aignostics 0.2.48__tar.gz → 0.2.52__tar.gz

{aignostics-0.2.48 → aignostics-0.2.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.48
+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-0.2.48 → aignostics-0.2.52}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.48",
+#     "aignostics==0.2.52",
 # ]
 # ///
 

{aignostics-0.2.48 → aignostics-0.2.52}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.48"
+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 = "0.2.48"
+current_version = "0.2.52"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.48 → aignostics-0.2.52}/src/aignostics/application/_cli.py

@@ -1,7 +1,9 @@
 """CLI of application module."""
 
+import json
 import sys
 import time
+import zipfile
 from pathlib import Path
 from typing import Annotated
 
@@ -9,7 +11,7 @@ import typer
 
 from aignostics.bucket import Service as BucketService
 from aignostics.platform import NotFoundException
-from aignostics.utils import console, get_logger, get_user_data_directory
+from aignostics.utils import console, get_logger, get_user_data_directory, sanitize_path
 
 from ._service import DownloadProgress, DownloadProgressState, Service
 from ._utils import (
@@ -96,6 +98,102 @@ def application_list(
         console.print("No applications available.")
 
 
+@cli.command("dump-schemata")
+def application_dump_schemata(  # noqa: C901
+    id: Annotated[  # noqa: A002
+        str,
+        typer.Argument(
+            help="Id of the application or application_version to dump the output schema for. "
+            "If application id is given the latest version of the application will be used."
+        ),
+    ],
+    destination: Annotated[
+        Path,
+        typer.Option(
+            help="Path pointing to directory where the input and output schemata will be dumped.",
+            exists=False,
+            file_okay=False,
+            dir_okay=True,
+            writable=True,
+            readable=True,
+            resolve_path=True,
+        ),
+    ] = Path().cwd(),  # noqa: B008,
+    zip: Annotated[  # noqa: A002
+        bool,
+        typer.Option(
+            help="If set, the schema files will be zipped into a single file, with the schema files deleted.",
+        ),
+    ] = False,
+) -> None:
+    """Output the input schema of the application in JSON format."""
+    try:
+        application_version = Service().application_version(id, True)
+        application = Service().application(application_version.application_id)
+    except (NotFoundException, ValueError) as e:
+        message = f"Failed to load application version with ID '{id}', check your input: : {e!s}."
+        logger.warning(message)
+        console.print(f"[warning]Warning:[/warning] {message}")
+        sys.exit(2)
+    except (Exception, RuntimeError) as e:
+        message = f"Failed to load application version with ID '{id}': {e!s}."
+        logger.exception(message)
+        console.print(f"[warning]Error:[/warning] {message}")
+        sys.exit(1)
+    try:
+        destination.mkdir(parents=True, exist_ok=True)
+    except OSError as e:
+        console.print(f"[error]Error:[/error] Failed to create directory '{destination}': {e}")
+        sys.exit(1)
+
+    created_files: list[Path] = []
+
+    for input_artifact in application_version.input_artifacts:
+        if input_artifact.metadata_schema:
+            file_path: Path = sanitize_path(
+                Path(destination / f"{application_version.application_version_id}_input_{input_artifact.name}.json")
+            )  # type: ignore
+            file_path.write_text(data=json.dumps(input_artifact.metadata_schema, indent=2), encoding="utf-8")
+            created_files.append(file_path)
+
+    for output_artifact in application_version.output_artifacts:
+        if output_artifact.metadata_schema:
+            file_path = sanitize_path(
+                Path(destination / f"{application_version.application_version_id}_output_{output_artifact.name}.json")
+            )  # type: ignore
+            file_path.write_text(data=json.dumps(output_artifact.metadata_schema, indent=2), encoding="utf-8")
+            created_files.append(file_path)
+
+    md_file_path: Path = sanitize_path(Path(destination / f"{application_version.application_version_id}_schemata.md"))  # type: ignore
+    with md_file_path.open("w", encoding="utf-8") as md_file:
+        md_file.write(f"# Schemata for Aignostics Application {application.name}\n")
+        md_file.write(f"* ID: {application.application_id}\n")
+        md_file.write(f"* Version ID: {application_version.application_version_id}\n")
+        md_file.write(f"\n## Description: \n{application.description}\n\n")
+        md_file.write("\n## Input Artifacts\n")
+        for input_artifact in application_version.input_artifacts:
+            md_file.write(
+                f"- {input_artifact.name}: "
+                f"{application_version.application_version_id}_input_{input_artifact.name}.json\n"
+            )
+        md_file.write("\n## Output Artifacts\n")
+        for output_artifact in application_version.output_artifacts:
+            md_file.write(
+                f"- {output_artifact.name}: "
+                f"{application_version.application_version_id}_output_{output_artifact.name}.json\n"
+            )
+    created_files.append(md_file_path)
+
+    if zip:
+        zip_filename = sanitize_path(Path(destination / f"{application_version.application_version_id}_schemata.zip"))
+        with zipfile.ZipFile(zip_filename, "w", zipfile.ZIP_DEFLATED) as zipf:
+            for file_path in created_files:
+                zipf.write(file_path, arcname=file_path.name)
+        console.print(f"Zipped {len(created_files)} files to [bold]{zip_filename}[/bold]")
+        for file_path in created_files:
+            file_path.unlink()
+
+
 @cli.command("describe")
 def application_describe(
     application_id: Annotated[str, typer.Argument(help="Id of the application to describe")],

{aignostics-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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-0.2.48 → 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.
         """