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Merge branch 'release_25.1' into dev

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This commit is contained in:
Nicola Soranzo
2026-01-17 12:19:00 +00:00
parent a467c8d885 ec810e47a7
commit 1c211faff6
8 changed files with 66 additions and 10 deletions
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client/src/components/User/UserPreferencesForm.vue
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@@ -2,7 +2,6 @@
import { BAlert } from "bootstrap-vue";
import { storeToRefs } from "pinia";
import { computed, ref, watchEffect } from "vue";
import { useRouter } from "vue-router/composables";
import { isRegisteredUser } from "@/api";
import {
@@ -18,6 +17,7 @@ import LoadingSpan from "@/components/LoadingSpan.vue";
interface Props {
formId: UserPreferencesKey;
id?: string;
}
const props = defineProps<Props>();
@@ -29,13 +29,11 @@ const breadcrumbItems = computed(() => [{ title: "User Preferences", to: "/user"
const userStore = useUserStore();
const { currentUser } = storeToRefs(userStore);
const router = useRouter();
const loading = ref(true);
const model = computed<UserPreferencesModel | undefined>(() => {
if (router.currentRoute.params.id) {
return getUserPreferencesModel(router.currentRoute.params.id);
if (props.id) {
return getUserPreferencesModel(props.id);
} else if (isRegisteredUser(currentUser.value)) {
return getUserPreferencesModel(currentUser.value.id);
} else {
client/src/entry/analysis/router.js
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@@ -673,7 +673,10 @@ export function getRouter(Galaxy) {
{
path: "user/:formId",
component: UserPreferencesForm,
props: true,
props: (route) => ({
formId: route.params.formId,
id: route.query.id,
}),
redirect: redirectAnon(),
},
{
doc/schema_template.md
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@@ -34,6 +34,9 @@ $tag:tool|requirements://complexType[@name='Requirements']
$tag:tool|requirements|requirement://complexType[@name='Requirement']
$tag:tool|requirements|container://complexType[@name='Container']
$tag:tool|requirements|resource://complexType[@name='Resource']
$tag:tool|requirements|credentials://complexType[@name='Credentials']
$tag:tool|requirements|credentials|variable://complexType[@name='CredentialsVariable']
$tag:tool|requirements|credentials|secret://complexType[@name='CredentialsSecret']
$tag:tool|required_files://complexType[@name='RequiredFiles']
$tag:tool|required_files|include://complexType[@name='RequiredFileInclude']
$tag:tool|required_files|exclude://complexType[@name='RequiredFileExclude']
doc/source/admin/galaxy_options.rst
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@@ -2465,7 +2465,7 @@
:Description:
The BibTeX citation for Galaxy, to be displayed in the History
Tool Reference List
:Default: ``@article{Galaxy2024, title={The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update}, author={{The Galaxy Community}}, journal={Nucleic Acids Research}, year={2024}, doi={10.1093/nar/gkae410}, url={https://doi.org/10.1093/nar/gkae410}}``
:Default: ``@article{Galaxy2024, title="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update", author="{The Galaxy Community}", journal="Nucleic Acids Research", year="2024", doi="10.1093/nar/gkae410", url="https://doi.org/10.1093/nar/gkae410"}``
:Type: str
doc/source/admin/special_topics/vault.md
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@@ -111,4 +111,49 @@ In a file source the password could be used as follows:
password: ${user.user_vault.read_secret('preferences/ufz-nextcloud/password')}
```
This example assumes that the NextCloud username is identical to the Galaxy username. If this is not the case also the username could be a user preference that is stored in a vault.
This example assumes that the NextCloud username is identical to the Galaxy username. If this is not the case also the username could be a user preference that is stored in a vault.
## Tool Credentials System
Starting with Galaxy 25.1, tools can request credentials directly through a new tool credentials system. This system provides a secure, user-friendly way for tools to access external APIs and services using credentials stored in the vault.
