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Commit Graph
4123 Commits
Author SHA1 Message Date
John Chilton da26bfdc75 Merge pull request #7683 from mvdbeek/implicit_conversion_for_collection_parameters 
Implicit conversion for input collection parameters
 2019-04-09 10:55:17 -04:00
Martin Cech 1075a0e6bc Merge pull request #7659 from jmchilton/format2_import_default 
Allow import of format2 workflows by default for 19.05.
 2019-04-09 10:50:45 -04:00
Enis Afgan a8dc13da53 Merge pull request #7195 from machristie/keycloak-integration 
Custos integration
 2019-04-08 16:15:41 -04:00
mvdbeek 272a136970 Add test tools for implicit coversion of collection input 2019-04-08 18:33:57 +02:00
mvdbeek 54b9609896 Merge branch 'release_19.01' into dev 2019-04-08 18:29:11 +02:00
Martin Cech adfb7e65b3 Merge pull request #7682 from mvdbeek/fix_format_source_impicit_conversion 
[19.01] Fix format_source for implicit conversion inputs and fasta.gz upload
 2019-04-08 10:13:26 -04:00
Marius van den Beek 03b96f9eb3 Merge pull request #7650 from jmchilton/uuid_fixes 
Fix composite data and metadata file handling for UUID object stores
 2019-04-08 15:17:23 +02:00
Marius van den Beek 7ea8734796 Merge pull request #7367 from jmchilton/export_collections 
Rework and Generalize History Import and Export
 2019-04-08 14:24:45 +02:00
mvdbeek 966cad890e Fix fasta.gz uploads 
This looks like it may probably broke with https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b84f9cca2a4c48
 2019-04-07 23:15:35 +02:00
mvdbeek 5f578d4108 Add double conversion test 2019-04-07 23:15:35 +02:00
mvdbeek 3e3d15a84b Add test that verifies ftype is being set correctly 2019-04-07 23:15:35 +02:00
John Chilton 9dbace05b0 Merge pull request #7657 from jmchilton/integration_testing_refactor 
Refactor IntegrationTestCase to allow integration test functions.
 2019-04-06 13:09:02 -04:00
Sveinung Gundersen 28cd9948b7 Fixed bug when removing other tags than the first from a dataset. A space was erroneously added in front of these tags. 2019-04-06 03:52:35 +02:00
John Chilton 55f58cb627 Make heartbeat unit tests a bit more robust. 2019-04-04 15:08:52 -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
Marcus Christie e6878a0936 Removed raw_token column, bumped migration number 2019-04-04 10:31:43 -04:00
John Chilton 4b13917d86 Allow import format2 workflows by default. 
Setup forcing export of format2 workflows by default in next release. There should be a least one release between enabling them to be imported by default and exporting them by default anyway I think - so 19.09 workflows can still be used on slightly older Galaxy instances.
 2019-04-04 09:15:30 -04:00
John Chilton 8aa7a62f85 Default test suite to store objects by UUID. 
If we have to test one path or the other, test the slightly more exotic one.
