From 1453d617ede8507cacfb9c93f8f4f9852e3c1c20 Mon Sep 17 00:00:00 2001
From: guerler <aysam.guerler@gmail.com>
Date: Fri, 7 Aug 2026 07:30:42 +0300
Subject: [PATCH 1/2] Raise a clear fetch error when async tool-request URL
 input materialization fails

---
 lib/galaxy/managers/jobs.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/managers/jobs.py b/lib/galaxy/managers/jobs.py
index ce9b0c45c5d..1e28b8aeb92 100644
--- a/lib/galaxy/managers/jobs.py
+++ b/lib/galaxy/managers/jobs.py
@@ -2267,7 +2267,11 @@ class JobSubmitter:
                 # API dataset materialization is immutable and produces new datasets
                 # here we just created the datasets - lets just materialize them in place
                 # and avoid extra and confusing input copies
-                self.hda_manager.materialize(materialize_request, sa_session(), in_place=True)
+                materialized = self.hda_manager.materialize(materialize_request, sa_session(), in_place=True)
+                if not materialized:
+                    raise RequestParameterInvalidException(
+                        f"Failed to fetch dataset from '{to_materialize.request.url}'"
+                    )
             if request.data_manager_mode:
                 tool_request.request["__data_manager_mode"] = request.data_manager_mode
             credentials_context = (

From ee7210f97ae68e3aae738f36da870e255fd19d64 Mon Sep 17 00:00:00 2001
From: galaxybot <galaxybot@users.noreply.github.com>
Date: Sat, 8 Aug 2026 03:33:29 +0000
Subject: [PATCH 2/2] Update Python dependencies

by running `make update-dependencies`.
---
 lib/galaxy/dependencies/dev-requirements.txt  | 40 +++++-----
 .../dependencies/pinned-lint-requirements.txt |  2 +-
 .../dependencies/pinned-requirements.txt      | 77 ++++++++++---------
 .../dependencies/pinned-test-requirements.txt | 40 +++++-----
 .../pinned-typecheck-requirements.txt         | 14 ++--
 5 files changed, 87 insertions(+), 86 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 7a5c97c3f85..427c2ed2b13 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -7,7 +7,7 @@ aiosignal==1.4.0
 alabaster==1.0.0
 annotated-types==0.8.0
 ase==3.29.0
-ast-serialize==0.6.0
+ast-serialize==0.8.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
 axe-selenium-python==2.1.6 ; python_full_version < '3.12'
@@ -16,23 +16,23 @@ babel==2.18.0
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 black==26.5.1
-boto3==1.43.46
-botocore==1.43.46
+boto3==1.43.56
+botocore==1.43.56
 build==1.5.0
 cachecontrol==0.14.4
-cachetools==7.1.6
+cachetools==7.1.7
 cattrs==26.1.0
 certifi==2026.7.22
-cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
+cffi==2.1.1 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 click==8.4.2
-cloudbridge==4.3.0
+cloudbridge==4.3.1
 codespell==2.4.3
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 colorlog==6.12.0
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.15.2
+coverage==7.15.4
 cryptography==50.0.0
 cwltest==2.6.20251216093331
 cycler==0.12.1
@@ -52,17 +52,17 @@ frozenlist==1.8.0
 fsspec==2026.7.0
 galaxy-release-util==0.4.2
 gcsfs==2026.7.0
-google-api-core==2.33.0
-google-auth==2.56.2
+google-api-core==2.34.0
+google-auth==2.56.3
 google-auth-oauthlib==1.4.0
-google-cloud-core==2.6.0
-google-cloud-storage==3.13.0
-google-cloud-storage-control==1.12.0
+google-cloud-core==2.6.1
+google-cloud-storage==3.13.1
+google-cloud-storage-control==1.13.0
