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WIP: updated branch with changes to support linkml schema #456

Merged
merged 52 commits into from
Jun 14, 2024
Merged

WIP: updated branch with changes to support linkml schema #456

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b5474b8
[wip] linkml version with shacl, context and pydantic
djarecka Feb 2, 2024
cd233a6
removing some unnecessary any_of; regenerate context
djarecka Feb 13, 2024
62bc4a8
changing comments to description; fixing types (string vs langString)…
djarecka Feb 16, 2024
7013c1c
Updated linkml schema and corresponding updates to context
satra Feb 17, 2024
10fefc5
Move TimedOut to an enumeration for missing
satra Feb 17, 2024
3be0933
update autogenerated files
satra Feb 17, 2024
aabafc3
Add generated shacl
satra Feb 17, 2024
379d329
more fixes
satra Feb 17, 2024
f7e1357
change name to also allow importing reproschema
satra Feb 17, 2024
b0a72cb
remove slot_usage of value for some classes
satra Feb 19, 2024
885f9b7
adding AllowSkip and fixing activity1
djarecka Feb 19, 2024
b9f81dc
Merge pull request #457 from djarecka/satra_ref/linkml
satra Feb 19, 2024
99f220b
changing LangString to Dict[str, str]
djarecka Feb 21, 2024
c7c5348
fixing vocab in the context file
djarecka Feb 21, 2024
efb74e1
Merge pull request #459 from djarecka/satra_ref/linkml1
satra Feb 21, 2024
577009b
fixing alt label so it is also langString, adding altLabel to the exa…
djarecka Feb 23, 2024
543ce44
Merge pull request #460 from djarecka/satra_ref/linkml1
djarecka Feb 23, 2024
083a8cc
fixing context for additionalNotesObj
djarecka Feb 23, 2024
3ea58a5
Merge pull request #461 from djarecka/satra_ref/linkml1
djarecka Feb 23, 2024
f88f74b
adding container to choices in the context
djarecka Feb 26, 2024
5c2fa67
Merge pull request #462 from djarecka/satra_ref/linkml1
djarecka Feb 26, 2024
7dbffe3
adding additional container=set to the context
djarecka Mar 1, 2024
27949dc
removing old contexts and renaming the new one
djarecka Mar 1, 2024
72c8ae5
Merge pull request #463 from djarecka/satra_ref/linkml1
djarecka Mar 1, 2024
953087b
updates based on the examples from reproschema-library
djarecka Mar 29, 2024
e5bf779
Merge pull request #468 from djarecka/satra_ref/linkml1
djarecka Mar 29, 2024
befbd8c
additional changes based on testing library: adding CreativeWork to R…
djarecka Apr 2, 2024
a1d0421
Merge pull request #469 from djarecka/satra_ref/linkml1
djarecka Apr 2, 2024
fcea6fd
fixing compute
djarecka Apr 4, 2024
5a4788f
adding MissingType to the Response value
djarecka Apr 4, 2024
2ea709f
adding AllowAltResponse option
djarecka Apr 5, 2024
bd7a412
Merge pull request #470 from djarecka/satra_ref/linkml1
djarecka Apr 5, 2024
362330b
adding CreativeWork to most of the classes; adding description to Cre…
djarecka Apr 13, 2024
2c2f930
adding title to enum, and modyfing label so it include reproschema
djarecka Apr 26, 2024
5cdd349
adding Thing and use it instead of CreativeWork in some classes
djarecka Apr 26, 2024
e87941e
adding back CreativeWork to ResponseOption and Activity
djarecka Apr 27, 2024
53b8f05
Merge pull request #471 from djarecka/satra_ref/linkml1
djarecka May 2, 2024
d76dd78
moving category to Thing and removing Creative Work; removing imageUr…
djarecka May 9, 2024
5f9c2ac
removing imageUrl and CreativeWork from the context
djarecka May 11, 2024
c000f79
Merge pull request #488 from djarecka/satra_ref/linkml1
djarecka May 11, 2024
4d01c40
add proprietary flag to activities
satra May 15, 2024
4e808fd
Merge pull request #489 from ReproNim/satra-patch-1
satra May 15, 2024
ff24fa2
removing decimal
djarecka Jun 11, 2024
939ae79
Merge pull request #493 from djarecka/satra_ref/linkml1
djarecka Jun 11, 2024
cd95b13
cleaning: removing some fles and changing test (will not work before …
djarecka Jun 14, 2024
3e6b2bf
Merge pull request #495 from djarecka/satra_ref/linkml1
djarecka Jun 14, 2024
e601ae7
running pre-commit
djarecka Jun 14, 2024
cfc79c9
Merge pull request #496 from djarecka/satra_ref/linkml1
djarecka Jun 14, 2024
5318a51
resolving conflicts
djarecka Jun 14, 2024
fff1522
Merge pull request #497 from djarecka/satra_ref/linkml1
djarecka Jun 14, 2024
7a7b9c4
removing link to validation
djarecka Jun 14, 2024
aa710a5
Merge pull request #498 from djarecka/satra_ref/linkml1
djarecka Jun 14, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/pythonpackage.yml
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Expand Up @@ -27,7 +27,7 @@ jobs:
- name: Test with pyshacl
run: |
python scripts/jsonParser.py
reproschema -l DEBUG validate --shapefile validation/reproschema-shacl.ttl examples
reproschema validate examples
- name: Make a release
run: |
python scripts/makeRelease.py ci-release
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1 change: 0 additions & 1 deletion README.md
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Expand Up @@ -12,7 +12,6 @@ This repository contains:
- the [different terms of the ReproSchema](./terms)
- the [corresponding context files](./contexts)
- a example of [a protocol based on the reproschema](./examples)
- the [validation SHACL files](./validation)
- the [documentation](./docs)


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18 changes: 0 additions & 18 deletions contexts/base
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279 changes: 0 additions & 279 deletions contexts/generic
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