cwl2click 0.2.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cwl2click-0.2.0/.github/workflows/docs.yaml +43 -0
- cwl2click-0.2.0/.github/workflows/package.yaml +70 -0
- cwl2click-0.2.0/.gitignore +7 -0
- cwl2click-0.2.0/LICENSE +202 -0
- cwl2click-0.2.0/NOTICE +5 -0
- cwl2click-0.2.0/PKG-INFO +50 -0
- cwl2click-0.2.0/README.md +23 -0
- cwl2click-0.2.0/docs/adopters.md +76 -0
- cwl2click-0.2.0/docs/crosswalk.md +16 -0
- cwl2click-0.2.0/docs/execution.md +162 -0
- cwl2click-0.2.0/docs/index.md +17 -0
- cwl2click-0.2.0/mkdocs.yaml +83 -0
- cwl2click-0.2.0/pyproject.toml +71 -0
- cwl2click-0.2.0/src/cwl2click/__about__.py +15 -0
- cwl2click-0.2.0/src/cwl2click/__init__.py +201 -0
- cwl2click-0.2.0/src/cwl2click/cli.py +143 -0
- cwl2click-0.2.0/src/cwl2click/templates/command_line_tools.py +31 -0
- cwl2click-0.2.0/tests/__init__.py +3 -0
- cwl2click-0.2.0/tests/test_place_holder.py +10 -0
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# Copyright 2025 Terradue
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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name: docs
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on:
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# Only rebuild website when docs have changed
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# Copyright 2025 Terradue
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# limitations under the License.
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name: publish-to-pypi
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release:
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contents: read
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environment: release
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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run: |
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pip install hatch
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run: |
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hatch build
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run: |
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hatch test
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if: github.ref == 'refs/heads/main'
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cwl2click-0.2.0/LICENSE
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Apache License
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To apply the Apache License to your work, attach the following
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boilerplate notice, with the fields enclosed by brackets "[]"
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replaced with your own identifying information. (Don't include
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the brackets!) The text should be enclosed in the appropriate
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comment syntax for the file format. We also recommend that a
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file or class name and description of purpose be included on the
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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright [yyyy] [name of copyright owner]
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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cwl2click-0.2.0/NOTICE
ADDED
cwl2click-0.2.0/PKG-INFO
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Metadata-Version: 2.4
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Name: cwl2click
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Version: 0.2.0
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Project-URL: Documentation, https://github.com/Terradue/cwl2click#readme
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Project-URL: Issues, https://github.com/Terradue/cwl2click/issues
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Project-URL: Source, https://github.com/Terradue/cwl2click
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Author-email: Simone Tripodi <simone.tripodi@terradue.com>, Fabrice Brito <fabrice.brito@terradue.com>
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License-Expression: MIT
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License-File: LICENSE
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License-File: NOTICE
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Classifier: Development Status :: 4 - Beta
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: Implementation :: CPython
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Classifier: Programming Language :: Python :: Implementation :: PyPy
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Requires-Python: >=3.8
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Requires-Dist: click>=8.2.1
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Requires-Dist: cwl-loader>=0.14.0
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Requires-Dist: cwl-utils>=0.40
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Requires-Dist: jinja2>=3.1.6
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Requires-Dist: loguru
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Description-Content-Type: text/markdown
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# cwl2click
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Boostrap a Python CLI using `click` from a CWL `CommandLineTool`(s).
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[](https://pypi.org/project/cwl2click)
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[](https://pypi.org/project/cwl2click)
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-----
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## Table of Contents
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- [Installation](#installation)
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- [License](#license)
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## Installation
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```console
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pip install cwl2click
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```
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## License
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`cwl2click` is distributed under the terms of the [Apache-2.0](https://spdx.org/licenses/Apache-2.0.html) license.
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# cwl2click
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Boostrap a Python CLI using `click` from a CWL `CommandLineTool`(s).
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[](https://pypi.org/project/cwl2click)
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[](https://pypi.org/project/cwl2click)
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-----
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## Table of Contents
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- [Installation](#installation)
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- [License](#license)
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## Installation
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```console
|
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pip install cwl2click
|
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+
```
|
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## License
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`cwl2click` is distributed under the terms of the [Apache-2.0](https://spdx.org/licenses/Apache-2.0.html) license.
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# Adopters recommendations
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## On CWL
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When submitting CWL document(s) to `cwl2click`, please mind the following constraints:
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- `CommandLineTool`s only will be taken in consideration;
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- The `click.Command` name is derived from `baseCommand` and `arguments` declarations, accepting the patterns below:
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|
|
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both `baseCommand` and `arguments` are declared
|
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|
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```yaml
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baseCommand: runner
|
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arguments:
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- crop-cli
|
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+
```
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```yaml
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baseCommand:
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- runner
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arguments:
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- crop-cli
|
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```
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`baseCommand` only is declared:
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```
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baseCommand:
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- runner
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- crop-cli
|
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arguments: []
|
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```
|
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In all the cases above, the resulting `click.Command` will result being `crop-cli`
|
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Any other case will force `cwl2click` not able to detect the command name, then an exception will be thrown.
|
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- `click.Option` parameter declaration is derived from `inputs[].inputBinding.prefix`, i.e.
|
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|
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```yaml
|
|
40
|
+
- class: CommandLineTool
|
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+
id: crop
|
|
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|
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baseCommand:
|
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|
+
- runner
|
|
44
|
+
arguments:
|
|
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|
+
- crop-cli
|
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+
inputs:
|
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+
item:
|
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type: Directory
|
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|
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inputBinding:
|
|
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|
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prefix: --input-item
|
|
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|
+
...
