mvdbeek
259bee364b
Don't set tool if we don't have a tool dir
2025-05-12 10:54:55 +02:00
mvdbeek
e73ec140ca
Rebuild client schema
2025-05-12 10:54:54 +02:00
mvdbeek
b007fc1341
Subclass generic for readable model title
2025-05-12 10:54:53 +02:00
mvdbeek
7c52e9fc79
Skip unprivileged tool resolution if we don't have appropriate permissions
2025-05-12 10:54:53 +02:00
mvdbeek
74a6f31f4f
Implement roles to restrict custom tool permissions
2025-05-12 10:54:52 +02:00
mvdbeek
40e1be1632
Fix up tool source display for user tools
2025-05-12 10:54:52 +02:00
mvdbeek
9815e8204c
Move dynamic_tool_models to tool_util_models
2025-05-12 10:54:50 +02:00
mvdbeek
fde572dfc0
Update import path
2025-05-12 10:54:50 +02:00
mvdbeek
86e823304f
Add missing `Literal` import
2025-05-12 10:54:49 +02:00
mvdbeek
1ea07735c2
Don't require validators for select parameters
2025-05-12 10:54:49 +02:00
mvdbeek
1c8090e7ad
Fix local import in __resolvers_dict
2025-05-12 10:54:47 +02:00
mvdbeek
c3e167bba4
Move dynamic tool models to tool_util
2025-05-12 10:54:47 +02:00
mvdbeek
ddaf5d3021
Fix linting issues with new API routes
2025-05-12 10:54:46 +02:00
mvdbeek
22d111e0ac
Add required name and version to embedded tool
2025-05-12 10:54:45 +02:00
mvdbeek
4ae1ea2010
Fix toolbox.get_tool return type annotation
2025-05-12 10:54:45 +02:00
mvdbeek
ef409b27c2
Fix admin tool deactivation, dynamic tool endpoint mixup
2025-05-12 10:54:45 +02:00
mvdbeek
280208f777
Fix duplicate import
2025-05-12 10:54:44 +02:00
mvdbeek
d9ea2fde61
Type fixes for workflow_run_dict
2025-05-12 10:54:44 +02:00
mvdbeek
a52b78bf16
Add a few annotations to test out schema info rendering
2025-05-12 10:54:44 +02:00
mvdbeek
e6b0783194
Enable (Javascript) requirements on frontend/backend
2025-05-12 10:54:42 +02:00
mvdbeek
791ab043ff
Exclude defaults from unprivileged tool api response
2025-05-12 10:54:32 +02:00
mvdbeek
301bb62974
Use native type discriminator for UserToolSource model
2025-05-12 10:54:32 +02:00
mvdbeek
152bc2ffa5
Add runtime model to API
...
Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
2025-05-12 10:54:30 +02:00
mvdbeek
5884fa9835
Enable single container key
2025-05-12 10:54:28 +02:00
mvdbeek
bfaad0773c
Enable unprivileged tool preview endpoint
2025-05-12 10:54:28 +02:00
mvdbeek
841e19d4ad
Fix admin-only dynamic tools
2025-05-12 10:54:26 +02:00
mvdbeek
1a0de476b0
Fetch dynamic tool for job
2025-05-12 10:54:25 +02:00
mvdbeek
d9dd54d5b3
Add monaco-based tool editor with json schema support
2025-05-12 10:54:25 +02:00
mvdbeek
d6121d543e
Enable access to dynamic tools via toolbox.get_tool
2025-05-12 10:54:24 +02:00
mvdbeek
746935b7fc
Return unprivileged tool api return types
2025-05-12 10:54:23 +02:00
mvdbeek
a6d6477122
Bypass global toolbox for unprivileged tools
2025-05-12 10:54:23 +02:00
mvdbeek
1767ad21a9
Test tool run
2025-05-12 10:54:22 +02:00
mvdbeek
a234ec565a
Add separate unprivileged tools endpoint
2025-05-12 10:54:22 +02:00
mvdbeek
4b1c336218
Add user_dynamic_tool_association migration
2025-05-12 10:54:21 +02:00
mvdbeek
cbddc5196e
Add unprivileged tools endpoint and models
2025-05-12 09:07:57 +02:00
mvdbeek
bafb615c1f
Add user_tool role types
2025-05-12 09:07:56 +02:00
mvdbeek
024d688e58
Minor fix to restore admin-style dynamic tools
2025-05-12 09:07:56 +02:00
mvdbeek
5228e32a14
Create UserToolSource pydantic model
2025-05-12 09:07:54 +02:00
mvdbeek
855d359f0c
Add an experimental non-cheetah way of building command lines
...
The primary benefit is that the command section does not have access the
app or any dangling reference to the database connection or any other
secrets. There are two flavors here, one uses base_command and
arguments, and allows building up an (escaped) argv list, the other is a
shortcut for writing shell scripts and feels maybe a bit more like
writing a very simple cheetah section.
base_command:
```yml
name: base_command tool
class: GalaxyTool
version: 1.0.0
base_command: cat
arguments:
- $(inputs.input.path)
- '>'
- output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
shell_command style:
```yml
name: shell_command tool
class: GalaxyTool
version: 1.0.0
shell_command: cat '$(inputs.input.path)' > output.fastq
inputs:
- type: data
name: input
outputs:
output:
type: data
from_work_dir: output.fastq
name: output
```
2025-05-12 09:07:24 +02:00
mvdbeek
eb38fd8ec9
Merge branch 'release_24.2' into dev
2025-05-12 09:05:28 +02:00
mvdbeek
65d265fd51
Merge branch 'release_24.1' into release_24.2
2025-05-12 09:02:07 +02:00
mvdbeek
c5c0599a2d
Merge branch 'release_24.0' into release_24.1
2025-05-12 09:01:27 +02:00
mvdbeek
4fb1388e50
Fix invocation failure dataset reference
...
Fixes https://github.com/galaxyproject/galaxy/issues/20049 .
Many thanks for pointing me at the real issue @jdavcs!
2025-05-10 10:57:00 +02:00
John Chilton
e3c6ea3a3e
Tweak API tests for small test tool tweaks.
2025-05-09 17:39:41 -04:00
John Chilton
7304573e2d
Add selenium test for creating a paired/unpaired list from a workflow input.
2025-05-09 17:39:41 -04:00
John Chilton
6c9bc27d47
More test coverage for workflow running with collections.
2025-05-09 17:39:41 -04:00
John Chilton
cf6a1a4f5f
Typo/format fix.
2025-05-09 17:39:41 -04:00
John Chilton
7141c402cd
Bugfixes around specified multiple collection types for wf inputs.
2025-05-09 17:39:41 -04:00
John Chilton
e6df994faa
Fixes for using paired list creator from workflow form.
2025-05-09 17:39:41 -04:00
John Chilton
be6de1273f
Apply Rules on Collection Element Index.
2025-05-09 17:39:40 -04:00
mvdbeek