Martin Cech
1cac9ad54f
Merge branch 'dev' of github.com:galaxyproject/galaxy into dev
2018-01-19 11:06:45 -05:00
mvdbeek
dedb1d3f4c
Fix history import by file on multi-handler setups
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The uploaded archive was going to be deleted before the job started running.
2018-01-19 11:06:24 -05:00
Marius van den Beek
8f65cd46b0
Merge pull request #5180 from bgruening/bam_unsorted
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Add BamNative datatype
2018-01-19 16:37:36 +01:00
Martin Cech
8fa785427c
Merge pull request #5344 from mvdbeek/history_import_fixes
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[17.09] History import fixes
2018-01-19 10:27:55 -05:00
mvdbeek
89d45416fb
Import Registry directly
2018-01-19 15:27:55 +01:00
mvdbeek
654ed86b37
Setup a dummy registry to allow some more operations, e.g. accessing metadata
2018-01-19 15:09:38 +01:00
guerler
662440e730
Add quotes
2018-01-19 14:55:57 +01:00
mvdbeek
ca51898bc4
Fix cleanup datasets script
2018-01-19 14:50:08 +01:00
Jelle Scholtalbers
4947ab0738
use safemakedirs instead of private _ensure_directory
2018-01-19 13:51:54 +01:00
mvdbeek
208dcb9196
Stop walking up to parent HDA
2018-01-19 13:39:31 +01:00
Marius van den Beek
33bd54079b
Merge pull request #4916 from scholtalbers/add_maintenance_script
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Add maintenance script..
2018-01-19 12:26:42 +01:00
mvdbeek
b5d0030b3e
Fix history import by file on multi-handler setups
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The uploaded archive was going to be deleted before the job started running.
2018-01-19 12:15:16 +01:00
guerler
b82676b8ee
Switch to transparent readmode for history tarfiles
2018-01-19 12:14:35 +01:00
mvdbeek
5554c2f9b9
Fix import by url for history archive import tool
2018-01-19 12:14:24 +01:00
ValentinChCloud
747309b278
Fix tool-shed-config-validate
2018-01-19 10:28:14 +00:00
Jelle Scholtalbers
8be4addaa9
update ldap role creation based on comments on PR #5136 and PR #5136
2018-01-19 11:25:04 +01:00
Nicola Soranzo
c8a7b7b07c
Merge pull request #5335 from mvdbeek/no_check_data
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Work around (temporarily) wrong getsize() output
2018-01-19 08:58:26 +00:00
mvdbeek
161467513b
Use a for loop when checking size in object store
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and adjust `empty()` to use the new code. Thanks @nsoranzo.
2018-01-19 08:23:50 +01:00
mvdbeek
16344a62d3
Alternative fix for missing metadata on datasets that report output size 0
2018-01-19 08:23:50 +01:00
mvdbeek
1a43ef5b83
Work around (temporarily) wrong getsize() output
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I'm not sure how/why this happens, but this can be reproduced by copying a file to a location in one process, while checking the size in another process:
Run this to copy a file indefinitely:
```
import os
import shutil
open('test').write("foo")
while True:
shutil.copy('test', 'test.file')
os.remove('test.file')
```
In the same directory run this
```
import os
count = 0
wrong_size = False
while True:
try:
size = os.path.getsize('test.file')
if size == 0:
wrong_size = True
wrong_count = count
elif wrong_size and os.path.getsize('test.file') != 0:
# We have seen the wrong size being reported, but now it's correct again
print("Got wrong file size at %dnd try, was fixed in %dnd try" % (wrong_count, count))
break
except Exception:
pass
count += 1
```
It'll (probably) fail like this:
```
Got wrong file size at 0nd try, was fixed in 1nd try
```
or more often:
```
Got wrong file size at 31nd try, was fixed in 32nd try
```
This seems to be fixed when running os.path.getsize() another time,
so we simply do that here.
2018-01-19 08:23:50 +01:00
Martin Cech
4993249ab6
Merge pull request #5340 from dannon/tour_path_tweak
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Disable galaxy tour 'path' navigation
2018-01-18 20:57:18 -05:00
Dannon Baker
7af6381e24
Disable galaxy tour 'path' navigation -- this style of tour nav behaves very poorly with Galaxy and it's pretty easy to get a tour completely *stuck* in reload loops from the user experience, forcing manual cache cleaning or the like to make Galaxy usable again.
