Add tool to import OPeNDAP datasets using xarray (#181)

* Add tool to import OPeNDAP dataset using xarray

This uses xarray and netcdf4 to open remote datasets available over OPeNDAP

* fix linting and tests

* fix python linting

* fix import order, docs and test output type

* add validator for protocol

Author: knl88

tools/xarray_import_data/.shed.yml

@@ -0,0 +1,11 @@
+categories:
+    - Ecology
+owner: ecology
+remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/xarray_import_data
+homepage_url: http://xarray.pydata.org
+long_description: |
+  A data import tool for opening OPeNDAP datasets and storing as netCDF files.
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "A data import tool for opening OPeNDAP datasets and storing as netCDF files: {{ tool_name }}."

tools/xarray_import_data/xarray_import_data.py

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+"""Import OPeNDAP dataset using xarray to a netCDF file."""
+
+import argparse
+
+import xarray as xr
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument(
+    "opendap_url",
+    help=(
+        "A valid OPeNDAP URL, also see "
+        "https://docs.xarray.dev/en/stable/user-guide/io.html#opendap"
+    ),
+)
+parser.add_argument(
+    "decode_times",
+    type=lambda x: x == "true",
+    help='If time should be decoded, e.g. "True" or "False"',
+)
+parser.add_argument(
+    "decode_cf",
+    type=lambda x: x == "true",
+    help=(
+        "Whether to decode according to "
+        'CF conventions e.g. "true" or "false"'
+    ),
+)
+parser.add_argument("output_dataset", help="netCDF file to output")
+args = parser.parse_args()
+
+xr.open_dataset(
+    args.opendap_url.strip(),
+    decode_cf=args.decode_cf,
+    decode_times=args.decode_times,
+).to_netcdf(args.output_dataset)

tools/xarray_import_data/xarray_import_data.xml

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+<tool id="xarray_import_data" name="Xarray Import Data" version="0.1.0" profile="22.05">
+    <description>
+        Import a dataset from an OPeNDAP URL and convert it to a local NetCDF file using xarray.
+    </description>
+    <requirements>
+        <requirement type="package" version="2025.4.0">xarray</requirement>
+        <requirement type="package" version="3">python</requirement>
+        <requirement type="package" version="1.6.0">netcdf4</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/xarray_import_data.py' '$opendap_url' '$decode_times' '$decode_cf' '$output_dataset' 
+    ]]></command>
+    <inputs>
+        <param name="opendap_url" type="text" format="netcdf" label="OPeNDAP URL"
+            help="OPeNDAP URL to a dataset, also see https://docs.xarray.dev/en/stable/user-guide/io.html#opendap"
+            optional="false">
+            <validator type="regex" message="Type a valid url">^(https:|http:|\.)\S*</validator>
+        </param>
+        <param name="decode_times" type="boolean" label="Decode times"
+            help="If true, decode time variables to datetime objects. If false, keep them as raw data."
+            checked="true" />
+        <param name="decode_cf" type="boolean" label="Decode CF conventions"
+            help="Whether to decode according to CF conventions"
+            checked="true" />
+    </inputs>
+    <outputs>
+        <data name="output_dataset" from_work_dir="xarray_imported_data" format="netcdf"
+            label="xarray dataset" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="opendap_url"
+                value="http://test.opendap.org:8080/opendap/catalog/data/nc/data.nc" />
+            <output name="output_dataset" ftype="netcdf">
+                <assert_contents>
+                    <has_size min="17K" max="18K" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+==================
+Xarray Import Data
+==================
+
+**What it does**
+
+Open a dataset from an OPeNDAP URL and convert it to a NetCDF file using xarray and netcdf4.
+
+|
+
+**How to use it**
+
+Pass a valid OPeNDAP URL to the `opendap_url` parameter. The tool will download the dataset and save it as a local NetCDF file.
+
+For big datasets consider subsetting the dataset in the url using `<URL>?var_name1[start:step:end],var_name2[start:step:end]`
+
+|
+
+**Links**
+ https://docs.xarray.dev/en/stable/user-guide/io.html#opendap
+ https://www.opendap.org/
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.5334/jors.148</citation>
+    </citations>
+</tool>