|
|
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|
+
```
|
|
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|
+
|
|
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will result to
|
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|
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|
|
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```python
|
|
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|
+
cli.add_command(
|
|
58
|
+
click.Command(
|
|
59
|
+
name="crop-cli",
|
|
60
|
+
callback=crop_command,
|
|
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|
+
params=[
|
|
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click.Option(
|
|
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|
+
["--input-item"],
|
|
64
|
+
"item",
|
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|
+
type=click.Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=False, dir_okay=True),
|
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multiple=False,
|
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required=True,
|
|
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is_flag=False,
|
|
69
|
+
|
|
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),
|
|
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|
+
...
|
|
72
|
+
```
|
|
73
|
+
|
|
74
|
+
If `inputs[].inputBinding.prefix` is not found, it will follow up on `--{{inputs[].id}}`
|
|
75
|
+
|
|
76
|
+
- Users have in charge to implement all the callback functions - `click2cwl` generates the interface only, concrete implementations must be provided by implementors!
|
|
@@ -0,0 +1,16 @@
|
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|
1
|
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# Crosswalk
|
|
2
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|
|
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|
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| CWL Type | Click Type |
|
|
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|-----------------------------------------------------------------------------------|---------------------------------------------------|
|
|
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| `int` | `click.INT` |
|
|
6
|
+
| `long` | `click.INT` |
|
|
7
|
+
| `double` | `click.FLOAT` |
|
|
8
|
+
| `float` | `click.FLOAT` |
|
|
9
|
+
| `boolean` | `click.BOOL` |
|
|
10
|
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| `string` | `click.STRING` |
|
|
11
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+
| `Directory` | `click.Path(file_okay=False, dir_okay=True)` |
|
|
12
|
+
| `File` | `click.Path(file_okay=True, dir_okay=False)` |
|
|
13
|
+
| `https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#DateTime` | `click.DateTime(formats=['%Y-%m- %d T%H:%M:%S'])` |
|
|
14
|
+
| `https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#UUID` | `click.UUID` |
|
|
15
|
+
|
|
16
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+
Any other unsupported type is threated like a `click.STRING`.
|
|
@@ -0,0 +1,162 @@
|
|
|
1
|
+
# Execution
|
|
2
|
+
|
|
3
|
+
Based on a KISS approach:
|
|
4
|
+
|
|
5
|
+
```
|
|
6
|
+
$ cwl2click --help
|
|
7
|
+
Usage: cwl2click [OPTIONS] WORKFLOW
|
|
8
|
+
|
|
9
|
+
Options:
|
|
10
|
+
--workflow-id TEXT ID(s) of the CommandLineTools
|
|
11
|
+
--output PATH Output directory path [required]
|
|
12
|
+
--help Show this message and exit.
|
|
13
|
+
```
|
|
14
|
+
|
|
15
|
+
Users can generate `Click` code by executing:
|
|
16
|
+
|
|
17
|
+
```
|
|
18
|
+
cwl2click \
|
|
19
|
+
--output /path/to/your-project/src/your-module \
|
|
20
|
+
https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl
|
|
21
|
+
```
|
|
22
|
+
|
|
23
|
+
and monitor the execution:
|
|
24
|
+
|
|
25
|
+
```
|
|
26
|
+
2025-12-24 10:55:57.416 | DEBUG | cwl_loader:load_cwl_from_location:228 - Loading CWL document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl...
|
|
27
|
+
2025-12-24 10:55:57.664 | DEBUG | cwl_loader:_load_cwl_from_stream:231 - Reading stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl...
|
|
28
|
+
2025-12-24 10:55:57.689 | DEBUG | cwl_loader:load_cwl_from_stream:203 - CWL data of type <class 'ruamel.yaml.comments.CommentedMap'> successfully loaded from stream
|
|
29
|
+
2025-12-24 10:55:57.689 | DEBUG | cwl_loader:load_cwl_from_yaml:143 - No needs to update the Raw CWL document since it targets already the v1.2
|
|
30
|
+
2025-12-24 10:55:57.689 | DEBUG | cwl_loader:load_cwl_from_yaml:145 - Parsing the raw CWL document to the CWL Utils DOM...
|
|
31
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:158 - Raw CWL document successfully parsed to the CWL Utils DOM!
|
|
32
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:160 - Dereferencing the steps[].run...
|
|
33
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl#crop must be externally imported...
|
|
34
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:82 - run_url: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl - uri: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl
|
|
35
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl#norm_diff must be externally imported...
|
|
36
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:82 - run_url: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl - uri: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl
|
|
37
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:78 - Checking if https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl#otsu must be externally imported...
|
|
38
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_on_process:82 - run_url: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl - uri: https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl
|
|
39
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:167 - steps[].run successfully dereferenced! Dereferencing the FQNs...
|
|
40
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:171 - CWL document successfully dereferenced! Now verifying steps[].run integrity...
|
|
41
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:175 - All steps[].run link are resolvable!
|
|
42
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:178 - Sorting Process instances by dependencies....
|
|
43
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:load_cwl_from_yaml:180 - Sorting process is over.
|
|
44
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl_loader:_load_cwl_from_stream:240 - Stream from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl successfully load!
|
|
45
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:main:89 - Input CWL Document from https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl is a $graph:
|
|
46
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:72 - * Checking 'norm_diff'...
|
|
47
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:74 - 'norm_diff' is a CommandLineTool instance
|
|
48
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:83 - Include list not defined, processing 'norm_diff'
|
|
49
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:72 - * Checking 'otsu'...
|
|
50
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:74 - 'otsu' is a CommandLineTool instance
|
|
51
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:83 - Include list not defined, processing 'otsu'
|
|
52
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:72 - * Checking 'crop'...
|
|
53
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:74 - 'crop' is a CommandLineTool instance
|
|
54
|
+
2025-12-24 10:56:04.305 | DEBUG | cwl2click.cli:_add_if_eligible:83 - Include list not defined, processing 'crop'
|
|
55
|
+
2025-12-24 10:56:04.306 | DEBUG | cwl2click.cli:_add_if_eligible:72 - * Checking 'pattern-12'...