### Overview
The tool credentials system allows tool developers to declaratively specify credential requirements in their tool XML, and Galaxy automatically:
- Presents a user-friendly credential management interface in the tool form
- Stores sensitive credentials (secrets) encrypted in the configured vault
- Injects credentials as environment variables when tools execute
- Provides centralized credential management in User Preferences
### How it works
1. **Tool Definition**: Tool developers add a `<credentials>` element to their tool XML defining required secrets (API keys, passwords) and optional variables (endpoints, usernames).
2. **User Experience**: When users run a tool requiring credentials, they see a credential management section in the tool form where they can provide or select existing credentials.
3. **Secure Storage**: All secrets are automatically stored encrypted in the vault (configured via `vault_config_file`).
4. **Automatic Injection**: When the tool runs, Galaxy injects the credentials as environment variables into the tool's execution environment.
### Vault Configuration Requirements
The tool credentials system requires a properly configured vault. Any of the supported vault backends (hashicorp, custos, or database) can be used. Ensure you have:
1. Set up your vault configuration as described in the sections above
2. Configured the `vault_config_file` setting in `galaxy.yml`
3. Tested that the vault is working properly
The tool credentials system will automatically use the configured vault to store all tool secrets.
### Admin Considerations
- **No additional configuration needed**: Unlike the older user preferences approach, the tool credentials system requires no admin configuration in `user_preferences_extra_conf.yml`. Tools can define their own credential requirements.
- **Vault is required**: The tool credentials system only works when a vault is configured. If no vault is configured, tools requesting credentials will not function properly.
- **User isolation**: Each user's credentials are isolated in the vault. Credentials cannot be shared between users.
- **Migration from user preferences**: If you previously configured tool credentials via `user_preferences_extra_conf.yml`, those can be gradually phased out as tools migrate to the new system. Both systems can coexist.
### API Access
The tool credentials system provides a REST API at `/api/users/{user_id}/credentials` for programmatic credential management. This can be useful for:
- Automating credential setup for multiple users
- Building custom credential management interfaces
- Integrating with external identity management systems
For more information on the tool credentials system from a developer perspective, see the [Tool XML Schema documentation](https://docs.galaxyproject.org/en/master/dev/schema.html#tool-requirements-credentials).
doc/source/releases/25.1_announce.rst
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@@ -97,6 +97,13 @@ Deprecation Notices
* `Galaxy Monitoring with Telegraf and Grafana <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__
* `Galaxy Monitoring with gxadmin <https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html>`__
**Deprecation of Python 3.9 support in Galaxy release 26.0**
Since Python 3.9 reached its end-of-life in October 2025, support for it will
be removed in Galaxy 26.0.
Administrators should upgrade their Python environment to version 3.10 or
higher to avoid security vulnerabilities and ensure a smooth transition to
Galaxy 26.0 and beyond.
Release Team
===========================================================
lib/galaxy/config/sample/galaxy.yml.sample
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@@ -1518,7 +1518,7 @@ galaxy:
# The BibTeX citation for Galaxy, to be displayed in the History Tool
# Reference List
#citation_bibtex: '@article{Galaxy2024, title={The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update}, author={{The Galaxy Community}}, journal={Nucleic Acids Research}, year={2024}, doi={10.1093/nar/gkae410}, url={https://doi.org/10.1093/nar/gkae410}}'
#citation_bibtex: '@article{Galaxy2024, title="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update", author="{The Galaxy Community}", journal="Nucleic Acids Research", year="2024", doi="10.1093/nar/gkae410", url="https://doi.org/10.1093/nar/gkae410"}'
# The URL linked by the "Galaxy Version" link in the "Help" menu.
#release_doc_base_url: https://docs.galaxyproject.org/en/release_
lib/galaxy/config/schemas/config_schema.yml
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@@ -1834,7 +1834,7 @@ mapping:
citation_bibtex:
type: str
default: "@article{Galaxy2024, title={The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update}, author={{The Galaxy Community}}, journal={Nucleic Acids Research}, year={2024}, doi={10.1093/nar/gkae410}, url={https://doi.org/10.1093/nar/gkae410}}"
default: '@article{Galaxy2024, title="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update", author="{The Galaxy Community}", journal="Nucleic Acids Research", year="2024", doi="10.1093/nar/gkae410", url="https://doi.org/10.1093/nar/gkae410"}'
required: false
per_host: true
desc: |