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Author SHA1 Message Date
Nate Coraor d1d5944387 Mention cookie_path in the nginx/Apache docs just for anyone who had it 
set and might be confused about why it's no longer documented.
 2019-04-16 17:48:36 -04:00
Nate Coraor fed86eb598 Remove cookie_path configuration documentation since it's now set 
automatically.
 2019-04-16 17:48:36 -04:00
Nate Coraor 58d311f2e0 Make the cookie_path an attribute on trans so that consumers don't need 
to duplicate logic. Unfortunately it isn't usable for the proxy setup
since trans isn't available when the command line is generated.
 2019-04-16 17:48:36 -04:00
Nate Coraor 449932b229 Automatically set cookie_path using url_for() 2019-04-16 17:48:34 -04:00
Marius van den Beek 7c233a9c2d Merge pull request #7754 from jmchilton/fix_for_docker_on_mac_kubernetes_test 
Fix Kubernetes integration tests for Docker on Mac.
 2019-04-16 16:20:53 +02:00
Dannon 6db36b4192 Merge pull request #7719 from guerler/fix_toolpanel_label_spacing 
Fix spacing in tool panel labels
 2019-04-16 09:24:29 -04:00
John Chilton cfa763ff29 Merge pull request #7748 from nsoranzo/follow-up_on_7659 
Replace ``enable_beta_export_format2_default`` with ``default_workflow_export_format``
 2019-04-16 08:55:50 -04:00
John Chilton 74bf94f445 Fix kubernetes integration tests for Docker on Mac. 2019-04-16 08:28:36 -04:00
Nicola Soranzo 4eee583037 Merge branch 'release_19.01' into dev 2019-04-16 11:47:24 +01:00
Marius van den Beek 848a963da9 Merge pull request #7744 from natefoo/pulsar-0.9.0 
Upgrade pulsar-galaxy-lib to 0.9.0
 2019-04-16 11:49:49 +02:00
Aysam Guerler 03d30d81f0 Merge pull request #7751 from dannon/message_sanitization 
Sanitize html in messages using galaxy.util.sanitize_html
 2019-04-15 23:24:39 -04:00
Martin Cech 30ccb0d7a5 Merge pull request #7743 from mvdbeek/rename_future_to_default 
Rename _future_expose_api to expose_api, expose_api to legacy_expose_api
 2019-04-15 16:33:37 -04:00
Dannon Baker 8bea4f5a9d Sanitize html using galaxy.util.sanitize_html (which in turn calls bleach with appropriate configuration) in message.mako 2019-04-15 16:19:52 -04:00
Nicola Soranzo 7f88f76d5b Merge pull request #7740 from dannon/dep-upgrades 
Python dependency upgrades
 2019-04-15 20:26:52 +01:00
Nicola Soranzo 305ca77cc2 Replace `enable_beta_export_format2_default with default_workflow_export_format` 
This allows future different formats to be included.

Also remove promises about next release.
 2019-04-15 20:11:26 +01:00
John Chilton 2d2c7ab36c Merge pull request #7737 from nsoranzo/more_migration_fixes 
Many more migration fixes
 2019-04-15 14:31:59 -04:00
Nicola Soranzoandmvdbeek 7ae6d700cc Replace from x import a as a instances 
Co-Authored-By: mvdbeek <m.vandenbeek@gmail.com>
 2019-04-15 20:29:47 +02:00
Dannon 5f65252d4d Merge pull request #7675 from gtrack/workflow_btn_dont_jump 
[19.01] Bugfix: "Run workflow" jumps when clicked
 2019-04-15 14:24:54 -04:00
John Chilton 06fc513d05 Merge pull request #7712 from mvdbeek/include_hostname 
Add hostname to task message queues
 2019-04-15 14:24:24 -04:00
John Chilton c33b4d4364 Merge pull request #7724 from mvdbeek/dependent_jobs 
Unpause dependent jobs when resuming jobs
 2019-04-15 14:16:47 -04:00
Nicola Soranzo 94fb97ecb7 Remove `pinned-dev-requirements.txt if empty 2019-04-15 18:35:15 +01:00
mvdbeek dc1834c93b Rename _future_expose_api to expose_api, expose_api to legacy_expose_api 2019-04-15 19:12:17 +02:00
Nate Coraor de24e9eb2b Upgrade pulsar-galaxy-lib to 0.9.0 for Python 3 fix. 2019-04-15 13:10:59 -04:00
Dannon Baker b8d6338334 Swap to docker-based dependency updating by default, for consistency across platforms. 2019-04-15 12:38:47 -04:00
Dannon Baker 448dd08fba Add makefile targets for building the dependency docker container and then using it. 2019-04-15 12:28:33 -04:00
Dannon Baker b812afb739 Leave sqlalchemy pinned to 1.2.18 2019-04-15 12:15:38 -04:00
Dannon Baker 271d947cdf Rerun using Docker-based dependency updater. 2019-04-15 12:13:47 -04:00
Dannon Baker c2a6731b46 Dependency upgrades pass 2019-04-15 11:31:40 -04:00
Martin Cech 51d5174a41 Merge pull request #7553 from guerler/add_data_dialog 
Add data dialog option to tool form data selector
 2019-04-15 11:25:53 -04:00
John Chilton 10be2cd8ac Merge pull request #7713 from mvdbeek/more_defensive_iteration 
Copy tools_by_id before collecting dependency status
 2019-04-15 08:23:07 -04:00
John Chilton 8f2e9246bf Merge pull request #7738 from nsoranzo/fix_comments 
Fix comments
 2019-04-15 08:19:19 -04:00
Nicola Soranzo 1b1f6e9cda Fix comments 2019-04-14 18:02:42 +01:00
guerler 47a67df265 Remove data dialog test visibility 2019-04-13 16:37:49 -04:00
Nicola Soranzo 061a07b020 More migration refactoring 2019-04-13 03:28:54 +01:00
Nicola Soranzo 3a9991ec95 Refactor migrations dropping indexes 2019-04-13 03:28:54 +01:00
Nicola Soranzo 262d9ba0ea Uniform handling of SQLAlchemy Migrate bug 
when adding a column with both a ForeignKey and a index in SQLite.

Also add proper downgrade to migration 37.
 2019-04-13 03:28:54 +01:00
Nicola Soranzo 73998b0c07 Fix foreign keys in migration 68 for SQLite 
SQLite does not always update foreign key constraints when the target
table is renamed, so we start with the table rename in both `upgrade()`
and `downgrade()`.

xref. https://www.sqlite.org/lang_altertable.html
 2019-04-13 03:28:54 +01:00
Nicola Soranzo cd4006679b Fix downgrade in migration 57 for non-SQLite databases 
`notify` column need to be re-added.
 2019-04-13 03:28:54 +01:00
Nicola Soranzo bb77981414 Add proper downgrade to migration 101 2019-04-13 03:28:54 +01:00
Nicola Soranzo bfc7b68848 Merge branch 'release_19.01' into dev 2019-04-12 23:18:49 +01:00
Björn Grüning a6c531e3c5 Merge pull request #7723 from nsoranzo/release_19.01_fix_safemembers 
[19.01] Fix check on links in ``CompressedFile.safemembers()``
 2019-04-12 22:24:41 +02:00
guerler 7ddd6e2b83 Fix download url test case for data dialog 2019-04-12 16:15:35 -04:00
guerler 4e45cfe438 Build download url for history datasets from record attributes 2019-04-12 15:02:30 -04:00
guerler cd3069ef7b Disable show dialog button, hide option by default for now 2019-04-12 14:50:56 -04:00
guerler b93e643b2d Use computed to handle nested v-models, better pattern 2019-04-12 13:58:10 -04:00
Nicola Soranzo 049732f46a Merge pull request #7727 from VJalili/send_to_cloud 
Commented-out cloudbridge requirement for the cloud/send tool.
 2019-04-12 18:57:30 +01:00
Enis Afgan ab6ad17c85 Merge pull request #7720 from machristie/custos-login-button 
OIDC login buttons based on configuration
 2019-04-12 13:56:25 -04:00
Nicola Soranzo 8e3d85697c Merge pull request #7248 from davebx/migration_stages 
Modest refactoring of the migration stages code.
 2019-04-12 17:31:47 +01:00
Nicola Soranzoanddavebx e88182345a Improve logic that filters files to check 
Co-Authored-By: davebx <dave@bx.psu.edu>
 2019-04-12 15:33:49 +01:00
Dave B 8034f8efbe Remove unused variable. 2019-04-12 15:33:49 +01:00