adding log messages with pkg_infra.logger

Author: daniele-bottazzi

omnipath_client/_client.py

@@ -3,18 +3,18 @@
 from __future__ import annotations
 
 from typing import Any
-import logging
 
-from omnipath_client._query import QueryBuilder
-from omnipath_client._types import BackendType
-from omnipath_client._download import Downloader
-from omnipath_client._response import parse_response
 from omnipath_client._constants import DEFAULT_BASE_URL
+from omnipath_client._download import Downloader
 from omnipath_client._endpoints import ParamDef, EndpointDef
 from omnipath_client._inventory import Inventory
+from omnipath_client._query import QueryBuilder
+from omnipath_client._response import parse_response
+from omnipath_client._session import get_logger, get_session
+from omnipath_client._types import BackendType
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class OmniPath:
@@ -36,12 +36,20 @@ def __init__(
         cache: bool = True,
     ) -> None:
 
+        get_session()
+
         self._base_url = base_url.rstrip('/')
         self._backend = backend
         self._inventory = Inventory(base_url=self._base_url)
         self._inventory.load()
         self._query_builder = QueryBuilder(self._inventory)
         self._downloader = Downloader(use_cache=cache)
+        logger.info(
+            'Initialized OmniPath client with base_url=%s backend=%s cache=%s',
+            self._base_url,
+            self._backend,
+            cache,
+        )
 
     def _fetch(
         self,
@@ -51,16 +59,29 @@ def _fetch(
     ) -> Any:
         """Internal: build query, download, parse response."""
 
+        logger.info(
+            'Starting request workflow for endpoint=%s backend=%s',
+            endpoint,
+            backend or self._backend,
+        )
         query = self._query_builder.build(endpoint, **params)
         result = self._downloader.fetch(query)
         fmt = query.endpoint.response_format
 
-        return parse_response(
+        parsed = parse_response(
             result,
             response_format=fmt,
             backend=backend or self._backend,
         )
 
+        logger.info(
+            'Completed request workflow for endpoint=%s format=%s',
+            endpoint,
+            fmt,
+        )
+
+        return parsed
+
     # --- Export endpoints ---
 
     def entities(
@@ -285,6 +306,7 @@ def _get_default() -> OmniPath:
     global _default_client
 
     if _default_client is None:
+        logger.info('Creating default OmniPath client singleton')
         _default_client = OmniPath()
 
     return _default_client

omnipath_client/_download.py

@@ -3,18 +3,18 @@
 from __future__ import annotations
 
 import io
-from typing import Any
-import logging
 from pathlib import Path
+from typing import Any
 
-from omnipath_client._query import Query
 from omnipath_client._errors import (
     OmniPathAPIError,
     OmniPathConnectionError,
 )
+from omnipath_client._query import Query
+from omnipath_client._session import get_logger
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 class Downloader:
@@ -41,6 +41,11 @@ def __init__(
 
         self._dm = DownloadManager(**dm_kwargs)
         self._use_cache = use_cache
+        logger.info(
+            'Initialized downloader with cache=%s cache_dir=%s',
+            use_cache,
+            cache_dir,
+        )
 
     def fetch(self, query: Query) -> str | io.BytesIO:
         """Download the response for a query.
@@ -62,38 +67,58 @@ def fetch(self, query: Query) -> str | io.BytesIO:
 
         url = query.resolved_url
         method = query.endpoint.method
+        payload = query.json_body if method == 'POST' else query.query_params
+
+        logger.info(
+            'Fetching %s %s with parameter keys=%s',
+            method,
+            url,
+            sorted(payload.keys()) if payload else [],
+        )
 
         try:
             dl_kwargs: dict[str, Any] = {}
 
             if method == 'POST':
                 dl_kwargs['post'] = True
                 dl_kwargs['json'] = True
-                dl_kwargs['query'] = query.json_body or {}
-            elif query.query_params:
-                dl_kwargs['query'] = query.query_params
+                dl_kwargs['query'] = payload or {}
+            elif payload:
+                dl_kwargs['query'] = payload
 
             dest = None if self._use_cache else False
             result = self._dm.download(url, dest=dest, **dl_kwargs)
 
         except Exception as e:
-            raise OmniPathConnectionError(
-                f'Failed to download from {url}: {e}',
-            ) from e
+            message = f'Failed to download from {url}: {e}'
+            logger.exception(message)
+            raise OmniPathConnectionError(message) from e
 
