turbomam / mixs-subset-examples-first Goto Github PK

• #58
• start with simple structure pattern settings #56
• add multivalued settings

see also

• #64

ERROR:root:Error compiling generated python code: name 'Agriculture' is not defined
Traceback (most recent call last):
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/bin/linkml-run-examples", line 8, in
sys.exit(cli())
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 306, in cli
runner.process_examples()
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 136, in process_examples
self.process_examples_from_list(input_examples, fmt, False)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 195, in process_examples_from_list
obj = self._load_from_dict(input_dict, target_class=tc)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 245, in _load_from_dict
v2 = self._load_from_dict(v, target_class=islot.range)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 250, in _load_from_dict
return [self._load_from_dict(x, target_class) for x in dict_obj]
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 250, in
return [self._load_from_dict(x, target_class) for x in dict_obj]
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 247, in _load_from_dict
py_target_class = getattr(self.python_module, camelcase(target_class))
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/workspaces/example_runner.py", line 99, in python_module
self._python_module = pygen.compile_module()
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/generators/pythongen.py", line 82, in compile_module
raise e
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml/generators/pythongen.py", line 78, in compile_module
return compile_python(pycode)
File "/home/mark/.cache/pypoetry/virtualenvs/mixs-subset-examples-first-1BdAgHnd-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/compile_python.py", line 47, in compile_python
exec(spec, module.dict)
File "test", line 187, in
File "test", line 195, in Database
NameError: name 'Agriculture' is not defined
make: *** [Makefile:159: examples/output] Error 1

No conflicts between soil, water and (empty)!

Lots of conflicts with agriculture.

What might have a small number of conflicts?

Usage of terms in Checklist classes would be completely redundant. In the output of XXX, we informally model these usages? assignments? in terms of a "core" grouping

Already have

• checklist oriented class-slot assignment and requirement sheet: data/core_requirements_recommended_required_curated.tsv

Starting on

• environmental package usage sheet, based on data/mixs_v6_environmental_packages.tsv
  • #47

just need to avoid curly quotes

internal_separator: "|"

not

internal_separator: “|”

https://github.com/microbiomedata/mixs_fresh_start/blob/main/project.Makefile

or at least provide an index

presentation.md

It was in a curated input. I have removed it.

• #23
• #24
• #25

• #50
• #51

would be based on data/mixs_v6_environmental_packages.tsv

That doesn't take advantage of previous Environmental package and Structured comment name cleanups that went into XXX?

How to look for malformed names in YAML after the fact?

Must include

• Environmental package -> class
• Structured comment name -> slot
• Requirement -> recommended and required

Global

  mims_soil_set:
    name: mims_soil_set
    from_schema: https://github.com/turbomam/mixs-subset-examples-first/tree/main/src/mixs_subset_examples_first

Database slot_usage

      mims_soil_set:
        name: mims_soil_set
        multivalued: true
        range: MimsSoil
        inlined_as_list: true

esp TTL

and SQLite

probably with run-linkml-examples

data/core_requirements_recommended_required_curated.tsv

etc.

data/Database.tsv

data/duplicated_scns_by_id.tsv

data/mixs_combined_all_modified.tsv

data/mixs_combined_all_modified_lossy_deduped.tsv

data/mixs_requirement_codes.tsv

mixs_citation = https://github.com/GenomicsStandardsConsortium/mixs/wiki/5.-MIxS-checklists

data/mixs_v6_checklists_env_packages_classes_curated.tsv

https://github.com/microbiomedata/mixs_fresh_start/tree/main/src/mixs_fresh_start/datamodel

• don't say class or slot (term)
• inheritance may not be useful... say combination of ...
• applicable classes have been lost from slot pages

data/mixs_combined_all_modified.tsv

will require edits to project.Makefile

like the schema should in src/mixs-subset-examples-first/schema/mixs-subset-examples-first.yaml

• will this be hard to do with schemasheets? two different inner keys in two different columns
• or put {dicts} in a single column?
• how about yq

contains

• exactly one [
• exactly one ]
• at least one |
• no {
• no }
• no ;

see also

• #78

samp_name?

see #11

MIxS provides examples of yes, no, true, etc.

• usefulness?
• compatibility with strange element names?
  • python data classes doesn't like element with names that start with digits
  • #64
• execution time?
  • markdown
  • excel
• customization, like closed jsonschema

from https://github.com/microbiomedata/submission-schema/blob/main/project.Makefile

examples/output/README.md: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \
src/data/invalid src/data/valid
	mkdir -p $(dir $@)
	# RDF/TTL generation is failing
	# https://github.com/microbiomedata/submission-schema/issues/13
	$(RUN) linkml-run-examples \
		--output-formats json \
		--output-formats yaml \
		--counter-example-input-directory $(word 2,$^) \
		--input-directory $(word 3,$^) \
		--output-directory $(dir $@) \
		--schema $< > $@

https://github.com/turbomam/mixs-subset-examples-first/actions/runs/4671863919/jobs/8273368033

Or GH pages just hadn't been setup yet?

Harshad and Sujay have suggested deleting the GH pages branch when this happens, but I didn't even have on when I got this error

Kai had reported a similar situation in which he solved the problem by allowing write permissions by ? on ??

like this?

https://github.com/turbomam/mixs-subset-examples-first/actions/runs/4668090785/jobs/8264692805

TypeError: linkml_runtime.linkml_model.meta.PatternExpression() argument after ** must be a mapping, not extended_str

maybe needs an inner key?

emphasize MimsSoil

how can we make it easier to filter the available classes at the time of generation?

data/mixs_combined_all_modified_lossy_deduped.tsv

also in examples

these can't be generated as proprieties of a class in the Python Data Classes