medenv: fix Copernicus credentials accessibility (#214)

* Update cmems_username and cmems_password retrieval

* Bump version to 0.1.1 in med_environ.xml

Updated version number from 0.1.0 to 0.1.1 in med_environ.xml.

* First try new credentials feature

Added CMEMS credentials for accessing the Copernicus Marine Service API.

* Remove config section

Removed cmems_credentials configuration section from med_environ.xml.

* Fix secret name for CMEMS password in XML

* Update credentials in med_environ.xml

Updated the profile version and modified credential handling for CMEMS.

* update command

Added prompt for CMEMS credentials when test_boolean is true.

* Change secret to variable for CMEMS username

* Update tools/medenv/med_environ.xml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Remove credential prompt and keyfile input

* Remove keyfile argument and related logic

Removed keyfile handling for environment variables.

* Remove unused import of os module

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

Author: PaulineSGN

tools/medenv/med_environ.py

@@ -2,7 +2,6 @@
 
 # Standard imports
 import argparse
-import os
 import pathlib
 from datetime import datetime
 
@@ -50,14 +49,6 @@ def environment_dataset(args):
     # "true" or the string "false" that we need to convert to a bool
     verbose = True if args.verbose == "true" else False
 
-    if args.keyfile is not None and os.path.exists(args.keyfile):
-        with open(args.keyfile, "r") as fh:
-            key_lines = fh.readlines()
-            cmems_username = key_lines[0].split(":")[1].strip()
-            cmems_password = key_lines[1].split(":")[1].strip()
-            os.environ["CMEMS_USERNAME"] = cmems_username
-            os.environ["CMEMS_PASSWORD"] = cmems_password
-
     features = args.variables.split(",")
     fetcher = medenv.Fetcher(features, reduction="mean")
 
@@ -95,7 +86,6 @@ def __main__():
     parser.add_argument("--depth_key", type=int, required=True)
     parser.add_argument("--variables", type=str, required=True)
     parser.add_argument("--tol_spatial_coordinates", type=float, required=True)
-    parser.add_argument("--keyfile", type=pathlib.Path, default=None)
     parser.add_argument("--verbose", type=str, default=False)
     args = parser.parse_args()
 

tools/medenv/med_environ.xml

@@ -1,20 +1,20 @@
-<tool id="iabiodiv_smartbiodiv_med_environ" name="Adds environment variables" version="0.1.0" profile="22.05">
+<tool id="iabiodiv_smartbiodiv_med_environ" name="Adds environment variables" version="0.1.1" profile="25.1">
     <description>
         From Copernicus and etopo given geolocalized and timestamped observations
     </description>
     <requirements>
         <requirement type="package" version="2.1.3">pandas</requirement>
         <requirement type="package" version="4.9.3">lxml</requirement>
         <requirement type="package" version="1.1.0">medenv</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="CMEMS_USERNAME" optional="false" label="CMEMS Username" description="Your Copernicus Marine Service Username. Get it from your Copernicus account."/>
+            <secret name="password" inject_as_env="CMEMS_PASSWORD" optional="false" label="CMEMS password" description="Your Copernicus Marine Service password."/>
+         </credentials>
     </requirements>
     <creator>
         <person givenName="Jérémy" familyName="Fix" url="http://www.github.com/jeremyfix/" email="jeremy.fix@centralesupelec.fr"/>
     </creator>
     <command><![CDATA[
-        #set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
-        #if $cmems_username != ""
-            cp '$cmems_credentials' ~/.medenvkey &&
-        #end if
 
 python '$__tool_directory__/med_environ.py'
     --datafile '${input}'
@@ -25,17 +25,8 @@ python '$__tool_directory__/med_environ.py'
     --depth_key '${depth_key}'
     --variables '${env_variables}'
     --tol_spatial_coordinates '${tol_spatial_coordinates}'
-    --keyfile ~/.medenvkey
     --verbose '${verbose}'
         ]]></command>
-    <configfiles>
-        <configfile name="cmems_credentials"><![CDATA[
-            #set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
-            #set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
-            cmems_username: $cmems_username
-            cmems_password: $cmems_password
-        ]]></configfile>
-    </configfiles>
     <inputs>
         <param name="input" type="data" format="tabular" label="Input dataset"/>
         <param name="env_variables" type="select" label="Which variables to add" multiple="true">