fractal-server 2.18.3a0__py3-none-any.whl → 2.18.3a2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.18.3a0"
+__VERSION__ = "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/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/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/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.dist-info → fractal_server-2.18.3a2.dist-info}/METADATA

@@ -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-2.18.3a0.dist-info → fractal_server-2.18.3a2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=dEhdl9EtyqOPj5CiMlEv2OAVTTkU6dc3GeZ002YM4p8,25
+fractal_server/__init__.py,sha256=Rzw6TOYnnUFPK6rCXCcX9YI2QCykuOzwafCf3c0dUAk,25
 fractal_server/__main__.py,sha256=QeKoAgqoiozLJDa8kSVe-Aso1WWgrk1yLUYWS8RxZVM,11405
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -25,7 +25,7 @@ fractal_server/app/routes/admin/v2/__init__.py,sha256=VF4wg09fvz6gVgIFe-r7LoCU9t
 fractal_server/app/routes/admin/v2/_aux_functions.py,sha256=fqA5sUCFuD2iVANQt2WUUfVOEVz5egQA7inzUKYGCw0,1684
 fractal_server/app/routes/admin/v2/accounting.py,sha256=xNXyQYpa0K0bOjd5WNVKfU6zBhvT2-Xgrx2F4vdS9C0,3512
 fractal_server/app/routes/admin/v2/impersonate.py,sha256=ictDjuvBr3iLv3YtwkVRMNQRq5qtPAeAXbbC7STSsEg,1125
-fractal_server/app/routes/admin/v2/job.py,sha256=nishNH472KMmz9Au8_w6xOOAXEN3tqVSUX1IraO1Hr0,10430
+fractal_server/app/routes/admin/v2/job.py,sha256=UaUwD5vsIPslc6KrbUPs2OsGcJOsLd7UeE2a5GRZnD0,10837
 fractal_server/app/routes/admin/v2/profile.py,sha256=DwLlA9K3hkl9BqzyifIDiaWeHOM_N_17kqB5CSJOhSI,3165
 fractal_server/app/routes/admin/v2/resource.py,sha256=c2z6b_D_W6_dqVnxNF8F8OdlI5Z4asex8Zgfwzjbi2Q,6330
 fractal_server/app/routes/admin/v2/sharing.py,sha256=x7RtbDPapyENEU_s4-glPoEeEOxxj2VBgduVQ1V7wkE,3796
@@ -65,7 +65,7 @@ fractal_server/app/routes/auth/_aux_auth.py,sha256=gKdYTWUzxcU44Iep787zReWwdAs4k
 fractal_server/app/routes/auth/current_user.py,sha256=uDWttWo9isG69Jv1EGnnr2Ki5ZGd0D76jgjVDQMkn8c,3251
 fractal_server/app/routes/auth/group.py,sha256=uR98vdQHH-7BFl-Czj85ESPxT2yQymy4qtagaMrnUPU,6491
 fractal_server/app/routes/auth/login.py,sha256=buVa5Y8T0cd_SW1CqC-zMv-3SfPxGJknf7MYlUyKOl0,567
-fractal_server/app/routes/auth/oauth.py,sha256=NxrwOWBGPe7hLPEnD66nfWPGMWzDM80LIrwtmONVw-4,2731
+fractal_server/app/routes/auth/oauth.py,sha256=ocQjyy6OfuEORDYVVzQSgcisSwL-YLZxacq7FuzwJF4,3673
 fractal_server/app/routes/auth/register.py,sha256=IiUJhgY0ZrTs0RlBRRjoTv4wF5Gb3eXTInFV-dXkpsE,615
 fractal_server/app/routes/auth/router.py,sha256=Zip_fw9qJWtoXWjluznschyrCKb2n_rf3xWarSXMkgI,692
 fractal_server/app/routes/auth/users.py,sha256=5BagdH1dz-ZoXdvTgIo9QWBNFPW3p1pIZfY9BBu4eds,7397
@@ -103,9 +103,8 @@ fractal_server/config/_data.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 fractal_server/config/_database.py,sha256=0_FvboMkQEKKRxvr9uFdp98oiQwMTFbdCW3loTZNSY0,1846
 fractal_server/config/_email.py,sha256=vMwLHN9-beYp_-up-WkTpeyNUZk4EHwt3N2l6-PYnx4,4364
 fractal_server/config/_main.py,sha256=6splUmAPRD1J9HXkeZ-Vqif7Nw4ljJXIugpvRrcwPeI,2476
