aignostics 0.2.49__tar.gz → 0.2.52__tar.gz

{aignostics-0.2.49 → aignostics-0.2.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.49
+Version: 0.2.52
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/

{aignostics-0.2.49 → aignostics-0.2.52}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.49",
+#     "aignostics==0.2.52",
 # ]
 # ///
 

{aignostics-0.2.49 → aignostics-0.2.52}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.49"
+version = "0.2.52"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -355,7 +355,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.49"
+current_version = "0.2.52"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/application/_service.py

@@ -32,7 +32,7 @@ from aignostics.platform import (
     NotFoundException,
     OutputArtifactElement,
 )
-from aignostics.utils import BaseService, Health, get_logger, sanitize_path_component
+from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, get_logger, sanitize_path_component
 from aignostics.wsi import Service as WSIService
 
 from ._settings import Settings
@@ -155,13 +155,16 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)  # automatically loads and validates the settings
 
-    def info(self) -> dict[str, Any]:
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): If True, mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {"settings": self._settings.model_dump()}
+        return {"settings": self._settings.model_dump(context={UNHIDE_SENSITIVE_INFO: not mask_secrets})}
 
     def health(self) -> Health:  # noqa: PLR6301
         """Determine health of this service.

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/bucket/_service.py

@@ -8,7 +8,7 @@ import requests
 from botocore.client import BaseClient, Config
 from botocore.exceptions import ClientError
 
-from aignostics.utils import BaseService, Health, get_logger
+from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, get_logger
 
 from ._settings import Settings
 
@@ -28,13 +28,16 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)
 
-    def info(self) -> dict[str, Any]:
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): If True, mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {"settings": self._settings.model_dump()}
+        return {"settings": self._settings.model_dump(context={UNHIDE_SENSITIVE_INFO: not mask_secrets})}
 
     def health(self) -> Health:  # noqa: PLR6301
         """Determine health of this service.

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/dataset/_service.py

@@ -59,9 +59,12 @@ atexit.register(_cleanup_processes)
 class Service(BaseService):
     """Service of the IDC module."""
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:  # noqa: ARG002, PLR6301
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): Whether to mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/notebook/_service.py

@@ -220,9 +220,12 @@ def _get_runner() -> _Runner:
 class Service(BaseService):
     """Service of the Marimo module."""
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:  # noqa: ARG002, PLR6301
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): Whether to mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/platform/_service.py

@@ -6,7 +6,7 @@ from typing import Any
 import urllib3
 
 from aignostics.platform import Client
-from aignostics.utils import BaseService, Health, __version__, get_logger
+from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, __version__, get_logger
 
 from ._settings import Settings
 
@@ -24,13 +24,16 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)  # automatically loads and validates the settings
 
-    def info(self) -> dict[str, Any]:
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): Whether to mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {"settings": self._settings.model_dump()}
+        return {"settings": self._settings.model_dump(context={UNHIDE_SENSITIVE_INFO: not mask_secrets})}
 
     def _determine_api_public_health(self) -> Health:
         """Determine healthiness and reachability of Aignostics Platform API.

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/qupath/_service.py

@@ -25,7 +25,7 @@ from packaging.version import Version
 from psutil import Process, wait_procs
 from pydantic import BaseModel, computed_field
 
-from aignostics.utils import BaseService, Health, __project_name__, get_logger
+from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, __project_name__, get_logger
 
 from ._settings import Settings
 
@@ -34,6 +34,7 @@ logger = get_logger(__name__)
 QUPATH_VERSION = "0.6.0-rc5"
 DOWNLOAD_CHUNK_SIZE = 10 * 1024 * 1024
 QUPATH_LAUNCH_MAX_WAIT_TIME = 30  # seconds, maximum wait time for QuPath to start
+QUPATH_SCRIPT_MAX_EXECUTION_TIME = 60 * 60 * 2  # seconds, maximum wait time for QuPath to run a script
 
 PROJECT_FILENAME = "project.qpproj"
 ANNOTATIONS_BATCH_SIZE = 500000
@@ -203,13 +204,16 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)
 
-    def info(self) -> dict[str, Any]:
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): Whether to mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """
-        settings = self._settings.model_dump()
+        settings = self._settings.model_dump(context={UNHIDE_SENSITIVE_INFO: not mask_secrets})
         executable = Service.find_qupath_executable()
         version = Service.get_version()
         return {
@@ -936,8 +940,13 @@ class Service(BaseService):
             start_time = time.time()
             while True:
                 waited = time.time() - start_time
-                if time.time() - start_time > QUPATH_LAUNCH_MAX_WAIT_TIME:
-                    message = f"Timed out after {waited:.2f} seconds waiting for QuPath to start"
+                if script:
+                    if waited > QUPATH_SCRIPT_MAX_EXECUTION_TIME:
+                        message = f"Timed out after {waited:.2f} seconds waiting for QuPath script to complete"
+                        logger.error(message)
+                        return None
+                elif waited > QUPATH_LAUNCH_MAX_WAIT_TIME:
+                    message = f"Timed out after {waited:.2f} seconds waiting for QuPath to launch"
                     logger.error(message)
                     return None
 

