Martin Cech
42e274d334
Merge pull request #4122 from galaxyproject/release_17.01
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[17.05] merge Release 17.01
2017-05-30 10:11:51 -04:00
John Chilton
55336d2c31
Fix legacy Python path for genome diversity tools from miller lab.
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Fixes #4108 .
2017-05-28 19:34:20 -04:00
Dannon Baker
dd06a01746
Handle *both* paths for tag appending using the now-dict correctly.
2017-05-26 10:22:13 +01:00
Dannon Baker
b6e8d3e8ac
Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though.
2017-05-26 10:14:48 +01:00
Dannon Baker
68433b1eff
Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one)
2017-05-25 15:33:09 +01:00
Martin Cech
18ef6a6ab0
Update version to 17.05
2017-05-24 10:47:27 -04:00
Nicola Soranzo
31015a83af
Remove residual comment
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Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
2017-05-24 11:18:47 +01:00
Martin Cech
0268f5078c
Merge pull request #4107 from guerler/fix_repeats_in_workflows
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[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
2017-05-23 13:50:26 -04:00
Martin Cech
3d1da8e11d
Merge pull request #4089 from mvdbeek/no_global_changes
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[17.05] Do not modify self.app.config.tool_data_path
2017-05-23 13:19:41 -04:00
Martin Cech
aa8aafb109
Merge pull request #4104 from dannon/tags_continued
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[17.05] Change to only inheriting 'name' tags
2017-05-23 13:01:19 -04:00
guerler
6f8472e525
Fixes repeat handling in workflow editor, store values as passed from ui
2017-05-23 08:08:28 -04:00
Bjoern Gruening
9ec6c13fa9
update openbabel to version 2.4.1
2017-05-21 14:12:58 +02:00
mvdbeek
a1c14ee8fa
Do not modify self.app.config.tool_data_path
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and self.app.config.tool_data_table_config_path during metadata setting.
xref https://github.com/galaxyproject/tools-iuc/issues/1315 .
I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
2017-05-19 20:04:17 +02:00
Björn Grüning
4125f79161
Merge pull request #4034 from jmchilton/k8_name_fixed
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[17.05] Sanitize container names sending to Kubernetes.
2017-05-17 22:36:51 +02:00
Martin Cech
185c76605f
Merge pull request #4033 from jmchilton/dispatch_fix
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[17.05] Fixes for containerized job executions.
2017-05-12 17:36:32 -04:00
Martin Cech
0bafd683f1
Merge pull request #4020 from jmchilton/fix_explicit_container_resolver_from_config
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[17.05] Fix setting up explicit container resolution...
2017-05-12 17:34:56 -04:00
Nicola Soranzo
9940ae7030
Merge branch 'release_17.01' into release_17.05
2017-05-11 18:23:52 +01:00
Dannon Baker
3e079a9f2c
Fix for s3objectstore _clean_cache method, thanks to @zzsoni and @nsoranzo
2017-05-11 12:26:42 -04:00
mvdbeek
c38c0276af
Exit with error message when conda environemnt could not be activated (thx @nsoranzo).
2017-05-07 16:34:54 +02:00
mvdbeek
a0c59d8f05
Try activating conda environment again if previous activation failed
2017-05-05 19:52:41 +02:00
John Chilton
be7dea47d5
Sanitize container names sending to Kubernetes.
2017-05-05 13:25:50 -04:00
John Chilton
a9faa4873e
Do not attempt to use mulled containers if tool requires legacy Galaxy environment.
2017-05-05 13:20:45 -04:00
John Chilton
f26e358321
Fix docker_dispatch dynamic destination rule for container resolvers.
2017-05-05 13:19:16 -04:00
John Chilton
3332dfb671
[17.05] Fix setting up explicit container resolution from a container resolution config file.
2017-05-04 10:30:21 -04:00
Martin Cech
6ef7b9977a
Merge pull request #4015 from erasche/remote-user-bug
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[17.05] Typo in remote user / user preferences exception
2017-05-03 17:18:35 -04:00
mvdbeek
8dd5b153ed
Pass hdca and element_identifier to _serve_raw
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This is necessary for getting the new filenames introduced in #3985 if
downloading tabular datatypes. Closes #4016 .