|
|
56
|
+
2025-12-24 10:56:04.306 | WARNING | cwl2click.cli:_add_if_eligible:86 - 'pattern-12' is not a CommandLineTool instance, discarding
|
|
57
|
+
2025-12-24 10:56:04.306 | INFO | cwl2click.cli:main:101 - ------------------------------------------------------------------------
|
|
58
|
+
2025-12-24 10:56:04.306 | DEBUG | cwl2click.cli:main:102 - Processing CommadLineTools ['norm_diff', 'otsu', 'crop']
|
|
59
|
+
2025-12-24 10:56:04.306 | DEBUG | cwl2click.cli:main:110 - https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl was parsed from a URL, normalizing...
|
|
60
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting <cwl_utils.parser.cwl_v1_2.CommandInputArraySchema object at 0x7ce30a43bf40> CWL type to the related Click type...
|
|
61
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting Directory CWL type to the related Click type...
|
|
62
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI CWL type to the related Click type...
|
|
63
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting Directory CWL type to the related Click type...
|
|
64
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting Directory CWL type to the related Click type...
|
|
65
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI CWL type to the related Click type...
|
|
66
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting Directory CWL type to the related Click type...
|
|
67
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox CWL type to the related Click type...
|
|
68
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting https://raw.githubusercontent.com/eoap/schemas/main/ogc.yaml#BBox CWL type to the related Click type...
|
|
69
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting string CWL type to the related Click type...
|
|
70
|
+
2025-12-24 10:56:04.309 | DEBUG | cwl2click:to_click_type:94 - Converting https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml#URI CWL type to the related Click type...
|
|
71
|
+
2025-12-24 10:56:04.310 | SUCCESS | cwl2click.cli:main:128 - 'https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl' successfully converted to Click Python application in '/path/to/your-project/src/your-module/pattern-12.py'.
|
|
72
|
+
2025-12-24 10:56:04.310 | INFO | cwl2click.cli:main:130 - ------------------------------------------------------------------------
|
|
73
|
+
2025-12-24 10:56:04.310 | SUCCESS | cwl2click.cli:main:131 - BUILD SUCCESS
|
|
74
|
+
2025-12-24 10:56:04.310 | INFO | cwl2click.cli:main:139 - ------------------------------------------------------------------------
|
|
75
|
+
2025-12-24 10:56:04.310 | INFO | cwl2click.cli:main:140 - Total time: 6.8937 seconds
|
|
76
|
+
2025-12-24 10:56:04.310 | INFO | cwl2click.cli:main:141 - Finished at: 2025-12-24T10:56:04.310
|
|
77
|
+
```
|
|
78
|
+
|
|
79
|
+
As reported in the `SUCCESS` logging message, the `Click` application is serialized to the `/path/to/your-project/src/your-module/pattern-12.py` file:
|
|
80
|
+
|
|
81
|
+
```pyton
|
|
82
|
+
# File generated by cwl2click v0.30.0
|
|
83
|
+
# timestamp: 2025-12-24T10:56:04.309
|
|
84
|
+
|
|
85
|
+
from norm_diff_impl import execute as norm_diff_command
|
|
86
|
+
from otsu_impl import execute as otsu_command
|
|
87
|
+
from crop_impl import execute as crop_command
|
|
88
|
+
|
|
89
|
+
from pathlib import Path
|
|
90
|
+
|
|
91
|
+
import click
|
|
92
|
+
|
|
93
|
+
@click.group()
|
|
94
|
+
def cli() -> None:
|
|
95
|
+
pass
|
|
96
|
+
|
|
97
|
+
cli.add_command(
|
|
98
|
+
click.Command(
|
|
99
|
+
name="ndi-cli",
|
|
100
|
+
callback=norm_diff_command,
|
|
101
|
+
# CODE OMITTED FOR SIMPLICITY
|
|
102
|
+
)
|
|
103
|
+
)
|
|
104
|
+
|
|
105
|
+
cli.add_command(
|
|
106
|
+
click.Command(
|
|
107
|
+
name="otsu-cli",
|
|
108
|
+
callback=otsu_command,
|
|
109
|
+
params=[
|
|
110
|
+
click.Option(
|
|
111
|
+
["--input-ndi"],
|
|
112
|
+
"raster",
|
|
113
|
+
type=click.Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=False, dir_okay=True),
|
|
114
|
+
multiple=False,
|
|
115
|
+
required=True,
|
|
116
|
+
is_flag=False,
|
|
117
|
+
|
|
118
|
+
),
|
|
119
|
+
click.Option(
|
|
120
|
+
["--item"],
|
|
121
|
+
"item",
|
|
122
|
+
type=click.Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=False, dir_okay=True),
|
|
123
|
+
multiple=False,
|
|
124
|
+
required=True,
|
|
125
|
+
is_flag=False,
|
|
126
|
+
|
|
127
|
+
),
|
|
128
|
+
click.Option(
|
|
129
|
+
["None"],
|
|
130
|
+
"collection",
|
|
131
|
+
type=click.STRING,
|
|
132
|
+
multiple=False,
|
|
133
|
+
required=True,
|
|
134
|
+
is_flag=False,
|
|
135
|
+
|
|
136
|
+
),
|
|
137
|
+
]
|
|
138
|
+
)
|
|
139
|
+
)
|
|
140
|
+
|
|
141
|
+
cli.add_command(
|
|
142
|
+
click.Command(
|
|
143
|
+
name="crop-cli",
|
|
144
|
+
callback=crop_command,
|
|
145
|
+
# CODE OMITTED FOR SIMPLICITY
|
|
146
|
+
)
|
|
147
|
+
)
|
|
148
|
+
```
|
|
149
|
+
|
|
150
|
+
#### Include list
|
|
151
|
+
|
|
152
|
+
By default, `cwl2click` will transpile _all_ the `CommandLineTool` found instances inside the CWL, in case users are interested in just one sub-set, can use the `--workflow-id` option:
|
|
153
|
+
|
|
154
|
+
```
|
|
155
|
+
cwl2click \
|
|
156
|
+
--output /path/to/your-project/src/your-module \
|
|
157
|
+
--workflow-id crop \
|
|
158
|
+
--workflow-id otsu \
|
|
159
|
+
https://raw.githubusercontent.com/eoap/application-package-patterns/refs/heads/main/cwl-workflow/pattern-12.cwl
|
|
160
|
+
```
|
|
161
|
+
|
|
162
|
+
By executing this example, `ndi-cli` won't be generated.
