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yml->yaml in README.md
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PeterKraus authored Nov 9, 2023
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Expand Up @@ -21,12 +21,12 @@ their pracical use is shown in the [API](https://github.com/marda-alliance/metad
The repository contains two user-facing schemas:

- ``FileType`` schema, used to specify the types of files passed to the extractors by users.
The schema definition is located in [``filetype.yml``](./schemas/filetype.yml).
The schema definition is located in [``filetype.yaml``](./schemas/filetype.yaml).

- ``Extractor`` schema, used to specify the download, installation, and usage instructions,
allowing for machine execution of the defined extractor/parser code, as well as a list of
``FileTypes`` compatible with the ``Extractor``.
The schema definition is located in [``extractor.yml``](./schemas/extractor.yml).
The schema definition is located in [``extractor.yaml``](./schemas/extractor.yaml).

## Usage
### Validation
Expand All @@ -43,11 +43,11 @@ pip install -r requirements.txt

Then, you can check the validity of your filetype or extractor definition against the provided
schemas using ``linkml-validate``. For example, to validate the provided example filetype definition
in [``biologic_mpr.yml``](./examples/filetype/biologic_mpr.yml) against the ``FileType`` schema
from ``schemas/filetype.yml``, run:
in [``FileType-netcdf.yaml``](./examples/FileType-netcdf.yaml) against the ``FileType`` class
from ``schemas/filetype.yaml``, run:

```
linkml-validate -s schemas/filetype.yml -C FileType examples/filetype/biologic_mpr.yml
linkml-validate -s schemas/filetype.yaml -C FileType examples/FileType-netcdf.yaml
```

If successful, you should see "``✓ No problems found``" returned by ``linkml-validate``.
Expand All @@ -58,9 +58,9 @@ The LinkML schemas provided here can be automatically translated to other format
JSONSchema, Python dataclasses, or Pydantic classes:

```
gen-json-schema schemas/filetype.yml >> filetype.json
gen-python schemas/filetype.yml >> filetype.py
gen-pydantic schemas/filetype.yml >> filetype.py
gen-json-schema schemas/extractor.yaml >> extractor.json
gen-python schemas/filetype.yaml >> filetype.py
gen-pydantic schemas/extractor.yaml >> extractor.py
```

The generated files can be used in downstream codes such as in the [validation function](https://github.com/marda-alliance/metadata_extractors_registry/blob/main/tasks.py#L33)
Expand All @@ -70,6 +70,8 @@ of the [MaRDA Metadata Extractors Registry](https://github.com/marda-alliance/me

Contributions are welcome. We pledge to follow the [Contributor Covenant Code of Conduct](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).

In particular, if you have any suggestions, technical queries, or a feature request related
If you wish to contribute a new `FileType` or a new `Extractor` to the Registry, please open a pull request at [the Registry repo](https://github.com/marda-alliance/metadata_extractors_registry).

If you have any suggestions, technical queries, or a feature request related
to the schemas, please do not hesitate to open an issue in this repository. For general
questions related to the MaRDA Metadata Extractors WG, please use the [discussion board](https://github.com/marda-alliance/metadata_extractors/discussions).

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