fractal-server 2.18.3a0__tar.gz → 2.18.3a2__tar.gz

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/PKG-INFO

@@ -1,35 +1,29 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.3a0
+Version: 2.18.3a2
 Summary: Backend component of the Fractal analytics platform
+Author: Tommaso Comparin, Marco Franzon, Yuri Chiucconi, Jacopo Nespolo
+Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>, Marco Franzon <marco.franzon@exact-lab.it>, Yuri Chiucconi <yuri.chiucconi@exact-lab.it>, Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
 License-Expression: BSD-3-Clause
-License-File: LICENSE
-Author: Tommaso Comparin
-Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.11,<3.15
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
-Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: fabric (>=3.2.2,<3.3.0)
-Requires-Dist: fastapi (>=0.120.0,<0.121.0)
-Requires-Dist: fastapi-users[oauth] (>=15,<16)
-Requires-Dist: gunicorn (>=23.0,<24.0)
-Requires-Dist: packaging (>=25.0.0,<26.0.0)
-Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
-Requires-Dist: pydantic (>=2.12.0,<2.13.0)
-Requires-Dist: pydantic-settings (==2.11.0)
-Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (==0.0.27)
-Requires-Dist: tomli_w (>=1.2.0,<1.3.0)
-Requires-Dist: uvicorn (>=0.38.0,<0.39.0)
-Requires-Dist: uvicorn-worker (==0.4.0)
-Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server
-Project-URL: Homepage, https://github.com/fractal-analytics-platform/fractal-server
-Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-server
+Requires-Dist: fastapi>=0.120.0,<0.121.0
+Requires-Dist: sqlmodel==0.0.27
+Requires-Dist: sqlalchemy[asyncio]>=2.0.23,<2.1
+Requires-Dist: fastapi-users[oauth]>=15,<16
+Requires-Dist: alembic>=1.13.1,<2.0.0
+Requires-Dist: uvicorn>=0.38.0,<0.39.0
+Requires-Dist: uvicorn-worker==0.4.0
+Requires-Dist: pydantic>=2.12.0,<2.13.0
+Requires-Dist: pydantic-settings==2.11.0
+Requires-Dist: packaging>=25.0.0,<26.0.0
+Requires-Dist: fabric>=3.2.2,<3.3.0
+Requires-Dist: gunicorn>=23.0,<24.0
+Requires-Dist: psycopg[binary]>=3.1.0,<4.0.0
+Requires-Dist: tomli-w>=1.2.0,<1.3.0
+Requires-Python: >=3.11, <3.15
 Project-URL: changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
+Project-URL: documentation, https://fractal-analytics-platform.github.io/fractal-server
+Project-URL: homepage, https://github.com/fractal-analytics-platform/fractal-server
+Project-URL: repository, https://github.com/fractal-analytics-platform/fractal-server
 Description-Content-Type: text/markdown
 
 # Fractal Server
@@ -63,4 +57,3 @@ See https://fractal-analytics-platform.github.io/fractal-server.
 Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
 
 Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
-

fractal_server-2.18.3a2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.18.3a2"

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/fractal_server/app/routes/admin/v2/job.py

@@ -17,6 +17,7 @@ from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import HistoryRun
 from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import JobV2
+from fractal_server.app.models.v2.project import ProjectV2
 from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.app.routes.aux._runner import _check_shutdown_is_supported
@@ -37,6 +38,7 @@ router = APIRouter()
 @router.get("/", response_model=PaginationResponse[JobRead])
 async def view_job(
     id: int | None = None,
+    resource_id: int | None = None,
     user_id: int | None = None,
     project_id: int | None = None,
     dataset_id: int | None = None,
@@ -84,6 +86,13 @@ async def view_job(
     if id is not None:
         stm = stm.where(JobV2.id == id)
         stm_count = stm_count.where(JobV2.id == id)
+    if resource_id is not None:
+        stm = stm.join(ProjectV2, ProjectV2.id == JobV2.project_id).where(
+            ProjectV2.resource_id == resource_id
+        )
+        stm_count = stm_count.join(
+            ProjectV2, ProjectV2.id == JobV2.project_id
+        ).where(ProjectV2.resource_id == resource_id)
     if user_id is not None:
         stm = (
             stm.join(

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/fractal_server/app/routes/auth/oauth.py