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
# Introduction
|
|
2
|
+
|
|
3
|
+
## Rationale
|
|
4
|
+
|
|
5
|
+
Taking inspiration from the [Contract-First Development](https://openpracticelibrary.com/practice/contract-first-development/) approach, this small tool aims to simplify the development of Python CLI with [Click](https://click.palletsprojects.com/en/stable/) to be integrated in [CWL Command Line Tool](https://www.commonwl.org/user_guide/topics/command-line-tool.html).
|
|
6
|
+
|
|
7
|
+
Defining the Interface(s) first in the CWL not only speeds up the development, it also alleviates developers to manually write the boilerplate code to implement the CLIs.
|
|
8
|
+
|
|
9
|
+
## Usage
|
|
10
|
+
|
|
11
|
+
### Installation
|
|
12
|
+
|
|
13
|
+
`cwl2click` is published on [Pypi](https://pypi.org/project/cwl2click/), users just have to execute
|
|
14
|
+
|
|
15
|
+
```
|
|
16
|
+
pip install cwl2click
|
|
17
|
+
```
|
|
@@ -0,0 +1,83 @@
|
|
|
1
|
+
# Copyright 2025 Terradue
|
|
2
|
+
#
|
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
4
|
+
# you may not use this file except in compliance with the License.
|
|
5
|
+
# You may obtain a copy of the License at
|
|
6
|
+
#
|
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
|
8
|
+
#
|
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
12
|
+
# See the License for the specific language governing permissions and
|
|
13
|
+
# limitations under the License.
|
|
14
|
+
|
|
15
|
+
site_name: CWL2Click
|
|
16
|
+
site_url: https://eoepca.github.io/cwl2ckick/
|
|
17
|
+
site_author: Fabrice Brito, Simone Tripodi
|
|
18
|
+
repo_url: https://github.com/Terradue/cwl2ckick/
|
|
19
|
+
repo_name: Terradue/cwl2ckick
|
|
20
|
+
|
|
21
|
+
theme:
|
|
22
|
+
logo: imgs/icon-eoap.png
|
|
23
|
+
name: material
|
|
24
|
+
|
|
25
|
+
palette:
|
|
26
|
+
- media: "(prefers-color-scheme: light)"
|
|
27
|
+
scheme: default
|
|
28
|
+
toggle:
|
|
29
|
+
icon: material/toggle-switch-off-outline
|
|
30
|
+
name: Switch to dark mode
|
|
31
|
+
- media: "(prefers-color-scheme: dark)"
|
|
32
|
+
scheme: slate
|
|
33
|
+
toggle:
|
|
34
|
+
icon: material/toggle-switch
|
|
35
|
+
name: Switch to light mode
|
|
36
|
+
|
|
37
|
+
plugins:
|
|
38
|
+
- search
|
|
39
|
+
- mermaid2:
|
|
40
|
+
version: 11.4.1
|
|
41
|
+
- mkdocs-jupyter:
|
|
42
|
+
execute: true
|
|
43
|
+
show_input: True
|
|
44
|
+
no_input: False
|
|
45
|
+
|
|
46
|
+
markdown_extensions:
|
|
47
|
+
- pymdownx.details
|
|
48
|
+
- abbr
|
|
49
|
+
- admonition
|
|
50
|
+
- footnotes
|
|
51
|
+
- pymdownx.caret
|
|
52
|
+
- pymdownx.mark
|
|
53
|
+
- pymdownx.tilde
|
|
54
|
+
- pymdownx.arithmatex:
|
|
55
|
+
generic: true
|
|
56
|
+
- pymdownx.superfences
|
|
57
|
+
- pymdownx.tabbed
|
|
58
|
+
- pymdownx.superfences:
|
|
59
|
+
custom_fences:
|
|
60
|
+
- name: mermaid
|
|
61
|
+
class: mermaid
|
|
62
|
+
format: !!python/name:pymdownx.superfences.fence_div_format
|
|
63
|
+
- attr_list
|
|
64
|
+
- pymdownx.snippets:
|
|
65
|
+
base_path: './'
|
|
66
|
+
- pymdownx.highlight:
|
|
67
|
+
line_spans: __span
|
|
68
|
+
|
