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35080 Commits
Author SHA1 Message Date
mvdbeek ce7f58408d Also set is_webapp in tests 2023-08-26 10:08:14 +02:00
mvdbeek 413adc1f51 Set is_webapp earlier 2023-08-26 10:08:14 +02:00
mvdbeek b6a95696bb Drop delay 2023-08-26 10:08:14 +02:00
mvdbeek 5bee3e514b Parse help and tests only in webapp 2023-08-26 10:08:13 +02:00
mvdbeek df4ccd5100 Drop now unneeded threading lock 2023-08-26 10:08:13 +02:00
mvdbeek 75fcbc3df2 Fix RST linter 2023-08-26 10:08:13 +02:00
mvdbeek 0a8ba61da6 Fix errors uncovered by improved typing of Tool 2023-08-26 10:08:13 +02:00
mvdbeek eb8a49d805 Drop delayed_tool_init config setting 2023-08-26 10:08:13 +02:00
mvdbeek 02c4a94d1b Fix type errors 2023-08-26 10:08:13 +02:00
mvdbeek 324efe3aee Fix up help_by_page 2023-08-26 10:08:12 +02:00
mvdbeek edbe6e79b9 Assign so ruff doesn't complain 
This needs a whole bunch of refactoring.
 2023-08-26 10:08:12 +02:00
mvdbeek 90116029cc Stop newer docutils from failing to parse help text 
This is in the docutils source code:
```
        if level >= self.halt_level:
            raise SystemMessage(msg, level)
```
and it's not being caught. Might be new in new docutils?
 2023-08-26 10:08:12 +02:00
mvdbeek cbc1a5283e Tweak tool memory consumption 2023-08-26 10:08:12 +02:00
mvdbeek 8d5feb4fa1 Merge branch 'release_23.0' into release_23.1 2023-08-26 10:01:32 +02:00
M Bernt 99ffa0e5ce remove debug code 2023-08-26 08:32:16 +02:00
M BerntandMarius van den Beek 913e890c6a Fix _GALAXY_JOB_TMP_DIR 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-08-26 08:32:13 +02:00
Matthias Bernt efef30d6ab make sure that TMP, TEMP, and TMPDIR are set 
seems needed for docker volume strings (an empty
variable would lead to `-v "::rw"` which causes
`docker: invalid spec: ::rw: empty section between colons.`)
 2023-08-26 08:32:09 +02:00
mvdbeek e93e986ad6 Fix new_dataset._extra_files_path just in case something still uses it 2023-08-26 08:30:16 +02:00
mvdbeek 0477581217 Push extra files from object store cache to object store 2023-08-26 08:30:16 +02:00
mvdbeek 27991b950d Fix writing data bundle manifest to object store 2023-08-26 08:30:16 +02:00
mvdbeek 3c4e1195f7 Implement downloading directories from S3 2023-08-26 08:30:16 +02:00
John Chilton d00e01ed18 Merge pull request #16592 from jmchilton/fix_parameters 
[23.1] Fix replacement parameters for subworkflows.
 2023-08-25 13:33:35 -04:00
Marius van den Beek 84afacf004 Merge pull request #16594 from bernt-matthias/release_23.1_tmp 
[23.1] make sure that TMP, TEMP, and TMPDIR are set
 2023-08-25 18:31:39 +02:00
mvdbeek 1a9a402f2e Bump minimum tpv version to 2.3.2 
This version fixes the version parsing for tools that don't use PEP 440
versions (https://github.com/galaxyproject/total-perspective-vortex/issues/111)
 2023-08-25 16:53:00 +02:00
M Bernt b1ffd47ab8 remove debug code 2023-08-25 16:03:11 +02:00
M BerntandMarius van den Beek 34c781e604 Fix _GALAXY_JOB_TMP_DIR 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-08-25 16:02:22 +02:00
Matthias Bernt f39f4b982c make sure that TMP, TEMP, and TMPDIR are set 
seems needed for docker volume strings (an empty
variable would lead to `-v "::rw"` which causes
`docker: invalid spec: ::rw: empty section between colons.`)
 2023-08-25 14:09:50 +02:00
John Chilton eea5fb1a53 Fix mapping parent workflow formal inputs to subworkflow informal replacement parameters. 2023-08-24 14:12:39 -04:00
mvdbeek 3af41be3eb Merge branch 'release_23.0' into release_23.1 2023-08-24 17:03:02 +02:00
John Chilton 72070dbd0a Merge pull request #16541 from mvdbeek/fix_extra_files_path_handling 
[23.0] Fix extra files path handling
 2023-08-24 10:54:35 -04:00
John Chilton c3d0191f32 Merge pull request #16585 from mvdbeek/dont_read_body_into_memory 
[23.0] Don't read request body into memory
 2023-08-24 10:53:13 -04:00
mvdbeek 96b1f7aaac Reuse code for getting extra files rewrite path, make pick up location more consistent 2023-08-24 10:44:41 +02:00
mvdbeek ba0a649066 Pick up extra files from outputs directory 2023-08-24 10:44:41 +02:00
mvdbeek 56ee745ed8 "Use `object_store.construct_path` to build paths" 
This allows us to figure out what the extra)path for tools to consume should
be without having to create the directory up front ... which would fail
many tools that start with `mkdir`
 2023-08-24 10:44:41 +02:00
mvdbeek 1c32d95ea6 Use string cast to get the correct rewritten path 2023-08-24 10:44:40 +02:00
mvdbeek e8aeedaf7a Defer to compute_environment.input_extra_files_rewrite for path_rewrite 2023-08-24 10:44:40 +02:00
mvdbeek 3cffba23a7 Drop files_path bypass, use ComputeEnvironment 
to calculate output_extra_files_path also for `files_path`.

