
6fb42ab
@cmdoret
feat: allow adding reference genomes
d03eafe
@cmdoret
chore: update poetry lock
b05494d
@cmdoret
test: add reference to test data
78495c6
@cmdoret
test: update test cases + fix object creation
8190b52
@cmdoret cmdoret merged commit 76c95e7 into main Jan 17, 2024
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@cmdoret cmdoret deleted the feat/schema branch February 7, 2024 09:05
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@almutlue almutlue almutlue left review comments

@AssafSternberg AssafSternberg Awaiting requested review from AssafSternberg

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@cmdoret @almutlue