|
69
|
+
extra_css:
|
|
70
|
+
- styles/css/app.css
|
|
71
|
+
|
|
72
|
+
extra_javascript:
|
|
73
|
+
- javascripts/config.js
|
|
74
|
+
- https://polyfill.io/v3/polyfill.min.js?features=es6
|
|
75
|
+
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
|
|
76
|
+
|
|
77
|
+
nav:
|
|
78
|
+
- index.md
|
|
79
|
+
- execution.md
|
|
80
|
+
- adopters.md
|
|
81
|
+
- crosswalk.md
|
|
82
|
+
|
|
83
|
+
copyright: <a href="https://www.apache.org/licenses/LICENSE-2.0"><img src="https://img.shields.io/badge/license-Apache%20License%202.0-blue"" alt="Apache License, Version 2.0" /></a>
|
|
@@ -0,0 +1,71 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["hatchling"]
|
|
3
|
+
build-backend = "hatchling.build"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "cwl2click"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = ''
|
|
9
|
+
readme = "README.md"
|
|
10
|
+
requires-python = ">=3.8"
|
|
11
|
+
license = "MIT"
|
|
12
|
+
keywords = []
|
|
13
|
+
authors = [
|
|
14
|
+
{ name = "Simone Tripodi", email = "simone.tripodi@terradue.com" },
|
|
15
|
+
{ name = "Fabrice Brito", email = "fabrice.brito@terradue.com" }
|
|
16
|
+
]
|
|
17
|
+
classifiers = [
|
|
18
|
+
"Development Status :: 4 - Beta",
|
|
19
|
+
"Programming Language :: Python",
|
|
20
|
+
"Programming Language :: Python :: 3.8",
|
|
21
|
+
"Programming Language :: Python :: 3.9",
|
|
22
|
+
"Programming Language :: Python :: 3.10",
|
|
23
|
+
"Programming Language :: Python :: 3.11",
|
|
24
|
+
"Programming Language :: Python :: 3.12",
|
|
25
|
+
"Programming Language :: Python :: Implementation :: CPython",
|
|
26
|
+
"Programming Language :: Python :: Implementation :: PyPy",
|
|
27
|
+
]
|
|
28
|
+
dependencies = [
|
|
29
|
+
"cwl-loader>=0.14.0",
|
|
30
|
+
"cwl-utils>=0.40",
|
|
31
|
+
"click>=8.2.1",
|
|
32
|
+
"Jinja2>=3.1.6",
|
|
33
|
+
"loguru"
|
|
34
|
+
]
|
|
35
|
+
|
|
36
|
+
[project.scripts]
|
|
37
|
+
cwl2click = "cwl2click.cli:main"
|
|
38
|
+
|
|
39
|
+
[project.urls]
|
|
40
|
+
Documentation = "https://github.com/Terradue/cwl2click#readme"
|
|
41
|
+
Issues = "https://github.com/Terradue/cwl2click/issues"
|
|
42
|
+
Source = "https://github.com/Terradue/cwl2click"
|
|
43
|
+
|
|
44
|
+
[tool.hatch.version]
|
|
45
|
+
path = "src/cwl2click/__about__.py"
|
|
46
|
+
|
|
47
|
+
[tool.hatch.envs.types]
|
|
48
|
+
extra-dependencies = [
|
|
49
|
+
"mypy>=1.0.0",
|
|
50
|
+
]
|
|
51
|
+
[tool.hatch.envs.types.scripts]
|
|
52
|
+
check = "mypy --install-types --non-interactive {args:src/cwl2click tests}"
|
|
53
|
+
|
|
54
|
+
[tool.coverage.run]
|
|
55
|
+
source_pkgs = ["cwl2click", "tests"]
|
|
56
|
+
branch = true
|
|
57
|
+
parallel = true
|
|
58
|
+
omit = [
|
|
59
|
+
"src/cwl2click/__about__.py",
|
|
60
|
+
]
|
|
61
|
+
|
|
62
|
+
[tool.coverage.paths]
|
|
63
|
+
cwl2click = ["src/cwl2click", "*/cwl2click/src/cwl2click"]
|
|
64
|
+
tests = ["tests", "*/cwl2click/tests"]
|
|
65
|
+
|
|
66
|
+
[tool.coverage.report]
|
|
67
|
+
exclude_lines = [
|
|
68
|
+
"no cov",
|
|
69
|
+
"if __name__ == .__main__.:",
|
|
70
|
+
"if TYPE_CHECKING:",
|
|
71
|
+
]
