first draft layout

CITATION.cff

@@ -2,10 +2,13 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: Tool Spec Python template
+title: Metacatalog GeoCube aggregator
 message: >-
-  Please replace this citation information with appropriate
-  metadata for your tool
+  This tool is designed to be used together with the V-FOR-WaTer Metacatalog data loader.
+  It uses a number of data source files along with either a metacatalog entry or JSON dumps
+  of the metadata.
+  The data is aggregated to a target precision (temporal) and spatial resolution and then
+  ingested into a geocube that is stored as a netCDF file.
 type: software
 authors:
   - given-names: Mirko
@@ -15,14 +18,7 @@ authors:
       Institute for Water and Environment, Hydrology,
       Karlsruhe Institute for Technology (KIT)
     orcid: 'https://orcid.org/0000-0002-0424-2651'
-  - given-names: Alexander
-    family-names: Dolich
-    email: [email protected]
-    affiliation: >-
-      nstitute for Water and Environment, Hydrology,
-      Karlsruhe Institute for Technology (KIT)
-    orcid: 'https://orcid.org/0000-0003-4160-6765'
-repository-code: 'https://github.com/VForWaTer/tool_template_python'
+repository-code: 'https://github.com/hydrocode-de/metacatalog_aggregator'
 url: 'https://vforwater.github.io/tool-specs/'
 abstract: >-
   This is a Github repository template for scientific data
@@ -34,6 +30,10 @@ keywords:
   - docker
   - tool-spec
   - V-For-WaTer
+  - MetaCatalog
+  - netCDF
+  - DataCube
+  - open data cube
 license: CC-BY-4.0
-version: '0.5'
-date-released: '2024-07-30'
+version: '0.1'
+date-released: '2024-08-20'

Dockerfile

@@ -1,16 +1,16 @@
 # Pull any base image that includes python3
-FROM python:3.12
+FROM python:3.12.2
 
 # install the toolbox runner tools
-RUN pip install "json2args[data]>=0.6.2"
-
-# if you do not need data-preloading as your tool does that on its own
-# you can use this instread of the line above to use a json2args version
-# with less dependencies
-# RUN pip install json2args>=0.6.2
-
-# Do anything you need to install tool dependencies here
-RUN echo "Replace this line with a tool"
+RUN pip install "json2args>=0.6.2" \
+    metacatalog==0.9.2 \    
+    ipython==8.26.0 \ 
+    pandas==2.2.2 \
+    geopandas==1.0.1 \
+    xarray[complete]==2024.7.0 \ 
+    rioxarray==0.17.0 \
+    polars-lts-cpu==1.1.0 \
+    geocube==0.6.0
 
 # create the tool input structure
 RUN mkdir /in

README.md

@@ -1,86 +1,50 @@
-# tool_template_python
+# Metacatalog aggregator
 
-[![Docker Image CI](https://github.com/VForWaTer/tool_template_python/actions/workflows/docker-image.yml/badge.svg)](https://github.com/VForWaTer/tool_template_python/actions/workflows/docker-image.yml)
-[![DOI](https://zenodo.org/badge/558416591.svg)](https://zenodo.org/badge/latestdoi/558416591)
 
-This is the template for a generic containerized Python tool following the [Tool Specification](https://vforwater.github.io/tool-specs/) for reusable research software using Docker.
+This tool is designed to be used together with the V-FOR-WaTer [Metacatalog data loader](https://github.com/VForWaTer/tool_vforwater_loader).
+It uses a number of data source files along with either a metacatalog entry or JSON dumps of the metadata. The data is aggregated to a target precision (temporal) and spatial resolution and then ingested into a geocube that is stored as a netCDF file.
 
-This template can be used to generate new Github repositories from it.
+This tool is based on the [Python template](https://github.com/vforwater/tool_template_python) for a generic containerized Python tool following the [Tool Specification](https://vforwater.github.io/tool-specs/) for reusable research software using Docker.
 
 
-## How generic?
-
-Tools using this template can be run by the [toolbox-runner](https://github.com/hydrocode-de/tool-runner). 
-That is only convenience, the tools implemented using this template are independent of any framework.
-
-The main idea is to implement a common file structure inside container to load inputs and outputs of the 
-tool. The template shares this structures with the [R template](https://github.com/vforwater/tool_template_r),
-[NodeJS template](https://github.com/vforwater/tool_template_node) and [Octave template](https://github.com/vforwater/tool_template_octave), 
-but can be mimiced in any container.
-
-Each container needs at least the following structure:
+## Structure
 
 ```
 /
 |- in/
-|  |- parameters.json
+|  |- input.json
 |- out/
 |  |- ...
 |- src/
 |  |- tool.yml
 |  |- run.py
+|  |- CITATON.cff
 ```
 
