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1367 Commits
Author SHA1 Message Date
Marius van den Beek 9415df899e Merge pull request #17422 from wm75/data_source_tools_fixes 
Fix data_source and data_source_async bugs
 2024-02-15 12:36:25 +01:00
Marius van den Beek ddabba7c2f Merge pull request #17087 from mvdbeek/from_url_option 
Add select parameter with options from remote resources
 2024-02-14 18:47:40 +01:00
mvdbeek 84604bd2cb Merge branch 'release_23.2' into dev 2024-02-14 18:44:36 +01:00
mvdbeek 5aabab9c93 Implement request header and body templating 2024-02-13 14:51:16 +01:00
mvdbeek 2eca43e175 Allow expression evaluation to fail, so default value can be set in expression 2024-02-12 15:48:01 +01:00
mvdbeek 648b29bf7e Fix tool schema for `postprocess_expression` 2024-02-12 15:48:01 +01:00
mvdbeek d96dc3dfa5 Add test cases against usegalaxy.org's genomes api 2024-02-12 15:48:00 +01:00
mvdbeek 6fc51bd897 Implement postprocessing using javascript sandbox expression evaluation 2024-02-12 15:48:00 +01:00
mvdbeek 5eecab4248 Allow templating URL with cheetah 
Context are the user context values, we could extend that as needed.
 2024-02-12 15:48:00 +01:00
mvdbeek 67ab6a0ff0 Basic support for getting select options from URLs 
Updating regular tool data tables for frequently changing data is a
little tricky, and it was requested that we allow loading options
dynamically from a URL. The eventual goals of this work is to enable
exploring resources with great APIs (NCBI datasets is a good exmaple)
from within Galaxy tools.

This doesn't do any of that yet ... it's just a simple URL one can
query with a GET request, and the data there must be in the format
["name", "value", True|False].

Following steps:
  - [x] allow templating (Cheetah ? JS?)
  - [x] allow post-processing to extract name-value pairs
    - jq-like syntax ?
    - [x] JS expression ?
  - add pagination (requires work on vue-multiselect)
  - add request caching

Some potential issues:
  - Slow server responses: use async library and cancel request after N
    seconds ?
  - Large respons ... stream response and cancel after configurable max
    response size ?
 2024-02-12 15:47:59 +01:00
mvdbeek 880977943e Add templating to test IT 2024-02-10 12:15:12 +01:00
Wolfgang Maier 870af6d68f Try to fix API test 
The test tool needs to declare a recent enough profile to expect modern
tool-provided metadata.
 2024-02-08 21:14:07 +01:00
Matthias Bernt 181d5d2598 add test cases showing bug 2024-01-10 14:34:14 +01:00
mvdbeek d65d3112ac Make framework tool tests use driver fixture 2024-01-01 15:05:19 +02:00
mvdbeek 0cc9225ca0 Add file_name property on DatasetFilenameWrapper 2023-12-01 19:57:38 +01:00
mvdbeek 686ec6fac4 Merge branch 'release_23.1' into dev 2023-11-21 09:36:51 +01:00
John Chilton edcc043b61 Make testing tool panel views a little easier. 2023-11-15 11:04:28 -05:00
John Chilton ea0fe8053b Merge pull request #14955 from jmchilton/default_uris_2 
Implement default locations for data and collection parameters.
 2023-11-06 10:05:00 -05:00
Nicola Soranzo 1e86672f83 Allow non-optional integer/float params without `value` attribute 
Previously a tool with such an input would fail to load.

Add test tool.
 2023-11-02 17:19:43 +00:00
John Chilton dce53769bd Implement default locations for data and collection parameters. 
Works for both files and collections. Workflow defaults override tool defaults.