|
|
@@ -0,0 +1,15 @@
|
|
|
1
|
+
# Copyright 2025 Terradue
|
|
2
|
+
#
|
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
4
|
+
# you may not use this file except in compliance with the License.
|
|
5
|
+
# You may obtain a copy of the License at
|
|
6
|
+
#
|
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
|
8
|
+
#
|
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
12
|
+
# See the License for the specific language governing permissions and
|
|
13
|
+
# limitations under the License.
|
|
14
|
+
|
|
15
|
+
__version__ = "0.2.0"
|
|
@@ -0,0 +1,201 @@
|
|
|
1
|
+
# Copyright 2025 Terradue
|
|
2
|
+
#
|
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
4
|
+
# you may not use this file except in compliance with the License.
|
|
5
|
+
# You may obtain a copy of the License at
|
|
6
|
+
#
|
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
|
8
|
+
#
|
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
12
|
+
# See the License for the specific language governing permissions and
|
|
13
|
+
# limitations under the License.
|
|
14
|
+
|
|
15
|
+
from cwl_loader.utils import (
|
|
16
|
+
contains_process,
|
|
17
|
+
search_process
|
|
18
|
+
)
|
|
19
|
+
from cwl_utils.parser import CommandLineTool
|
|
20
|
+
from datetime import datetime
|
|
21
|
+
from jinja2 import (
|
|
22
|
+
Environment,
|
|
23
|
+
PackageLoader
|
|
24
|
+
)
|
|
25
|
+
from loguru import logger
|
|
26
|
+
from importlib.metadata import (
|
|
27
|
+
version,
|
|
28
|
+
PackageNotFoundError
|
|
29
|
+
)
|
|
30
|
+
from typing import (
|
|
31
|
+
Any,
|
|
32
|
+
List,
|
|
33
|
+
Mapping,
|
|
34
|
+
TextIO
|
|
35
|
+
)
|
|
36
|
+
|
|
37
|
+
import re
|
|
38
|
+
import time
|
|
39
|
+
|
|
40
|
+
pattern = re.compile(r'(?<!^)(?=[A-Z])')
|
|
41
|
+
|
|
42
|
+
def to_snake_case(name: str) -> str:
|
|
43
|
+
return pattern.sub('_', name.replace('-', '_')).lower()
|
|
44
|
+
|
|
45
|
+
def is_nullable(
|
|
46
|
+
type_: Any
|
|
47
|
+
) -> bool:
|
|
48
|
+
return isinstance(type_, list) and "null" in type_
|
|
49
|
+
|
|
50
|
+
def is_required(
|
|
51
|
+
type_: Any
|
|
52
|
+
) -> bool:
|
|
53
|
+
return not is_nullable(type_)
|
|
54
|
+
|
|
55
|
+
def is_flag(
|
|
56
|
+
type_: Any
|
|
57
|
+
) -> bool:
|
|
58
|
+
return isinstance(type_, list) and "boolean" in type_ or "boolean" == type_
|
|
59
|
+
|
|
60
|
+
def get_command_name(
|
|
61
|
+
clt: CommandLineTool
|
|
62
|
+
) -> str:
|
|
63
|
+
if clt.baseCommand:
|
|
64
|
+
if isinstance(clt.baseCommand, list):
|
|
65
|
+
if len(clt.baseCommand) > 1:
|
|
66
|
+
return clt.baseCommand[1]
|
|
67
|
+
|
|
68
|
+
if clt.arguments:
|
|
69
|
+
if isinstance(clt.arguments, list):
|
|
70
|
+
return clt.arguments[0]
|
|
71
|
+
return str(clt.arguments)
|
|
72
|
+
|
|
73
|
+
raise Exception(f"Impossible to extract the sub-command from CommandLineTool '{clt.id}':\n- `clt.baseCommand` contains the tool only or is empty;\n-no `clt.arguments` provided.")
|
|
74
|
+
raise Exception(f"CommandLineTool '{clt.id}' does not define a 'baseCommand' property, impossible to map it to a `click.Command`")
|
|
75
|
+
|
|
76
|
+
_STRING_FORMAT_SCHEMA_: str = "https://raw.githubusercontent.com/eoap/schemas/main/string_format.yaml"
|
|
77
|
+
|
|
78
|
+
_CWL_CLICK_MAP_: Mapping[Any, str] = {
|
|
79
|
+
"int": "INT",
|
|
80
|
+
"long": "INT",
|
|
81
|
+
"double": "FLOAT",
|
|
82
|
+
"float": "FLOAT",
|
|
83
|
+
"boolean": "BOOL",
|
|
84
|
+
"string": "STRING",
|
|
85
|
+
"Directory": "Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=False, dir_okay=True)",
|
|
86
|
+
"File": "Path(path_type=Path, exists=True, readable=True, resolve_path=True, file_okay=True, dir_okay=False)",
|
|
87
|
+
f"{_STRING_FORMAT_SCHEMA_}#DateTime": "DateTime(formats=['%Y-%m-%dT%H:%M:%S'])",
|
|
88
|
+
f"{_STRING_FORMAT_SCHEMA_}#UUID": "UUID"
|
|
89
|
+
}
|
|
90
|
+
|
|
91
|
+
def to_click_type(
|
|
92
|
+
type_: Any
|
|
93
|
+
) -> str:
|
|
94
|
+
logger.debug(f"Converting {type_} CWL type to the related Click type...")
|
|
95
|
+
|
|
96
|
+
key = None
|
|
97
|
+
|
|
98
|
+
if isinstance(type_, str):
|
|
99
|
+
key = type_
|
|
100
|
+
elif isinstance(type_, list):
|
|
101
|
+
key = [item_type for item_type in type_ if "null" != item_type][0]
|
|
102
|
+
elif hasattr(type_, "class_"):
|
|
103
|
+
key = type_.class_ # type: ignore
|
|
104
|
+
elif hasattr(type_, "symbols"):
|
|
105
|
+
return f"Choice({list(map(lambda symbol : symbol.split('/')[-1], type_.symbols))})"
|
|
106
|
+
|
|
107
|
+
if key and not isinstance(key, str) and hasattr(key, "symbols"):
|
|
108
|
+
return f"Choice({list(map(lambda symbol : symbol.split('/')[-1], key.symbols))})"
|
|
109
|
+
|
|
110
|
+
return _CWL_CLICK_MAP_.get(key, "STRING")
|
|
111
|
+
|
|
112
|
+
_CWL_PYTHON_MAP_: Mapping[Any, str] = {
|
|
113
|
+
"int": "int",
|
|
114
|
+
"long": "int",
|
|
115
|
+
"double": "float",
|
|
116
|
+
"float": "float",
|
|
117
|
+
"boolean": "bool",
|
|
118
|
+
"string": "str",
|
|
119
|
+
"Directory": "str",
|
|
120
|
+
"File": "str"
|
|
121
|
+
}
|
|
122
|
+
|
|
123
|
+
def to_python_type(
|
|
124
|
+
type_
|
|
125
|
+
) -> str:
|
|
126
|
+
logger.debug(f"Converting {type_} CWL type to the related Python type...")
