Update logging configuration and exclude folder from Ruff analysis (#23)

* chores: exclude the  folder from being analyzed by Ruff

* chores: add script to verify the pkg_infra session, logger with ontograph. Different downloaders can be used here

* chores: modify loggeing levels in the work directory config file.

Author: ecarrenolozano

04_workdir.yaml

@@ -2,30 +2,49 @@
 # ----      Logging               -----
 # -------------------------------------
 logging:
-  handlers:
-    file:
-      filename: "logs/my_saezapp_logger.log"
+    handlers:
+        file:
+            filename: logs/my_saezapp_logger.log
+
+    loggers:
+        default:
+            level: DEBUG
+        pkg_infra:
+            level: INFO
+            handlers: [file, console]
+            propagate: false
+        download_manager:
+            level: INFO
+            handlers: [file, console]
+            propagate: false
+        ontograph:
+            level: INFO
+            handlers: [file, console]
+            propagate: false
+
+    root:
+        level: WARNING
+        handlers: [file, console]
 
 # -------------------------------------
 # ----      Integrations          -----
 # -------------------------------------
 integrations:  # New question: store the big yaml?
   # OntoGraph
-  ontograph:
-    settings:
-      - enabled: true  # This will be switch <--- what should be the default value?
-      - cache_path: "ontograph_config.yaml"
-      - source_ontology: "chebi"
-      - backend: "graphblas"
+    ontograph:
+        settings:
+        -   enabled: true # This will be switch <--- what should be the default value?
+        -   cache_path: ontograph_config.yaml
+        -   source_ontology: chebi
+        -   backend: graphblas
 
   # Download manager
-  download_manager:
-    settings:
-      enabled: true   # This will be switch <--- what should be the default value?
-      path: "/tmp"
-      backend: "requests"
-      
-      url: "https://getsamplefiles.com/download/txt/sample-1.txt"
-      dest: false
-      newer_than: null
-      older_than: null
+    download_manager:
+        settings:
+            enabled: true # This will be switch <--- what should be the default value?
+            path: /tmp
+            backend: requests
+            url: https://getsamplefiles.com/download/txt/sample-1.txt
+            dest: false
+            newer_than:
+            older_than:

pyproject.toml

@@ -152,6 +152,9 @@ report_level = "INFO"
 
 # ---- Ruff: a fast Python linter and formatter.
 [tool.ruff]
+exclude = [
+    "sandbox/"
+]
 extend-include = ["*.ipynb"]
 line-length = 80
 target-version = "py312"

sandbox/use_case_downloaders.py

@@ -0,0 +1,39 @@
+import pkg_infra
+
+from ontograph.client import ClientCatalog, ClientOntology
+from ontograph.downloader import PoochDownloaderAdapter
+from ontograph.config.settings import DEFAULT_CACHE_DIR
+
+def main():
+    workspace = './'
+
+    # Create a session for the app
+    session = pkg_infra.get_session(workspace=workspace, include_location=True)
+
+    # Get logger from the session
+    logger = session.get_logger()
+
+    # Add simple messages to the current logger
+    logger.info('This is an INFO message')
+    logger.debug('This is a DEBUG message')
+    logger.warning('This is a WARNING message')
+    logger.error('This is an ERROR message')
+    logger.critical('This is a CRITICAL message')
+
+    # Call a given downloader from OntoGraph
+    downloader = PoochDownloaderAdapter(cache_dir=DEFAULT_CACHE_DIR)
+
+    # Download a catalog
+    catalog = ClientCatalog(cache_dir='./data/out', downloader=downloader)
+    catalog.load_catalog()
+
+    # print the schema tree
+    #catalog.print_catalog_schema_tree()
+
+    # Download a given ontology
+    client = ClientOntology(cache_dir='./data/out', downloader=downloader)
+    client.load(source='go')  # catalog download
+
+if __name__ == '__main__':
+
+    main()