This should fix the working/working issue in
https://github.com/galaxyproject/pulsar/issues/296
 2023-08-24 10:44:40 +02:00
mvdbeek 92128ea44c Don't read body into memory 2023-08-24 10:03:38 +02:00
mvdbeek 6d067f47b5 Merge branch 'release_23.0' into release_23.1 2023-08-23 17:09:50 +02:00
Marius van den Beek 66ec43c074 Merge pull request #16579 from mvdbeek/resource_param_fix 
[23.1] Ignore errors with user-set job resources
 2023-08-23 16:39:06 +02:00
John Chilton 81a1705573 Merge pull request #16584 from mvdbeek/when_expression_repeat 
[23.0] Fix conditional step evaluation with datasets in repeats
 2023-08-23 10:19:36 -04:00
mvdbeek c001ce0dcc Fix conditional step evaluation with datasets in repeats 
For instance when this is the step state:

```
{
    queries: [
        {
            __index__: 0,
            inputs2: ["<galaxy.model.HistoryDatasetAssociation(141277566) at 0x7fc2099417f0>"]
        }
    ],
when: False
}
```

as seen in https://sentry.galaxyproject.org/share/issue/995445a10402461aa80328db5ceba491/
 2023-08-22 18:14:25 +02:00
mvdbeek cb35441822 Ignore errors with user-set job resources 
Fixes
https://sentry.galaxyproject.org/share/issue/735cef91223e42888ff9bc54ec93c2cb/,
which is a problem that happens when a workflow with resource parameters
is imported from another Galaxy instance, or when we change the
available resource parameters and the selection becomes invalid.

Medium-term we need to stop doing this completely IMO and work with more
abstract job requirements IMO, as this is a big barrier to transfer
workflows from instance to instance and having them just work.
 2023-08-22 15:29:03 +02:00
mvdbeek 6221bf5493 Don't use `docker run` --user flag on OSX 
On OSX files touched by the docker daemon belong to the proper user.
Using `--user` actually breaks permissions when mounting $TMPDIR in a
really bizarre way.
 2023-08-18 11:34:52 +02:00
davelopez 6f3e7228a8 Fix incorrect request host in ASGI 2023-08-18 11:32:07 +02:00
mvdbeek 62677c951e Make sure job_wrapper uses a consistent metadata strategy 
This should fix https://github.com/galaxyproject/galaxy/issues/16309#issue-1774159663
 2023-08-17 17:10:23 +02:00
mvdbeek 71e5756ff8 Merge branch 'release_23.0' into release_23.1 2023-08-17 11:40:01 +02:00
John Davis 21a35b84a7 Merge pull request #16537 from mvdbeek/tool_document_cache 
[23.1] Limit tool document cache to tool configs with explicit cache path
 2023-08-15 04:32:02 +10:00
mvdbeek 98b3642fe2 Drop unused tool_cache_data_dir config setting 2023-08-10 12:08:43 +02:00
mvdbeek 90a6b67464 Include RuntimeError in exceptions that should disable the tool cache 2023-08-10 12:00:16 +02:00