feat: Update Dockerfile and add coscine_api_retrieval module

- Dockerfile.dynamics_learning: Created .logs directory to store log files.
- coscine_api_retrieval.py: Added new module for retrieving data from Coscine API with logging configuration.
- main.py: Integrated the coscine_api_retrieval module to download resource content.
- requirements.txt: Updated dependencies to reflect necessary packages for the new functionalities.

dynamics_learning/Dockerfile.dynamics_learning

@@ -2,6 +2,8 @@ FROM nvcr.io/nvidia/tensorflow:24.04-tf2-py3
 
 WORKDIR /app
 
+RUN mkdir .logs
+
 # COPY . .
 
 # Make entrypoint executeable

dynamics_learning/dynamics_learning/data_retrieval/coscine_api_retrieval.py

+#!/usr/bin/python3
+# -*- coding:utf-8 -*-
+# Copyright Leon Gorissen
+# Released under MIT License
+# Contact us for other licensing options.
+
+import logging
+import coscine
+import os
+from pathlib import Path
+from typing import List
+
+# Configure logging
+logger = logging.getLogger('coscine_data_retrieval_logger')  # Create a logger named 'coscine_receiver_logger'
+logger.setLevel(logging.INFO)  # Set the logging level to INFO
+
+# Create and configure console handler
+console_handler = logging.StreamHandler()  # Create a stream handler to log to console
+console_handler.setLevel(logging.INFO)  # Set the logging level for the console handler
+
+# Create and configure file handler
+file_handler = logging.FileHandler('/app/.logs/coscine_data_retrieval.log')  # Create a file handler to log to a file
+file_handler.setLevel(logging.INFO)  # Set the logging level for the file handler
+
+# Create a formatter for log messages
+formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+console_handler.setFormatter(formatter)  # Set formatter for console handler
+file_handler.setFormatter(formatter)  # Set formatter for file handler
+
+# Add handlers to the logger
+logger.addHandler(console_handler)  # Add console handler to logger
+logger.addHandler(file_handler)  # Add file handler to logger
+
+# Retrieve environment variables for API token
+def get_env_variable(var_name):
+    value = os.environ.get(var_name)
+    if value is None:
+        raise EnvironmentError(f"The environment variable {var_name} is not set.")
+    return value
+
+try:
+    API_TOKEN = get_env_variable("COSCINE_API_TOKEN") 
+except EnvironmentError as e:
+    print(e)
+    # Handle the error appropriately, e.g., exit the program or set default values
+    API_TOKEN = None
+
+CLIENT = coscine.ApiClient(API_TOKEN)
+PROJECT = CLIENT.project("IoP Ws A.III FER WWL Demo")  # Connect to the specified Coscine project
+logger.info(f"Connecting to Coscine Project\n{PROJECT}")  # Log the connection to the project
+RESOURCE = PROJECT.resource("Trajectory Data")  # Address the specific resource in the project
+logger.info(f"Addressing resource\n{RESOURCE}")
+
+def download_resource_content(resource:coscine.resource.Resource=RESOURCE) -> None:
+    """Downloads none-existend contents of the resource.
+
+    Args:
+        resource (coscine.resource.Resource, optional): The resource to download from. Defaults to RESOURCE.
+    """    
+    resource_files = set(get_resource_content(resource))
+    existing_files = set(get_downloaded_files())
+    unique_elements = resource_files.symmetric_difference(existing_files)
+    missing_files = list(unique_elements)
+    if missing_files:
+        logger.info(f"Files not yet downloaded are {missing_files}. These files will now be downloaded.")
+    for file in missing_files:
+        try:
+            resource.file(file).download(path=f"./Trajectory Data/{file}")
+        except Exception as e:
+            logger.warn(f"{e}\nLikely you have local copy of a file that is not on coscine.")
+
+def get_resource_content(resource:coscine.resource.Resource=RESOURCE) -> List:
+    """Get the contents the specified resource.
+
+    Args:
+        resource (coscine.resource.Resource, optional): Coscine Resource to use. Defaults to RESOURCE.
+
+    Returns:
+        List: List of resource contents.
+    """    
+    files = []
+    for file in resource.files(recursive=True):
+        if not str(file).endswith("/"):
+            files.append(file.path)
+    return files
+
+
+def get_downloaded_files(root_dir:str=f"./{RESOURCE.name}/") -> List:
+    """Looks which whiles have been downloaded from the resource.
+
+    Args:
+        root_dir (str, optional): Directory where stored files are saved. Defaults to f"./{RESOURCE.name}/".
+
+    Returns:
+        List: List of downloaded files.
+    """    
+    root_path = Path(root_dir)
+    files = []
+    for path in root_path.rglob('*'):
+        if path.is_file():
+            file = str(path).split("/", 1)[1]
+            if file != "":
+                files.append(file)
+    return files
+
+if __name__ == "__main__":
+    download_resource_content()
+    #get_resource_content()
+    #get_downloaded_files()
\ No newline at end of file

dynamics_learning/dynamics_learning/main.py

+from dynamics_learning.data_retrieval.coscine_api_retrieval import download_resource_content
+
+if __name__ == "__main__":
+    download_resource_content()
\ No newline at end of file