Copernicus Marine Data Store tool: Update credential system and copernicusmarine package. (#220)

* Update Copernicus Marine tool version and credentials

Updated tool profile version and modified credentials handling.

* Remove deprecated '--force-download' command option

Deprecate the '--force-download' option in command.

* match with flake8 linting

* Modify comment on '--force-download' option

Updated comment regarding the '--force-download' option.

* Update tools/ocean/copernicusmarine.xml

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>

* Update tools/ocean/copernicusmarine.xml

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>

* Update tools/ocean/copernicusmarine.xml

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>

* Update tools/ocean/copernicusmarine.xml

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>

* Update tools/ocean/copernicusmarine.xml

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>

* Fix indentation for assert_stderr in XML test

* Remove unnecessary assertion from Copernicus Marine test

Removed assertion for '_NCProperties' from test.

* Update divandfull.xml

* Update macro.xml

* Update and rename macro.xml to macros.xml

* revert

* Update argo_getdata.xml

---------

Co-authored-by: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>
Co-authored-by: Marie Jossé <84919248+Marie59@users.noreply.github.com>

Author: 3 people

tools/ocean/argo_getdata.xml

@@ -1,7 +1,7 @@
 <tool id="argo_getdata" name="Argo data access" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>for global ocean in situ observing system</description>
     <macros>
-        <import>macro.xml</import>
+        <import>macros.xml</import>
     </macros>
     <expand macro="argo_requirements">
     </expand>

tools/ocean/check.py

@@ -77,8 +77,9 @@ def main():
         sys.exit(1)
 
     # Append '--force-download' option to the command
-    if "--force-download" not in command:
-        command += " --force-download"
+    # -> depreciated with copernicusmarine V2.0.0
+    # if "--force-download" not in command:
+    #    command += " --force-download"
 
     # Execute the command
     try:

tools/ocean/copernicusmarine.xml

@@ -1,31 +1,22 @@
-<tool id="copernicusmarine" name="Copernicus Marine Data Store" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
+<tool id="copernicusmarine" name="Copernicus Marine Data Store" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="MIT">
     <description>retrieve marine data</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.3.3</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">2.3.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">copernicusmarine</requirement>
+        <credentials name="cmems_credentials" version="1.0" label="CMEMS Credentials" description="Credentials for accessing Copernicus Marine Service API.">
+            <variable name="username" inject_as_env="COPERNICUSMARINE_SERVICE_USERNAME" optional="false" label="CMEMS Username" description="Your Copernicus Marine Service Username. Get it from your Copernicus account."/>
+            <secret name="password" inject_as_env="COPERNICUSMARINE_SERVICE_PASSWORD" optional="false" label="CMEMS password" description="Your Copernicus Marine Service password."/>
+         </credentials>
     </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        bash '$cmems_credentials' &&
+    <command detect_errors="exit_code"><![CDATA[ 
         
         echo -e '$input_text' > config_file_with_my_command &&
         python '$__tool_directory__/check.py' 'config_file_with_my_command'
+        
     ]]></command>
-    <configfiles>
-        <configfile name="cmems_credentials">
-#import os 
-#set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
-#set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
-#if $cmems_username == "" or $cmems_password == ""
-    #set $cmems_username = os.getenv('CMEMS_USERNAME', '')
-    #set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
-#end if
-export cmems_username='$cmems_username'
-export cmems_password='$cmems_password'
-        </configfile>
-    </configfiles>
     <inputs>
         <param name="input_text" label="Paste API Request" type="text" area="true">
             <sanitizer invalid_char="">
@@ -45,13 +36,11 @@ export cmems_password='$cmems_password'
         <data name="output_netcdf" label="Copernicus marine data" from_work_dir="./*.nc" format="netcdf"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test expect_failure="true">
             <param name="input_text" value="copernicusmarine subset --dataset-id cmems_mod_med_phy_my_4.2km-climatology_P1M-m --variable bottomT_avg --variable bottomT_std --variable mlotst_avg --variable mlotst_std --variable so_avg --variable so_std --variable thetao_avg --variable thetao_std --variable uo_avg --variable uo_std --variable vo_avg --variable vo_std --variable zos_avg --variable zos_std --start-datetime 1993-12-01T00:00:00 --end-datetime 1993-12-01T00:00:00 --minimum-longitude 10.283266521135577 --maximum-longitude 12.139348881644054 --minimum-latitude 38.461936025366256 --maximum-latitude 39.82957565942514 --minimum-depth 1.0182366371154785 --maximum-depth 1.0182366371154785"/>
-            <output name="output_netcdf">
-                <assert_contents>
-                    <has_text text="_NCProperties"/>
-                </assert_contents>
-            </output>
+            <assert_stderr>
+                <has_text text="Downloading Copernicus Marine data requires a Copernicus Marine username and password"/>
+            </assert_stderr>
         </test>
     </tests>
     <help><![CDATA[