-* `parameters.json` are parameters. Whichever framework runs the container, this is how parameters are passed.
+* `input.json` are parameters. Whichever framework runs the container, this is how parameters are passed.
 * `tool.yml` is the tool specification. It contains metadata about the scope of the tool, the number of endpoints (functions) and their parameters
-* `run.py` is the tool itself, or a Python script that handles the execution. It has to capture all outputs and either `print` them to console or create files in `/out`
+* `run.py` is the tool itself
+* `CITATION.cff` is a citation file that describes the tool and its authors. It is used by the
 
 ## How to build the image?
 
 You can build the image from within the root of this repo by
 ```
-docker build -t tbr_python_tempate .
+docker build -t metacatalog_geocube .
 ```
 
-Use any tag you like. If you want to run and manage the container with [toolbox-runner](https://github.com/hydrocode-de/tool-runner)
-they should be prefixed by `tbr_` to be recognized. 
-
-Alternatively, the contained `.github/workflows/docker-image.yml` will build the image for you 
-on new releases on Github. You need to change the target repository in the aforementioned yaml.
-
 ## How to run?
 
-This template installs the json2args python package to parse the parameters in the `/in/parameters.json`. This assumes that
-the files are not renamed and not moved and there is actually only one tool in the container. For any other case, the environment variables
-`PARAM_FILE` can be used to specify a new location for the `parameters.json` and `TOOL_RUN` can be used to specify the tool to be executed.
+This template installs the json2args python package to parse the parameters in the `/in/input.json`. This assumes that
+the files are not renamed and not moved and there is actually only one tool in the container. For any other case, the environment variables `PARAM_FILE` can be used to specify a new location for the `parameters.json` and `TOOL_RUN` can be used to specify the tool to be executed.
 The `run.py` has to take care of that.
 
 To invoke the docker container directly run something similar to:
 ```
-docker run --rm -it -v /path/to/local/in:/in -v /path/to/local/out:/out -e TOOL_RUN=foobar tbr_python_template
+docker run --rm -it -v /path/to/local/in:/in -v /path/to/local/out:/out -e TOOL_RUN=geocube metacatalog_geocube
 ```
 
 Then, the output will be in your local out and based on your local input folder. Stdout and Stderr are also connected to the host.
 
-With the [toolbox runner](https://github.com/hydrocode-de/tool-runner), this is simplyfied:
-
-```python
-from toolbox_runner import list_tools
-tools = list_tools() # dict with tool names as keys
-
-foobar = tools.get('foobar')  # it has to be present there...
-foobar.run(result_path='./', foo_int=1337, foo_string="Please change me")
-```
-The example above will create a temporary file structure to be mounted into the container and then create a `.tar.gz` on termination of all 
-inputs, outputs, specifications and some metadata, including the image sha256 used to create the output in the current working directory.
-
-## What about real tools, no foobar?
-
-Yeah. 
 
-1. change the `tool.yml` to describe your actual tool
-2. add any `pip install` or `apt-get install` needed to the dockerfile
-3. add additional source code to `/src`
-4. change the `run.py` to consume parameters and data from `/in` and useful output in `out`
-5. build, run, rock!
 

RELEASE.md

@@ -1,5 +1,7 @@
-# tool_template_python
+# Metacatalog aggregator
 
-This is the template for a generic containerized Python tool following the [Tool Specification](https://vforwater.github.io/tool-specs/) for reusable research software using Docker.
 
-This template can be used to generate new Github repositories from it.
+This tool is designed to be used together with the V-FOR-WaTer [Metacatalog data loader](https://github.com/VForWaTer/tool_vforwater_loader).
+It uses a number of data source files along with either a metacatalog entry or JSON dumps of the metadata. The data is aggregated to a target precision (temporal) and spatial resolution and then ingested into a geocube that is stored as a netCDF file.
+
+This tool is based on the [Python template](https://github.com/vforwater/tool_template_python) for a generic containerized Python tool following the [Tool Specification](https://vforwater.github.io/tool-specs/) for reusable research software using Docker.

src/tool.yml

@@ -1,8 +1,12 @@
 tools:
-  foobar:
-    title: Foo Bar
-    description: A dummy tool to exemplify the YAML file
-    version: 0.1
+  geocube:
+    title: Metacatalog GeoCube
+    description: |
+      This tool is designed to be used together with the V-FOR-WaTer Metacatalog data loader.
+      It uses a number of data source files along with either a metacatalog entry or JSON dumps
+      of the metadata.
+      The data is aggregated to a target precision (temporal) and spatial resolution and then
+      ingested into a geocube that is stored as a netCDF file.
     parameters:
       foo_int: 
         type: integer