2017-05-03 20:08:40 +02:00
Eric Rasche
460d1737be
typo
2017-05-03 17:42:24 +00:00
John Chilton
8db51db702
Update version to 17.05.rc1
2017-05-02 14:56:20 -04:00
John Chilton
06d0e4fce5
Merge remote-tracking branch 'upstream/release_17.01' into dev
2017-05-02 14:54:05 -04:00
Nate Coraor
d224bedd39
Implicitly set use_volumes = False if using Docker swarm
2017-05-02 12:04:34 -04:00
John Chilton
1c8370cf33
Restore line accidentally removed as part of #3985 .
2017-05-02 10:19:32 -04:00
Nicola Soranzo
de46a0edba
Merge pull request #3935 from jmchilton/more_maf_fixes
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[17.01] More careful inspection of fixes for MAF tools requiring Galaxy.
2017-05-02 14:53:08 +01:00
Martin Cech
a6415b25fd
Merge pull request #3909 from mvdbeek/speedup_toolbox
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Speedup startup and toolbox operations
2017-05-02 09:29:37 -04:00
John Chilton
86ebe28667
Enhance filenames with collection context when downloading datasets from GUI.
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- Reduce duplication related to calculating filename.
- Formalized pattern for normal dataset download using string.Tempalte - "Galaxy${hid}-[${name}].${ext}".
- In the context of collections, hid and name of the datasets are pretty worthless so I used a second pattern for collections based on where it is in the current GUI frame. The new pattern is "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}".
- The patterns make this a little more tweakable - for people who want something different it should be pretty straight forward to make these patterns configurable.
Fixes #2140 I think.
2017-05-01 21:19:13 -04:00
Eric Rasche
09404117b9
Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes
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Rework Jupyter IE for additional_ids handling.
2017-05-01 18:08:43 +00:00
mvdbeek
af156a8f74
Build search index at startup, rebuild repository cache during toolbox or datamanager reload
2017-05-01 16:06:48 +02:00
mvdbeek
2587ab55b8
Remove operations from custom_datatype_manager
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Updating the upload file formats is handled when loading the datatype
into the registry, and reloading the upload tool seems unnecessary and
insufficient, since this would only affect the current web handler. In
any case removed and added datatypes are immediately propagated to the
upload tool.
2017-05-01 16:06:48 +02:00
mvdbeek
cdad5bee9b
Attempt to speedup proprietary datatype loading
2017-05-01 16:06:48 +02:00
mvdbeek
86684df5ef
Skip time-based reloading, rely on detecting DetachedInstanceErrors to trigger cache rebuild
2017-05-01 16:06:47 +02:00
mvdbeek
b666649c81
Work around InstanceDetached errors
2017-05-01 16:06:47 +02:00
mvdbeek
84351de20b
Send control task as postfork function
2017-05-01 16:06:47 +02:00
mvdbeek
ff1b66afb3
Fix thread local cache use
2017-05-01 16:06:47 +02:00
mvdbeek
b4e4f3ce7a
Use current session
2017-05-01 16:06:47 +02:00
mvdbeek
f199d5b434
Keep cache thread-local
2017-05-01 16:06:47 +02:00
mvdbeek
5a26896745
Write out datatype registry when loading set_metadata tool
2017-05-01 16:06:46 +02:00
mvdbeek
5e7da2c910
Don't fail tests without internet connectivity
2017-05-01 16:06:46 +02:00
mvdbeek
f88304b65b
Build toolbox search in a local control task
2017-05-01 16:06:46 +02:00
mvdbeek
3079d0c239
Write out the datatype registry only once
2017-05-01 16:06:46 +02:00
mvdbeek
869d7bf481
Replace getchildren(), which has been deprecated ( https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren )
2017-05-01 16:06:46 +02:00
mvdbeek
73c7c364a2
Use tool_shed_repository_cache in populate_tool_shed_info
2017-05-01 16:06:46 +02:00
Martin Cech