TODO:

- Unit test case to ensure this only works for non-default, non-multi data parameters.
- Implement XSD once syntax is finalized.
 2023-11-01 11:52:44 -04:00
guerler bf02dc9948 Drop library_data input type 2023-10-17 10:29:26 +03:00
mvdbeek 0f2ef4dc0c Merge branch 'release_23.1' into dev 2023-09-14 13:43:50 +02:00
mvdbeek 90c8438a83 Fix and extend extended metadata outputs to working directory tests 2023-09-12 13:07:10 +02:00
Marius van den Beek f43f350982 Merge pull request #16668 from bernt-matthias/topic/samtools-bump 
Bump samtools converters
 2023-09-10 10:17:26 +02:00
Matthias Bernt 8841408406 fix functional test 2023-09-09 13:19:47 +02:00
mvdbeek 33aab28217 Merge branch 'release_23.1' into dev 2023-09-08 14:43:01 +02:00
Matthias Bernt 2117385d13 fix framework test 
by allowing lines_diff
 2023-09-08 13:16:52 +02:00
M BerntandNicola Soranzo 3199134aa8 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-09-07 22:02:15 +02:00
Matthias Bernt 85124d8500 xsd: allow name attrbute of test collections 
already supported by the framework

fixes: https://github.com/galaxyproject/galaxy/issues/16654
 2023-09-07 20:16:26 +02:00
mvdbeek effd5e8ade Merge branch 'release_23.1' into dev 2023-08-24 17:03:44 +02:00
mvdbeek 3af41be3eb Merge branch 'release_23.0' into release_23.1 2023-08-24 17:03:02 +02:00
mvdbeek 90d04a017e Always create output 
I think that's always been required, we just didn't test this ??
 2023-08-24 10:44:41 +02:00
mvdbeek 7986110c9e Extend pulsar test cases with composite_output_tests 2023-08-24 10:44:40 +02:00
mvdbeek 61f8123b68 Test files path and extra files path 2023-08-24 10:44:40 +02:00
Laila Los c52dba0c3a add selenium test for reordering repeat blocks 2023-08-14 10:29:45 +02:00
Matthias Bernt 13b59afa67 add framework test for profile behavior of format="input" 
stumbled over this here: https://github.com/galaxyproteomics/tools-galaxyp/pull/679
could not find a test
 2023-07-30 18:49:55 +02:00
Marius van den Beek fa64fc646d Merge pull request #15825 from bernt-matthias/validation_metadata 
Add ability to assert metadata properties on input dataset parameters
 2023-07-29 12:00:32 +02:00
davelopez 2298f42ed7 Update XSD schema docs 
- Remove checksum support for inputs for now
 2023-06-28 12:31:42 +02:00
davelopez 49719e20cc Partially revert #15510 
This solution was suboptimal as it moved around too much unnecessary data
 2023-06-28 12:28:06 +02:00
Marius van den Beek 71d70a9275 Merge pull request #15483 from bernt-matthias/tests-fix 
Fixes for two framework test tools
 2023-06-21 22:02:22 +02:00
Marius van den Beek a68a453608 Merge pull request #15085 from bernt-matthias/topic/decompress-assertions 
Decompress history data for testing assertions
 2023-06-21 20:05:10 +02:00
Matthias Bernt 4a28bc3525 restructure tests and add tests for explicit container resolvers 2023-06-14 15:28:43 +01:00
Matthias Bernt 9e48ceb169 containers: do not mount /tmp/ 
fixes https://github.com/galaxyproject/galaxy/issues/15673

- singularity: add `--no_mount tmp` (analogous to docker's default)
- do not bind `$TMPDIR:rw,$TMP:rw,$TEMP:rw` by default
- instead (by default )provide a writable `/tmp` via
  `$_GALAXY_JOB_TMP_DIR/:/tmp:rw` note that this dir is still also
  available as `$_GALAXY_JOB_TMP_DIR:rw`
 2023-06-14 15:28:38 +01:00
Matthias Bernt 0e059f854a add value_json 2023-06-06 10:02:30 +02:00
Matthias Bernt 12a4464b48 finish metadata equal validator 2023-06-06 10:02:30 +02:00
John Chilton 1f56fa37d7 WIP: metadata validation. 2023-06-06 10:02:29 +02:00
Marius van den Beek ec9f216b73 Merge pull request #15978 from mvdbeek/fix_recording_param_path 
Record input datasets and collections at full parameter path
 2023-06-04 17:47:51 +02:00
mvdbeek 5e0d80bd34 Test `format_source` with conditional inputs 2023-06-01 17:50:30 +02:00
mvdbeek c1a055ff2f Merge branch 'release_23.0' into dev 2023-05-25 16:36:34 +02:00
mvdbeek dca783b185 Add test tool for triggering implicit bigwig to wig converter 2023-05-24 10:54:31 +02:00