-fractal_server/config/_oauth.py,sha256=UTmlFppDZcOQhr3RvkiG5XMqvr54XRAQ_Y-iR0V8N-8,2024
+fractal_server/config/_oauth.py,sha256=kktD0MEZ_NV4QOK6RmOXDK1x8RCrFEkqC6WLY-DzRIY,2390
 fractal_server/config/_settings_config.py,sha256=tsyXQOnn9QKCFJD6hRo_dJXlQQyl70DbqgHMJoZ1xnY,144
-fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/exceptions.py,sha256=l6aZDk_6u_9PwDaQSoIFdI40ekpzqOJaxjx5rhW-HVI,141
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -183,7 +182,7 @@ fractal_server/runner/config/slurm_mem_to_MB.py,sha256=6KmrIC-NymQjb9-bIQjNYQx6m
 fractal_server/runner/exceptions.py,sha256=N8DLn7tuV8zMSdr8xdJN0aIdytPveSCeQ1Y5IoxXW-8,1778
 fractal_server/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/runner/executors/base_runner.py,sha256=h8uE5gr6zFEwpjhasJDc-eNTMIw3RwmQQLYD6U5w8E0,7116
-fractal_server/runner/executors/call_command_wrapper.py,sha256=n6c9haKyIudBlz9-d3GQb19rewBR54qLG8jlrma6okk,1415
+fractal_server/runner/executors/call_command_wrapper.py,sha256=yLFfwkYdfGAp6TSLx0omymW3IxaDNdxV-DDk-3oqNx0,1828
 fractal_server/runner/executors/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/runner/executors/local/get_local_config.py,sha256=oI32JawlG3ixYdjxJDRfT0sreEnoHekhiAHzlejl2aM,1694
 fractal_server/runner/executors/local/runner.py,sha256=0s0u5ONasXdsvS2WD5zxksQgved_XGXtaxCEiBJoAlM,12297
@@ -268,8 +267,7 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=zt
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=-rjg8QTXQcKweXjn0NcmETFs1_uM9PGnbl0Q7c4ERPM,2181
 fractal_server/zip_tools.py,sha256=Uhn-ax4_9g1PJ32BdyaX30hFpAeVOv2tZYTUK-zVn1E,5719
-fractal_server-2.18.3a0.dist-info/METADATA,sha256=gvMqw6he1Mg5FoCHcVzHL1i3ywNWUhVfVz_Lqa_XF5I,4277
-fractal_server-2.18.3a0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fractal_server-2.18.3a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.18.3a0.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.18.3a0.dist-info/RECORD,,
+fractal_server-2.18.3a2.dist-info/WHEEL,sha256=ZyFSCYkV2BrxH6-HRVRg3R9Fo7MALzer9KiPYqNxSbo,79
+fractal_server-2.18.3a2.dist-info/entry_points.txt,sha256=3TpdcjmETRYWJxFyAh3z-9955EWua9jdkSnBwxES1uE,60
+fractal_server-2.18.3a2.dist-info/METADATA,sha256=gaWGl_yrUyqMMTGt-z2Aw53MAlLURTYVObPvmskNmY8,4163
+fractal_server-2.18.3a2.dist-info/RECORD,,

fractal_server-2.18.3a2.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.9.18
+Root-Is-Purelib: true
+Tag: py3-none-any

fractal_server-2.18.3a2.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+fractalctl = fractal_server.__main__:run
+

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.

fractal_server-2.18.3a0.dist-info/WHEEL

@@ -1,4 +0,0 @@
-Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
-Root-Is-Purelib: true
-Tag: py3-none-any

fractal_server-2.18.3a0.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-fractalctl=fractal_server.__main__:run
-

fractal_server-2.18.3a0.dist-info/licenses/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.