|
|
127
|
+
|
|
128
|
+
key: str
|
|
129
|
+
if isinstance(type_, str):
|
|
130
|
+
key = type_
|
|
131
|
+
elif isinstance(type_, list):
|
|
132
|
+
key = [item_type for item_type in type_ if "null" != item_type][0]
|
|
133
|
+
else:
|
|
134
|
+
key = type_.class_ # type: ignore
|
|
135
|
+
|
|
136
|
+
if "enum" == key:
|
|
137
|
+
key = "string"
|
|
138
|
+
|
|
139
|
+
return _CWL_PYTHON_MAP_.get(key, str(type_))
|
|
140
|
+
|
|
141
|
+
def _to_mapping(
|
|
142
|
+
functions: List[Any]
|
|
143
|
+
) -> Mapping[str, Any]:
|
|
144
|
+
mapping: Mapping[str, Any] = {}
|
|
145
|
+
|
|
146
|
+
for function in functions:
|
|
147
|
+
mapping[function.__name__] = function
|
|
148
|
+
|
|
149
|
+
return mapping
|
|
150
|
+
|
|
151
|
+
def is_array(
|
|
152
|
+
type_
|
|
153
|
+
) -> bool:
|
|
154
|
+
return isinstance(type, list) or hasattr(type_, "class_") and "array" == type_.class_
|
|
155
|
+
|
|
156
|
+
def _get_version() -> str:
|
|
157
|
+
try:
|
|
158
|
+
return version("cwl2puml")
|
|
159
|
+
except PackageNotFoundError:
|
|
160
|
+
return 'N/A'
|
|
161
|
+
|
|
162
|
+
_jinja_environment = Environment(
|
|
163
|
+
loader=PackageLoader(
|
|
164
|
+
package_name='cwl2click'
|
|
165
|
+
)
|
|
166
|
+
)
|
|
167
|
+
_jinja_environment.filters.update(
|
|
168
|
+
_to_mapping(
|
|
169
|
+
[
|
|
170
|
+
get_command_name,
|
|
171
|
+
is_array,
|
|
172
|
+
is_flag,
|
|
173
|
+
is_required,
|
|
174
|
+
is_nullable,
|
|
175
|
+
to_click_type,
|
|
176
|
+
to_python_type,
|
|
177
|
+
to_snake_case,
|
|
178
|
+
]
|
|
179
|
+
)
|
|
180
|
+
)
|
|
181
|
+
_jinja_environment.tests.update(
|
|
182
|
+
_to_mapping(
|
|
183
|
+
[ is_array ]
|
|
184
|
+
)
|
|
185
|
+
)
|
|
186
|
+
|
|
187
|
+
def to_click(
|
|
188
|
+
command_line_tools: List[CommandLineTool],
|
|
189
|
+
module_name: str,
|
|
190
|
+
output_stream: TextIO
|
|
191
|
+
):
|
|
192
|
+
template = _jinja_environment.get_template(f"command_line_tools.py")
|
|
193
|
+
|
|
194
|
+
output_stream.write(
|
|
195
|
+
template.render(
|
|
196
|
+
version=_get_version(),
|
|
197
|
+
timestamp=datetime.fromtimestamp(time.time()).isoformat(timespec='milliseconds'),
|
|
198
|
+
module_name=module_name,
|
|
199
|
+
command_line_tools=command_line_tools
|
|
200
|
+
)
|
|
201
|
+
)
|
|
@@ -0,0 +1,143 @@
|
|
|
1
|
+
# Copyright 2025 Terradue
|
|
2
|
+
#
|
|
3
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
4
|
+
# you may not use this file except in compliance with the License.
|
|
5
|
+
# You may obtain a copy of the License at
|
|
6
|
+
#
|
|
7
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
|
8
|
+
#
|
|
9
|
+
# Unless required by applicable law or agreed to in writing, software
|
|
10
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
11
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
12
|
+
# See the License for the specific language governing permissions and
|
|
13
|
+
# limitations under the License.
|
|
14
|
+
|
|
15
|
+
from . import (
|
|
16
|
+
to_click,
|
|
17
|
+
to_snake_case
|
|
18
|
+
)
|
|
19
|
+
from cwl_loader import load_cwl_from_location
|
|
20
|
+
from cwl_utils.parser import (
|
|
21
|
+
Process,
|
|
22
|
+
CommandLineTool
|
|
23
|
+
)
|
|
24
|
+
from datetime import datetime
|
|
25
|
+
from loguru import logger
|
|
26
|
+
from pathlib import Path
|
|
27
|
+
from os.path import (
|
|
28
|
+
basename,
|
|
29
|
+
splitext
|
|
30
|
+
)
|
|
31
|
+
from typing import List
|
|
32
|
+
from urllib.parse import urlparse
|
|
33
|
+
|
|
34
|
+
import click
|
|
35
|
+
import time
|
|
36
|
+
|
|
37
|
+
@click.command()
|
|
38
|
+
@click.argument(
|
|
39
|
+
'workflow',
|
|
40
|
+
required=True
|
|
41
|
+
)
|
|
42
|
+
@click.option(
|
|
43
|
+
'--workflow-id',
|
|
44
|
+
required=False,
|
|
45
|
+
type=click.STRING,
|
|
46
|
+
multiple=True,
|
|
47
|
+
help="ID(s) of the CommandLineTools"
|
|
48
|
+
)
|
|
49
|
+
@click.option(
|
|
50
|
+
'--output',
|
|
51
|
+
type=click.Path(
|
|
52
|
+
path_type=Path
|
|
53
|
+
),
|
|
54
|
+
required=True,
|
|
55
|
+
default=Path("."),
|
|
56
|
+
help="Output directory path"
|
|
57
|
+
)
|
|
58
|
+
def main(
|
|
59
|
+
workflow: str,
|
|
60
|
+
workflow_id: List[str],
|
|
61
|
+
output: Path
|
|
62
|
+
):
|
|
63
|
+
start_time = time.time()
|
|
64
|
+
|
|
65
|
+
click.STRING
|
|
66
|
+
|
|
67
|
+
cwl_document: Process | List[Process] = load_cwl_from_location(path=workflow)
|
|
68
|
+
|
|
69
|
+
clts: List[CommandLineTool] = []
|
|
70
|
+
|
|
71
|
+
def _add_if_eligible(process: Process):
|
|
72
|
+
logger.debug(f"* Checking '{process.id}'...")
|
|
73
|
+
if isinstance(process, CommandLineTool):
|
|
74
|
+
logger.debug(f" '{process.id}' is a CommandLineTool instance")
|
|
75
|
+
if workflow_id:
|
|
76
|
+
logger.debug(f" Checking if '{process.id}' is in the include list {workflow_id}...")
