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c6fcd051c8e252cd2c6786b85cfed68150f129cd
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160 Commits
Author SHA1 Message Date
John Chilton c6fcd051c8 Cleanup integration test configuration code. 
Remove copy and paste problems, remote excess configuration unrelated to the what is being tested (handler configuration, multiple worker counts, etc..).
 2019-05-02 08:45:11 -04:00
John Chilton faae919af1 Add file missing from #7694 2019-05-02 08:27:04 -04:00
Nicola Soranzo d53112aa43 Use `yaml.safe_load() instead of load()` 
See https://msg.pyyaml.org/load
 2019-04-23 16:50:55 +01:00
John Chilton 74bf94f445 Fix kubernetes integration tests for Docker on Mac. 2019-04-16 08:28:36 -04:00
John Chilton 74a6615488 Fix pulsar with metadata_strategy == 'directory'. 2019-04-08 16:30:15 -04:00
John Chilton 4527293ce4 Refactor IntegrationTestCase to allow integration test functions. 
I want to be able to make more integration tests like test_pulsar_embedded.py, where we just define a configuration and then some tool tests to run. In particular this will be useful for extended metadata testing of the most interesting tools.
 2019-04-04 14:58:55 -04:00
John Chilton 0fe13b7e5a Seperate tool and job script standard I/O. 
This should allow Galaxy to reason about what the tool reports vs. what dependency resolution and metadata reports, allow us to enable logging during metadata collection, and allow us to reason about the tool's I/O from inside the job script during cleanup/metadata collection at the end.
 2019-03-04 15:39:07 -05:00
mvdbeek b0f3d92149 Don't use skip_unless_docker decorator 
This is handled in setupClass. Also drop
unused skip_unless_singularity.
 2019-03-02 12:19:14 +01:00
mvdbeek e293a74e66 Add test for tool using python dependencies 2019-02-19 20:17:16 +01:00
mvdbeek 7cf161ba01 Allow adding multiple volume claims 2019-02-19 20:17:16 +01:00
mvdbeek e52bb5daa7 Import from correct module 2019-02-19 13:36:28 +01:00
mvdbeek 54c964011a Take ceiling of kubernetes cpu value 2019-02-19 13:28:18 +01:00
mvdbeek c61c790fcc Make kubernetes pass GALAXY_SLOTS and GALAXY_MEMORY_MB 
Also drops __transform_cpu_value, incoming values are always
strings, so this wasn't functional in any case.
 2019-02-19 13:28:18 +01:00
mvdbeek 5c5f199f81 Add job properties test 2019-02-19 13:27:27 +01:00
mvdbeek 9019916ae2 Fix test skipping 2019-02-19 13:22:11 +01:00
mvdbeek 4e39c0fc84 Test cancelling jobs, running mulled containers on kubernetes 2019-02-19 13:22:10 +01:00
mvdbeek 3498f87d87 Use sh as job shell for kubernetes test, bash is not available in default container 2019-02-19 13:11:09 +01:00
mvdbeek 879d7c22b6 Add basic kubernetes integration test 
Currently times out becasue jobs aren't monitored succesfully.
 2019-02-19 13:11:09 +01:00
mvdbeek c0b63a18c7 Fix container integration tests 2019-01-06 15:01:31 +01:00
mvdbeek fd4b009089 Skip singualrity integration tests if singularity not available 2019-01-06 15:01:31 +01:00
mvdbeek b41d969d68 Add integration test for singularity resolution 2019-01-06 15:01:31 +01:00
mvdbeek 50d8e3079d Add integration test for un/install with resolver_type 2019-01-06 15:01:31 +01:00
John Chilton 1222f80ae9 Merge pull request #7129 from natefoo/serializable-job-assignment 
Perform job assignment using DB serialization techniques
 2019-01-05 20:22:56 -05:00
Nate Coraor df7f8b425d Integration tests for handler assignment methods 2019-01-04 16:46:29 -05:00
John Chilton 0727f17ade Fixes for Pulsar error handling. 
More uniform error hanlding to fix test. Simplify test case of resubmission to test just jobs resubmit properly (no need to test Pulsar-to-Pulsar resubmission in particular here I don't think, maybe as a second test - but not a first?).
