Commit Graph
6543 Commits
Author SHA1 Message Date
Dannon Baker fd4134e827 hyphy-vision: swap to gulp build so we can drop static deps and rebuild reliably 2020-02-17 17:02:14 -05:00
Marius van den Beek 6306b20fa4 Merge pull request #9367 from dannon/fix-styleguide
[20.01] Styleguide fixes
2020-02-14 15:55:42 +01:00
Nicola Soranzo cbb071fc49 Remove GenomeSpace tools, OpenID, UI and requirements 2020-02-13 09:50:29 +00:00
Dannon Baker 2c23c11506 reincorporate toplevel components 2020-02-12 14:00:04 -05:00
Dannon Baker 83150b334a Reorder sections, drop uncategorized components temporarily. 2020-02-12 13:50:40 -05:00
Dannon Baker 316931bdf9 Fix styleguide for new webpack config approach. 2020-02-12 13:17:55 -05:00
mvdbeek 572eeac529 Fix circster launch and saving
Fixes:
```
Error - <class 'binascii.Error'>: decoding with 'hex' codec failed (Error: Odd-length string)
URL: http://127.0.0.1:8080/visualization/circster?id=undefined
File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/middleware/error.py', line 154 in __call__
  app_iter = self.application(environ, sr_checker)
File '/Users/mvandenb/src/galaxy/.venv/lib/python3.6/site-packages/paste/recursive.py', line 85 in __call__
  return self.application(environ, start_response)
File '/Users/mvandenb/src/galaxy/.venv/lib/python3.6/site-packages/paste/httpexceptions.py', line 640 in __call__
  return self.application(environ, start_response)
File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/base.py', line 143 in __call__
  return self.handle_request(environ, start_response)
File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/base.py', line 222 in handle_request
  body = method(trans, **kwargs)
File '/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/controllers/visualization.py', line 764 in circster
  vis = self.get_visualization(trans, id, check_ownership=False, check_accessible=True)
File '/Users/mvandenb/src/galaxy/lib/galaxy/webapps/base/controller.py', line 651 in get_visualization
  visualization = trans.sa_session.query(trans.model.Visualization).get(trans.security.decode_id(id))
File '/Users/mvandenb/src/galaxy/lib/galaxy/security/idencoding.py', line 84 in decode_id
  return int(unicodify(id_cipher.decrypt(codecs.decode(obj_id, 'hex'))).lstrip("!"))
Error: decoding with 'hex' codec failed (Error: Odd-length string)
```
among other things. This happens when a new circster instance is created
and it doens't have an id yet. `id` then is `undefined`, which is not a
valid id.
2020-02-07 13:27:41 +01:00
Dannon b703548d5d Merge pull request #9316 from mvdbeek/fix_and_enhance_reports
[20.01] Various fixes and enhancements to reports
2020-02-05 13:48:33 -05:00
mvdbeek 5ede51c4ce Also quote job_parameters example
I rarely read entire help texts (shame on me, I know), so I missed the
example below that was quoting when there is a whitespace.
For consistency it's probably better too to qute all parameters.
2020-02-05 11:11:43 +01:00
Dannon Baker 617b310887 Fix tag display coloring calculation to match the history. Also formats nametags/hashtags as appropriate. 2020-01-29 16:18:34 -05:00
Dannon 8e16fcb4cc Merge pull request #9233 from dannon/external-auth-login-refinement
[20.01] External auth login refinement
2020-01-28 13:22:55 -05:00
Dannon Baker fbcafb19e8 Patches for fixing user duplication w/ custos authnz, and logout loop. 2020-01-17 13:15:27 -05:00
Dannon Baker 6a4a3b89ac Formatting. 2020-01-17 12:57:53 -05:00
Dannon Baker 6218b313a7 Allow mailto addresses (for support/contact) in menu items. 2020-01-17 12:57:20 -05:00
Dannon Baker 254ce7c37b Merge remote-tracking branch 'upstream/release_19.09' into release_20.01 2020-01-14 15:14:26 -05:00
Kai Kruse 6f68f2a7e2 Ensure visible overflow on nav ba container so that we can push
the genome navigation into the title element. Fixes #9205
2020-01-14 15:48:14 +01:00
Dannon Baker 5b0e30834e Client formatting. 2019-12-19 16:09:25 -05:00
