Copernicus marine data retrieving tool

tools/ocean/.shed.yml

@@ -2,7 +2,7 @@ categories:
     - Ecology
 owner: ecology
 remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean
-homepage_url: https://github.com/Marie59/FE-ft-ESG/tree/main/argo
+homepage_url: https://github.com/Marie59/FE-ft-ESG/tree/main/ocean
 long_description: |
   Access, process, visualise oceanographic data for the Earth System
 type: unrestricted

tools/ocean/check.py

@@ -0,0 +1,88 @@
+import os
+import subprocess
+import sys
+
+
+def validate_command(command):
+    # Example validation: Ensure the command does not contain
+    # potentially dangerous substrings
+    forbidden_substrings = ["rm",
+                            "rm -rf",
+                            "sudo",
+                            "dd if=",
+                            "curl",
+                            "wget",
+                            ";",
+                            "&&"]
+    for substring in forbidden_substrings:
+        if substring in command:
+            message = f"Error: Command has forbidden substring '{substring}'"
+            return False, message
+
+    # Check if the command starts with 'copernicusmarine'
+    if not command.startswith("copernicusmarine"):
+        return False, "Error: Command must start with 'copernicusmarine'"
+
+    # Remove 'copernicusmarine' from the start
+    command = command[len("copernicusmarine"):].strip()
+
+    # Check for specific commands and their arguments
+    if command.startswith("subset"):
+        # Check for required arguments for 'subset' command
+        if not ("--dataset-id" in command or "--dataset-url" in command):
+            message = (
+                "Error: 'subset' command must have '--dataset-id' or "
+                "'--dataset-url'"
+            )
+            return False, message
+    elif command.startswith("get"):
+        # Check for required arguments for 'get' command
+        if not ("--dataset-id" in command or "--dataset-url" in command):
+            message = (
+                "Error: 'get' command must have '--dataset-id' or "
+                "'--dataset-url'"
+            )
+            return False, message
+    elif command.startswith("login") or command.startswith("describe"):
+        message = "This tool only accepts 'subset' and 'get' commands."
+        return False, message
+    else:
+        return False, "Error: Command must be 'subset' or 'get'"
+
+    return True, None
+
+
+def main():
+    # Check if a filename argument is provided
+    if len(sys.argv) != 2:
+        print("Usage: python check.py <config_file>")
+        sys.exit(1)
+
+    # Get the filename from the command line argument
+    config_file = sys.argv[1]
+
+    # Check if the file exists
+    if not os.path.isfile(config_file):
+        print(f"Error: File '{config_file}' does not exist.")
+        sys.exit(1)
+
+    # Read the content of the file
+    with open(config_file, "r") as file:
+        command = file.read().strip()
+
+    # Validate the command
+    is_valid, error_message = validate_command(command)
+    if not is_valid:
+        print(error_message)
+        sys.exit(1)
+
+    # Execute the command
+    try:
+        subprocess.run(command, shell=True, check=True)
+    except subprocess.CalledProcessError as e:
+        print(f"Error: Command failed with exit code {e.returncode}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

tools/ocean/copernicusmarine.xml

@@ -0,0 +1,114 @@
+<tool id="copernicusmarine" name="Copernicue Marine Data Store" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT">
+    <description>retrieve marine data</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.3.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">copernicusmarine</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    #import re
+        #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 $cmems_password = os.getenv('CMEMS_PASSWORD', '')
+
+            echo "Using global ENVs" &&
+
+            #if re.match(r"^(?=.*[a-z])(?=.*[A-Z])(?=.*\d).{8,}$", $cmems_password):
+                echo "Password meets the required criteria" &&
+            #else:
+                echo "Password does not meet the required criteria" &&
+            #end if
+
+        #end if
+
+        #if $cmems_username != ""
+            echo 'Error. Set your CMEMS credentials via: User -> Preferences -> Manage Information'  &&
+        #end if
+
+        #set $filename="config_file_with_my_command"
+        echo -e '$input_text' > $filename --force-download --username $cmems_username --password $cmems_password &&
+
+        python '$__tool_directory__/check.py' $filename
+    ]]></command>
+    <configfiles>
+        <configfile name="cmems_credentials">
+            #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_text" label="Paste API Request" type="text" area="true">
+            <sanitizer invalid_char="">
+                <valid initial="string.letters,string.digits">
+                    <add value="_" />
+                    <add value="-" />
+                    <add value=" " />
+                    <add value=":" />
+                    <add value="." />
+                    <add value=" " />
+                </valid>
+            </sanitizer>
+            <validator type="regex">[0-9a-zA-Z_:\-\. ]+</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_netcdf" label="Copernicus marine data" from_work_dir="./*.nc" format="netcdf"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <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>
+        </test>
+    </tests>
+    <help><![CDATA[
+============================
+Copernicus Marine Data Store
+============================
+
+** Context **
+This tool is a wrapper to retrieve data from the Copernicus Marine Environment Monitoring Service (CMEMS).
+
+- It allows to retrieve data from the Copernicus Marine Service.
+- Any user willing to use this tool needs to `create a new account <https://data.marine.copernicus.eu/login>`_.
+- Set your Copernicus CMEMS API Key via: User > Preferences > Manage Information
+- Enter your username and password for Copernicus CMEMS
+- Compose your request directly on Copernicus Marine Data Store 
+    - Choose there which data interest you click on the download button
+    - Then on the top right click again on the big download butto
+    - Log in
+    - Click on "Automate"
+    - You should have a pop-up window called "Automate download"
+    - Copy the ">_Command-Line Interface" proposed there
+- Back on Galaxy paste it in the input field "Paste API Request".
+
+For more information on the Command-Line Interface (CLI) go on `Copernicus Marine Toolbox CLI - Subset <https://help.marine.copernicus.eu/en/articles/7972861-copernicus-marine-toolbox-cli-subset>`
+
+** Input **
+Command line from the Copernicus marine services copy paste as a text.
+
+** Output **
+A netcdf file containing the the data chose by the user from the Copernicus Marine Data Store.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex"> 
+        @misc{Copernicus, 
+        title={Copernicus Marine Data Store}, 
+        url={https://data.marine.copernicus.eu/products}, 
+        note={E.U. Copernicus Marine Service Information}, 
+        author={Copernicus, E.U.} 
+        }
+        </citation>
+    </citations>
+</tool>