 2018-12-21 11:16:38 -05:00
John Chilton cd119d641a Merge remote-tracking branch 'jmchilton/dev' into pulsar_resubmit 2018-12-21 09:51:10 -05:00
Martin Cech 11428a03b8 Merge pull request #7019 from jmchilton/path-aware-workflows 
File-based Workflow Editor
 2018-12-07 16:18:26 -05:00
Nuwan Goonasekera 263d10ca1c Added test for pulsar resubmission 2018-11-28 22:41:38 +05:30
John Chilton a2b7521140 Fix resubmission on tool error detection. 
Parts of this were wired up before but pieces were missing and so it was broken.
 2018-11-23 14:32:04 +01:00
John Chilton 9bac3c44fa Path-aware workflows. 
- Allow workflows to be uploaded via path using the GUI and and API for admins.
- Track the path and resync workflows on save (both .ga and format 2 workflows) - this will allow Planemo to leverage the Galaxy workflow editor to interactively save workflows.
 2018-11-20 15:49:51 +01:00
Marius van den Beekandnuwang ae78691707 Update test/integration/test_chained_dynamic_destinations.py 
Co-Authored-By: nuwang <nuwan.goonasekera@gmail.com>
 2018-11-16 17:12:45 +05:30
Nuwan Goonasekera 5ba1c24a14 Added integration test for rules_module overrides 2018-11-16 12:27:32 +05:30
Nuwan Goonasekera ca7e2b9e68 Added integration test for chained destinations 2018-11-16 12:04:09 +05:30
John Chilton f035d642ce Merge pull request #6844 from jmchilton/compressed_types_and_extra_files 
Infrastructure/API Support for Composite Uploads/Downloads
 2018-11-01 10:57:09 -04:00
mvdbeek d80e4bd0a1 Fix test logic 2018-10-30 09:27:25 +01:00
mvdbeek 48bdc97fce Verify state of uploaded datasets and download datasets to verify that the file is intact after upload 2018-10-30 09:27:25 +01:00
mvdbeek b74f225f18 Map fastqsolex to fastq datatype in integration test 2018-10-30 09:27:25 +01:00
mvdbeek 7ce69df57c Add integration test for uploading datasets of known datatype 
We upload everything in lib/galaxy/datatypes/test and make sure
that we get the correct datatype.
For datatypes that have a sniffer we use `auto`, otherwise we set the
correct datatype.

This is fairly basic for now, but it would be trivial to extend this
to also verify file integrity and metadata elements as well as testing
options that affect uploads, like `auto_decompress` settings.
 2018-10-30 09:27:24 +01:00
mvdbeek 9a24338d12 Name datatype test files according to datatype extension 2018-10-30 09:27:24 +01:00
John Chilton c2a49de6ce Directory datatype for Galaxy. 2018-10-24 09:39:06 -04:00
mvdbeek 20526ceb50 Share ssh key generation across tests 
Closes https://github.com/galaxyproject/galaxy/issues/6860
 2018-10-14 18:08:17 +02:00
Nicola Soranzo bc226e6d41 Use more generic destination name 
xref. https://github.com/galaxyproject/galaxy/pull/6845#pullrequestreview-163617248
 2018-10-12 09:53:47 +01:00
Nicola Soranzo 5e71401a7e Merge branch 'release_18.09' into dev 2018-10-12 09:47:34 +01:00
Nicola Soranzo d22f652f91 Merge branch 'release_18.05' into release_18.09 2018-10-12 09:44:18 +01:00
Nicola Soranzo ac3e1ca1d0 Use Crypto to generate SSH keys 
Also remove key files in `stop_ssh_docker()`.
 2018-10-10 16:22:05 +01:00
mvdbeek b08c6219c3 Simplify ssh key handling in integration test 2018-10-10 14:56:05 +02:00
mvdbeek 5e12e509bf Fix selection of job plugin and image 
Thanks @nsoranzo.
 2018-10-10 14:56:05 +02:00
mvdbeek 5844bdc7aa Add integration test for remote shell CLI runners 
This tests both the SecureShell and Paramiko shell plugins and the
Slurm and Torque CLI runner.
 2018-10-10 10:10:51 +02:00
Nicola Soranzo 0c931235af Change all remaining old-style classes to new style 2018-09-17 12:26:07 +01:00
Nicola Soranzo e14b871eb9 Add test for scripts/galaxy-main 2018-09-06 11:00:08 +01:00