Commit Graph
41638 Commits
Author SHA1 Message Date
Martin Cech 1bdbb77044 client auto format 2019-08-02 09:41:03 -04:00
Helena Rasche d50cec0866 Improve color relationships between text and background (#8388)
Improve color relationships between text and background
2019-08-02 09:53:25 +02:00
Martin Cech 1376d96510 Merge pull request #8331 from janani-prasad/favbtn_toggle
Issue#8105: Make tool favourite query a toggle
2019-08-01 15:10:54 -04:00
Martin Cech 8d7280db4b use standard naming and format 2019-08-01 15:09:55 -04:00
guerler 00a9d7caf4 Use text color for dark gray 2019-08-01 14:08:27 -04:00
guerler 41e8b04e29 Determine dark grays from text colors 2019-08-01 11:53:32 -04:00
guerler e236758f50 Move text colors below brand colors in theme file to highlight settings 2019-08-01 11:31:56 -04:00
guerler c89d02dae0 Apply selected brand colors to select2 popup 2019-08-01 11:14:39 -04:00
Martin Cech b95751cbd4 Merge pull request #8371 from WilliamHolden/ui_bootstrap_fix
Use bootstrap classes to fix form css issue
2019-08-01 11:10:04 -04:00
Marius van den Beek fcaeb857b8 Merge pull request #7730 from bernt-matthias/topic/test-asserts
Fix assert_command is not executed
2019-08-01 11:41:22 +02:00
M Bernt 32aeb78a6d Revert "test asserts: check if asserts work as expected"
This reverts commit 53cb2c1c484dc6dcd59614faf84996a06b652bfc.
2019-08-01 09:26:11 +02:00
mvdbeek 4437021938 Fix ignored assert_command tests
These were swalled becasue the `raw_test_dict` already
lists them under `command_line`, not `command`.
(https://github.com/galaxyproject/galaxy/blob/418f1220c8f6b21bcf3b4ddcf9d19f29bdb2c373/lib/galaxy/tools/test.py#L49)
2019-08-01 09:26:11 +02:00
M Bernt 62fcf2d43f test asserts: check if asserts work as expected 2019-08-01 09:26:11 +02:00
guerler a060f1ba0a Fix hover on panel header buttons 2019-07-31 02:35:36 -04:00
guerler c45a837352 Use brand-light for background overlay 2019-07-31 00:12:12 -04:00
guerler c17c2827f1 Remove custom gray tone from pair list builder help text 2019-07-30 17:51:14 -04:00
guerler 148955e60f Use text-muted, fix comment 2019-07-30 16:40:37 -04:00
guerler a633246b45 Fix search field visibility in multipanel view header 2019-07-30 15:45:26 -04:00
will 08e07654b3 Only wrap on medium size screens and smaller and make use of extra space in dropdown select field 2019-07-30 15:36:12 -04:00
guerler b72e20bb19 Increase background contrast 2019-07-30 15:11:27 -04:00
guerler 308b376a77 Refactor theming, improve color contrast relationships between text and background 2019-07-30 14:43:42 -04:00
Martin Cech 38e57d7fec Merge pull request #8386 from jmchilton/puslar_fixes
Better isolation of embedded Pulsar tests.
2019-07-30 11:24:41 -04:00
John Chilton 955018e79c Better isolation of embedded Pulsar tests. 2019-07-29 13:29:51 -04:00
Marius van den Beek 74d5381fa5 Merge pull request #8376 from guerler/fix_viz_routes
Identify visualization static path from absolute path
2019-07-29 16:32:39 +02:00
John Chilton 5178695684 Merge pull request #8385 from bernt-matthias/topic/univa-drmaa-py
univa runner: fix check for drmaa python module
2019-07-29 10:25:12 -04:00
John Chilton e2a73fa2b3 Merge pull request #8377 from mvdbeek/fix_session_exception
Fix exception thrown with invalid session key
2019-07-29 10:23:27 -04:00
M Bernt 49ef5f48da univa runner: fix check for drmaa python module
the runner name was changed at some point and we forgot to change it here

(also looks much better now)
2019-07-29 13:19:43 +02:00
guerler 766d0d062c Remove unused import 2019-07-25 17:15:37 -04:00
guerler 5c7fddc15c Replace message exception with log statement, a static path is optional 2019-07-25 17:00:47 -04:00
guerler 70363cd0b3 Add error logging and use avoid usage of regex 2019-07-25 14:00:39 -04:00
Marius van den Beek 4e42446a6c Merge pull request #8373 from guerler/fix_references_flag
Hide references card if array is empty
2019-07-25 13:44:36 +02:00
mvdbeek 27971c0943 Fix exception thrown with invalid session key
Move session lookup into try/except, user will then just get a new
session. Fixes
```
127.0.0.1 - - [25/Jul/2019:13:24:23 +0200] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/75.0.3770.142 Safari/537.36"
Traceback (most recent call last):
  File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "lib/galaxy/web/framework/base.py", line 143, in __call__
    return self.handle_request(environ, start_response)
  File "lib/galaxy/web/framework/base.py", line 199, in handle_request
    trans = self.transaction_factory(environ)
  File "lib/galaxy/web/framework/webapp.py", line 82, in <lambda>
    self.set_transaction_factory(lambda e: self.transaction_chooser(e, galaxy_app, session_cookie))