 google-crc32c==1.8.0
-google-resumable-media==2.10.0
-googleapis-common-protos==1.75.0
+google-resumable-media==2.10.1
+googleapis-common-protos==1.75.1
 greenlet==3.5.4
-grpc-google-iam-v1==0.14.4
+grpc-google-iam-v1==0.14.5
 grpcio==1.83.0
 grpcio-status==1.83.0
 h11==0.16.0
@@ -89,7 +89,7 @@ jsonschema-specifications==2025.9.1
 junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.5.0
-librt==0.13.0 ; platform_python_implementation != 'PyPy'
+librt==0.15.0 ; platform_python_implementation != 'PyPy'
 lxml==6.1.1
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.2.0 ; python_full_version >= '3.11'
@@ -116,19 +116,19 @@ oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==7.6.2
-packaging==26.2
+packaging==26.3
 pathspec==1.1.1
 pfzy==0.3.4
 pillow==12.3.0
 pkce==1.0.3
-platformdirs==4.11.0
+platformdirs==4.11.1
 playwright==1.62.0
 pluggy==1.6.0
 port-for==1.0.0
 prettytable==3.18.0
 prompt-toolkit==3.0.53
 propcache==0.5.2
-proto-plus==1.28.2
+proto-plus==1.28.3
 protobuf==7.35.1
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.4
@@ -214,7 +214,7 @@ tenacity==9.1.4
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==12.3.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
-tinydb==4.8.2
+tinydb==4.9.0
 toml==0.10.2
 tomli==2.4.1 ; python_full_version <= '3.11'
 total-perspective-vortex==3.2.1
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index 698e6005a9b..c5979de5901 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.16.1
+ruff==0.16.2
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 86fa40b4a50..6458b3b4cb5 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -2,24 +2,24 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-aiobotocore==3.8.0
+aiobotocore==3.9.0
 aiofile==3.9.0 ; python_full_version < '3.11'
-aiofile==3.11.1 ; python_full_version >= '3.11'
+aiofile==3.12.3 ; python_full_version >= '3.11'
 aiofiles==25.1.0
 aiohappyeyeballs==2.7.1
 aiohttp==3.14.3
 aioitertools==0.13.0
 aiosignal==1.4.0
-alembic==1.18.5
+alembic==1.19.0
 amqp==5.3.1
 annotated-doc==0.0.5
 annotated-types==0.8.0
-anthropic==0.120.2
+anthropic==0.121.0
 anyio==4.14.2
 apispec==6.10.0
 appdirs==1.4.4
 arcp==0.2.1
-argcomplete==3.7.0
+argcomplete==3.7.2
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
 authlib==1.7.2
@@ -37,14 +37,15 @@ bioblend==1.9.0
 bleach==6.4.0
 boltons==26.1.0
 boto==2.49.0
-botocore==1.43.46
+botocore==1.43.56
 bx-python==0.14.0
 cachecontrol==0.14.4
-cachetools==7.1.6
-caio==0.9.25
+cachetools==7.1.7
+caio==0.9.25 ; python_full_version < '3.11'
+caio==0.12.2 ; python_full_version >= '3.11'
 celery==5.6.3
 certifi==2026.7.22
-cffi==2.1.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
+cffi==2.1.1 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 circus==0.19.0
 click==8.4.2
@@ -60,7 +61,7 @@ ct3==3.4.0.post5
 cwl-upgrader==1.2.15
 cwl-utils==0.42
 cwltool==3.2.20260720092025
-cyclopts==4.22.3
+cyclopts==4.22.5
 defusedxml==0.7.1
 deprecated==1.3.1
 dictobj==0.4
@@ -77,20 +78,20 @@ et-xmlfile==2.0.0
 exceptiongroup==1.3.1
 executing==2.2.1
 fastapi==0.141.1
-fastmcp==3.4.5
-fastmcp-slim==3.4.5
+fastmcp==3.4.6
+fastmcp-slim==3.4.6
 filelock==3.32.2
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
 fsspec==2026.7.0
 future==1.0.0
-genai-prices==0.1.0
-google-api-core==2.33.0
-google-auth==2.56.2
-google-cloud-batch==0.22.1
-google-genai==2.16.0
-googleapis-common-protos==1.75.0
+genai-prices==0.1.1
+google-api-core==2.34.0
+google-auth==2.56.3
+google-cloud-batch==0.22.2
+google-genai==2.17.0
+googleapis-common-protos==1.75.1
 gravity==1.2.3
 greenlet==3.5.4 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
 griffelib==2.1.0
@@ -132,10 +133,10 @@ kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==5.8.0
-logfire==4.39.0
-logfire-api==4.39.0
+logfire==4.40.0
+logfire-api==4.40.0
 lxml==6.1.1
-mako==1.3.12
+mako==1.4.1
 markdown==3.10.3
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.2.0 ; python_full_version >= '3.11'
@@ -158,7 +159,7 @@ numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.6 ; python_full_version == '3.11.*'
 numpy==2.5.1 ; python_full_version >= '3.12'
 oauthlib==3.3.1
-openai==2.52.0
+openai==2.53.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.44.0
@@ -171,17 +172,17 @@ opentelemetry-sdk==1.44.0
 opentelemetry-semantic-conventions==0.65b0
 opentelemetry-util-http==0.65b0
 orjson==3.11.9
-packaging==26.2
+packaging==26.3
 paramiko==5.0.0
 parsley==1.3
 paste==3.10.1
 pathable==0.6.0
 pebble==5.2.0
 pillow==12.3.0
-platformdirs==4.11.0
+platformdirs==4.11.1
 prompt-toolkit==3.0.53
 propcache==0.5.2
-proto-plus==1.28.2
+proto-plus==1.28.3
 protobuf==7.35.1
 prov==1.5.1
 psutil==7.2.2
@@ -193,13 +194,13 @@ pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
 pydantic==2.13.4
-pydantic-ai==2.22.0
-pydantic-ai-slim==2.22.0
+pydantic-ai==2.26.0
+pydantic-ai-slim==2.26.0
 pydantic-core==2.46.4
-pydantic-evals==2.22.0
+pydantic-evals==2.26.0
 pydantic-extra-types==2.11.1
-pydantic-graph==2.22.0
-pydantic-settings==2.14.2
+pydantic-graph==2.26.0
+pydantic-settings==2.15.0
 pydantic-tes==0.4.0
 pydicom==3.0.2
 pydot==4.0.1
@@ -249,13 +250,13 @@ setuptools==81.0.0
 six==1.17.0
 slowapi==0.1.10
 sniffio==1.3.1
-social-auth-core==5.0.2
+social-auth-core==5.1.0
 sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.51
 sqlparse==0.5.5
-sse-starlette==3.4.6
-starlette==1.3.1
+sse-starlette==3.4.8
+starlette==1.4.1
 starlette-context==0.5.1
 supervisor==4.3.0
 svgwrite==1.4.3
@@ -265,13 +266,13 @@ tifffile==2025.5.10 ; python_full_version < '3.11'
 tifffile==2026.3.3 ; python_full_version == '3.11.*'
 tifffile==2026.7.31 ; python_full_version >= '3.12'
 tiktoken==0.13.0
-tinydb==4.8.2
+tinydb==4.9.0
 tomli==2.4.1 ; python_full_version < '3.11'
-tornado==6.5.7
+tornado==6.5.8
 tqdm==4.70.0
 truststore==0.10.4
 tuspy==1.1.0
-tuspyserver==4.2.12
+tuspyserver==4.2.13
 typing-extensions==4.16.0
 typing-inspection==0.4.2
 tzdata==2026.3
@@ -279,13 +280,13 @@ tzlocal==5.4.4
 ubiquerg==0.9.3
 uncalled-for==0.3.2
 urllib3==2.7.0
-uvicorn==0.52.0
+uvicorn==0.52.1
 uvloop==0.22.1
 vine==5.1.0
 watchfiles==1.2.0
 wcwidth==0.8.2
 webencodings==0.5.1
-webob==1.8.10
+webob==1.8.11
 websockets==16.1.1
 whoosh==2.7.4
 wrapt==2.3.0
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index 62cc724d4cc..8ada9729294 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -6,27 +6,27 @@ aiohttp==3.14.3
 aiosignal==1.4.0
 annotated-types==0.8.0
 ase==3.29.0
-ast-serialize==0.6.0
+ast-serialize==0.8.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
 axe-selenium-python==2.1.6 ; python_full_version < '3.12'
 axe-selenium-python==3.0.0 ; python_full_version >= '3.12'
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
-boto3==1.43.46
-botocore==1.43.46
+boto3==1.43.56
+botocore==1.43.56
 cachecontrol==0.14.4
-cachetools==7.1.6
+cachetools==7.1.7
 cattrs==26.1.0
 certifi==2026.7.22
-cffi==2.1.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
+cffi==2.1.1 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.9
 click==8.4.2
-cloudbridge==4.3.0
+cloudbridge==4.3.1
 colorama==0.4.6 ; sys_platform == 'win32'
 colorlog==6.12.0
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.15.2
+coverage==7.15.4
 cryptography==50.0.0
 cwltest==2.6.20251216093331
 cycler==0.12.1
@@ -41,17 +41,17 @@ fonttools==4.63.0
 frozenlist==1.8.0
 fsspec==2026.7.0
 gcsfs==2026.7.0
-google-api-core==2.33.0
-google-auth==2.56.2
+google-api-core==2.34.0
+google-auth==2.56.3
 google-auth-oauthlib==1.4.0
-google-cloud-core==2.6.0
-google-cloud-storage==3.13.0
-google-cloud-storage-control==1.12.0
+google-cloud-core==2.6.1
+google-cloud-storage==3.13.1
+google-cloud-storage-control==1.13.0
 google-crc32c==1.8.0
-google-resumable-media==2.10.0
-googleapis-common-protos==1.75.0
+google-resumable-media==2.10.1
+googleapis-common-protos==1.75.1
 greenlet==3.5.4
-grpc-google-iam-v1==0.14.4
+grpc-google-iam-v1==0.14.5
 grpcio==1.83.0
 grpcio-status==1.83.0
 h11==0.16.0
@@ -70,7 +70,7 @@ jsonschema==4.26.0
 jsonschema-specifications==2025.9.1
 junit-xml==1.9
 kiwisolver==1.5.0
-librt==0.13.0 ; platform_python_implementation != 'PyPy'
+librt==0.15.0 ; platform_python_implementation != 'PyPy'
 lxml==6.1.1
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.2.0 ; python_full_version >= '3.11'
@@ -91,19 +91,19 @@ oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==7.6.2
-packaging==26.2
+packaging==26.3
 pathspec==1.1.1
 pfzy==0.3.4
 pillow==12.3.0
 pkce==1.0.3
-platformdirs==4.11.0
+platformdirs==4.11.1
 playwright==1.62.0
 pluggy==1.6.0
 port-for==1.0.0
 prettytable==3.18.0
 prompt-toolkit==3.0.53
 propcache==0.5.2
-proto-plus==1.28.2
+proto-plus==1.28.3
 protobuf==7.35.1
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.4
@@ -166,7 +166,7 @@ tenacity==9.1.4
 testfixtures==8.3.0 ; python_full_version < '3.11'
 testfixtures==12.3.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
-tinydb==4.8.2
+tinydb==4.9.0
 toml==0.10.2
 tomli==2.4.1 ; python_full_version <= '3.11'
 total-perspective-vortex==3.2.1
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index 7a8b7013957..8e22004df31 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,15 +1,15 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=typecheck
 annotated-types==0.8.0
-ast-serialize==0.6.0
-boto3-stubs==1.43.62
+ast-serialize==0.8.0
+boto3-stubs==1.43.67
 botocore-stubs==1.43.14
-cffi==2.1.0 ; platform_python_implementation != 'PyPy'
+cffi==2.1.1 ; platform_python_implementation != 'PyPy'
 cryptography==50.0.0
-librt==0.13.0 ; platform_python_implementation != 'PyPy'
+librt==0.15.0 ; platform_python_implementation != 'PyPy'
 lxml-stubs==0.5.1
 mypy==2.3.0
-mypy-boto3-s3==1.43.50
+mypy-boto3-s3==1.43.66
 mypy-extensions==1.1.0
 pathspec==1.1.1
 pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
@@ -26,12 +26,12 @@ types-docutils==0.22.3.20260724
 types-html5lib==1.1.11.20260518
 types-markdown==3.10.2.20260712
 types-paramiko==5.0.0.20260724
-types-python-dateutil==2.9.0.20260716
+types-python-dateutil==2.9.0.20260807
 types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20260724
 types-requests==2.33.0.20260712
 types-s3transfer==0.16.0
-types-setuptools==83.0.0.20260724
+types-setuptools==83.0.0.20260807
 types-six==1.17.0.20260724
 types-webencodings==0.5.0.20260408
 typing-extensions==4.16.0