@@ -3,6 +3,8 @@ from httpx_oauth.clients.github import GitHubOAuth2
 from httpx_oauth.clients.google import GoogleOAuth2
 from httpx_oauth.clients.openid import OpenID
 from httpx_oauth.clients.openid import OpenIDConfigurationError
+from httpx_oauth.exceptions import GetIdEmailError
+from httpx_oauth.exceptions import GetProfileError
 
 from fractal_server.config import OAuthSettings
 from fractal_server.config import get_oauth_settings
@@ -13,6 +15,29 @@ from . import cookie_backend
 from . import fastapi_users
 
 
+class FractalOpenID(OpenID):
+    """
+    Subclass of `httpx_oauth.clients.openid.OpenID` with customizable name for
+    the `"email"` claim.
+    """
+
+    def __init__(self, *, email_claim: str, **kwargs):
+        super().__init__(**kwargs)
+        self.email_claim = email_claim
+
+    # TODO-requires-py312: add `@override` decorator
+    async def get_id_email(self, token: str) -> tuple[str, str | None]:
+        """
+        Identical to the parent-class method (httpx-oauth version 0.16.1),
+        apart from making `"email"` configurable.
+        """
+        try:
+            profile = await self.get_profile(token)
+        except GetProfileError as e:
+            raise GetIdEmailError(response=e.response) from e
+        return str(profile["sub"]), profile.get(self.email_claim)
+
+
 def _create_client_github(cfg: OAuthSettings) -> GitHubOAuth2:
     return GitHubOAuth2(
         client_id=cfg.OAUTH_CLIENT_ID.get_secret_value(),
@@ -29,10 +54,11 @@ def _create_client_google(cfg: OAuthSettings) -> GoogleOAuth2:
 
 def _create_client_oidc(cfg: OAuthSettings) -> OpenID:
     try:
-        open_id = OpenID(
+        open_id = FractalOpenID(
             client_id=cfg.OAUTH_CLIENT_ID.get_secret_value(),
             client_secret=cfg.OAUTH_CLIENT_SECRET.get_secret_value(),
             openid_configuration_endpoint=cfg.OAUTH_OIDC_CONFIG_ENDPOINT.get_secret_value(),  # noqa
+            email_claim=cfg.OAUTH_EMAIL_CLAIM,
         )
     except OpenIDConfigurationError as e:
         OAUTH_OIDC_CONFIG_ENDPOINT = (

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/fractal_server/config/_oauth.py

@@ -28,6 +28,11 @@ class OAuthSettings(BaseSettings):
             String to be used as `redirect_url` argument in
             `fastapi_users.get_oauth_router`, and then in
             `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`.
+        OAUTH_EMAIL_CLAIM:
+            Name of the OIDC claim with the user's email address. This is
+            `"email"` by default, but can be customized (e.g. to `"mail"`) to
+            fit with the response from the userinfo endpoint - see
+            https://openid.net/specs/openid-connect-core-1_0.html#UserInfoResponse
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -43,6 +48,7 @@ class OAuthSettings(BaseSettings):
     OAUTH_CLIENT_SECRET: SecretStr | None = None
     OAUTH_OIDC_CONFIG_ENDPOINT: SecretStr | None = None
     OAUTH_REDIRECT_URL: str | None = None
+    OAUTH_EMAIL_CLAIM: str = "email"
 
     @model_validator(mode="after")
     def check_configuration(self: Self) -> Self:

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/fractal_server/runner/executors/call_command_wrapper.py

@@ -6,6 +6,18 @@ import subprocess  # nosec
 from fractal_server.runner.exceptions import TaskExecutionError
 from fractal_server.string_tools import validate_cmd
 
+MAX_LEN_STDERR = 100_000
+
+
+def placeholder_if_too_long(stderr: str) -> str:
+    """Returns a placeholder if the string is too long"""
+    if len(stderr) > MAX_LEN_STDERR:
+        return (
+            f"Cannot display stderr of length {len(stderr)}. You can find the "
+            "detailed logs by downloading the job-log folder."
+        )
+    return stderr
+
 
 def call_command_wrapper(*, cmd: str, log_path: str) -> None:
     """
@@ -46,6 +58,7 @@ def call_command_wrapper(*, cmd: str, log_path: str) -> None:
         if os.path.isfile(log_path):
             with open(log_path) as fp_stderr:
                 stderr = fp_stderr.read()
+            stderr = placeholder_if_too_long(stderr)
         raise TaskExecutionError(
             f"Task failed with returncode={result.returncode}.\n"
             f"STDERR: {stderr}"