  File "lib/galaxy/web/framework/webapp.py", line 115, in transaction_chooser
    return GalaxyWebTransaction(environ, galaxy_app, self, session_cookie)
  File "lib/galaxy/web/framework/webapp.py", line 219, in __init__
    self._ensure_valid_session(session_cookie)
  File "lib/galaxy/web/framework/webapp.py", line 446, in _ensure_valid_session
    self.app.model.GalaxySession.table.c.is_valid == true())).options(joinedload("user")).first()
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3222, in first
    ret = list(self[0:1])
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3012, in __getitem__
    return list(res)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3324, in __iter__
    return self._execute_and_instances(context)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3349, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute
    return meth(self, multiparams, params)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement
    distilled_params,
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context
    e, statement, parameters, cursor, context
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1468, in _handle_dbapi_exception
    util.reraise(*exc_info)
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 154, in reraise
    raise value
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context
    cursor, statement, parameters, context
  File "/Users/mvandenb/src/galaxy/.venv3/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 550, in do_execute
    cursor.execute(statement, parameters)
ValueError: A string literal cannot contain NUL (0x00) characters.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "lib/galaxy/web/framework/middleware/batch.py", line 80, in __call__
    return self.application(environ, start_response)
  File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__
    return self.app(environ, start_response)
  File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__
    return self.app(environ, start_response)
  File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__
    return self.application(environ, replacement_start_response)
  File "lib/galaxy/web/framework/middleware/error.py", line 164, in __call__
    exc_info)
  File "lib/galaxy/web/framework/middleware/translogger.py", line 70, in replacement_start_response
    return start_response(status, headers, exc_info)
SystemError: <built-in function uwsgi_spit> returned a result with an error set
```
Which can be provoked by switching between python 3 and python 2.
2019-07-25 13:33:30 +02:00
guerler 31e99a932e Validate static path before joining path extensions 2019-07-24 20:54:45 -04:00
will 58d4bea616 add margin in between ui select buttons when they wrap vertically 2019-07-24 18:58:50 -04:00
guerler ae535f8307 Identify visualization static path from absolute path 2019-07-24 15:54:34 -04:00
guerler cef7eeb7be Hide references card if array is empty 2019-07-23 00:57:28 -04:00
Martin Cech e7c106b01d Merge pull request #8366 from bernt-matthias/topic/sortlist-missing-when
Sort Collection: add missing when tags
2019-07-22 23:28:08 -04:00
John Chilton 43e10aab24 Merge pull request #8363 from ic4f/update_rst_files
Update RST files to reflect code structure changes
2019-07-22 15:03:30 -04:00
John Chilton 34f9c91dd0 Merge pull request #8365 from ic4f/dev_unittests_refactor_tools
Remove some test interdependencies in unit/tools
2019-07-22 15:01:07 -04:00
will 924dedd734 add right margin for form field 2019-07-22 14:24:24 -04:00
will b7cb02664e Use bootstrap classes to fix css issue 2019-07-22 14:18:13 -04:00
Marius van den Beek 9606690ac2 Merge pull request #8360 from mvdbeek/fix_default_involucro_path
Fix default involucro path
2019-07-22 10:44:26 +02:00
Marius van den Beek 15c8fdd88c Merge pull request #8362 from wm75/zipfile-fix
Fix autodetection of zip file format (including xlsx)
2019-07-22 10:43:03 +02:00
M Bernt a2e2139d5d Sort Collection: add missing when tags 2019-07-22 10:23:33 +02:00
Sergey Golitsynskiy a3c4d753b9 [Commit to squash] (restart test/undo prev edit) 2019-07-21 21:35:31 -04:00
Sergey Golitsynskiy f060d3c1f2 [Commit to squash] (restart tests) 2019-07-21 21:33:27 -04:00
Sergey Golitsynskiy e345bcab98 Remove some test interdependencies in unit/tools
Factor out BaseParameterTestCase into a helper module.
2019-07-21 19:41:10 -04:00
Sergey Golitsynskiy df5252c887 Update RST files to reflect code structure changes
Also, clean out obsolete RST files.
2019-07-21 12:42:58 -04:00
Wolfgang Maier 652f19a422 Use more elegant way to test stream type 2019-07-21 10:59:09 +02:00
Wolfgang Maier b66eeea526 Fix and improve unit tests 2019-07-21 10:48:15 +02:00