# HG changeset patch
# User climate
# Date 1624127750 0
# Node ID b768e517a7d09cc1d9a0d5ba70766c39baaf7073

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"

diff -r 000000000000 -r b768e517a7d0 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,25 @@
+
+# Copernicus Atmosphere Data Store (ADS)
+
+This tool allows you to retrieve [Copernicus Atmosphere Data Store (ADS)](https://ads.atmosphere.copernicus.eu/cdsapp#!/home).
+
+- Any user willing to use this tool needs to [create a new account](https://ads.atmosphere.copernicus.eu/user/register?destination=/).
+- Compose your request directly on ADS and copy/paste it in the input field "Request"
+- Users need to add their ADS API Key to Galaxy (see below). Documentation on where to get the ADS API key can be found [here](https://ads.atmosphere.copernicus.eu/api-how-to).
+- Be aware that for being able to download dataset from ADS, users also need to agree to their term of use (Licence to use Copernicus Products) on the ADS website.
+
+## Set up user credentials on Galaxy
+
+To enable users to set their credentials and provide their ADS API Key for this tool,
+make sure the file `config/user_preferences_extra.yml` has the following section:
+
+```
+    cads_account:
+        description: Your Copernicus ADS API Key (Copernicus Atmosphere Data Store API Key)
+        inputs:
+            - name: cads_apikey
+              label: Copernicus ADS API Key
+              type: password
+              required: True
+```
+
diff -r 000000000000 -r b768e517a7d0 cads.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cads.sh	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+if [ -f download.tar.gz ]; then
+   tar zxvf  download.tar.gz
+   cat *.grib > tmp.grib
+   cdo setgridtype,regular tmp.grib tmpg.grib
+   cdo -f nc -t ecmwf copy tmpg.grib tmp.nc
+elif [ -f download.zip ]; then
+   unzip download.zip
+   cat *.grib > tmp.grib
+   cdo setgridtype,regular tmp.grib tmpg.grib
+   cdo -f nc -t ecmwf copy tmpg.grib tmp.nc
+elif [ -f download.grib ]; then
+   cdo -f nc -t ecmwf copy download.grib tmp.nc
+elif [ -f download.nc ]; then
+   mv download.nc tmp.nc
+else
+   echo "No data found! Check your request and/or credentials."
+fi
diff -r 000000000000 -r b768e517a7d0 cads.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cads.xml	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,111 @@
+<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05">
+    <description>for retrieving data from the Atmosphere Monitoring Service</description>
+    <requirements>
+        <requirement type="package" version="3">python</requirement>
+        <requirement type="package" version="0.5.1">cdsapi</requirement>
+        <requirement type="package" version="1.9.9">cdo</requirement>
+        <requirement type="package" version="1.34">tar</requirement>
+        <requirement type="package" version="6.0">unzip</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        export HOME=`pwd`  &&
+        #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
+        #if $cads_apikey == ''
+            echo 'Error. Set your CADS credentials via: User -> Preferences -> Manage Information'  &&
+            echo 'Will try to use tool adsapirc file (used for testing)' &&
+            cp '$__tool_directory__/adsapirc.cfg' .cdsapirc &&
+        #else
+            cp '$cads_key_file' .cdsapirc &&
+        #end if
+
+        python3 '$__tool_directory__/cads_retrieve.py' 
+        #if str($is_file.has_req).strip() == 'yes'
+            --request '$is_file.api_req_file' 
+        #else
+            --request '$req_from_paste'
+        #end if
+        --output request.txt &&
+        bash '$__tool_directory__/cads.sh' &&
+        echo "Data retrieval from Copernicus Atmosphere Data Store is done"
+    ]]></command>
+    <configfiles>
+        <configfile name="cads_key_file"><![CDATA[
+#set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
+         url: https://ads.atmosphere.copernicus.eu/api/v2
+         key: $cads_apikey
+        ]]></configfile>
+        <configfile name="req_from_paste"><![CDATA[
+       #if str($is_file.has_req).strip() == 'no'
+$is_file.api_req_text
+       #end if
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="is_file">
+            <param name="has_req" type="select" label="Provide CADS request">
+                <option value="no">paste as text</option>
+                <option value="yes" selected="true">give a filename</option>
+            </param>
+            <when value="yes">
+                <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
+            </when>
+            <when value="no">
+                <param name="api_req_text" type="text" label="Paste API Request" area="true" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="request" format="txt" from_work_dir="request.txt"/>
+        <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="is_file">
+                <param name="has_req" value="yes" />
+                <param name="api_req_file" ftype="txt" value="req.txt" />
+            </conditional>
+            <output name="request" value="req_out.txt" compare="sim_size" delta="10"/>
+            <output name="ofilename" ftype="netcdf" value="output.nc" compare="sim_size" delta="100"/>
+        </test>
+        <test>
+            <conditional name="is_file">
+                <param name="has_req" value="yes" />
+                <param name="api_req_file" ftype="txt" value="req-timeseries.txt" />
+            </conditional>
+            <output name="request" value="timeseries_out.txt" compare="sim_size" delta="10"/>
+            <output name="ofilename" ftype="netcdf" value="timeseries.nc" compare="sim_size" delta="100"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**Copernicus Atmosphere Data Store (ADS)**
+=======================================================================================================
+
+This tool is a wrapper to retrieve data from the Copernicus Atmosphere Data Store.
+
+- It allows to retrieve data from the Copernicus Atmosphere Monitoring Service.
