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Author SHA1 Message Date
mvdbeek cbcee585b5 Use contextmanager when using compression_util.get_fileobj() 2017-06-30 11:56:59 +02:00
Dannon Baker 8169129981 Merge pull request #4253 from bwlang/refactor_tag_manager 
refactors tag manager to use only what it needs…
 2017-06-28 11:40:32 -04:00
Anton Nekrutenko dd0336e7d2 Merge pull request #4113 from erasche/security-policy 
[PROCEDURES] Security policy
 2017-06-28 14:36:06 +02:00
Brad Langhorst 8f416951bf TagManager in toolshed is not related 
To GalaxyTagManager
Fixes toolshed failing test
 2017-06-28 08:15:38 +02:00
Nicola Soranzo 40cd2df06b Merge pull request #4239 from dpryan79/sniffSkipComments 
Enable skipping comment lines while sniffing files
 2017-06-28 08:15:03 +02:00
Devon Ryan e5e83833d1 Style and ignore '' comment_designators 2017-06-28 07:19:16 +02:00
Marius van den Beek 6cd026bc7b Merge pull request #4237 from dpryan79/fastqSniffer_implement3571 
Sniff fastqsanger and prefer it over fastq if the quality scores match
 2017-06-28 00:34:08 +02:00
Devon Ryan e6278a778d Remove camel case 2017-06-28 00:27:44 +02:00
Brad Langhorst 49ccf2f49c Should address too much indentation flake issue 2017-06-27 23:30:20 +02:00
Martin Cech e98378160a Merge pull request #4232 from pvanheus/dev 
add public-only filter for data libraries
 2017-06-27 21:41:15 +02:00
Brad Langhorst 7c86c5480b refactors tag manager to use only what it needs… 
an sql_alchemy session, not the full app.
This makes it possible to use the tag manager from
the model.
 2017-06-27 18:32:34 +02:00
Devon Ryan e21e9ec15f Ugh, there were multiple places where the sniffing order was specified (binary formats are different). 2017-06-27 15:21:34 +02:00
Nate Coraor 153b8d4dca Merge pull request #4096 from bernt-matthias/dev 
get real user name from username and email (for submission as real user with drmaa)
 2017-06-27 13:54:22 +02:00
Devon Ryan 3bb3ecb09b Typo 2017-06-27 11:31:35 +02:00
Devon Ryan 907bd53776 Make the phred range stricter and more explicit. 2017-06-27 11:11:19 +02:00
Devon Ryan f3853a0956 Test a non-fastqsanger file and ensure it doesn't pass the sniff test. 2017-06-27 11:01:46 +02:00
Devon Ryan 9c10b6ce5d For file sniffing, allow get_headers() to skip comment lines, which should prevent at least some instances of #3148. 2017-06-27 10:53:31 +02:00
Martin Cech 6a43fad892 Merge branch 'dev' into lib_exclude_restricted 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
 2017-06-27 10:49:56 +02:00
Martin Cech c41b284999 adjust logic to match the include deleted checkbox 
also make client and set default user preference
 2017-06-27 10:41:22 +02:00
Devon Ryan 8eaede3110 Fix sequence.py unit test 2017-06-27 10:11:30 +02:00
Devon Ryan 798b73eb68 Fix line reordering 2017-06-27 09:46:05 +02:00
Devon Ryan ab1127334f Remove debugging stuff, since everything works inside of docker 2017-06-27 09:44:39 +02:00
Nicola Soranzo a57b4c1715 Merge branch 'release_17.05' into dev 
Conflicts:
	static/maps/mvc/tool/tool-form-base.js.map
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/tool/tool-form-base.js
 2017-06-27 03:25:44 +02:00
Devon Ryan bc13a16f83 Add the compressed datatypes to the sniffer lsit 2017-06-26 22:18:38 +02:00
Björn Grüning 46dbf8d10c Merge pull request #3076 from peterjc/gff3_filter_by_attribute 
GFF3 support in filter by attribute
 2017-06-26 18:00:45 +02:00
Peter van Heusden e63ababa79 add public-only filter for data libraries 2017-06-26 17:10:45 +02:00
Devon Ryan 0a942d79a3 Checking the quality lines will make fastqsanger checks rather more relevant. 2017-06-26 16:36:17 +02:00
Nicola Soranzo ce1316d680 Merge pull request #4226 from dpryan79/CompressedFastqLines_implement4144 
Running a word count on a compressed fastq file now runs wc on the un…
 2017-06-26 14:06:26 +02:00
Devon Ryan 8a6ef05858 Single quote file names 2017-06-26 13:56:56 +02:00
Devon Ryan 694d8c8555 Sniff FastqSanger before Fastq, in the former case checking the quality scores for compatibility 2017-06-26 13:55:12 +02:00
peterjc 005f3d9f98 Defensive code in case standard GFF fields missing 2017-06-26 11:16:14 +01:00
peterjc c87e0eedb7 Cope with GFF3 as well as legacy GFF. 
In GFF3 have key=value rather than space separated
as in legacy GFF and GTF format. Closes #3068.
 2017-06-26 11:16:06 +01:00
peterjc cb40b01db8 Ignore blank lines and comments in GFF files 
Previously would wrongly issue warnings about valid # lines.
Closes #3067
 2017-06-26 11:15:08 +01:00
Devon Ryan 4ee1848992 Running a word count on a compressed fastq file now runs wc on the uncompressed file 2017-06-26 12:03:57 +02:00
pvanheus b1477a8b87 Merge pull request #4 from galaxyproject/dev 
Merge just before GCC2017
 2017-06-26 09:32:21 +02:00
John Chilton 3ec2c7831d Merge pull request #4224 from nsoranzo/fix_get_datatype_by_extension 
Fix Registry.get_datatype_by_extension() to return None if ext is unknown
 2017-06-26 04:26:47 +00:00
Nicola Soranzo e8c2313640 Small fixes 2017-06-26 01:30:48 +01:00
Nicola Soranzo 02ffcd5c8f Fix import order and Python3 compatibility for lib/galaxy/datatypes/registry.py 
xref. https://github.com/galaxyproject/galaxy/issues/1715
 2017-06-26 01:30:44 +01:00
Nicola Soranzo 0bfa1df72f Fix Registry.get_datatype_by_extension() to return None if ext is unknown 
Without this fix, the Cheetah expression:

$dataset.is_of_type('unknown_ext')

in a tool command would be equivalent to:

$dataset.is_of_type('txt')

meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.

xref. https://github.com/galaxyproject/tools-iuc/issues/1373

Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
 2017-06-26 00:43:41 +01:00
Björn Grüning 73faf7c8b6 Merge pull request #4223 from pvanheus/patch-3 
Correct name of neo4j datatype class
 2017-06-24 05:44:38 +02:00
pvanheus 00928743bf Correct name of neo4j datatype class 
Its neo4j.Neo4jDB: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/neo4j.py#L89
 2017-06-23 23:25:09 +02:00
Dannon Baker a910763cd8 Merge pull request #4208 from jmchilton/singularity_volume_fix_2 
Add missing lines for fixing Singularity volumes.
 2017-06-22 18:01:06 -04:00
Dannon Baker c18479b79c Merge remote-tracking branch 'guerler/grids_published' into dev 2017-06-22 17:15:50 -04:00
John Chilton 27e843bfc1 Merge pull request #4213 from bgruening/improve_search_plugin 
Improve search plugin
 2017-06-22 15:49:00 -04:00
John Chilton 739fb083f0 Merge pull request #4216 from thobalose/neo4j-ie 
Upgrading Neo4j IE to 3.1
 2017-06-22 15:47:14 -04:00
Martin Cech 9dca211e2f Merge pull request #4214 from guerler/revise_tool_url 
[17.05] Improve resilience of tool url building
 2017-06-22 14:06:52 -04:00
Martin Cech 9cec283b5a make the overlay icon toggleable, change wording 2017-06-22 11:28:32 -04:00
Thoba Lose 009f44c25f using sanbi-sa image. 2017-06-22 15:00:03 +02:00
guerler a498390bef Fix basic version changes for reloaded tools 2017-06-21 23:06:15 -04:00
guerler 69e76f98fa Remove redundancy of tool_id parameter 2017-06-21 17:10:52 -04:00