Nicola Soranzo
9eb1db82ca
Do not convert spaces to tabs when importing datasets into a library.
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Reported (with fix provided) by Fabien Mareuil in
http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-header-td4669160.html
2016-03-22 20:03:32 +00:00
Björn Grüning
30750c32e4
Merge pull request #1880 from dannon/fix_migration_0131_mysql
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[16.01] Fixes to subworkflow migration 0131
2016-03-22 14:14:43 +01:00
Dannon Baker
566f556b07
Merge pull request #1952 from guerler/fix_tool_access_000
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[16.01] Fix tool access rights and forwarding
2016-03-21 19:29:31 -04:00
Dannon Baker
377ccbe23b
Merge pull request #1967 from jmchilton/fix_optional_numeric_params
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[16.01] Fix #1721 .
2016-03-21 16:18:27 -04:00
John Chilton
2efd9c2687
Fix #1721 .
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TODO: write test...
2016-03-21 13:51:26 +00:00
John Chilton
9e9dfdfd55
Fix workflow scheduler log message.
2016-03-21 00:51:18 +00:00
guerler
054fdf76f0
Parse user when filtering tools
2016-03-18 20:48:24 -04:00
guerler
bd0439d9b7
Fix tool access rights and forwarding
2016-03-18 20:12:21 -04:00
Dannon Baker
98c65dcee0
Swap back to the first fix, update metrics api to use new signature.
2016-03-17 13:13:19 -04:00
Dannon Baker
87bcb5f5a1
Fix in a different way not requiring signature change; still not thrilled about overlapping kwarg names w/ stdlib module names.
2016-03-17 12:09:02 -04:00
Dannon Baker
f277f99aed
Fix handling of time in fluent logger.
2016-03-17 11:43:52 -04:00
Dannon Baker
9a343efe8b
Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam
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[16.01] Ensure chrom, start, end as bytestring in BamDataProvider
2016-03-15 16:16:22 -04:00
Marius van den Beek
18473a187e
Ensure chrom, start, end as bytestring in BamDataProvider
2016-03-15 19:41:09 +01:00
Nicola Soranzo
5a50a4691c
Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship
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[16.01] Backport PR #1868
2016-03-11 14:49:06 +00:00
Marius van den Beek
d6e38c7d48
remove unused import
2016-03-11 13:10:08 +01:00
Marius van den Beek
b3e9398c3a
Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship
2016-03-11 13:10:02 +01:00
Martin Cech
3abd2c213a
Merge pull request #1898 from dannon/quota_api_fix_fabien
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[16.01] Quota API issue with serialization to JSON of Decimal
2016-03-10 20:23:00 -05:00
Dannon Baker
a351c75687
Extra documentation for @mvdbeek
2016-03-09 11:31:18 -05:00
Dannon Baker
f0b7a34dd3
Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html
2016-03-09 11:07:12 -05:00
Dannon Baker
c6f3e9b5b2
Slight cleanup, remove outdated comment regarding tabixfile.close()
2016-03-09 10:52:31 -05:00
Dannon Baker
50f1089c72
Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam.
2016-03-09 10:40:19 -05:00
Dannon Baker
0f97b50e9c
Different logic for mysql (just don't worry about keys, due to the agony -- access to the database is entirely procedural and due to this we'd likely see any issues breaking these fk constraints in postgres before mysql (if ever) anyway.
2016-03-07 18:14:04 -05:00
Dannon Baker
ad6273307d
We can't flip storedworkflow back to non-nullable in a downgrade step here, so don't try. Just leave it alone.
2016-03-07 11:57:51 -05:00
Dannon Baker
b23c354f91
Replace testing keynames with real ones.
2016-03-07 10:05:51 -05:00
Dannon Baker
6442cbc3d4
Fix downgrade attempting to drop parent_workflow_id off the wrong table.
2016-03-07 09:53:07 -05:00
Dannon Baker
0e0c1caec4
Fixing subworkflow migration (0131) to work with mysql
2016-03-07 09:53:01 -05:00
guerler
0445fcda51
Add workflow building mode check to collection parameter handling
2016-03-04 09:26:16 -05:00
John Chilton
e0ce68cc58
Fix lack of output when discovering large collections...
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Example log statement collected for each dataset:
```
galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output].
```
2016-03-03 11:48:56 +00:00
Nate Coraor
a494011897
Improve dataset error log message
2016-03-02 11:40:45 -05:00
Dannon Baker
7534182d7a
Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that.
2016-03-01 08:59:14 -05:00
Dannon Baker
16280c6323
Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application.
2016-03-01 08:01:14 -05:00
Dannon Baker
93494a833e
This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure.
2016-03-01 08:01:05 -05:00
John Chilton
56076db848
Disable command isolation for Pulsar...
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... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better.
2016-02-26 12:15:56 +00:00
Nate Coraor
5677c2ee4f
Update version to 16.01
2016-02-24 15:29:14 -05:00
Nate Coraor
e845d649c6
Security fixes for tool shed hg push and capsule/tarball uploads
2016-02-24 11:18:23 -05:00
Nate Coraor
e4a1d57278
Security fixes for tool shed repository browsing
2016-02-24 11:18:23 -05:00
Nate Coraor
cd8b96553f
Remove sample tracking manual external service transfer due to security concerns
2016-02-24 11:18:23 -05:00
Nate Coraor
5da91bddcd
Security fixes for object store paths
2016-02-24 11:18:23 -05:00
Nate Coraor
bf1c77d171
Security fixes for history imports
2016-02-24 11:18:23 -05:00
Nate Coraor
f540a16768
Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory
2016-02-24 11:18:23 -05:00
Daniel Blankenberg
6bb43aa4af
Merge pull request #1786 from jmchilton/format_source_restrictive
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[16.01] format_source in workflow editor is too restrictive.
2016-02-23 17:57:47 -05:00
John Chilton
a5c30c563e
Merge pull request #1771 from mvdbeek/16.01_fix_ies
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[16.01] Remove len(stderr), breaks on recent docker versions
2016-02-23 17:42:27 -05:00
John Chilton
b402093479
format_source in workflow editor is too restrictive.
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Case made well by @erasche on #1746 , fixes #1746 .
To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch.
2016-02-23 17:16:27 +00:00
Nicola Soranzo
5ce771b70e
Strip URL of download_file and download_by_url install actions.
2016-02-23 14:47:23 +00:00
Marius van den Beek
a47a4f40b4
Remove len(stderr), breaks on recent docker versions
2016-02-22 11:56:21 +01:00
Nicola Soranzo
b5e91d2377
Merge branch 'release_15.10' into release_16.01
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Conflicts:
lib/galaxy/util/__init__.py
2016-02-19 11:41:10 +00:00
Nicola Soranzo
ef93629719
Fix pretty_print_time_interval for MySQL. Fix #1619 .
2016-02-18 20:08:14 +00:00
Daniel Blankenberg
b4c823f2cd
Merge pull request #1758 from jmchilton/ts_section_fix
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[16.01] Fix updating in-memory tools for tool shed installs into sections.
2016-02-18 15:03:52 -05:00
Nicola Soranzo
3f34131ff5
Merge branch 'release_15.10' into release_16.01
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Conflicts:
lib/galaxy/version.py
2016-02-18 19:40:14 +00:00
Nicola Soranzo
587d450402
Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702 .
2016-02-18 17:44:08 +00:00
Nicola Soranzo