John Chilton
2d9ae75cae
Fix another bad merge issue?
2017-08-29 15:48:19 -04:00
John Chilton
2ede34659b
Fix bad merge of security patch from 17.05 into dev.
2017-08-28 16:28:27 -04:00
Martin Cech
9337c9fdc1
Merge branch 'release_17.05' into merge-release1705
2017-08-28 12:36:41 -04:00
E Rasche
e6155367e6
2017-08 Security Patch
2017-08-28 10:58:33 +02:00
E Rasche
1d485390b0
2017-08 Security Patch
2017-08-28 10:53:47 +02:00
Dannon Baker
df0507e494
Merge pull request #4471 from erasche/reports-sentry-dsn
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needed for sentry functionality in reports webapp
2017-08-25 06:23:34 -04:00
Dannon Baker
0e467b73bc
Fixes for reports sentry dsn (lint and missing import).
2017-08-24 21:45:16 -04:00
Dannon Baker
c89233c7cb
Merge pull request #4477 from nsoranzo/vcf_bcf_fixes
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Fixes for VCF/BCF datatypes
2017-08-24 20:28:30 -04:00
Dannon Baker
b80ee79b43
Remove /mobile and associated templates. It has been deactivated for almost three years now.
2017-08-24 17:17:56 -04:00
guerler
5d04c593b6
Removes unused comma from subworkflow populator
2017-08-24 14:55:37 -04:00
Dannon Baker
001d94ae4e
Merge pull request #4479 from nsoranzo/use_pysam_in_verify
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Use pysam instead of samtools binary
2017-08-24 11:45:45 -04:00
Eric Rasche
a83438159c
Merge pull request #4458 from xgaia/interactive_environment
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don't uppercase envoverride
2017-08-23 20:36:21 +02:00
guerler
ce7d8a2fc1
Validate workflow step after step argument injection
2017-08-23 11:31:04 -04:00
Nicola Soranzo
d3ae7351f7
Use pysam instead of samtools binary
...
This will make it possible to remove the requirement of having `samtools`
installed when testing tools, e.g. in the tools-iuc TravisCI setup:
https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L59
2017-08-22 20:42:57 +01:00
Nicola Soranzo
a63af63b41
Add requirement for bcftools to set_metadata tool
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The `bcftools` binary is used by the `set_meta()` method of the `Bcf`
datatype class. Having a `<requirement>` for it in the set_metadata tool
makes it possible to use conda to resolve the dependency instead of
forcing the admin to install `bcftools` on the PATH of the Galaxy user.
This will also fix errors like
https://travis-ci.org/galaxyproject/tools-iuc/jobs/266923024#L1994
when running
```
planemo test --conda_dependency_resolution --conda_auto_install
```
2017-08-22 18:29:51 +01:00
Nicola Soranzo
8dc0e697d3
Fix vcf_bgzip datatype
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In https://github.com/galaxyproject/galaxy/pull/4254 `vcf_bgzip` was made
a proper datatype with the introduction of the `VcfGz` class, but was
still described as a subclass in `datatypes_conf.xml` .
Also fix `file_ext` attribute in `BaseVcf` and subclasses.
2017-08-22 17:53:40 +01:00
Nicola Soranzo
da5b72a030
Alias bcf_bgzip datatype to bcf. Add bcf_uncompressed and converters
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Since https://bitbucket.org/galaxy/galaxy-central/pull-requests/353
(only) compressed BCF files have been sniffed as `bcf`, so the `bcf_bgzip`
datatype (introduced 2 years later in
https://github.com/galaxyproject/galaxy/pull/1148 ) is an unused duplicate.
This adds also a distinct `bcf_uncompressed` datatype (and converters) for
the rare cases when it may be useful.
