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Cloud ObjectStore #4352

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538ef00
Also load yaml sample files. cc @jmchilton, is this ok?
hexylena Aug 8, 2017
3e8919c
correct name to type
hexylena Aug 8, 2017
5563ecc
fix import order
hexylena Aug 10, 2017
00ee109
fix css class
hexylena Aug 10, 2017
4c36b5a
not a useful test in this location
hexylena Aug 10, 2017
a2b0206
Remove unneeded messages.mako.
jmchilton Aug 10, 2017
4146123
rebuild client
hexylena Aug 10, 2017
6d7d4e9
Merge pull request #4305 from erasche/bug-report-actions
jmchilton Aug 10, 2017
fcd06a9
Merge pull request #4408 from erasche/grt-pardir
jmchilton Aug 10, 2017
e3de5e2
Merge pull request #4329 from glormph/collection_list_sort
jmchilton Aug 10, 2017
bcdf2c8
Merge pull request #4254 from ffinfo/vcf_gz_datatype
jmchilton Aug 10, 2017
583765c
Merge branch 'dev' into revise_grid_forms
guerler Aug 10, 2017
be19b36
Merge branch 'revise_grid_forms' into admin_grid_roles
guerler Aug 10, 2017
b38ccbc
Merge branch 'admin_grid_roles' into admin_grid_groups
guerler Aug 10, 2017
ad2f39c
Fix lint
guerler Aug 10, 2017
6a7cc34
Bring Galaxy, reports, and shed run scripts in sync.
jmchilton Aug 22, 2016
72e5a00
Centralize launching server for reports and tool shed.
jmchilton Aug 23, 2016
1bdb99b
Update galaxy.util.properties to allow YAML.
jmchilton Aug 25, 2016
8189a1f
Scripts to manage configuration infrastructure.
jmchilton Aug 26, 2016
7973a91
Add uwsgi_schema.yml.
jmchilton Aug 26, 2016
90e899d
Update tool shed to use newer configuration schema.
jmchilton Aug 23, 2016
102566d
Update Galaxy Reports to use newer configuration schema.
jmchilton Aug 26, 2016
50d426e
Add reports documentation to ``doc/``.
jmchilton Aug 26, 2016
4945f55
Makefile shortcuts for configuration script.
jmchilton Aug 26, 2016
ef46a60
Add required dependency on uwsgi.
jmchilton Aug 26, 2016
8191fd4
Add pykwalify as dependency for the new config validation stuff.
jmchilton Sep 15, 2016
ffe295e
Fix Python 3 linting problem with test_config_manage.py.
jmchilton Nov 16, 2016
1ce93cc
Pin version of uWSGI to freshly released 2.0.15 available on wheels.g…
jmchilton Mar 13, 2017
539a62f
Fix ORM scripts for #3179.
jmchilton Apr 6, 2017
98ca8ce
Update config overhaul branch for introduction of galaxy.web.stack pa…
jmchilton Apr 11, 2017
23db89b
Merge remote-tracking branch 'jmchilton/dev' into install_workflow_an…
jmchilton Aug 10, 2017
7dd3ddc
Require admin for new import_tools function in workflows API.
jmchilton Aug 10, 2017
6353704
Merge pull request #4039 from VJalili/patch-11
jmchilton Aug 10, 2017
e49ba40
Generalize allow_library_path_paste to allow_path_paste.
jmchilton Aug 9, 2017
f97efa6
Remove unused dataset_info in parameters.grouping.
jmchilton Aug 10, 2017
33acc1f
Merge branch 'admin_grid_groups' into admin_grid_toolversion
guerler Aug 10, 2017
ba3249a
Add missing chemical formats to datatypes_conf.xml.sample
nsoranzo Aug 10, 2017
61d172f
Update pin for flake8-docstrings
nsoranzo Aug 11, 2017
a249dc0
Use container-based infrastructure (sudo: false) in TravisCI
nsoranzo Apr 26, 2017
ef2c32a
Fix lint
guerler Aug 11, 2017
600b0aa
Merge pull request #4377 from guerler/revise_grid_forms
martenson Aug 11, 2017
33c794d
Merge pull request #4385 from guerler/admin_grid_roles
jmchilton Aug 11, 2017
10285b8
Tweak Excel format phrasing based on review from @nsoranzo.
