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4273 Commits
Author SHA1 Message Date
Marius van den Beek c654406725 Merge pull request #8046 from jmchilton/selenium_workflow_data 
Fix Selenium DatasetPopulator for more interesting uploads.
 2019-05-28 14:42:47 +02:00
John Chilton 79ce86bce5 Fix Selenium DatasetPopulator for more interesting uploads. 
This is a bug, that interface consumes files and so should this method.
 2019-05-27 17:56:55 -04:00
Nicola Soranzo 0e14a47e6c Merge branch 'release_19.05' into dev 2019-05-27 22:50:04 +01:00
John Chilton 0e33056989 Merge pull request #8039 from mvdbeek/non_legacy_object_store_fix 
[19.05] Backport 7939: Fix non-eager object store with nested object stores
 2019-05-27 12:09:34 -04:00
mvdbeek 5b05866545 Explicitly create extra_files_path when discovering outputs with extra files 2019-05-27 14:37:53 +02:00
mvdbeek 563ae4d7d3 Raise ObjectNotFound if file does not exist in object store 
And return an empty string if a path does not exist when calling
`get_filename` or` get_extra_files_path` on a Dataset.
 2019-05-27 14:37:53 +02:00
John Chilton 7ea502be77 Run API tests with a nested object store. 2019-05-27 14:37:53 +02:00
mvdbeek 62f5572a43 Add carriage return unit test 2019-05-27 11:35:20 +02:00
Nicola Soranzo d9b0f54906 Try to verify tool test output first as Unicode 2019-05-26 15:07:36 +01:00
Martin Cech a8d1a4f965 Merge pull request #8023 from mvdbeek/fix_column_assign_bug 
Fix column assign bug
 2019-05-24 16:14:27 -04:00
Martin Cech 81a64e9c13 Merge pull request #8024 from dannon/history_menu_trimming 
History menu (cog) updates.
 2019-05-24 15:26:43 -04:00
mvdbeek 93419bc3ce Add workflow testcase for ColumSetAction PJA 2019-05-24 10:07:03 +02:00
Dannon Baker 4bcd3b4b39 Move 'test_saved_histories' to 'test_histories_list' 2019-05-23 15:39:55 -04:00
Dannon Baker 55bf2fea06 Go ahead and update saved_histories -> histories everywhere in selenium tests 2019-05-23 15:38:30 -04:00
Dannon Baker c8facb6191 Update selenium navigation target for Saved Histories (now just histories) 2019-05-23 15:36:36 -04:00
John Chilton e461918201 VueJs component to show job metrics. 
- Can operate from a job_id or dataset_id.
- New API endpoint to support this.
 2019-05-23 07:10:49 -04:00
mvdbeek 2d71b0bdfe Use io.open with errors="repalce" instead of comparing byte strings 2019-05-23 11:07:06 +02:00
mvdbeek ab7a38631e Unit test verify module 2019-05-22 17:45:00 +02:00
Dannon f6011bab5b Merge pull request #7992 from jmchilton/more_packages 
Add galaxy-tool-util and galaxy-job-metrics packages.
 2019-05-20 16:36:11 -04:00
mvdbeek 9c06527bbb Simplify convert_newlines_sep2tabs 
Just call convert_newlines with a compiled regex
 2019-05-19 09:30:26 +02:00
mvdbeek b67ddbf036 Drop (seemingly?) unused sep2tabs function 2019-05-19 09:30:26 +02:00
Björn Grüning b8f9d9a75c Merge pull request #7993 from msauria/mcooler 
Add mcool datatypeand extend h5 tool output testing
 2019-05-18 10:11:37 +02:00
mvdbeek 3c5c7a0da2 Parametrize sniff_test 2019-05-17 15:41:14 -04:00
mvdbeek 6878e3973a Fix test_sniff unittest 2019-05-17 15:41:14 -04:00
John Chilton 0e707f2901 Improve sniffing test cases. 2019-05-17 15:41:13 -04:00
John Chilton d3f2ce009e Attempt binary conversion of newlines if UTF conversion fails. 2019-05-17 15:41:13 -04:00
John Chilton 85f9ead2a2 Improved newline conversion handling. 
- Fix bug where sep2tabs didn't work with '\r\n'
- Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines.
- Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(.
- Simplify convert_newlines to just let universal newline handling handle the conversion.
 2019-05-17 15:41:13 -04:00
John Chilton 6000f79b6d Fix extra newlines in peek code. 
Behavior changes:
 - Now includes a trailing new line if the input contained a trailing newline.
 - Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT.
