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

fractal_server-2.18.3a0/LICENSE

@@ -0,0 +1,29 @@
+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-2.18.3 → fractal_server-2.18.3a0}/PKG-INFO

@@ -1,29 +1,35 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.3
+Version: 2.18.3a0
 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
-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
+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
 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
@@ -57,3 +63,4 @@ 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-2.18.3a0/fractal_server/__init__.py

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

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

@@ -17,7 +17,6 @@ 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
@@ -38,7 +37,6 @@ 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,
@@ -86,13 +84,6 @@ 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-2.18.3 → fractal_server-2.18.3a0}/fractal_server/app/routes/auth/oauth.py

@@ -3,8 +3,6 @@ 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
@@ -15,29 +13,6 @@ 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(),
@@ -54,11 +29,10 @@ def _create_client_google(cfg: OAuthSettings) -> GoogleOAuth2:
 
 def _create_client_oidc(cfg: OAuthSettings) -> OpenID:
     try:
-        open_id = FractalOpenID(
+        open_id = OpenID(
             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-2.18.3 → fractal_server-2.18.3a0}/fractal_server/config/_oauth.py

@@ -28,11 +28,6 @@ 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)
@@ -48,7 +43,6 @@ 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/data_migrations/README.md

@@ -0,0 +1,6 @@
+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.

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

@@ -6,18 +6,6 @@ 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:
     """
@@ -58,7 +46,6 @@ 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-2.18.3 → fractal_server-2.18.3a0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.18.3"
+version = "2.18.3a0"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -37,51 +37,54 @@ changelog = "https://github.com/fractal-analytics-platform/fractal-server/blob/m
 [project.scripts]
 fractalctl = "fractal_server.__main__:run"
 
-[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"
-]
-
-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"
-]
-
-
 [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"]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
 
+[tool.poetry]
+requires-poetry = ">=2.0"
+packages = [
+    {include="fractal_server"}
+]
+exclude = [
+    "fractal_server/data_migrations/old",
+    "fractal_server/json_schemas",
+    "fractal_server/migrations/script.py.mako",
+]
 
+[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"
 
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
@@ -92,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.18.3"
+current_version = "2.18.3a0"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.18.3/fractal_server/__init__.py

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