jmchilton Aug 11, 2017
fbde34f
Add EDAM format for excel.xls datatype.
jmchilton Aug 11, 2017
cca00ea
Merge pull request #4404 from jmchilton/allow_path_paste
martenson Aug 11, 2017
c6e45e7
Merge pull request #4410 from jmchilton/excel97
bgruening Aug 11, 2017
331851b
Merge pull request #3179 from jmchilton/web_config_overhaul_0
bgruening Aug 12, 2017
7a1fbd3
Fix bug in upload HTML checker.
jmchilton Aug 11, 2017
59aa118
Add configuration option to disable upload content checking.
jmchilton Aug 9, 2017
53b0b25
Better error reporting in test/base/populators.py.
jmchilton Aug 9, 2017
bee6af1
Allow API tests to work with admin users (not just admin keys).
jmchilton Jul 15, 2017
fec1eab
Add ability to arbitrarily not decompress files on upload via API.
jmchilton Aug 9, 2017
fc861cd
Merge pull request #3064 from manabuishii/install_workflow_and_tools
jmchilton Aug 12, 2017
06ca789
Configuration tests for the last few upload enhancements.
jmchilton Aug 9, 2017
5f1b7d5
Show verison button in workflow editor and trigger on_change
mvdbeek Aug 3, 2017
25e05b6
Do postchange action only when modifiying tool versions in the workfl…
mvdbeek Aug 3, 2017
5afe490
Fix qunit test
mvdbeek Aug 3, 2017
36ce911
Keep spacing consistent (thx @nsoranzo)
mvdbeek Aug 3, 2017
526e98e
Reset outputs when changing tool versions in wf-editor
mvdbeek Aug 5, 2017
db2ea85
Now thing are mostly working -- input and output connections are corr…
mvdbeek Aug 6, 2017
ea1f4f8
Fix the occasional loading of the wrong workflow. Turns out that some…
mvdbeek Aug 6, 2017
bc95f5e
Now adding/removing datasets and multiple version switches work fine,…
mvdbeek Aug 7, 2017
92fedc0
Fix logic for adding and removing outputs
mvdbeek Aug 7, 2017
1c286b1
Remove extra newlines
mvdbeek Aug 7, 2017
2e95026
Remove unused old_version variable
mvdbeek Aug 7, 2017
31c423a
Fix typo and remove leftover comment (thanks @nsoranzo)
mvdbeek Aug 7, 2017
df91881
Remove unused workflow outputs
mvdbeek Aug 8, 2017
d0b06a3
Don't cast tool_version to string if tool_version is None-type
mvdbeek Aug 13, 2017
73f4141
Add static JS
mvdbeek Aug 13, 2017
f849c7e
Merge pull request #4417 from jmchilton/upload_enhance
bgruening Aug 14, 2017
6ad6fd9
Rebuild tool_version_cache on DetachedInstanceError
mvdbeek Aug 14, 2017
8e192db
Merge pull request #4397 from jmchilton/api_test_enhancement
mvdbeek Aug 14, 2017
e594152
Merge pull request #4394 from jmchilton/subworkflow_loading_fix
mvdbeek Aug 14, 2017
0f5ad34
Merge pull request #4413 from nsoranzo/release_17.01_really_add_datat…
mvdbeek Aug 14, 2017
4faf496
Merge branch 'release_17.01' into release_17.05
nsoranzo Aug 14, 2017
9cbabef
Merge branch 'release_17.05' into dev
nsoranzo Aug 14, 2017
4dd5030
Update conda channel order to sync with Bioconda
nsoranzo Aug 10, 2017
420e7a4
Remove _ensure_conda_context() function
nsoranzo Aug 14, 2017
cdbac05
Override channel list on the command line instead of modifying condarc
nsoranzo Aug 14, 2017
