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Commit Graph
3750 Commits
Author SHA1 Message Date
Mason 1b18e9ea2d More linting fun 2018-11-06 21:26:46 -08:00
Mason 10723c789f Added white space to pass linter 2018-11-06 21:24:53 -08:00
Mason a8eb9463a6 test/selenium_tests/test_library_contents.py 2018-11-06 15:17:14 -08:00
John Chilton 82a8eb05d6 Merge remote-tracking branch 'jmchilton/release_18.09' into dev_merge_1 2018-11-06 09:10:22 -05:00
Dannon Baker 4405d15fea Merge branch 'window_monitor' into dev 2018-11-05 18:02:51 -05:00
Dannon e9f2693933 Merge pull request #6729 from scrathat/admin.data.manager.vue.steps 
Vue rewrite of admin data manager (local data) in steps
 2018-11-05 15:00:20 -05:00
Mason 11375a5692 Merge branch 'dev' into window_monitor 2018-11-05 09:19:27 -08:00
Marius van den Beek c3dc2392ce Merge pull request #6954 from jmchilton/workflow_tests_2 
Small API Workflow Test Improvements.
 2018-11-05 14:22:59 +01:00
Marius van den Beek c1e4b0111a Merge pull request #6911 from jmchilton/workflow_mapping_refactor 
Refactor collection mapping workflows toward independence from tools.
 2018-11-05 14:04:09 +01:00
mvdbeek 9b42032098 Fill in default state for test_optional_workflow_output 2018-11-05 13:09:31 +01:00
Sebastian Kapust 45d0f161c9 Fix functional test case test_1460_data_managers 2018-11-03 14:11:43 +01:00
Sebastian Kapust 8789713b95 Merge branch 'dev' into admin.data.manager.vue.steps 2018-11-03 09:59:36 +01:00
M Bernt 4e098c5d52 tests: add parameter to output_filter 2018-11-01 17:23:17 +01:00
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
John Chilton 06aea92eb8 cleaner test test_run_subworkflow_runtime_parameters 2018-11-01 10:37:51 -04:00
John Chilton d4b6bf28b5 Test for parameter replacement of GUI-style normalized parameters. 2018-11-01 10:37:49 -04:00
Mason 66a7db9405 Merged dev 2018-10-31 12:25:27 -07:00
M Bernt 717605af96 added test 2018-10-31 12:52:25 +01:00
Dannon Baker 51273658fb Merge remote-tracking branch 'upstream/dev' into unified_webpack4 2018-10-30 11:06:24 -04:00
Mason 04242c7503 Renamed selenium utility function 2018-10-30 07:10:19 -07:00
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 81155c635a Rename 2.shuffled.bam to 2.shuffled.unsorted.bam 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
Mason ef5e01da82 White space awesomeness 2018-10-29 22:07:58 -07:00
Mason 734c39d4f5 added global monitor for window.Galaxy 2018-10-29 21:03:24 -07:00
Dannon d41837cd9c Merge pull request #6933 from jmchilton/mutable_default 
Eliminate some mutable defaults in populators.py.
 2018-10-29 17:52:15 -04:00
M Bernt 1ec18484df added test 2018-10-29 14:47:57 +01:00
John Chilton 09e6b1dcde Eliminate some mutable defaults in populators.py. 2018-10-29 09:41:31 -04:00
John Chilton f0bf1694c5 Tweak testing toward being a bit more robust. 2018-10-26 14:02:16 -04:00
jra001k 9319ddf989 Rename "Test Dataset". 
Rename test dataset from "Test Dataset" to "Test_Dataset" to prevent CWL error below:
<--
if not ACCEPTLIST_RE.match(f["basename"]):
    raise WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"]))
--->
This error occur when running the test below:
test/api/test_workflows_cwl.py:CwlWorkflowsTestCase.test_simplest_wf
 2018-10-26 14:02:00 -04:00
John Chilton 7bd7abb5ee Fix linting of dev. 2018-10-26 10:01:56 -04:00
John Chilton 4919805f81 Merge pull request #6924 from natefoo/quiesce-handler 
Be more precise with the job runner worker thread join timeout and improve documentation
 2018-10-26 09:48:33 -04:00
Marius van den Beek dda297c408 Merge pull request #6776 from jmchilton/gxformat2_integration 
Allow API import/export of format 2 workflows.
 2018-10-26 14:10:33 +02:00
Nate Coraor e7156bdd23 Restore monitor_thread_join_timeout to 5 for tests 2018-10-25 14:55:25 -04:00
Nicola Soranzo f4203ca051 Fix errors reported by flake8 3.6.0 
Ignore W504.
 2018-10-24 23:22:19 +01:00
John Chilton e3bc005a86 Implement API endpoint for indexing extra files in a dataset. 2018-10-24 09:55:25 -04:00
John Chilton dd6b185ab8 Implement composite uploads on arbitrary datatypes. 
Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files.

These may be specified one at a time or in directory structures via tar files.
 2018-10-24 09:55:25 -04:00
Marius van den Beek 210cdc998a Merge pull request #6916 from nsoranzo/fix_exception_logging 
Do not log exception info twice
 2018-10-24 15:50:33 +02:00
John Chilton c2a49de6ce Directory datatype for Galaxy. 2018-10-24 09:39:06 -04:00
John Chilton b1fe6fee93 Refactor collection mapping workflows toward independence from tools. 
Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface.
 2018-10-24 09:34:40 -04:00
Nicola Soranzo 949dcfdbc3 Do not log exceptions twice 
`logging.exception()` already adds the the exception information after
the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-10-24 12:57:05 +01:00
mvdbeek 19c98b2745 Fix tests and name tool more appropriately 2018-10-24 12:11:52 +02:00
mvdbeek 26680e0ca1 Add test for remove_value form dynamic options 
Unfortunately you can select an invalid value (in the API, not the UI)
and Galaxy will replace the invalid value with the first valid value.
 2018-10-24 11:34:09 +02:00
Pierrick ROGER 35093e38fc Remove spaces in blank line. 2018-10-18 11:16:29 +02:00
Pierrick ROGER efc7864cab Merge branch 'dev' into feature/isa_data_type 2018-10-18 10:36:49 +02:00
Dannon Baker 03b44a84a6 Merge remote-tracking branch 'upstream/dev' into unified_webpack4 2018-10-17 22:47:57 -04:00
Dannon Baker 84ae932e8b Add back extra link to base.css for selenium testing (and assumedly other deployments which have custom mappings?). We need to drop all these extra handles eventually, to consolidate the interface to single endpoints with chunked bundles. 2018-10-17 21:04:29 -04:00