Dannon Baker 0bfeda6726 Fix logout/login redirect loop. We changed logout to go home in a workaround for the loop, but this is a more robust solution that'll also work with require_login 2019-12-19 16:05:19 -05:00
Dannon Baker 9091727668 Simplification of oidc icon presentation. 2019-12-19 14:21:03 -05:00
Dannon Baker c5d7dc0765 Fix icons for oidc idps without defined fancy ones. 2019-12-19 13:39:05 -05:00
John Chilton 003dbe8865 Markdown export of pages. 2019-12-18 17:18:06 -05:00
John Chilton eca65e9c01 PDF generation for reports. 2019-12-18 17:18:05 -05:00
Martin Cech 4af20ef104 Merge pull request #9137 from guerler/modify_toolshed_reset_text
Fix toolshed monitor confirmation message
2019-12-18 13:30:47 -05:00
Marius van den Beek a72847b2cd Merge pull request #9133 from guerler/workflow_list_update
Add click prevent to workflow list dropdowns
2019-12-18 19:28:46 +01:00
Marius van den Beek 9646d590d6 Merge pull request #9115 from machristie/auto-redirect-single-oidc-provider
Automatically redirect to OIDC provider when only auth option
2019-12-18 18:45:57 +01:00
guerler a25b13594b Fix toolshed monitor confirmation message 2019-12-17 19:37:50 -05:00
guerler a582d76438 Remove legacy installation monitor from admin panel 2019-12-17 18:18:06 -05:00
guerler cd7db6104d Fix typo in admin panel label 2019-12-17 18:17:52 -05:00
guerler 4eaf3dbd3b Add prevent handler to dropdown actions in workflow list 2019-12-17 17:52:56 -05:00
Marius van den Beek c10a434fcc Merge pull request #8512 from jmchilton/page_format
Markdown-based Galaxy Pages.
2019-12-17 22:37:21 +02:00
Marius van den Beek 4704610ef6 Merge pull request #9018 from guerler/refactor_dataset_grid
Implement datasets grid as vue component
2019-12-17 22:31:33 +02:00
Marius van den Beek 9c46e852b1 Merge pull request #9086 from jmchilton/revise_workflow_inputs_2
Even Richer Workflow Inputs
2019-12-17 22:26:08 +02:00
Martin Cech 1afb1f65a3 Merge pull request #9062 from guerler/disable_brand
Add a config option to allow customizing the brand title
2019-12-17 14:58:25 -05:00
guerler f0baec7b34 Indicate that dataset name is missing in dataset list 2019-12-17 13:50:46 -05:00
guerler c4ed764624 Add tooltips for dataset list icons 2019-12-17 13:26:24 -05:00
Martin Cech eefc0efc26 minor polish, change config option name 2019-12-17 12:17:47 -05:00
Dannon Baker ebe2deb4dd Merge remote-tracking branch 'upstream/release_19.09' into dev 2019-12-16 13:04:40 -05:00
Dannon Baker 868d6c9987 Fix word salad. 2019-12-16 12:19:47 -05:00
Dannon Baker b25cb15b83 Add HMR blurb. 2019-12-16 11:59:49 -05:00
John Chilton fbd508ada2 client-format 2019-12-16 10:12:46 -05:00
Dannon Baker a0203007e9 Job info displays in multiple spots; handle it all the same. 2019-12-16 10:05:19 -05:00
Dannon 45aff50809 Merge pull request #9104 from nsoranzo/merge_release_19.09
Merge release_19.09 into dev
2019-12-16 09:59:57 -05:00
mvdbeek a53c3636b8 Fix embedding history with dataset collections
`getGalaxyInstance` returns undefined, so the debug statements
cause the load to fail. Certainly not correct, I guess getGalaxyInstance
should always work ?
2019-12-16 07:25:17 -05:00
John Chilton 5fc7c3b8b2 Implement Markdown pages w/editor toolbar. 2019-12-16 07:25:16 -05:00
John Chilton 92c65d5add Refactor DataDialog to allow selection of workflows, collections as well. 2019-12-16 07:25:16 -05:00
Marcus Christie 9ce6c0cc97 Automatically redirect to OIDC provider when only auth option 2019-12-14 11:28:32 -05:00
Dannon d05f442be2 Merge pull request #9105 from jmchilton/select_type_workflow_threshold
add option select_type_workflow_threshold (rebase)
2019-12-13 09:07:42 -05:00
John Chilton 7c239f2ec9 Merge remote-tracking branch 'galaxyproject/dev' into emailnotify 2019-12-12 13:50:54 -05:00
Frederic Sapet a83f0d6a0a Forgot to run Prettier? Yes ! 2019-12-12 13:41:16 -05:00
Frederic Sapet 02a95d5355 add option select_type_workflow_threshold 2019-12-12 13:41:11 -05:00