+- Any user willing to use this tool needs to `create a new account <https://ads.atmosphere.copernicus.eu/user/register?destination=/api-how-to|>`_.
+- Set your CADS API Key via: User -> Preferences -> Manage Information"
+- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
+- Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file.
+- Be aware that for being able to download dataset from ADS, users also need to agree to their term of use (Licence to use Copernicus Products) on the ADS website.
+
+License:
+~~~~~~~~
+
+Generated using Copernicus Atmosphere Monitoring Service information [2021]
+Neither the European Commission nor ECMWF is responsible for any use 
+that may be made of the Copernicus information or data it contains.
+    ]]></help>
+    <citations>
+    </citations>
+    <edam_topics>
+      <edam_topic>topic_3855</edam_topic>
+      <edam_topic>topic_3318</edam_topic>
+    </edam_topics>
+    <edam_operations>
+      <edam_operation>operation_2422</edam_operation>
+      <edam_operation>operation_3357</edam_operation>
+      <edam_operation>operation_0335</edam_operation>
+    </edam_operations>
+</tool>
diff -r 000000000000 -r b768e517a7d0 cads_retrieve.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cads_retrieve.py	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,56 @@
+import argparse
+import ast
+from os import environ, path
+
+import cdsapi
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-i", "--request", type=str, help="input API request")
+parser.add_argument("-o", "--output", type=str, help="output API request")
+args = parser.parse_args()
+
+mapped_chars = {
+    '>': '__gt__',
+    '<': '__lt__',
+    "'": '__sq__',
+    '"': '__dq__',
+    '[': '__ob__',
+    ']': '__cb__',
+    '{': '__oc__',
+    '}': '__cc__',
+    '@': '__at__',
+    '#': '__pd__',
+    "": '__cn__'
+}
+
+with open(args.request) as f:
+    req = f.read()
+
+    # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
+    for key, value in mapped_chars.items():
+        req = req.replace(value, key)
+
+print("req = ", req)
+c3s_type = req.split('c.retrieve')[1].split('(')[1].split(',')[0].strip(' "\'\t\r\n')
+
+c3s_req = '{' + req.split('{', 1)[1].rsplit('}', 1)[0].replace('\n', '') + '}'
+c3s_req_dict = ast.literal_eval(c3s_req)
+
+c3s_output = req.rsplit('}', 1)[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n')
+
+with open(args.output, "w") as f:
+    f.write(f'dataset to retrieve: {c3s_type}\nrequest: {c3s_req}\noutput filename: {c3s_output}')
+
+print("start retrieving data...")
+
+cdapi_file = path.join(environ.get('HOME'), '.cdsapirc')
+
+if path.isfile(cdapi_file):
+    c = cdsapi.Client()
+
+    c.retrieve(
+        c3s_type,
+        c3s_req_dict,
+        c3s_output)
+
+    print("data retrieval successful")
diff -r 000000000000 -r b768e517a7d0 test-data/output.nc
Binary file test-data/output.nc has changed
diff -r 000000000000 -r b768e517a7d0 test-data/req-timeseries.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/req-timeseries.txt	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,19 @@
+import cdsapi
+  
+c = cdsapi.Client()
+
+c.retrieve(
+    'cams-solar-radiation-timeseries',
+    {
+        'sky_type': 'clear',
+        'location': {
+            'latitude': 60,
+            'longitude': 11,
+        },
+        'altitude': '-999.',
+        'date': '2021-06-17/2021-06-17',
+        'time_step': '15minute',
+        'time_reference': 'universal_time',
+        'format': 'netcdf',
+    },
+    'download.nc')
diff -r 000000000000 -r b768e517a7d0 test-data/req.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/req.txt	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,21 @@
+import cdsapi
+
+c = cdsapi.Client()
+
+c.retrieve(
+    'cams-europe-air-quality-forecasts',
+    {
+        'variable': 'nitrogen_dioxide',
+        'model': 'ensemble',
+        'level': '0',
+        'date': '2021-06-16/2021-06-16',
+        'type': 'analysis',
+        'time': '00:00',
+        'leadtime_hour': '0',
+        'format': 'netcdf',
+        'area': [
+            59.96, 10.66, 59.87,
+            10.9,
+        ],
+    },
+    'download.nc')
diff -r 000000000000 -r b768e517a7d0 test-data/req_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/req_out.txt	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,3 @@
+dataset to retrieve: cams-europe-air-quality-forecasts
+request: {        'variable': 'nitrogen_dioxide',        'model': 'ensemble',        'level': '0',        'date': '2021-06-16/2021-06-16',        'type': 'analysis',        'time': '00:00',        'leadtime_hour': '0',        'format': 'netcdf',        'area': [            59.96, 10.66, 59.87,            10.9,        ],    }
+output filename: download.nc
\ No newline at end of file
diff -r 000000000000 -r b768e517a7d0 test-data/timeseries.nc
Binary file test-data/timeseries.nc has changed
diff -r 000000000000 -r b768e517a7d0 test-data/timeseries_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/timeseries_out.txt	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,3 @@
+dataset to retrieve: cams-solar-radiation-timeseries
+request: {        'sky_type': 'clear',        'location': {            'latitude': 60,            'longitude': 11,        },        'altitude': '-999.',        'date': '2021-06-17/2021-06-17',        'time_step': '15minute',        'time_reference': 'universal_time',        'format': 'netcdf',    }
+output filename: download.nc
\ No newline at end of file