https://github.com/eoap/quickwin-inline-code
https://github.com/eoap/quickwin-inline-code
Last synced: 4 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/eoap/quickwin-inline-code
- Owner: eoap
- License: apache-2.0
- Created: 2023-12-01T08:28:52.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-29T16:21:17.000Z (about 2 years ago)
- Last Synced: 2024-03-29T17:33:05.657Z (about 2 years ago)
- Language: Jupyter Notebook
- Size: 37.1 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Quickwin - An Application Package with inline Python code
This repository contains a simple Python application `app.py` including a simple unit test as a demonstration of a "real" yet very simple Python EO application.
Using CWL's [InitialWorkDirRequirement](https://www.commonwl.org/v1.2/CommandLineTool.html#InitialWorkDirRequirement), a requirement that defines a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool, the Python script `app.py` is staged and executed in a container.
For easing the development of the Python script `app.py`, its content is added to a template named `workflow.cwl.template` by this repository Github actions.
The CWL document generated is available in the [releases section](https://github.com/eoap/quickwin-inline-code/releases/tag/1.0.0).
## Generate the Application Package with the inline code
Update the Application Package template `workflow.cwl.template` with the Python `app.py` as the inline code to run:
```
content=`cat app.py` yq eval '.$graph[1].requirements.InitialWorkDirRequirement.listing[0].entry=strenv(content)' workflow.cwl.template > workflow.cwl
```
Here's a breakdown of the command:
* `cat app.py`: This command outputs the contents of the `app.py` file.
* `yq eval '.$graph[1].requirements.InitialWorkDirRequirement.listing[0].entry=strenv(content)' workflow.cwl.template`: This command uses yq to evaluate a YAML expression on the `workflow.cwl.template` file. The expression modifies the entry at a specific path in the CWL `InitialWorkDirRequirement`, setting it to the content of `app.py`.
* `> workflow.cwl`: This part of the command redirects the modified output to a new file named `workflow.cwl`.
## Run the Application Package
The new `workflow.cwl` can be executed with:
```
cwltool workflow.cwl params.yaml
```
Where `params.yaml` contains:
```yaml
item: "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A"
aoi: "-121.399,39.834,-120.74,40.472"
epsg: "EPSG:4326"
```
## Run the released Application Package
The release 1.0.0 contains the released Application Package include the update docker reference published in the Github container registry.
Run the released Application Package with:
```
cwltool \
https://github.com/eoap/quickwin-inline-code/releases/download/1.0.0/app-water-body-inline-code.1.0.0.cwl \
params.yaml
```
## Explanation
The Application Package defines a workflow for detecting water bodies based on Normalized Difference Water Index (NDWI) and Otsu threshold using Sentinel-2 data.
The key components of this CWL document are:
* Name: Water bodies detection based on NDWI and the Otsu threshold.
* Description: Workflow for detecting water bodies based on NDWI and Otsu threshold applied to a single Sentinel-2 Cloud-Optimized GeoTIFF (COG) SpatioTemporal Asset Catalog (STAC) item.
* Inputs:
* `aoi`: Area of interest as a bounding box.
* `epsg`: EPSG code (default: "EPSG:4326").
* `bands`: Bands used for NDWI (default: ["green", "nir"]).
* `item`: Reference to a STAC item.
* Outputs:
* `stac_catalog`: Output directory containing the STAC catalog.
* Steps:
* `node_detect`: Executes the detect-water-body tool with specified inputs and produces a STAC catalog in the output directory.
* Tool: detect-water-body:
* A CommandLineTool written in Python that uses various libraries such as rasterio, skimage, pyproj, shapely and loguru.
* It performs operations like cropping, thresholding, and creating a STAC catalog for the detected water bodies.
* It takes inputs like STAC item URL, area of interest, EPSG code, and band names.
* Tool Requirements:
* Uses Docker.
* Specifies resource requirements (`coresMax: 1`, `ramMax: 512`).
* Sets up initial working directory with an entry script (`app.py`).
* Execution:
* The workflow runs the detect-water-body tool with specified inputs.
* Generates a STAC catalog with the detected water bodies.
* Cleans up temporary files after completion.
The webpage of the documentation is https://eoap.github.io/quickwin-inline-code/.
[](https://creativecommons.org/licenses/by-sa/4.0/)