 2019-05-17 15:41:13 -04:00
John Chilton 96d6b0508a Merge pull request #7995 from mvdbeek/jmchilton-newline_fixes 
Datatype I/O fixes
 2019-05-17 15:39:26 -04:00
John Chilton 6bcac4a8a9 Merge pull request #7939 from mvdbeek/jmchilton-objectstore_fix 
Fix non-eager object store with nested object stores
 2019-05-17 13:12:07 -04:00
mvdbeek 5ab6e799f8 Simplify convert_newlines_sep2tabs 
Just call convert_newlines with a compiled regex
 2019-05-17 17:45:04 +02:00
mvdbeek 2e6743e897 Drop (seemingly?) unused sep2tabs function 2019-05-17 16:14:44 +02:00
msauria 9da400a5dd Removed testing using 'containsh5keys' attribute 2019-05-17 10:02:43 -04:00
msauria a563375610 Updated PR based on comments 
Removed log statements from proxy.js
Added space back to validation_hdf5.xml
Changed Mcool class to inherit from Cool in binary.py
 2019-05-17 09:23:23 -04:00
mvdbeek 3d2c243b4d Explicitly create extra_files_path when discovering outputs with extra files 2019-05-17 14:04:23 +02:00
mvdbeek da4887877d Parametrize sniff_test 2019-05-17 12:26:41 +02:00
Nicola Soranzo 75d9e33363 Merge branch 'release_19.05' into dev 2019-05-17 10:10:16 +01:00
mvdbeek 1d967dc7d0 Fix test_sniff unittest 2019-05-17 10:58:23 +02:00
John Chilton caa3d4243a Create galaxy-job-metrics package to share with Pulsar. 2019-05-16 16:45:41 -04:00
John Chilton 939e7774a8 Create galaxy-tool-util package. 
This is (so far a subset of) the tool utilities from galaxy-lib. galaxy-lib mocked out a fake galaxy.tools to allow these to all exist below the galaxy.tools - but this was a terrible hack - in order for the new packages to be true subsets of Galaxy they need to be refactored into a new package that doesn't depend on models, SA, galaxy.jobs, etc...

[x] galaxy.tools.deps -> galaxy.tool_util.deps
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.cwl -> galaxy.tool_util.cwl
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.fetcher -> galaxy.tool_util.fetcher
[x] galaxy.tools.locations -> galaxy.tool_util.locations
[x] galaxy.tools.parser -> galaxy.tool_util.parser
 2019-05-16 16:45:25 -04:00
msauria dfaaf5a5bf Added tool test for recursive subset of h5 keys 2019-05-16 15:52:30 -04:00
John Chilton 28c0a3b077 Improve sniffing test cases. 2019-05-16 15:10:54 -04:00
John Chilton 5496aad8a1 Fix Selenium tests. 
https://jenkins.galaxyproject.org/job/docker-selenium/6478/artifact/6478-test-errors/test_admin_server_display2019051612081558008530/

Likely broken with https://github.com/galaxyproject/galaxy/pull/7790.
 2019-05-16 14:01:48 -04:00
John Chilton fc5d068044 Attempt binary conversion of newlines if UTF conversion fails. 2019-05-15 15:57:44 -04:00
John Chilton 8ae1dd1e4d Improved newline conversion handling. 
- Fix bug where sep2tabs didn't work with '\r\n'
- Fix bug where sep2tabs didn't work with '\r' - we were opening it with universal newlines.
- Fix memory bug where convert_newlines would read unbounded buffers - other methods still do though :(.
- Simplify convert_newlines to just let universal newline handling handle the conversion.
 2019-05-15 15:57:44 -04:00
John Chilton 9913ecdee3 Fix extra newlines in peek code. 
Behavior changes:
 - Now includes a trailing new line if the input contained a trailing newline.
 - Now returns only as many lines as are present if the file contains fewer lines than LINE_COUNT.
 2019-05-15 15:56:06 -04:00
John Chilton 703c968788 Merge pull request #7944 from mvdbeek/expression_tool_improvements 
[19.05] Allow mapping over of expression tool params
 2019-05-14 08:12:38 -04:00
mvdbeek 556ee003ae Fix parse_values_from_file tool and tests 2019-05-14 00:14:34 +02:00
mvdbeek 974f45b043 Allow mapping over of expression tool params 
This allows feeding a collection of parameters values to a parameter
value. This enables https://github.com/galaxyproject/tools-iuc/pull/2404#issuecomment-491740393
for instance, where we normalize a collection based on a computed
parameter.
 2019-05-14 00:14:34 +02:00
John Chilton 3cd0e8f2e8 Fix populators.py workflow testing for non-text inputs. 2019-05-13 17:50:38 -04:00