John Chilton
b477a0891b
Merge pull request #12105 from natefoo/dependency-resolution-config-docs
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Update dependency resolver docs and drop sample XML file in favor of direct configuration under the dependency_resolvers key of galaxy.yml
2021-06-09 11:03:26 -04:00
Martin Cech
75bb4de6b3
Merge pull request #12114 from martenson/label-change
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docs: change GIEs label to interactive-tools
2021-06-09 16:09:02 +02:00
Martin Cech and Nicola Soranzo
b2be4564bf
proper ordering
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-06-09 14:50:53 +02:00
Martin Cech
d9d531697e
docs: change GIEs label to interactive-tools
2021-06-09 14:36:58 +02:00
Björn Grüning
038850977d
Merge pull request #12101 from kxk302/new_irods_client
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Upgraded irods client to v1.0.0
2021-06-09 07:56:29 +02:00
Björn Grüning
28201c1c53
Merge pull request #12108 from jmchilton/type_redundancy
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Fix up some typing redundancy.
2021-06-09 07:53:13 +02:00
John Chilton
f7a88314b7
Fix up some typing redundancy.
2021-06-08 15:33:11 -04:00
Nate Coraor
15e1b06ba5
A few more updates to the tool deps documentation
2021-06-07 20:54:23 -04:00
Nate Coraor
2ddc310711
Update dependency resolver docs and drop sample XML file in favor of
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direct configuration under the dependency_resolvers key of galaxy.yml.
2021-06-07 18:16:07 -04:00
Kaivan Kamali
92a801b791
Upgraded irods client to v1.0.0
2021-06-07 09:41:59 -04:00
Nicola Soranzo
c1eae49615
Merge branch 'release_21.05' into dev
2021-06-06 20:10:04 +01:00
Nicola Soranzo
2e926a7b5e
Merge branch 'release_21.01' into release_21.05
2021-06-06 20:09:13 +01:00
Marius van den Beek
e82cdcbd90
Merge pull request #12096 from nsoranzo/release_21.01_backport_11830
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[21.01] Backport #11830
2021-06-05 07:53:56 +02:00
Mason Houtz
58c6be8475
Fixed uploader link on tool list and legacy empty history message
2021-06-05 01:28:31 +01:00
Sergey Golitsynskiy
796026daa6
Merge pull request #12089 from ic4f/dev_sa_1.4.17
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Update SQLAlchemy to 1.4.17
2021-06-03 17:10:12 -04:00
Sergey Golitsynskiy
050e710b1f
Merge pull request #12090 from jmchilton/webapp_name
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Rework variable name to clarify this is a wsgi application.
2021-06-03 16:32:40 -04:00
John Chilton
9d950af3b0
Rework variable name to clarify this is a wsgi application.
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Working on the architecture slides and I think this improves the readibility and clarity of this code.
2021-06-03 14:05:30 -04:00
Sergey Golitsynskiy
94ce70aa8b
Update SQLAlchemy to 1.4.17
2021-06-03 12:22:54 -04:00
Marius van den Beek
7be3099d91
Merge pull request #12080 from OlegZharkov/fix_edit_field_reactivity
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[21.05] Fix edit field reactivity in libraries
2021-06-03 12:52:05 +02:00
mvdbeek
bf78f40bf6
Merge branch 'release_21.05' into dev
2021-06-03 10:23:52 +02:00
mvdbeek
90dff9af5b
Merge branch 'release_21.01' into release_21.05
2021-06-03 09:54:23 +02:00
John Chilton
65e702b5d8
Merge pull request #12088 from mvdbeek/fix_fetch_data_dicovered_output_metadata_setting
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[21.01] Fix set metadata for primary discovered outputs
2021-06-02 16:06:35 -04:00
Oleg Zharkov
a79207245b
lint
2021-06-02 20:38:23 +02:00
Oleg Zharkov
275cc67562
remove refs
2021-06-02 20:24:10 +02:00
Marius van den Beek
17078f5011
Merge pull request #12040 from Nerdinacan/standardize-mounts
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Normalize Vue mounts in analysis, admin endpoints
2021-06-02 20:22:25 +02:00
Marius van den Beek
cca54f5d29
Merge pull request #12072 from ic4f/dev_pytest_classes
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Enable pytest class-based tests
2021-06-02 18:56:42 +02:00
Marius van den Beek
edc56b399a
Merge pull request #12086 from OlegZharkov/select_all_in_collections
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[21.05] Fix export select_all in collections
2021-06-02 18:53:14 +02:00
Marius van den Beek
65254bcc89
Merge pull request #12087 from OlegZharkov/fix_filter_on_search
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[21.05] fix library search filter
2021-06-02 18:49:29 +02:00
mvdbeek
bd5596f382
Maybe skip setting metadata twice
2021-06-02 18:46:26 +02:00
mvdbeek
c16446b9a3
Use Job.states.OK
2021-06-02 18:46:26 +02:00
mvdbeek
5b5ebf90d5
Add API test for fetch_data with bam fails
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This fails without the preceding commit.
