merge linkML into main #44
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fix altLabel
…ue, updated to ResponseOption and image
updates to the model after testing library
* add print for testing * update clear_header * remove print * fix order and other errors * change ui yesno to radio * fix typo * update context, field->item, fix isVis * remove useless due to failed validation * remove visibility at the item level & remove matrixInfo * fix choice * remove identifier * updating validate command to the new pydantic model * updating/fixing the tests; updating the model to use CreativeWork; changes in formating * fix conversion tests * remove test output * change test output directory * final improvments on tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * model version after adding Thing class * updating model after removing CreativeWork and ImageUrl * adding tests to initialize the model classes * fixing load_file; adding write_obj_jsonld function and expanding test_schema * changing redcap2reproschema to use ned pydantic classes; some small changes to the pydantic model * changing name from string to landstring with en as language * fixing jsonld files * Adding option to return compact schema to load_file * fixing the protocol jsonld file * changing reproschema2redcap to use the new model * adding contectfile to write_obj_jsonld function and improving test; improving compact option for load_file * fixing reproschema2redcap and tests * removing file with the context and fixing references to the context_url (for now the link rfom the ref/linkm branch * updating the reproschema2redcap to work for activity/items from urls * improving error message for file_load and validate; checking the suffix of the file before treating it as jsonld * fixing identify_model_class, so Item and Field are treated the same * fixing reproschema2redcap so it reads responseOptions from another file * rewriting parts of redcap2reproschema, fixing some bugs[wip] * fixing compute: removing isvis condition * fixing process_csv so it doesn't go multiple time through the same condition * changes to input and value mapping (mapping explicitly or raising errors if not found); fixing choices and adding slider; adding sql to compute types (this does not work properly right now); adding many comments * adding output for redcap2reproschema command; removing argparse * model without decimal; revert changes to valueType in the model * adding migrade command * fixing multiple issues with redcap2rp and rp2redcap: adding compute, fixing preamble (can be either activity level or issue level * WIP: addining test to test rp2redcap and redcap2repo using nimh exampl * fixing paths in the tests, should run now * ignore .DS_Store files in validation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: yibeichan <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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okay, I merged the PR to ref/linkml, but forgot to rebase.... now we need to solve some conflicts...