microbiomedata / cleanroom-schema Goto Github PK

intermittent

see

• linkml/linkml#1154

mark@nuc-two-ups:~/gitrepos/cleanroom-schema$ make update
./utils/get-value.sh: 4: Bad substitution
./utils/get-value.sh: 4: Bad substitution
cruft update
bash: cruft: command not found
make: *** [Makefile:67: update-template] Error 127

This won't copy in tests, makefiles, or necessarily place artifacts in the same locations as nmdc-schema

Move this "issue" somewhere else

compared to when (last relevant publication)

• "best" or standardized practices
  • cookiecutter
  • jinja template documentation
    • some slot table problems
  • collecting data with dataharmonizer
    • but don't have a general purpose de-flattener

variety of data source

characteristics of the MongoDB back-end

NAPA protocol identifiers

performed a migration of MongoDB contents from schema v3.2 to v7

• rough code
• only Biosample identifiers are being relocated into type-specific list and being replaced with nmdc identiifers
• those nmdc Biosample local values are UUIDs, not NAPA patterns

the cookiecutter template provides an instantiation-based test script and data file based on the defult person info schema

nmdc-schema used ! jsonschema to confirm invalid content in the past. (Has recently been switched to ! check-jsonschema)

lots of sub dependencies

I think @pkalita-lbl had local solutions for this in the nmdc-schema. Maybe those should be pushed into the cookiecutter template

Annotations
3 warnings

test (3.10)
Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-python@v2
test (3.9)
Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-python@v2
Build and test cleanroom_schema: .github#L1
ubuntu-latest workflows will use ubuntu-22.04 soon. For more details, see actions/runner-images#6399

mark@nuc-two-ups:~/gitrepos/cleanroom-schema$ make update
./utils/get-value.sh: 4: Bad substitution
./utils/get-value.sh: 4: Bad substitution
cruft update
bash: cruft: command not found
make: *** [Makefile:67: update-template] Error 127

set value from mam-pypi-general-2022-12-08 into repository secret PYPI_PASSWORD

Schema YAML already included

$ ls -lR cleanroom_schema-0.1.0/src/
cleanroom_schema-0.1.0/src/:
total 4
drwxrwxr-x 4 mark mark 4096 Dec  8 11:11 cleanroom_schema

cleanroom_schema-0.1.0/src/cleanroom_schema:
total 12
drwxrwxr-x 2 mark mark 4096 Dec  8 11:11 datamodel
drwxrwxr-x 2 mark mark 4096 Dec  8 11:11 schema
-rw-r--r-- 1 mark mark  185 Dec  8 11:08 _version.py

cleanroom_schema-0.1.0/src/cleanroom_schema/datamodel:
total 24
-rw-r--r-- 1 mark mark 17394 Dec  8 11:08 cleanroom_schema.py
-rw-r--r-- 1 mark mark    32 Dec  8 11:08 __init__.py

cleanroom_schema-0.1.0/src/cleanroom_schema/schema:
total 8
-rw-r--r-- 1 mark mark 6370 Dec  8 11:08 cleanroom_schema.yaml