bsandbox

a place to do bottom up exercises

see

• https://linkml.io/

• use template or https://linkml.io/linkml/generators/project-generator.html?highlight=template ?

• start with linkml individuals in json

• convert to yaml?

• try/practice

  • exception handling
  • make
  • various virtual environments
  • cookie cutter
  • tox
  • nlp
  • visualization
  • builing package and publishing
  • testing
  • GitHub actions
  • cli (click)
  • docstrings
  • ...

---

• clone this repo and cd into it
• % python3 -m venv venv
• pip install -r requirements.txt
  • try other virtual env and package installers
• make all

Intel MacBook Pro 2020, macPS Big Sur 11.5.2

many of these:

DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at Homebrew/homebrew-core#76621

d9b496c0ab2e069eefefb28222deda558c2b5429

GEN: sqlddl SCHEMA: personinfo.yaml PARENT=personinfo/sqlschema WARNING:SQLDDLGenerator:Unrecognized prefix: skos ARGS: {'mergeimports': False} WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> WARNING:root:UNKNOWN: XSDDate // <class 'linkml_runtime.utils.yamlutils.extended_str'> ERROR:root:No PK for Address WRITING TO: personinfo/sqlschema/personinfo.sql

% ./venv/bin/linkml-convert -m personinfo/personinfo.py -o person_glance_data.yaml -t yaml -C Person -s personinfo.yaml person_glance_data.json

WARNING:root:There is no established path to personinfo/personinfo.py - compile_python may or may not work WARNING:JsonSchemaGenerator:Unrecognized prefix: skos