eccdc8c
Removed unreached message line
guerler Aug 14, 2017
fd5f42d
Merge branch 'dev' into admin_grid_groups
guerler Aug 14, 2017
68555f5
some unicoding
hexylena Aug 15, 2017
7f78ee7
Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast
jmchilton Aug 15, 2017
8721da8
Merge pull request #4426 from erasche/local-runner-unicode
jmchilton Aug 15, 2017
44548f8
Merge pull request #4409 from nsoranzo/fix_conda_channel_order
jmchilton Aug 15, 2017
07a3049
Merge branch 'release_17.05' into dev
nsoranzo Aug 15, 2017
aa7be28
Merge branch 'dev' into switch_versions_in_workflows
martenson Aug 15, 2017
27be249
Merge pull request #4373 from mvdbeek/switch_versions_in_workflows
martenson Aug 15, 2017
462b7de
Merge pull request #4427 from nsoranzo/merge_release_17.05
dannon Aug 15, 2017
e72948c
Merge branch 'dev' into admin_grid_groups
guerler Aug 15, 2017
b726c33
Merge branch 'admin_grid_groups' into admin_grid_toolversion
guerler Aug 15, 2017
a078ee0
Move form augmentation to form handler
guerler Aug 15, 2017
5cebb08
Add support for the MEME psp format
gregvonkuster Aug 15, 2017
4bddd61
Merge pull request #4405 from guerler/admin_grid_groups
martenson Aug 15, 2017
9dfee37
Optionally allow to show or hide select all
guerler Aug 15, 2017
a1897bd
Hide select all for role and group selectors
guerler Aug 15, 2017
d6f6a78
Use 'Save' as default title for configuration forms
guerler Aug 15, 2017
4688eef
Fix user id decoding, fix optional array handling
guerler Aug 15, 2017
96cad03
Fix label for default quotas
guerler Aug 15, 2017
09c4b10
Break connection in workflow editor if necessary
mvdbeek Aug 15, 2017
246489a
Fix messages
guerler Aug 15, 2017
f9e8892
Catch user input error for auto created roles and groups
guerler Aug 15, 2017
bebc5ff
Move decode id to correct location
guerler Aug 15, 2017
f1e13ce
More messages to validate inputs
guerler Aug 15, 2017
86cdaaf
Add validation messages if resource ids are not correct
guerler Aug 15, 2017
522ca9e
Fix private role validation
guerler Aug 15, 2017
2073151
Merge branch 'dev' into admin_grid_toolversion
guerler Aug 15, 2017
abe8117
Fix
guerler Aug 15, 2017
8eb487e
Merge pull request #4431 from mvdbeek/break_connections
jmchilton Aug 16, 2017
8063701
fix XML error
bgruening Aug 16, 2017
338abee
Separate input augmentation helpers from form views, augment inputs f…
guerler Aug 16, 2017
b6f0600
Merge pull request #4387 from jmchilton/tool_unit_test_cleanup
bgruening Aug 16, 2017
7af41d4
Simplify form wrapper calling
guerler Aug 16, 2017
c5a9149
Merge pull request #4432 from guerler/fix_role_association_check
dannon Aug 16, 2017
7dae650
Change Psp to MemePsp and misc fixes per initial review
gregvonkuster Aug 16, 2017
7ef9b4c
Remove spurious null check.
Aug 11, 2017
43ddd47
Add missing `var` declarations.
Aug 11, 2017
48b835c
Remove an unused variable.
Aug 14, 2017
8950d44
Move two variable definitions to combine them with their declarations.
Aug 16, 2017
57c6284
Run `make client`.