 2019-04-04 08:11:56 -04:00
Marcus Christie f9eda39a82 Fixing tests 2019-04-03 17:09:14 -04:00
Marcus Christie 62617d4c8a Merge branch 'keycloak-integration' into patch-5 2019-04-03 15:17:58 -04:00
Marcus Christie b14c487287 Simplified configuration based on provider name and realm 2019-04-03 15:12:35 -04:00
Marcus Christie a1cd661a4e Rename from generic "OIDC" to "Custos" 2019-04-03 15:12:35 -04:00
Marcus Christie 2256ae3e2b Rename OIDCAccessToken -> OIDCToken 2019-04-03 15:12:35 -04:00
Marcus Christie 98071a432e Automatically set env var when redirect_uri is http://localhost 2019-04-03 15:12:34 -04:00
Marcus Christie 679d3197d0 Implemented disconnect() for OIDCAuthnz 2019-04-03 15:12:34 -04:00
Marcus Christie 4d0d827624 Associate external id with currently logged in Galaxy user 2019-04-03 15:12:34 -04:00
Marcus Christie 7ed229ca1a Fixing py3 compatibility of oidc_authnz and tests 2019-04-03 15:12:34 -04:00
Marcus Christie 29d55e4349 Removed Keycloak from data model 2019-04-03 15:12:34 -04:00
Marcus Christie 96b360bb8f Generalized extra auth url params and claim mapping 2019-04-03 15:12:34 -04:00
Marcus Christie c6b3e3caef Rename keycloak_authnz -> oidc_authnz 2019-04-03 15:12:34 -04:00
Marcus Christie 0e479367ff Change db strategy to look up existing keycloak_access_token first 2019-04-03 15:12:34 -04:00
Marcus Christie 7f2e0aaed1 Added tests around Galaxy user creation, keycloak_access_token records 2019-04-03 15:12:34 -04:00
Marcus Christie 3474be5e77 Added unit tests, refactoring 2019-04-03 15:12:34 -04:00
vahid 4ed550363e Update custos unit test. 2019-04-03 11:52:52 -07:00
John Chilton 500c43884e Merge pull request #7524 from jmchilton/decompose 
Decompose Galaxy into Python libraries in-tree.
 2019-04-03 13:51:21 -04:00
Dannon ded476414c Merge pull request #7645 from mvdbeek/fix_test_broken_with_float_to_int_pr 
Adjust test_run_with_numeric_input_connection to extra line
 2019-04-02 17:17:13 -04:00
Dannon cf5770f2d3 Merge pull request #7642 from jmchilton/workflow_editor_nodes 
Provide feedback on why workflow editor nodes won't connect.
 2019-04-02 16:26:08 -04:00
mvdbeek 6653d3ae9d Adjust test_run_with_numeric_input_connection to extra line 
introduced in https://github.com/galaxyproject/galaxy/pull/7634
 2019-04-02 21:23:49 +02:00
Dannon 62eedc45d7 Merge pull request #7548 from mvdbeek/kombu_broadcast 
More robust task messaging
 2019-04-02 10:30:46 -04:00
Nicola Soranzo 057afbca9a Merge branch 'release_19.01' into dev 2019-04-02 11:02:46 +01:00
Dannon bb76daf754 Merge pull request #7633 from mvdbeek/fix_early_run 
[19.01] Delay workflow step execution for discovered & mapped-over input
 2019-04-01 17:00:58 -04:00
John Chilton 2f9c93aea1 Provide feedback on why workflow editor nodes won't connect. 2019-04-01 11:34:00 -04:00
mvdbeek 8db8ce5de4 Fix float to int casting 
Fixes https://github.com/galaxyproject/galaxy/issues/998
 2019-03-31 17:15:46 +02:00
mvdbeek e8ea08dd61 Add testcase for mapped over discovered dataset consumption 2019-03-31 13:56:42 +02:00
mvdbeek 4912f7a97d Don't unhide mapped-over outputs when job fails 
The parent dataset collection now shows the failed datasets,
and that is much easier to deal with when all jobs within
a large collection have failed.
Fixes https://github.com/galaxyproject/galaxy/issues/7492

One downside here is that we don't see anything in the history right
away (except for the failed dataset count) if a hidden collection
contains failed datasets.
 2019-03-30 14:49:59 +01:00
mvdbeek fc8916525e Allow a little more time for thread to start up in heartbeat unit test 2019-03-30 10:08:04 +01:00
mvdbeek 7b4cf5b61d Fully initialize empty databaseses if GALAXY_TEST_DBURI is set and DB doesn't exist 2019-03-29 21:46:18 +01:00
mvdbeek 34eb9468d4 Use ApplicationStack for accessing server name 2019-03-29 21:46:18 +01:00
mvdbeek 22b21fde62 Only run rabbitmq queue worker test if GALAXY_TEST_AMQP_INTERNAL_CONNECTION is set 2019-03-29 21:46:18 +01:00
mvdbeek f4d5ae61f6 Make tests use finalizer instead of yield 
and verify tasks get executed the expected number of times.
Since the part after the yield statement runs to early it
was shutting down the app(s) prematurely.
 2019-03-29 21:46:18 +01:00