|
|
77
|
+
if process.id in workflow_id:
|
|
78
|
+
logger.debug(f" '{process.id}' is in the include list {workflow_id}, processing")
|
|
79
|
+
clts.append(process)
|
|
80
|
+
else:
|
|
81
|
+
logger.warning(f" '{process.id}' not in the include list, discarding")
|
|
82
|
+
else:
|
|
83
|
+
logger.debug(f" Include list not defined, processing '{process.id}'")
|
|
84
|
+
clts.append(process)
|
|
85
|
+
else:
|
|
86
|
+
logger.warning(f" '{process.id}' is not a CommandLineTool instance, discarding")
|
|
87
|
+
|
|
88
|
+
if isinstance(cwl_document, list):
|
|
89
|
+
logger.debug(f"Input CWL Document from {workflow} is a $graph:")
|
|
90
|
+
for process in cwl_document:
|
|
91
|
+
_add_if_eligible(process)
|
|
92
|
+
else:
|
|
93
|
+
_add_if_eligible(cwl_document)
|
|
94
|
+
|
|
95
|
+
if not clts:
|
|
96
|
+
if workflow_id:
|
|
97
|
+
logger.error(f"{workflow_id} not found on in input CWL document, only {list(map(lambda p: p.id, cwl_document)) if isinstance(cwl_document, list) else [cwl_document.id]} available.")
|
|
98
|
+
else:
|
|
99
|
+
logger.error("No CommandLineTool(s) found in input CWL document")
|
|
100
|
+
else:
|
|
101
|
+
logger.info('------------------------------------------------------------------------')
|
|
102
|
+
logger.debug(f"Processing CommadLineTools {[clt.id for clt in clts]}")
|
|
103
|
+
|
|
104
|
+
output.mkdir(parents=True, exist_ok=True)
|
|
105
|
+
|
|
106
|
+
file_name = basename(workflow)
|
|
107
|
+
try:
|
|
108
|
+
result = urlparse(workflow)
|
|
109
|
+
if result.scheme in ('http', 'https') and result.netloc:
|
|
110
|
+
logger.debug(f"{workflow} was parsed from a URL, normalizing...")
|
|
111
|
+
file_name = basename(result.path)
|
|
112
|
+
else:
|
|
113
|
+
logger.debug(f"{workflow} was not parsed from a URL")
|
|
114
|
+
except Exception:
|
|
115
|
+
logger.debug(f"{workflow} was not parsed from a URL")
|
|
116
|
+
|
|
117
|
+
file_name, _ = splitext(file_name)
|
|
118
|
+
|
|
119
|
+
target: Path = Path(output, f"{to_snake_case(file_name)}.py")
|
|
120
|
+
module_name = basename(target.parent.absolute().as_posix())
|
|
121
|
+
|
|
122
|
+
try:
|
|
123
|
+
with target.open('w') as stream:
|
|
124
|
+
to_click(
|
|
125
|
+
command_line_tools=clts,
|
|
126
|
+
module_name=module_name,
|
|
127
|
+
output_stream=stream
|
|
128
|
+
)
|
|
129
|
+
|
|
130
|
+
logger.success(f"'{workflow}' successfully converted to Click Python application in '{target.absolute()}'.")
|
|
131
|
+
|
|
132
|
+
logger.info('------------------------------------------------------------------------')
|
|
133
|
+
logger.success('BUILD SUCCESS')
|
|
134
|
+
except Exception as e:
|
|
135
|
+
logger.info('------------------------------------------------------------------------')
|
|
136
|
+
logger.error('BUILD FAILED')
|
|
137
|
+
logger.error(f"An unexpected error occurred while generating {target}: {e}")
|
|
138
|
+
|
|
139
|
+
end_time = time.time()
|
|
140
|
+
|
|
141
|
+
logger.info('------------------------------------------------------------------------')
|
|
142
|
+
logger.info(f"Total time: {end_time - start_time:.4f} seconds")
|
|
143
|
+
logger.info(f"Finished at: {datetime.fromtimestamp(end_time).isoformat(timespec='milliseconds')}")
|
|
@@ -0,0 +1,31 @@
|
|
|
1
|
+
# File generated by cwl2click v{{ version }}
|
|
2
|
+
# timestamp: {{ timestamp }}
|
|
3
|
+
|
|
4
|
+
{% for clt in command_line_tools %}from {{module_name}}.{{clt.id | to_snake_case}}_impl import execute as {{clt.id | to_snake_case}}_command
|
|
5
|
+
{% endfor %}
|
|
6
|
+
from pathlib import Path
|
|
7
|
+
|
|
8
|
+
import click
|
|
9
|
+
|
|
10
|
+
@click.group()
|
|
11
|
+
def cli() -> None:
|
|
12
|
+
pass
|
|
13
|
+
{% for clt in command_line_tools %}
|
|
14
|
+
cli.add_command(
|
|
15
|
+
click.Command(
|
|
16
|
+
name="{{clt | get_command_name}}",
|
|
17
|
+
callback={{clt.id | to_snake_case}}_command,
|
|
18
|
+
params=[
|
|
19
|
+
{% for input in clt.inputs %} click.Option(
|
|
20
|
+
["{% if input.inputBinding.prefix %}{{input.inputBinding.prefix}}{% else %}--{{input.id}}{% endif %}"],
|
|
21
|
+
"{{input.id}}",
|
|
22
|
+
type=click.{{input.type_ | to_click_type}},
|
|
23
|
+
multiple={{input.type_ | is_array}},
|
|
24
|
+
required={{input.type_ | is_required}},
|
|
25
|
+
is_flag={{input.type_ | is_flag}},{% if input.doc %}
|
|
26
|
+
help="{{input.doc}}",{% endif %}
|
|
27
|
+
),
|
|
28
|
+
{% endfor %} ]
|
|
29
|
+
)
|
|
30
|
+
)
|
|
31
|
+
{% endfor %}
|