Aug 16, 2017
3026bf5
Remove strange import - no idea from where it originated
gregvonkuster Aug 16, 2017
1b7f25e
Merge pull request #4421 from xiemaisi/fix-lgtm-alerts
dannon Aug 16, 2017
c72f43d
Avoid adding `(imported from API)` to workflows
chambm Aug 16, 2017
9ef13a1
Remove `(imported from API)` suffix from test
chambm Aug 16, 2017
03a3d34
Remove `(imported from API)` suffix from test
chambm Aug 16, 2017
73d6bd0
Restore build model bypass
guerler Aug 16, 2017
1fc4bb1
Merge branch 'dev' into improve_form_modules
guerler Aug 16, 2017
a0217cb
Attempt to customize build model
guerler Aug 16, 2017
fdcd469
Remove unfilterable columns from group and quota search grids
guerler Aug 16, 2017
2c4cf68
Merge branch 'dev' into admin_grid_toolversion
martenson Aug 16, 2017
0458334
Merge pull request #4411 from guerler/admin_grid_toolversion
martenson Aug 16, 2017
25bd717
Remove print of non-existent attribute 'content'
chambm Aug 16, 2017
5b64e6d
Decouple model building
guerler Aug 16, 2017
2b94fa3
Fix MemePsp sniff entry
gregvonkuster Aug 16, 2017
3c4e892
Hide initial tool version message
guerler Aug 16, 2017
8b43348
Move workflow tool form model rebuilding to workflow forms
guerler Aug 16, 2017
192c4b1
Properly update workflow tool module
guerler Aug 16, 2017
6d87448
Add optional initial model caller
guerler Aug 16, 2017
4098672
Remove form dom removal through workflow manager
guerler Aug 16, 2017
0092600
Merge branch 'dev' into improve_form_modules
guerler Aug 16, 2017
d8925d7
Fix message style
guerler Aug 16, 2017
1b69b9a
Merge pull request #4439 from chambm/patch-2
bgruening Aug 17, 2017
008a1d8
Merge pull request #4434 from chambm/patch-1
bgruening Aug 17, 2017
5799fbc
change file_ext to be inline with memexml and co
bgruening Aug 17, 2017
9a5016f
Update CloudBridge to its current latest
VJalili Aug 17, 2017
21b44bf
Fix all E201 and E202 style errors
nsoranzo Aug 16, 2017
a353b2e
Fix E127 errors introduced by previous commit
nsoranzo Aug 17, 2017
a8d7b2d
Fix more indentation errors
nsoranzo Aug 17, 2017
a85ee59
Merge pull request #4440 from nsoranzo/fix_E201_E202
jmchilton Aug 17, 2017
03df496
Fix API tests broken in #4434
nsoranzo Aug 17, 2017
56c1f25
Fix help text style
guerler Aug 17, 2017
b8f11df
Improve error message for unknown module types when encountered.
jmchilton Jul 14, 2017
2131370
Print warning if any input connections are unused during workflow exe…
jmchilton Jul 16, 2017
7bf7f39
Cleanup a couple things in #4396 caught by @nsoranzo.
jmchilton Aug 9, 2017
35ab745
Merge pull request #4445 from nsoranzo/followup_on_4434
dannon Aug 17, 2017
cca1f9e
Merge pull request #4430 from gregvonkuster/psp_format
dannon Aug 17, 2017
df442ea
Fix E201 errors (spaces in parens) in new memepsp datatype
dannon Aug 17, 2017
7ef099f
Merge pull request #4446 from dannon/memepsp_formatting
nsoranzo Aug 17, 2017
5a91370
Fix title
guerler Aug 17, 2017
7bab16e
Preserve advanced search visibility
guerler Aug 17, 2017
ee4c8e2
Fix filters
guerler Aug 17, 2017
114997d
Prevent search tag duplication
guerler Aug 17, 2017
0fa287f
Add autopep8 script to help rebasing branches after #4440.
jmchilton Aug 17, 2017
1e1c549
added missing parameter to function ensure_installed
bernt-matthias May 10, 2017
a1b8a54
ensure_installed is now iterative instead of recursive
bernt-matthias May 10, 2017
349c9c8
version with no repetition at all
bernt-matthias May 10, 2017
a765472
Set timeout for aquiring lock to 5min
bernt-matthias May 11, 2017
748539a
Merge pull request #4450 from mvdbeek/fix_file_lock_error
dannon Aug 17, 2017
685b9de
Merge remote-tracking branch 'origin/release_17.01' into release_17.05
mvdbeek Aug 17, 2017
8c225ec
Merge branch 'release_17.05' into dev
nsoranzo Aug 17, 2017
68e8abc
Merge pull request #4447 from jmchilton/autopep8
dannon Aug 17, 2017
706741f
Merge pull request #4449 from guerler/fix_grid_search
martenson Aug 17, 2017
2596012
Merge branch 'dev' into improve_form_modules
guerler Aug 17, 2017
517f248
Overhaul of tool provided job metadata.
