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
John Chilton
1bc6214aca
Add a field-like -> list:paired example to rules spec.
2025-05-09 17:39:40 -04:00
John Chilton
2ff11415bd
Update __EXTRACT_DATASET__ for paired/unpaired...
2025-05-09 17:39:40 -04:00
John Chilton
0c78f3a8a9
Rule builder API test case for paired/unpaired datasets.
2025-05-09 17:39:40 -04:00
John Chilton
aea0bef8d4
Extend rule builder for record collections.
2025-05-09 17:39:40 -04:00
John Chilton
9195d54e73
Add test case for list:list building in the UI.
2025-05-09 17:39:40 -04:00
John Chilton
24c7e19e6b
Paired/unpaired test case and fix.
2025-05-09 17:39:39 -04:00
John Chilton
6ff9f58a99
Update Galaxy XSD collection_type for new collection types.
2025-05-09 17:39:39 -04:00
John Chilton
878dbed6d5
Activity for rule builder imports.
2025-05-09 17:39:38 -04:00
John Chilton
219796f049
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
John Chilton
1b037af74f
Start trying to formalize dataset collection semantics.
2025-05-09 16:38:20 -04:00
John Chilton
0b3b408b50
Migrate doctests to unit tests.
2025-05-09 16:38:19 -04:00
John Chilton
2c11e18951
Database migration for fixed length collection migraton.
2025-05-09 16:38:19 -04:00
John Chilton
17de736ccb
record ui.
2025-05-09 16:38:19 -04:00
John Chilton
518fa136d9
[WIP] Implement records - heterogenous dataset collections.
...
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
2025-05-09 16:38:19 -04:00
John Chilton
94ead7c8df
WIP: embedded list of pairs workflow run selenium test case.
2025-05-09 16:38:18 -04:00
John Chilton
8e3e86a706
Option for add_column_regex to be unmatched, improved testing.
...
Can easily be combined concatenate and such to get conditionals on rewriting values. Used for new tests in new collection types branch that mirror I think useful, real-world examples. Also extends the test framework a bit to allow testing errors during evaluation and not just errors that can be caught statically by inspecting the rule itself.
2025-05-09 16:38:18 -04:00
Marius van den Beek
2eac17db1e
Merge pull request #19936 from jdavcs/dev_13922_metrics
...
Drop old job metrics
2025-05-09 15:02:21 +02:00
mvdbeek