         # Check for HTTP errors via the downloader's state
         if hasattr(self._dm, '_last_downloader'):
             dl = self._dm._last_downloader
 
             if hasattr(dl, 'http_code') and dl.http_code >= 400:
+                logger.error(
+                    'HTTP error while fetching %s: status_code=%s',
+                    url,
+                    dl.http_code,
+                )
                 raise OmniPathAPIError(
                     status_code=dl.http_code,
                     detail=f'Request to {url} failed',
                 )
 
         if result is None:
+            logger.error('Downloader returned no data for %s', url)
             raise OmniPathConnectionError(
                 f'Download returned None for {url}',
             )
 
+        logger.info(
+            'Fetched response for %s into %s',
+            url,
+            type(result).__name__,
+        )
+
         return result

omnipath_client/_graph.py

@@ -3,10 +3,11 @@
 from __future__ import annotations
 
 from typing import Any
-import logging
 
+from omnipath_client._session import get_logger
 
-logger = logging.getLogger(__name__)
+
+logger = get_logger(__name__)
 
 
 def interactions_to_graph(df: Any) -> Any:
@@ -33,12 +34,15 @@ def interactions_to_graph(df: Any) -> Any:
 
     import polars as pl
 
+    logger.info('Converting interactions DataFrame to annnet graph')
+
     # Convert to polars if needed (annnet is polars-backed)
     if not isinstance(df, pl.DataFrame):
         import narwhals as nw
 
         nw_df = nw.from_native(df, eager_only=True)
         df = nw_df.to_native()
+        logger.debug('Converted interactions frame to polars backend')
 
     g = annnet.Graph(directed=True)
 
@@ -60,6 +64,7 @@ def interactions_to_graph(df: Any) -> Any:
             directed=row.get('is_directed', True),
         )
 
+    logger.info('Created interaction graph with %d edges', df.height)
     return g
 
 
@@ -87,11 +92,14 @@ def associations_to_graph(df: Any) -> Any:
 
     import polars as pl
 
+    logger.info('Converting associations DataFrame to annnet graph')
+
     if not isinstance(df, pl.DataFrame):
         import narwhals as nw
 
         nw_df = nw.from_native(df, eager_only=True)
         df = nw_df.to_native()
+        logger.debug('Converted associations frame to polars backend')
 
     g = annnet.Graph(directed=True)
 
@@ -112,4 +120,5 @@ def associations_to_graph(df: Any) -> Any:
             row['member_entity_id'],
         )
 
+    logger.info('Created association graph with %d edges', df.height)
     return g

omnipath_client/_inventory.py

@@ -8,17 +8,17 @@
 
 import json
 from typing import Any
-import logging
 
 from omnipath_client._constants import (
-    OPENAPI_PATH,
     DEFAULT_BASE_URL,
+    OPENAPI_PATH,
     STATIC_ENDPOINTS,
 )
 from omnipath_client._endpoints import ParamDef, EndpointDef
+from omnipath_client._session import get_logger
 
 
-logger = logging.getLogger(__name__)
+logger = get_logger(__name__)
 
 
 def _param_type_from_schema(schema: dict) -> str:
@@ -155,6 +155,12 @@ def parse_openapi(spec: dict[str, Any]) -> dict[str, EndpointDef]:
     paths = spec.get('paths', {})
     endpoints: dict[str, EndpointDef] = {}
 
+    logger.debug(
+        'Parsing OpenAPI spec with %d path(s) and %d schema(s)',
+        len(paths),
+        len(schemas),
+    )
+
     for path, methods in paths.items():
         for method, details in methods.items():
             key = path.lstrip('/')
@@ -250,6 +256,7 @@ def __init__(self, base_url: str = DEFAULT_BASE_URL) -> None:
         self._base_url = base_url.rstrip('/')
         self._endpoints: dict[str, EndpointDef] = {}
         self._loaded = False
+        logger.debug('Created inventory for base_url=%s', self._base_url)
 
     def load(self, force_refresh: bool = False) -> None:
         """Load the inventory from the server or static fallback.
@@ -260,6 +267,10 @@ def load(self, force_refresh: bool = False) -> None:
         """
 
         if self._loaded and not force_refresh:
+            logger.debug(
+                'Inventory already loaded for %s; skipping refresh',
+                self._base_url,
+            )
             return
 
         try:
@@ -272,6 +283,10 @@ def load(self, force_refresh: bool = False) -> None:
                 exc_info=True,
             )
             self._endpoints = _build_static_fallback()
+            logger.info(
+                'Loaded %d endpoints from static fallback',
+                len(self._endpoints),
+            )
 
         self._loaded = True
 
@@ -299,6 +314,10 @@ def endpoints(self) -> dict[str, EndpointDef]:
         """All registered endpoints."""
 
         if not self._loaded:
+            logger.debug(
+                'Inventory access triggered lazy load for %s',
+                self._base_url,
+            )
             self.load()
 
         return self._endpoints