https://github.com/cmungall/basin3d_schema
EXPERIMENTAL
https://github.com/cmungall/basin3d_schema
environmental-data exemplar linkml
Last synced: about 2 months ago
JSON representation
EXPERIMENTAL
- Host: GitHub
- URL: https://github.com/cmungall/basin3d_schema
- Owner: cmungall
- License: bsd-3-clause
- Created: 2022-09-21T19:56:41.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2022-09-22T15:22:04.000Z (over 2 years ago)
- Last Synced: 2025-02-17T10:54:37.999Z (3 months ago)
- Topics: environmental-data, exemplar, linkml
- Language: Python
- Homepage: https://cmungall.github.io/basin3d_schema
- Size: 884 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# basin3d_schema
EXPERIMENTAL rendering of basin3d as [linkml](https://linkml.io/linkml/)
## Website
* [https://cmungall.github.io/basin3d_schema](https://cmungall.github.io/basin3d_schema)
The above website is entirely generated from the source LinkML yaml files.
This generates pages for classes, including:
* [Feature](https://cmungall.github.io/basin3d_schema/Feature/)
Vocabularies/enums, e.g.
* [StatisticEnum](https://cmungall.github.io/basin3d_schema/StatisticEnum/)
Slots/fields, e.g.
* [observed_property](https://cmungall.github.io/basin3d_schema/observed_property/)
## Repository Structure
* [examples/](examples/) - example data
* [project/](project/) - project files (generated: do not edit these)
* [jsonschema](jsonschema/) - JSON schema, for validating JSON documents
* [sqlschema](sqlschema/) - SQL DDL (CREATE TABLE statements)
* [jdonld](jsonld/) - JSON-LD Contexts
* [shacl](shacl/) - SHACL shape definitions (for RDF validation)
* [src/](src/) - source files (edit these)
* [basin3d_schema](src/basin3d_schema)
* [schema](src/basin3d_schema/schema) -- LinkML schema (edit this)
* [datamodel](src/basin3d_schema/datamodel) -- Generated pydantic datamodel
* [tests](tests/) - python tests
## Usage
```bash
pip install basin3d_schema
```
(^^ may not work if this is a new repo)
### Creating Objects
Creating objects via generated Pydantic model:
```python
from basin3d_schema.datamodel.core import Observation, MonitoringFeature, Coordinate, AbsoluteCoordinate,
GeographicCoordinate
geo_coord = GeographicCoordinate(x=-5, y=20)
ft = FeatureTypeEnum.WATERSHED
feat = MonitoringFeature(description="test",
coordinates=Coordinate(absolute=AbsoluteCoordinate(horizontal_position=[geo_coord])))
obs = Observation(feature_of_interest=feat,
feature_of_interest_type=ft)
print(obs.json(exclude_unset=True, indent=True))
```
Generates:
```json
{
"feature_of_interest": {
"description": "test",
"coordinates": {
"absolute": {
"horizontal_position": [
{
"x": -5.0,
"y": 20.0
}
]
}
}
},
"feature_of_interest_type": "WATERSHED"
}
```
### Validating Objects
Pydantic auto-validates by default
E.g:
```python
ac = AbsoluteCoordinate(horizontal_position=geo_coord)
```
raises an exception as a list is expected:
```python
pydantic.error_wrappers.ValidationError: 1 validation error for AbsoluteCoordinate
horizontal_position
value is not a valid list (type=type_error.list)
```
See [test_models](https://github.com/cmungall/basin3d_schema/blob/main/tests/test_model.py) in the unit tests for
more examples
### Serialization/Deserialization
Pydantic objects naturally serialize/deserialize to JSON
Using the LinkML runtime framework it's possible to ser/de from:
- SQL Databases
- RDF
- TSVs (with caveats)
### Vocabularies
See the [generated enums page](https://cmungall.github.io/basin3d_schema/#enumerations)
The generated Python looks like:
```python
class TimeFrequencyEnum(str, Enum):
YEAR = "YEAR"
MONTH = "MONTH"
DAY = "DAY"
HOUR = "HOUR"
MINUTE = "MINUTE"
SECOND = "SECOND"
```
The underlying schema is more granular:
```yaml
enums:
TimeFrequencyEnum:
permissible_values:
YEAR:
meaning: UO:0000036 ## year
unit:
ucum_code: a
MONTH:
meaning: UO:0000035 ## month
unit:
ucum_code: mo
DAY:
meaning: UO:0000033 ## day
unit:
ucum_code: d
HOUR:
meaning: UO:0000032 ## hour
unit:
ucum_code: h
MINUTE:
meaning: UO:0000031 ## minute
unit:
ucum_code: min
SECOND:
meaning: UO:0000010 ## second
unit:
ucum_code: s
```
The additional metadata gives *interoperability hooks*
But using these is just like any normal Python enum
```python
Time(aggregation_duration=TimeFrequencyEnum.MONTH)
```
## Developer Documentation
Use the `make` command to generate project artefacts:
- `make all`: make everything
- `make deploy`: deploys site
## About
this project was made with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter)
Most of the content was autogenerated using semi-automated tools from the basin3 python codebase.
Any mistakes are my own!
This is intended mainly for conversation starting purposes