{fractal_server-2.18.3a0 → fractal_server-2.18.3a2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.18.3a0"
+version = "2.18.3a2"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -37,54 +37,51 @@ changelog = "https://github.com/fractal-analytics-platform/fractal-server/blob/m
 [project.scripts]
 fractalctl = "fractal_server.__main__:run"
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.poetry]
-requires-poetry = ">=2.0"
-packages = [
-    {include="fractal_server"}
+[dependency-groups]
+dev = [
+    "asgi-lifespan >2.0.0,<3.0.0",
+    "pytest>=8.4.0,<8.5.0",
+    "pytest-env >=1.1.5,<1.2.0",
+    "httpx >=0.28.0,<0.29.0",
+    "devtools ==0.12",
+    "pytest-asyncio >= 1.2.0,<1.3.0",
+    "bumpver >=2024.0",
+    "pre-commit ==4.2.0",
+    "coverage[toml]>=7.12.0,<7.13.0",
+    "pytest-docker >=3.2.0,<3.3.0",
+    "mypy >= 1.9",
+    "pytest-subprocess >=1.5.0,<1.6.0",
+    "a2wsgi >=1.10.0,<1.11.0",
+    "jinja2 >=3.1.3,<3.1.4",
+    "pyyaml>=6.0.0"
 ]
-exclude = [
-    "fractal_server/data_migrations/old",
-    "fractal_server/json_schemas",
-    "fractal_server/migrations/script.py.mako",
+
+docs = [
+    "mkdocs==1.6.1",
+    "mkdocstrings[python]==0.30.1",
+    "mkdocs-material==9.7.0",
+    "mkdocs-gen-files==0.5.0",
+    "mkdocs-literate-nav==0.6.2",
+    "mkdocs-section-index==0.3.10",
+    "mkdocs-include-markdown-plugin==7.2.0",
+    "mkdocs-render-swagger-plugin==0.1.2",
+    "pyyaml>=6.0.0",
+    "click == 8.2.1"
 ]
 
-[tool.poetry.group.dev]
-optional = true
-
-[tool.poetry.group.dev.dependencies]
-asgi-lifespan = "^2"
-pytest = "8.4.*"
-pytest-env = ">=1.1.5,<1.2.0"
-httpx = ">=0.28.0,<0.29.0"
-devtools = "^0.12"
-pytest-asyncio = "1.2.*"
-bumpver = ">=2024.0"
-pre-commit = "4.2.0"
-coverage = {extras = ["toml"], version = "7.5.*"}
-pytest-docker = {version = "3.2.*"}
-mypy = "^1.9"
-pytest-subprocess = "1.5.*"
-a2wsgi = "^1.10.0"
-jinja2 = "^3.1.3"
-pyyaml=">=6.0.0"
-
-[tool.poetry.group.docs]
-optional = true
-
-[tool.poetry.group.docs.dependencies]
-mkdocs="1.6.1"
-mkdocstrings = { extras = ["python"], version = "0.30.1" }
-mkdocs-material="9.7.0"
-mkdocs-gen-files="0.5.0"
-mkdocs-literate-nav="0.6.2"
-mkdocs-section-index="0.3.10"
-mkdocs-render-swagger-plugin="0.1.2"
-pyyaml=">=6.0.0"
-click = "8.2.1"
+
+[build-system]
+requires = ["uv_build>=0.9.18,<0.10.0"]
+build-backend = "uv_build"
+
+# See https://docs.astral.sh/uv/concepts/build-backend/#file-inclusion-and-exclusion
+[tool.uv.build-backend]
+module-name = "fractal_server"
+module-root = ""
+source-exclude = ["tmp*", "fractal_server/data_migrations/old", "fractal_server/data_migrations/README.md", "fractal_server/json_schemas", "fractal_server/migrations/script.py.mako"]
+wheel-exclude = ["tmp*", "fractal_server/data_migrations/old", "fractal_server/data_migrations/README.md", "fractal_server/json_schemas", "fractal_server/migrations/script.py.mako"]
+
+
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
@@ -95,7 +92,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.18.3a0"
+current_version = "2.18.3a2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.18.3a0/LICENSE

@@ -1,29 +0,0 @@
-BSD 3-Clause License
-
-Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and University of Zurich
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-* Neither the name of the copyright holder nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fractal_server-2.18.3a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.18.3a0"

fractal_server-2.18.3a0/fractal_server/data_migrations/README.md

@@ -1,6 +0,0 @@
-Modules in this folder are consumed from the `update_db_data` function in
-`fractal_server/__main__.py`. They must expose a `fix_db` function, and they
-must be named according to `_slugify_version` (e.g. both for versions `1.4.3`
-and `1.4.3a0` the module name is  `1_4_3.py`).
-Modules corresponding to old versions should be moved to the `old` subfolder,
-which is not included in the package wheel.