2018-01-18 17:12:45 -05:00
khillion
12917d933e
fix flake8
2018-01-18 16:52:28 -05:00
khillion
35469c122d
add example phylip and docstring test
2018-01-18 16:41:17 -05:00
Martin Cech
7659efc68c
Merge pull request #5105 from jmchilton/ini_to_yaml_config
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Convert options file to YAML and use uWSGI by default
2018-01-18 15:50:44 -05:00
khillion
b649886eb8
fix datatypes_conf sniffer and code gardening
2018-01-18 15:47:31 -05:00
Dannon Baker
d51ea5d200
Constrain the select2 container for the tags display, instead of the outer box; this prevents the prompt from (in some cases) taking the space.
2018-01-18 15:35:38 -05:00
Dannon Baker
7434326006
Constrain tag editor height, minor refactoring. Will be removed with the conversion to a vue component that can pop out with a more flexible display.
2018-01-18 15:32:08 -05:00
Martin Cech
b174dafa36
Merge pull request #5333 from dannon/jenkins_client_build_tweak
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Move the client build for selenium to in-repo script
2018-01-18 14:06:17 -05:00
Nate Coraor
dd0aeec500
Fix lint error
2018-01-18 12:53:42 -05:00
Nate Coraor
3fdbaa3dec
Regenerate galaxy.yml.sample and documentation for newly
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added/documented config options.
2018-01-18 12:31:41 -05:00
Nate Coraor
44c291bc66
Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config
2018-01-18 12:30:05 -05:00
Dannon Baker
e61d5cdadf
Build sourcemaps for the jenkins selenium tests -- I don't know that this actually gets resolved, but it doesn't have a huge impact on build time anyway
2018-01-18 11:26:59 -05:00
Dannon Baker
a48d0e9a7f
Merge remote-tracking branch 'upstream/release_17.09' into dev
2018-01-18 10:57:58 -05:00
Dannon Baker
3c85407ec8
Merge pull request #5331 from mvdbeek/data_manager_reload_fix
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[17.09] Prevent reloading when data table is being modified
2018-01-18 10:42:33 -05:00
Dannon Baker
3681a4b77f
Move the client build for selenium to run_tests.sh instead of in the external jenkins job configuration. Has the added benefit of skipping the client build when we don't want to run it.
2018-01-18 10:34:04 -05:00
Jelle Scholtalbers
729b0bf63b
fix toolshed test with missing config attribute
2018-01-18 15:48:29 +01:00
Jelle Scholtalbers
8553ea2c6e
move logic to webapps.py
2018-01-18 15:48:29 +01:00
Jelle Scholtalbers
ae3afae8f0
sort import order alphabetically
2018-01-18 15:48:29 +01:00
Jelle Scholtalbers
74e551d34c
one less variable..
2018-01-18 15:47:40 +01:00
Jelle Scholtalbers
5071b69871
Add option to auto create user_library_import_dir directories upon user login.
2018-01-18 15:47:40 +01:00
mvdbeek
8f91ae0db9
Reload tool data tables for 'undeclared_tables'
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Thanks @nsoranzo!
2018-01-18 15:25:39 +01:00
mvdbeek
8c1807c287
Trigger reload for each modified data table
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In unindeted one level too much in the previous commit, which would only reload
the last table (thanks @dannon). The alternative would be to reload all tables,
but I think this is more efficient.
2018-01-18 15:17:14 +01:00
mvdbeek
d94148ff79
Prevent reloading when data table is being modified
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Fixes https://github.com/galaxyproject/galaxy/issues/4783 .
2018-01-18 15:05:47 +01:00
khillion
e7f82f8fef
drop __init__
2018-01-18 07:59:38 -05:00
Dannon Baker
c3d145ce99
Merge pull request #5327 from martenson/fix-structured-lib-link
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[17.09] fix link to library from history structure view
2018-01-17 18:05:36 -05:00
Martin Cech
bf2c9bab34
Merge pull request #5321 from mvdbeek/rerun_without_dependent_jobs
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Add option to replace failed elements on job rerun
2018-01-17 16:42:37 -05:00
Martin Cech
6bef1fcbaa
remove an extra F from the folder ID
2018-01-17 15:50:06 -05:00
Martin Cech
d2530f4f24
Merge pull request #5258 from bernt-matthias/topic/getmicrobedata-quick-fix
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Topic/getmicrobedata quick fix
2018-01-17 14:49:29 -05:00
mvdbeek
8ecc86cb67
Simplify conda framework setup
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Thanks @nsoranzo!
2018-01-17 19:32:15 +01:00
Martin Cech