jmchilton Aug 16, 2017
72e361b
Allow discovering datasets directly from galaxy.json...
jmchilton Aug 16, 2017
6563e38
Allow discovering dataset collections in galaxy.json in a nested fash…
jmchilton Aug 16, 2017
39d4411
Move determining tool provided metadata style to tool parser.
jmchilton Aug 17, 2017
a8bec7a
Allow override of provided metadata location.
jmchilton Aug 17, 2017
1e1df67
Variety of fixes for #4437.
jmchilton Aug 17, 2017
4e17c8e
Add Cloud configuration to object_store_conf.xml.sample
VJalili Aug 18, 2017
2489499
possibility to don't uppercase env variables
xgaia Aug 18, 2017
cff9292
Uniform indentation of multiline if conditionals
nsoranzo Aug 17, 2017
d2d1f85
Fix import order and Python3 compatibility for lib/galaxy/util/pastes…
nsoranzo Aug 18, 2017
784e6f5
Merge pull request #4396 from jmchilton/workflow_warnings
nsoranzo Aug 18, 2017
4e75635
Use log.warning() instead of deprecated warn()
nsoranzo Aug 15, 2017
e32ad28
Remove container config log message from cleanup scripts logs
nsoranzo Aug 15, 2017
bd88524
Fix import order and Python3 compatibility
nsoranzo Aug 15, 2017
b459399
Merge pull request #4454 from xgaia/interactive_environment
hexylena Aug 18, 2017
8d132b2
More detailed sentry reports
hexylena Aug 18, 2017
dd89a9c
Merge pull request #4437 from jmchilton/galaxy_json_rev
mvdbeek Aug 18, 2017
e987b9b
swap id to username
hexylena Aug 18, 2017
30562c0
don't uppercase envoverride
xgaia Aug 18, 2017
e492494
Merge pull request #4456 from nsoranzo/logging_fixes
jmchilton Aug 18, 2017
9c6fd67
Merge pull request #4455 from nsoranzo/multiline_if_conditionals
dannon Aug 18, 2017
cd22de1
Merge pull request #4457 from erasche/sentry-extra-info
jmchilton Aug 18, 2017
7f50a8a
Merge pull request #4438 from guerler/improve_form_modules
dannon Aug 18, 2017
dd27c1e
Client rebuild, @guerler and I were trying to figure out what changed…
dannon Aug 18, 2017
2630183
Merge pull request #4464 from dannon/rebuild_000
martenson Aug 18, 2017
1342c2b
Integrated File Browsing and Workflow support for GenomeSpace
nuwang Feb 25, 2016
e39901e
Moved back some code to wrapper and added back data type sniffing.
nuwang Aug 7, 2016
ad1b613
Added support for pushing multiple files from GenomeSpace to Galaxy.