2021-06-02 18:46:26 +02:00
Oleg Zharkov
a664b9d8f1
change value to v-model typo in name
2021-06-02 17:02:35 +02:00
mvdbeek
82d66bdd29
That's needed for things set via galaxy.json
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But it does mean that we might be running set_meta twice.
Need to figure out a better way of doing this.
2021-06-02 12:47:47 +02:00
mvdbeek
bd6fe02aa8
Fix set metadata for primary discovered outputs
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We were previously setting metadata on the path that `filename_override`
points to, which (should be an output in the job working directory, or an
output in the object store.
That does not work for `unnnamed_outputs` that are inferred via
galaxy.json and that are discovered using collect_dynamic_outputs. In
most cases that doesn't lead to an exception, but it does fail for bam
files (and a small subset of other datatypes I would guess) if you
specify the extension explicitly (if the extension is not set, sniffing
on the empty dataset results in `data`, which will prevent the
exception). For datatypes that don't fail in `set_metadata` on empty
input files metadata would then be set again when collecting dynamic
outputs, this time using the correct path.
The fix here is to check whether the file we're setting metadata for is
actually an unnamed output, and override the path with the path to the
file in the working directory. To prevent setting metadata twice we also
skip setting metadata on files that already have a database id (which
should only be these primary discovered outputs).
2021-06-02 11:30:20 +02:00
Sergey Golitsynskiy
8df642edbc
Fix linting errors
2021-06-01 15:32:56 -04:00
Sergey Golitsynskiy
fb179aa66d
Rename unit test helper classes (workflow support)
2021-06-01 15:08:17 -04:00
Sergey Golitsynskiy
9f0996ad32
Rename unit test helper class (TestConfig)
2021-06-01 15:08:17 -04:00
Sergey Golitsynskiy
a4b199a181
Rename unit test helper class (TestComputeEnvironment)
2021-06-01 15:07:40 -04:00
Sergey Golitsynskiy
0a43b58d35
Rename unit test helpers, use fixtures
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1. Rename class TestFoo > Foo to avoid conflict with pytest's python test
discovery convention.
2. Use fixtures to reduce duplication, centralize object creation.
2021-06-01 12:56:55 -04:00
Sergey Golitsynskiy
0b094438e0
Enable pytest class-based tests; add flag if n/a
2021-06-01 12:30:25 -04:00
Aysam Guerler
7253dc8898
Merge pull request #12085 from hexylena/make-report-components-full
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Make components full width
2021-06-01 11:55:52 -04:00
John Chilton
7a9a058b5b
Merge pull request #12075 from mvdbeek/fix_double_scheduling
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[21.05] Don't start workflow scheduler for handler in job pool
2021-06-01 10:43:02 -04:00
John Chilton
52a5247b57
Merge pull request #12077 from maximskorik/patch-1
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Fix typo in `interactivetool_jupyter_notebook.xml` help section
2021-06-01 10:39:54 -04:00
John Chilton
6c1030a620
Merge pull request #12045 from ic4f/dev_declarative2
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Migrate model to declarative mapping
2021-06-01 10:38:36 -04:00
John Chilton
99048b6768
Merge pull request #12082 from OlegZharkov/select_all_backbone_modal
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[21.05] Fix select all in import from history backbone modal
2021-06-01 10:25:45 -04:00
John Chilton
4f14f3d57b
Merge pull request #12084 from bioflowy/fix_s3_multipart_upload_bug
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Open partfile in rb-mode in multipart uploading
2021-06-01 10:24:21 -04:00
Oleg Zharkov
637109b222
lint
2021-06-01 15:51:01 +02:00
Oleg Zharkov
3ba6230c3a
fix lint
2021-06-01 15:49:40 +02:00
Oleg Zharkov
126909be04
remove unused function
2021-06-01 15:32:56 +02:00
Oleg Zharkov
a78e99bca6
fix https://github.com/galaxyproject/galaxy/issues/12014
2021-06-01 15:32:46 +02:00
John Chilton