Add push to openbis to update masterdata in openBIS

[JosePizarro3]

We need to create a script to check and update the datamodel in the openBIS instance.

We could use the pyBIS methods new_... to create new object types/property types/vocabulary types if these do not exist in the instance. For this, the masterdata_checker is necessary.

@carlosmada22

TODO:

• Create CLI push_to_openbis which accepts:
  • --excel-file (same behavior as in import-from-excel):
  • --python-path
    • individual Python modules
    • directory with all Python modules to be checked
• Applies checker
• For each entity, uses _log_msgs:
  • If checker has been successful (no critical, error, warning), creates or updates entity in openBIS
  • Else: logger.info("The checking of the entity type {cls_name} did not pass. Please, check your entity definitions.

[JosePizarro3]

This is part of #11

[JosePizarro3]

@carlosmada22 I am not 100% sure we can export the Python directly into openBIS. The methods new_xxx_type() are related with parsing, not with defining entities in the schema.

Ok, I saw the documentation: https://openbis.readthedocs.io/en/latest/software-developer-documentation/apis/python-v3-api.html#create-sample-types-object-types
It is indeed possible by just simply doing save() at the end.

[JosePizarro3]

A small snippet for something that works creating entities and assigning properties:

from datetime import datetime

o = ologin()
code = "TEST_OBJECT_FROM_PYTHON"
objects_obis = [
    entity.get("code") for entity in o.get_object_types().df.to_dict(orient="records")
]
if code in objects_obis:
    obj = o.get_object_type(code)
    obj.description = f"New description changed at <<{datetime.now()}>> Testing object creation from pybis"
else:
    obj = o.new_object_type(
        code=code,
        description=f"<<{datetime.now()}>> Testing object creation from pybis",
        generatedCodePrefix="TEST2025JAN",
        autoGeneratedCode=True,
        validationPlugin="",
    )
obj.save()

## Assign properties to the object
properties_obis = [
    entity.get("code") for entity in o.get_property_types().df.to_dict(orient="records")
]
code_prop_1 = "$NAME"
if code_prop_1 in properties_obis:
    obj.assign_property(
        prop="$NAME",
        section="General information",
        mandatory=True,
        showInEditView=True,
    )
else:
    prop = o.new_property_type(
        code=code_prop_1,
        description="Name",
        dataType="VARCHAR",
        label="Name",
    )
    prop.save()
    obj.assign_property(
        prop="$NAME",
        section="General information",
        mandatory=True,
        showInEditView=True,
    )
code_prop_2 = "CHEMICAL"
if code_prop_2 in properties_obis:
    obj.assign_property(
        prop="CHEMICAL",
        section="General information",
        mandatory=True,
        showInEditView=True,
    )
else:
    prop = o.new_property_type(
        code=code_prop_2,
        description="Chemical",
        dataType="SAMPLE",
        label="Chemical",
    )
    prop.save()
    obj.assign_property(
        prop="CHEMICAL",
        section="General information",
        mandatory=True,
        showInEditView=True,
    )