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

* [wip] linkml version with shacl, context and pydantic

* removing some unnecessary any_of; regenerate context

* changing comments to description; fixing types (string vs langString) and adding @language:en to context; bringing back imageUrl; splitting UI class to multiple classes for UI for Activity, Field and Protocol

* Updated linkml schema and corresponding updates to context

* Move TimedOut to an enumeration for missing

* update autogenerated files

* Add generated shacl

* more fixes

* change name to also allow importing reproschema

* remove slot_usage of value for some classes

* adding AllowSkip and fixing activity1

* changing LangString to Dict[str, str]

* fixing vocab in the context file

* fixing alt label so it is also langString, adding altLabel to the example

* fixing context for additionalNotesObj

* adding container to choices in the context

* adding additional container=set to the context

* removing old contexts and renaming the new one

* updates based on the examples from reproschema-library

* additional changes based on testing library: adding CreativeWork to ResponseOption, dealing with dict-form of compute

* fixing compute

* adding MissingType to the Response value

* adding AllowAltResponse option

* adding CreativeWork to most of the classes; adding description to CreativeWork slots; slightly different formatting from  the linkml generator

* adding title to enum, and modyfing label so it include reproschema

* adding Thing and use it instead of CreativeWork in some classes

* adding back CreativeWork to ResponseOption and Activity

* moving category to Thing and removing Creative Work; removing imageUrl to have consistent with video and audio

* removing imageUrl and CreativeWork from the context

* add proprietary flag to activities

* removing decimal

* cleaning: removing some fles and changing test (will not work before merging reproschema-py)

* running pre-commit

* removing link to validation

---------

Co-authored-by: Dorota Jarecka <[email protected]>

Author: satra

.github/workflows/pythonpackage.yml

@@ -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

README.md

@@ -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)