nuwang Aug 8, 2016
b04ccbe
Fixed genomespace_importer.xml command block
Slugger70 Mar 7, 2017
cb1b086
Fixed pylint errors
nuwang Mar 22, 2017
46c04dc
Fix incorrect reference when determining file type through file ext
nuwang Jul 31, 2017
678d575
Improved recognition of compressed files
nuwang Aug 9, 2017
ae6ae8f
Added new config setting for GenomeSpace UI URL
nuwang Aug 17, 2017
517fd23
Fixed typo in exporter help text
nuwang Aug 17, 2017
b73e21b
Formatting and linting fixes for GenomeSpace tool
nuwang Aug 17, 2017
b995e55
Fixed alignment of buttons in Genomespace Importer
nuwang Aug 18, 2017
46dc4a2
Fixed template formatting according to review comments
nuwang Aug 18, 2017
3e8bf3c
Moved genomespace token to environment variable
nuwang Aug 18, 2017
52b26f4
Registered genomespace_importer as a tool needing Galaxy's python env
nuwang Aug 18, 2017
3240197
Rebuilt galaxy client files
nuwang Aug 18, 2017
fd51a61
Merge pull request #1814 from gvlproject/genomespace_workflows
martenson Aug 18, 2017
912da2f
Fix checking WorkflowInvocation for published workflows
mvdbeek Aug 18, 2017
413233e
Correctly raise Exception if invocation not found
mvdbeek Aug 19, 2017
0a4203e
Fix test to use invocation_id instead of history_id
mvdbeek Aug 19, 2017
80e264d
Check ownership of invocation, instead of stored_workflow
mvdbeek Aug 19, 2017
2d16470
Allow admin user to view workflow invocation (thx @nsoranzo)
mvdbeek Aug 20, 2017
cff306b
Only skip check_security checks if check_ownership and check_accessib…
mvdbeek Aug 20, 2017
64f8e74
Fix subworkflow tests
mvdbeek Aug 20, 2017
0e46888
Show up to 15 histories by default in saved histories menu
mvdbeek Aug 20, 2017
a9d5c7c
Show tag if < 3 tags on history
mvdbeek Aug 20, 2017
2346c0a
Merge pull request #4467 from mvdbeek/saved_history_tags
martenson Aug 21, 2017
e3b3457
Merge pull request #4465 from mvdbeek/workflow_invocation_security_check
jmchilton Aug 21, 2017
092ad6d
Fix quota function name
guerler Aug 21, 2017
63d1d42
Merge pull request #4469 from guerler/fix_quota_api
nsoranzo Aug 21, 2017
a6632f3
replace exclamation with a clock icon
martenson Aug 23, 2017
27bd713
Merge pull request #4485 from martenson/remove-exclamation
dannon Aug 23, 2017
351ac64
Rebase.
VJalili Jul 21, 2017
f51add2
Removed white spaces.
VJalili Aug 23, 2017
4546ff7
Merge remote-tracking branch 'origin/CloudObjectStore' into CloudObje…
VJalili Aug 23, 2017
a834381
Merge pull request #4458 from xgaia/interactive_environment
hexylena Aug 23, 2017
4b9d720
Added CloudBridge to the requirements list.
VJalili Jul 21, 2017
6cae07e
Added CloudBridge to the dependencies check.
VJalili Jul 21, 2017
d69807f
(1) Added Cloud to ObjectStore; (2) updated CloudBridge dependencies.
VJalili Jul 22, 2017
7e74613
- Updated `Cloud` to account for changes in `CloudBridge` interface.
VJalili Jul 26, 2017
1565fca
Reverted the changes on package versions, as these changes are
VJalili Jul 26, 2017
2a7a9bd
Changed boto import style.
VJalili Jul 28, 2017
8da60dc
Updated CloudBridge to its current latest version.
VJalili Aug 2, 2017
b256e8b
Commented on boto import, and removed a `use_reduced_redundancy` config.
VJalili Aug 2, 2017
916d8b1
Removed boto import, and replaced all S3-specific exception catches with
VJalili Aug 2, 2017
8742eb2
Consolidated two upload methods, i.e., upload from file and string,
VJalili Aug 2, 2017
36d49aa
Removed a S3-related comment, and swapped an if/else condition.
VJalili Aug 2, 2017
4e8e20f
Removed a comment section.
VJalili Aug 2, 2017
7bb5d21
Changed indentation of two lines.
VJalili Aug 7, 2017
e1ac03d
Update CloudBridge to its current latest
VJalili Aug 17, 2017
7df7ed2
Add Cloud configuration to object_store_conf.xml.sample
VJalili Aug 18, 2017
d1e5c41
Removed white spaces.
VJalili Aug 23, 2017
d3d0abe
Merge branch 'CloudObjectStore' of https://github.com/VJalili/galaxy …
VJalili Aug 23, 2017
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2 changes: 1 addition & 1 deletion lib/galaxy/webapps/galaxy/api/quotas.py
Original file line number Diff line number Diff line change
@@ -125,7 +125,7 @@ def delete(self, trans, id, **kwd):
params = self.get_quota_params(payload)

try:
message = self._mark_quota_deleted(quota, params)
message = self._delete_quota(quota, params)
if util.string_as_bool(payload.get('purge', False)):
message += self._purge_quota(quota, params)
except ActionInputError as e: