aignostics 0.2.36__tar.gz → 0.2.39__tar.gz

{aignostics-0.2.36 → aignostics-0.2.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.36
+Version: 0.2.39
 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-0.2.36 → aignostics-0.2.39}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.36",
+#     "aignostics==0.2.39",
 # ]
 # ///
 

{aignostics-0.2.36 → aignostics-0.2.39}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.36"
+version = "0.2.39"
 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 = [
@@ -356,7 +356,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.36"
+current_version = "0.2.39"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/__init__.py

@@ -2,7 +2,7 @@
 
 import os
 
-from .constants import MODULES_TO_INSTRUMENT
+from .constants import MODULES_TO_INSTRUMENT, WSI_SUPPORTED_FILE_EXTENSIONS
 from .utils.boot import boot
 
 # Add scheme to HTTP proxy environment variables if missing
@@ -12,3 +12,5 @@ for proxy_var in ["HTTP_PROXY", "HTTPS_PROXY"]:
         os.environ[proxy_var] = f"http://{proxy_url}"
 
 boot(modules_to_instrument=MODULES_TO_INSTRUMENT)
+
+__all__ = ["WSI_SUPPORTED_FILE_EXTENSIONS"]

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/application/_cli.py

@@ -300,7 +300,7 @@ def run_prepare(
 ) -> None:
     """Prepare metadata CSV file required for submitting a run.
 
-    (1) Scans source_directory for whole slide images (.tif, .tiff and .dcm.
+    (1) Scans source_directory for whole slide images.
     (2) Extracts metadata from whole slide images such as width, height, mpp.
     (3) Creates CSV file with columns as required by the given application version.
     (4) Optionally applies mappings to amend the metadata CSV file for columns

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/application/_service.py

@@ -15,6 +15,7 @@ import requests
 from pydantic import BaseModel, computed_field
 
 from aignostics.bucket import Service as BucketService
+from aignostics.constants import WSI_SUPPORTED_FILE_EXTENSIONS
 from aignostics.platform import (
     LIST_APPLICATION_RUNS_MAX_PAGE_SIZE,
     ApiException,
@@ -154,13 +155,13 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)  # automatically loads and validates the settings
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self) -> dict[str, Any]:
         """Determine info of this service.
 
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {}
+        return {"settings": self._settings.model_dump()}
 
     def health(self) -> Health:  # noqa: PLR6301
         """Determine health of this service.
@@ -350,7 +351,7 @@ class Service(BaseService):
         """Generate metadata from the source directory.
 
         Steps:
-        1. Recursively files ending with .tiff, .tif, .svs and .dcm in the source directory
+        1. Recursively files ending with supported extensions in the source directory
         2. Creates a dict with the following columns
             - reference (str): The reference of the file, by default equivalent to the absolute file name
             - source (str): The absolute filename
@@ -385,10 +386,9 @@ class Service(BaseService):
         application_version = Service().application_version(application_version_id, use_latest_if_no_version_given=True)  # noqa: F841
 
         metadata = []
-        file_extensions = [".tiff", ".tif", ".svs", ".dcm"]
 
         try:
-            for extension in file_extensions:
+            for extension in list(WSI_SUPPORTED_FILE_EXTENSIONS):
                 for file_path in source_directory.glob(f"**/*{extension}"):
                     # Generate CRC32C checksum with google_crc32c and encode as base64
                     hash_sum = google_crc32c.Checksum()  # type: ignore[no-untyped-call]

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/bucket/_cli.py

@@ -59,11 +59,9 @@ def upload(
 
     console.print(f"Uploading {source} to bucket...")
 
-    # Create a counter for total bytes
     total_bytes = 0
     files_count = 0
 
-    # First, calculate total size and count files
     if source.is_file():
         total_bytes = source.stat().st_size
         files_count = 1
@@ -75,14 +73,9 @@ def upload(
 
     console.print(f"Found {files_count} files with total size of {humanize.naturalsize(total_bytes)}")
 
-    # Generate base prefix with placeholders replaced
     username = psutil.Process().username()
     timestamp = datetime.datetime.now(tz=datetime.UTC).strftime("%Y%m%d_%H%M%S")
-
-    # Replace placeholders in the destination_prefix
     base_prefix = destination_prefix.format(username=username, timestamp=timestamp)
-
-    # Remove leading/trailing slashes for consistency
     base_prefix = base_prefix.strip("/")
 
     with Progress(
@@ -98,18 +91,14 @@ def upload(
         TransferSpeedColumn(),
         TextColumn("[progress.description]{task.description}"),
     ) as progress:
-        # Create a task for overall progress
         task = progress.add_task(f"Uploading to {base_prefix}/...", total=total_bytes)
 
-        # Callback function to update progress
         def update_progress(bytes_uploaded: int, file: Path) -> None:
             relpath = file.relative_to(source)
             progress.update(task, advance=bytes_uploaded, description=f"{relpath}")
 
-        # Upload with progress reporting
         results = Service().upload(source, base_prefix, update_progress)
 
-    # Print results summary
     if results["success"]:
         console.print(f"[green]Successfully uploaded {len(results['success'])} files:[/green]")
         for key in results["success"]:

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/bucket/_service.py

@@ -28,13 +28,13 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self) -> dict[str, Any]:
         """Determine info of this service.
 
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {}
+        return {"settings": self._settings.model_dump()}
 
     def health(self) -> Health:  # noqa: PLR6301
         """Determine health of this service.
@@ -97,7 +97,7 @@ class Service(BaseService):
         url = self._get_s3_client().generate_presigned_url(
             ClientMethod="put_object",
             Params={"Bucket": self._settings.name if bucket_name is None else bucket_name, "Key": object_key},
-            ExpiresIn=3600,
+            ExpiresIn=self._settings.upload_signed_url_expiration_seconds,
         )
         return cast("str", url)
 
@@ -163,7 +163,7 @@ class Service(BaseService):
         url = self._get_s3_client().generate_presigned_url(
             ClientMethod="get_object",
             Params={"Bucket": self._settings.name if bucket_name is None else bucket_name, "Key": object_key},
-            ExpiresIn=3600,
+            ExpiresIn=self._settings.download_signed_url_expiration_seconds,
         )
         return cast("str", url)
 

aignostics-0.2.39/src/aignostics/bucket/_settings.py

@@ -0,0 +1,86 @@
+"""Settings of the bucket module."""
+
+from enum import StrEnum
+from typing import Annotated
+
+from pydantic import Field, PlainSerializer, SecretStr
+from pydantic_settings import SettingsConfigDict
+
+from ..utils import OpaqueSettings, __env_file__, __project_name__  # noqa: TID252
+
+
+class BucketProtocol(StrEnum):
+    GS = "gs"
+    S3 = "s3"
+
+
+class Settings(OpaqueSettings):
+    """Settings."""
+
+    model_config = SettingsConfigDict(
+        env_prefix=f"{__project_name__.upper()}_BUCKET_",
+        extra="ignore",
+        env_file=__env_file__,
+        env_file_encoding="utf-8",
+    )
+
+    protocol: Annotated[
+        BucketProtocol,
+        Field(
+            description=("Protocol to access the cloud bucket, default is gs"),
+            default="gs",
+        ),
+    ]
+
+    name: Annotated[
+        str,
+        Field(description=("Name of the cloud bucket")),
+    ]
+
+    region_name: Annotated[
+        str,
+        Field(description=("Region of the cloud bucket"), default="EUROPE-WEST3"),
+    ]
+
+    hmac_access_key_id: Annotated[
+        SecretStr,
+        PlainSerializer(func=OpaqueSettings.serialize_sensitive_info, return_type=str, when_used="always"),
+        Field(description=("HMAC access key ID of the cloud bucket")),
+    ]
+
+    hmac_secret_access_key: Annotated[
+        SecretStr,
+        PlainSerializer(func=OpaqueSettings.serialize_sensitive_info, return_type=str, when_used="always"),
+        Field(description=("HMAC secret access key of the cloud bucket")),
+    ]
+
+    upload_signed_url_expiration_seconds: Annotated[
+        int,
+        Field(
+            description=("Expiration time for signed URLs created and used by the Python SDK to upload to the bucket."),
+            default=2
+            * 60
+            * 60,  # The Python SDK creates the signed upload URLs immediately before uploading, so 2h is sufficient.
+            ge=60,  # Minimum expiration time is 60 seconds, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+            le=7
+            * 24
+            * 60
+            * 60,  # Limit to 7 days as this is the max e.g. at AWS, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+        ),
+    ]
+
+    download_signed_url_expiration_seconds: Annotated[
+        int,
+        Field(
+            description=(
+                "Expiration time of the signed URLs provided by the Python SDK to the platform on submitting "
+                "application runs."
+            ),
+            default=7 * 24 * 60 * 60,  # The platform queues application runs, so we set a gracious default of 7d.
+            ge=60,  # Minimum expiration time is 60 seconds, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+            le=7
+            * 24
+            * 60
+            * 60,  # Limit to 7 days as this is the max e.g. at AWS, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+        ),
+    ]

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/constants.py

@@ -12,3 +12,4 @@ NOTEBOOK_APP = Path(__file__).parent.parent.parent / "examples" / "notebook.py"
 # Project specific configuration
 os.environ["MATPLOTLIB"] = "false"
 os.environ["NICEGUI_STORAGE_PATH"] = str(Path.home().resolve() / ".aignostics" / ".nicegui")
+WSI_SUPPORTED_FILE_EXTENSIONS = {".dcm", ".tiff", ".tif", ".svs"}

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/notebook/_notebook.py

@@ -27,7 +27,7 @@ def _():
     import matplotlib.pyplot as plt
     from cloudpathlib import GSPath
     from dotenv import load_dotenv
-    from aignostics import dataset
+    from aignostics import dataset, WSI_SUPPORTED_FILE_EXTENSIONS
     from wsidicom import WsiDicom
 
     mo.sidebar([
@@ -44,7 +44,6 @@ def _():
             orientation="vertical",
         ),
     ])
-    return Path, WsiDicom, dataset, mo, plt
 
 
 @app.cell
@@ -55,7 +54,7 @@ def _(Path, mo):
     mo.vstack([
         mo.ui.file_browser(
             Path(query_params["results_folder"]),
-            filetypes=[".dcm", ".tif", ".tiff", ".svs"],
+            filetypes=list(WSI_SUPPORTED_FILE_EXTENSIONS),
             multiple=True,
             restrict_navigation=True,
         )

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/platform/_service.py

@@ -24,13 +24,13 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)  # automatically loads and validates the settings
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self) -> dict[str, Any]:
         """Determine info of this service.
 
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {}
+        return {"settings": self._settings.model_dump()}
 
     def _determine_api_public_health(self) -> Health:
         """Determine healthiness and reachability of Aignostics Platform API.

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/platform/_settings.py

@@ -6,7 +6,15 @@ from pathlib import Path
 from typing import Annotated, TypeVar
 
 import appdirs
-from pydantic import Field, PlainSerializer, SecretStr, computed_field, model_validator
+from pydantic import (
+    Field,
+    FieldSerializationInfo,
+    PlainSerializer,
+    SecretStr,
+    computed_field,
+    field_serializer,
+    model_validator,
+)
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from aignostics.utils import OpaqueSettings, __project_name__, load_settings
@@ -47,22 +55,22 @@ class Settings(OpaqueSettings):
     client credentials, token storage, and other SDK behaviors.
 
     Attributes:
-        client_id_device (SecretStr): Client ID for device authorization flow.
-        client_id_interactive (SecretStr): Client ID for interactive authorization flow.
         api_root (str): Base URL of the Aignostics API.
-        scope (str): OAuth scopes required by the SDK.
-        scope_elements (list[str]): OAuth scopes split into individual elements.
         audience (str): OAuth audience claim.
+        authorization_backoff_seconds (int): Backoff time for authorization retries in seconds.
         authorization_base_url (str): Authorization endpoint for OAuth flows.
-        token_url (str): Token endpoint for OAuth flows.
-        redirect_uri (str): Redirect URI for OAuth authorization code flow.
+        cache_dir (str): Directory for caching tokens and other data.
+        client_id_device (SecretStr): Client ID for device authorization flow.
+        client_id_interactive (SecretStr): Client ID for interactive authorization flow.
         device_url (str): Device authorization endpoint for device flow.
         jws_json_url (str): URL for JWS key set.
+        redirect_uri (str): Redirect URI for OAuth authorization code flow.
         refresh_token (SecretStr | None): OAuth refresh token if available.
-        cache_dir (str): Directory for caching tokens and other data.
-        token_file (Path): Path to the token storage file.
         request_timeout_seconds (int): Timeout for API requests in seconds.
-        authorization_backoff_seconds (int): Backoff time for authorization retries in seconds.
+        scope (str): OAuth scopes required by the SDK.
+        scope_elements (list[str]): OAuth scopes split into individual elements.
+        token_file (Path): Path to the token storage file.
+        token_url (str): Token endpoint for OAuth flows.
     """
 
     model_config = SettingsConfigDict(
@@ -117,7 +125,13 @@ class Settings(OpaqueSettings):
     device_url: str
     jws_json_url: str
 
-    refresh_token: SecretStr | None = None
+    refresh_token: Annotated[
+        SecretStr | None,
+        PlainSerializer(
+            func=OpaqueSettings.serialize_sensitive_info, return_type=str, when_used="always"
+        ),  # allow to unhide sensitive info from CLI or if user presents valid token via API
+        Field(description="Refresh token for OAuth authentication", min_length=10, max_length=1000, default=None),
+    ] = None
 
     cache_dir: str = appdirs.user_cache_dir(__project_name__)
 
@@ -131,6 +145,10 @@ class Settings(OpaqueSettings):
         """
         return Path(self.cache_dir) / ".token"
 
+    @field_serializer("token_file")
+    def serialize_token_file(self, token_file: Path, _info: FieldSerializationInfo) -> str:  # noqa: PLR6301
+        return str(token_file.resolve())
+
     request_timeout_seconds: int = 30
     authorization_backoff_seconds: int = 3
 

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/qupath/_cli.py

@@ -172,33 +172,6 @@ def launch(
         sys.exit(1)
 
 
-@cli.command()
-def info() -> None:
-    """Get info about QuPath installation."""
-    if not Service().is_qupath_installed():
-        console.print("QuPath is not installed. Use 'uvx aignostics qupath install' to install it.", style="warning")
-        sys.exit(2)
-    try:
-        console.print_json(data=Service().info())
-    except Exception as e:
-        message = f"Failed to get QuPath info: {e!s}."
-        logger.exception(message)
-        console.print(message, style="error")
-        sys.exit(1)
-
-
-@cli.command()
-def settings() -> None:
-    """Show settings configured for Paquo based QuPath integration."""
-    console.print_json(data=Service().get_paquo_settings())
-
-
-@cli.command()
-def defaults() -> None:
-    """Show default settings of Paquo based QuPath integration."""
-    console.print_json(data=Service().get_paquo_defaults())
-
-
 @cli.command()
 def uninstall(
     version: Annotated[

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/qupath/_service.py

@@ -25,6 +25,7 @@ import requests
 from packaging.version import Version
 from pydantic import BaseModel, computed_field
 
+from aignostics import WSI_SUPPORTED_FILE_EXTENSIONS
 from aignostics.utils import BaseService, Health, __project_name__, get_logger
 
 from ._settings import Settings
@@ -35,7 +36,6 @@ QUPATH_VERSION = "0.6.0-rc5"
 DOWNLOAD_CHUNK_SIZE = 10 * 1024 * 1024
 LAUNCH_MAX_WAIT_TIME = 60  # seconds, maximum wait time for QuPath to start
 
-IMAGE_SUFFIXES = {".dcm", ".tiff", ".tif", ".svs"}
 PROJECT_FILENAME = "project.qpproj"
 ANNOTATIONS_BATCH_SIZE = 500000
 
@@ -152,17 +152,22 @@ class Service(BaseService):
         Returns:
             dict[str,Any]: The info of this service.
         """
-        application_path = Service.find_qupath()
+        settings = self._settings.model_dump()
+        settings.update({
+            "paquo": {
+                "current": self.get_paquo_settings(),
+                "defaults": self.get_paquo_defaults(),
+            },
+        })
+        app_path = Service.find_qupath()
         version = Service.get_version()
         return {
-            "qupath": {
-                "application_path": str(application_path) if application_path else "Not found",
+            "app": {
+                "path": str(app_path) if app_path else None,
                 "version": dict(version) if version else None,
+                "expected_version": Service.get_expected_version(),
             },
-            "paquo": {
-                "settings": self.get_paquo_settings(),
-                "defaults": self.get_paquo_defaults(),
-            },
+            "settings": settings,
         }
 
     def health(self) -> Health:
@@ -1085,7 +1090,7 @@ class Service(BaseService):
                 progress.status = AddProgressState.FINDING_IMAGES
                 progress_callable(progress)
 
-            supported_extensions = IMAGE_SUFFIXES
+            supported_extensions = WSI_SUPPORTED_FILE_EXTENSIONS
 
             def is_supported_image(file_path: Path) -> bool:
                 return file_path.is_file() and file_path.suffix.lower() in supported_extensions

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/utils/_settings.py

@@ -34,10 +34,16 @@ class OpaqueSettings(BaseSettings):
     def serialize_sensitive_info(input_value: SecretStr, info: FieldSerializationInfo) -> str | None:
         if not input_value:
             return None
-        if info.context.get(UNHIDE_SENSITIVE_INFO, False):  # type: ignore
+        if info.context and info.context.get(UNHIDE_SENSITIVE_INFO, False):
             return input_value.get_secret_value()
         return str(input_value)
 
+    @staticmethod
+    def serialize_path_resolve(input_value: Path, _info: FieldSerializationInfo) -> str | None:
+        if not input_value:
+            return None
+        return str(input_value.resolve())
+
 
 def load_settings(settings_class: type[T]) -> T:
     """

{aignostics-0.2.36 → aignostics-0.2.39}/src/aignostics/wsi/_service.py

@@ -6,14 +6,13 @@ from typing import Any
 
 import requests
 
+from aignostics import WSI_SUPPORTED_FILE_EXTENSIONS
 from aignostics.utils import BaseService, Health, get_logger
 
 logger = get_logger(__name__)
 
 TIMEOUT = 60  # 1 minutes
 
-FILE_TYPES_SUPPORTED = {".dcm", ".tiff", ".tif", ".svs"}
-
 
 class Service(BaseService):
     """Service of the application module."""
@@ -47,7 +46,7 @@ class Service(BaseService):
             PIL.Image.Image: Thumbnail of the image.
 
         Raises:
-            ValueError: If the file type is not supported (.dcm, .tiff, or .tif).
+            ValueError: If the file type is not supported.
             RuntimeError: If there is an error generating the thumbnail.
         """
         from ._openslide_handler import OpenSlideHandler  # noqa: PLC0415
@@ -56,8 +55,8 @@ class Service(BaseService):
             message = f"File does not exist: {path}"
             logger.warning(message)
             raise ValueError(message)
-        if path.suffix.lower() not in FILE_TYPES_SUPPORTED:
-            message = f"Unsupported file type: {path.suffix}. Supported types are .dcm, .tiff, and .tif."
+        if path.suffix.lower() not in WSI_SUPPORTED_FILE_EXTENSIONS:
+            message = f"Unsupported file type: {path.suffix}. Supported types are {WSI_SUPPORTED_FILE_EXTENSIONS!s}"
             logger.warning(message)
             raise ValueError(message)
         try:
@@ -106,8 +105,8 @@ class Service(BaseService):
             message = f"File does not exist: {path}"
             logger.warning(message)
             raise ValueError(message)
-        if path.suffix.lower() not in FILE_TYPES_SUPPORTED:
-            message = f"Unsupported file type: {path.suffix}. Supported types are .dcm, .tiff, and .tif."
+        if path.suffix.lower() not in WSI_SUPPORTED_FILE_EXTENSIONS:
+            message = f"Unsupported file type: {path.suffix}. Supported types are {WSI_SUPPORTED_FILE_EXTENSIONS}."
             logger.warning(message)
             raise ValueError(message)
         try:

aignostics-0.2.36/src/aignostics/bucket/_settings.py

@@ -1,53 +0,0 @@
-"""Settings of the bucket module."""
-
-from enum import StrEnum
-from typing import Annotated
-
-from pydantic import Field, SecretStr
-from pydantic_settings import SettingsConfigDict
-
-from ..utils import OpaqueSettings, __env_file__, __project_name__  # noqa: TID252
-
-
-class BucketProtocol(StrEnum):
-    GS = "gs"
-    S3 = "s3"
-
-
-class Settings(OpaqueSettings):
-    """Settings."""
-
-    model_config = SettingsConfigDict(
-        env_prefix=f"{__project_name__.upper()}_BUCKET_",
-        extra="ignore",
-        env_file=__env_file__,
-        env_file_encoding="utf-8",
-    )
-
-    protocol: Annotated[
-        BucketProtocol,
-        Field(
-            description=("Protocol to access the cloud bucket, default is gs"),
-            default="gs",
-        ),
-    ]
-
-    name: Annotated[
-        str,
-        Field(description=("Name of the cloud bucket")),
-    ]
-
-    region_name: Annotated[
-        str,
-        Field(description=("Region of the cloud bucket"), default="EUROPE-WEST3"),
-    ]
-
-    hmac_access_key_id: Annotated[
-        SecretStr,
-        Field(description=("HMAC access key ID of the cloud bucket")),
-    ]
-
-    hmac_secret_access_key: Annotated[
-        SecretStr,
-        Field(description=("HMAC secret access key of the cloud bucket")),
-    ]