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/qupath/scripts/add.groovy

@@ -169,28 +169,46 @@ try {
             
             // Add image to project
             println("Calling addImage... ")
+            def addImageStart = System.currentTimeMillis()
             def entry = project.addImage(builder)
+            def addImageDuration = (System.currentTimeMillis() - addImageStart) / 1000.0
+            println("addImage took ${addImageDuration} seconds")
 
             println("Calling setImageName... "+imageFile.getName())
+            def setImageNameStart = System.currentTimeMillis()
             entry.setImageName(imageFile.getName())
+            def setImageNameDuration = (System.currentTimeMillis() - setImageNameStart) / 1000.0
+            println("setImageName took ${setImageNameDuration} seconds")
 
             // Set a particular image type
             println("Calling readImageData... ")
+            def readImageDataStart = System.currentTimeMillis()
             def imageData = entry.readImageData()
+            def readImageDataDuration = (System.currentTimeMillis() - readImageDataStart) / 1000.0
+            println("readImageData took ${readImageDataDuration} seconds")
 
             println("Calling setImageType... ")
+            def setImageTypeStart = System.currentTimeMillis()
             imageData.setImageType(ImageData.ImageType.BRIGHTFIELD_H_DAB)
+            def setImageTypeDuration = (System.currentTimeMillis() - setImageTypeStart) / 1000.0
+            println("setImageType took ${setImageTypeDuration} seconds")
 
-            println("Calling setImageData... ")
+            println("Calling saveImageData... ")
+            def saveImageDataStart = System.currentTimeMillis()
             entry.saveImageData(imageData)
+            def saveImageDataDuration = (System.currentTimeMillis() - saveImageDataStart) / 1000.0
+            println("saveImageData took ${saveImageDataDuration} seconds")
 
             // Write a thumbnail if we can
             println("Calling getThumbnailRGB... ")
             var img = ProjectCommands.getThumbnailRGB(imageData.getServer());
+            def setThumbnailStart = System.currentTimeMillis()
             entry.setThumbnail(img)
+            def setThumbnailDuration = (System.currentTimeMillis() - setThumbnailStart) / 1000.0
+            println("setThumbnail took ${setThumbnailDuration} seconds")
             
             addedCount++
-            println("Done for image " + addedCount + " " + imageFile.getName())
+            println("Adding image completed for image " + addedCount + ", " + imageFile.getName())
             
         } catch (Exception e) {
             def errorMsg = "Error adding image '" + imageFile.getAbsolutePath() + "': " + e.getMessage()

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/system/_service.py

@@ -244,7 +244,7 @@ class Service(BaseService):
         return any(term in key_lower for term in string_match_terms)
 
     @staticmethod
-    def info(include_environ: bool = False, mask_secrets: bool = True) -> dict[str, Any]:
+    def info(include_environ: bool = False, mask_secrets: bool = True) -> dict[str, Any]:  # type: ignore[override]
         """
         Get info about configuration of service.
 
@@ -377,7 +377,7 @@ class Service(BaseService):
         for service_class in locate_subclasses(BaseService):
             if service_class is not Service:
                 service = service_class()
-                result_dict[service.key()] = service.info()
+                result_dict[service.key()] = service.info(mask_secrets=mask_secrets)
 
         logger.info("Service info: %s", result_dict)
         return result_dict

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/utils/_service.py

@@ -32,8 +32,19 @@ class BaseService(ABC):
 
     @abstractmethod
     def health(self) -> Health:
-        """Get health of this service. Override in subclass."""
+        """Get health of this service. Override in subclass.
+
+        Returns:
+            Health: Health status of the service.
+        """
 
     @abstractmethod
-    def info(self) -> dict[str, Any]:
-        """Get info of this service. Override in subclass."""
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:
+        """Get info of this service. Override in subclass.
+
+        Args:
+            mask_secrets: Whether to mask sensitive information in the output.
+
+        Returns:
+            dict[str, Any]: Information about the service.
+        """

{aignostics-0.2.49 → aignostics-0.2.52}/src/aignostics/wsi/_service.py

@@ -17,9 +17,12 @@ TIMEOUT = 60  # 1 minutes
 class Service(BaseService):
     """Service of the application module."""
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self, mask_secrets: bool = True) -> dict[str, Any]:  # noqa: ARG002, PLR6301
         """Determine info of this service.
 
+        Args:
+            mask_secrets (bool): Whether to mask sensitive information in the output.
+
         Returns:
             dict[str,Any]: The info of this service.
         """