2017-08-22 17:44:53 +01:00
E Rasche
ae48774f54
needed for sentry functionality in reports webapp
2017-08-21 15:21:56 +02:00
guerler
092ad6d67f
Fix quota function name
2017-08-21 08:28:25 -04:00
John Chilton
e3b3457b1f
Merge pull request #4465 from mvdbeek/workflow_invocation_security_check
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Fix checking WorkflowInvocation for published workflows
2017-08-21 07:10:08 -04:00
Martin Cech
2346c0aa7e
Merge pull request #4467 from mvdbeek/saved_history_tags
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More items per page in saved history and directly show tags
2017-08-20 23:21:18 -04:00
mvdbeek
0e46888eed
Show up to 15 histories by default in saved histories menu
2017-08-20 17:42:18 +02:00
mvdbeek
cff306b86b
Only skip check_security checks if check_ownership and check_accessible are false
2017-08-20 11:24:09 +02:00
mvdbeek
2d16470132
Allow admin user to view workflow invocation (thx @nsoranzo)
2017-08-20 11:21:01 +02:00
mvdbeek
80e264d35f
Check ownership of invocation, instead of stored_workflow
2017-08-19 16:07:53 +02:00
mvdbeek
413233eec3
Correctly raise Exception if invocation not found
2017-08-19 14:45:58 +02:00
mvdbeek
912da2f3b9
Fix checking WorkflowInvocation for published workflows
2017-08-19 14:45:58 +02:00
Nuwan Goonasekera
52b26f45a2
Registered genomespace_importer as a tool needing Galaxy's python env
2017-08-19 00:38:08 +05:30
Nuwan Goonasekera
b73e21b584
Formatting and linting fixes for GenomeSpace tool
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
ae6ae8ffe2
Added new config setting for GenomeSpace UI URL
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
cb1b086324
Fixed pylint errors
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
e39901ef06
Moved back some code to wrapper and added back data type sniffing.
2017-08-19 00:38:06 +05:30
Nuwan Goonasekera
1342c2bd70
Integrated File Browsing and Workflow support for GenomeSpace
2017-08-19 00:38:06 +05:30
John Chilton
cd22de114c
Merge pull request #4457 from erasche/sentry-extra-info
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More detailed sentry reports
2017-08-18 13:02:28 -04:00
Dannon Baker
9c6fd670cf
Merge pull request #4455 from nsoranzo/multiline_if_conditionals
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Uniform indentation of multiline if conditionals
2017-08-18 10:13:05 -04:00
John Chilton
e492494282
Merge pull request #4456 from nsoranzo/logging_fixes
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Logging fixes
2017-08-18 09:51:57 -04:00
xgaia
30562c09c5
don't uppercase envoverride
2017-08-18 15:13:57 +02:00
E Rasche
e987b9b9e4
swap id to username
2017-08-18 14:25:44 +02:00
Marius van den Beek
dd89a9c65f
Merge pull request #4437 from jmchilton/galaxy_json_rev
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Enhanced tool options for dataset discovery
2017-08-18 14:18:50 +02:00
E Rasche
8d132b2bca
More detailed sentry reports
2017-08-18 14:18:23 +02:00
Eric Rasche
b459399ede
Merge pull request #4454 from xgaia/interactive_environment
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Interactive Environment: possibility to don't uppercase env variables
2017-08-18 13:48:25 +02:00
Nicola Soranzo
bd88524a10
Fix import order and Python3 compatibility
2017-08-18 12:35:04 +01:00
Nicola Soranzo
e32ad2864f
Remove container config log message from cleanup scripts logs
2017-08-18 12:35:04 +01:00
Nicola Soranzo
4e75635d62
Use log.warning() instead of deprecated warn()
2017-08-18 12:35:04 +01:00
Nicola Soranzo
784e6f5fd3
Merge pull request #4396 from jmchilton/workflow_warnings
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Slightly improve workflow warnings/errors logging.
2017-08-18 12:34:14 +01:00
Nicola Soranzo
d2d1f857bb
Fix import order and Python3 compatibility for lib/galaxy/util/pastescript/serve.py
2017-08-18 12:18:42 +01:00
Nicola Soranzo
cff9292f07
Uniform indentation of multiline if conditionals
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Use 8-spaces indentation for the conditional continuation lines of an
`if`-statement where the conditional part spans multiple lines.
According to PEP-8, using 4-spaces "can produce a visual conflict with
the indented suite of code nested inside the `if`-statement", but the PEP
"takes no explicit position".
There were only 2 places in the whole codebase where 8 spaces were not
used, this will make it uniform.
2017-08-18 12:18:42 +01:00
xgaia
2489499fb6
possibility to don't uppercase env variables
2017-08-18 11:47:00 +02:00
John Chilton
1e1df6786a
Variety of fixes for #4437 .
2017-08-17 15:43:34 -04:00
John Chilton
a8bec7a275
Allow override of provided metadata location.
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Eliminates that terrible circular dependency between tools and jobs.
2017-08-17 15:41:11 -04:00
John Chilton