opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
53,224 Commits 63 Branches 243 Tags
53e7a2b2bcfb9ffb2b6452650aafaa51fe506f49
Commit Graph
53224 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
qiagu 53e7a2b2bc Add test data 2021-05-04 09:54:42 +02:00
qiagu e13287c091 Make datatype H5_Model for machine leaning models 2021-05-04 09:54:42 +02:00
Marius van den Beek eb3f3c816f Merge pull request #11832 from qiagu/dynamic_options 
Make tool parameter options capable of referring to metadata file
 2021-05-04 09:49:35 +02:00
John Chilton ad6b1ccb8c Merge pull request #11873 from mvdbeek/fix_file_source_uploads 
Fix "Choose remote files" uploads
 2021-05-03 20:54:39 -04:00
Marius van den Beek 21796c3359 Merge pull request #11908 from bernt-matthias/topic/2debugmsg 
improve three debug messages
 2021-05-03 19:53:14 +02:00
John Chilton 88366f7c9d Merge pull request #11918 from mvdbeek/stabilize_history_options_selenium_test 
Stabilize test_history_options selenium test
 2021-05-03 13:49:19 -04:00
Marius van den Beek 9c69ab331e Merge pull request #11877 from jmchilton/rev_mypy 
Rev mypy.
 2021-05-03 19:03:42 +02:00
mvdbeek 2edb301654 Move shared test setup to lib/galaxy_test/driver/integration_setup.py 2021-05-03 16:18:21 +02:00
Marius van den Beek df1df0d5cb Merge pull request #11882 from scholtalbers/feature/add_filter_invocation_by_dataset_id 
Allow to filter /api/invocations by job_id
 2021-05-03 16:15:07 +02:00
M BerntandMarius van den Beek f886978c40 Apply suggestions from code review 
- fix and simplify reading of env variable
- shorten doc

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-03 16:13:04 +02:00
mvdbeek ab451d5e1e Stabilize test_history_options selenium test 
By waiting for the uploaded dataset to be in OK state.
`wait_for_history` seems to return too early.

Fixes
```
_____________________ HistoryOptionsTestCase.test_options ______________________

self = <galaxy_test.selenium.test_history_options.HistoryOptionsTestCase testMethod=test_options>

    @selenium_test
    def test_options(self):
        self.register()
        self.perform_upload(self.get_filename("1.txt"))
        self.wait_for_history()
        self.click_history_options()

        menu_selector = self.navigation.history_panel.selectors.options_menu
        self.wait_for_visible(menu_selector)

        # Click away closes history options
        self.click_center()

        self.wait_for_absent_or_hidden(menu_selector)

        hid = 1
        self.history_panel_click_item_title(hid=hid, wait=True)
        item_component = self.history_panel_item_body_component(hid=hid)
        item_component.wait_for_visible()
>       self.history_panel_click_item_title(hid=hid, wait=True)

lib/galaxy_test/selenium/test_history_options.py:28:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/selenium/navigates_galaxy.py:1350: in history_panel_click_item_title
    details_component.wait_for_absent_or_hidden()
lib/galaxy/selenium/smart_components.py:79: in wait_for_absent_or_hidden
    self._has_driver.wait_for_absent_or_hidden(self._target, **kwds)
lib/galaxy/selenium/has_driver.py:145: in wait_for_absent_or_hidden
    **kwds
lib/galaxy/selenium/has_driver.py:167: in _wait_on
    return wait.until(condition, self._timeout_message(on_str))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <selenium.webdriver.support.wait.WebDriverWait (session="f6478ee5ab12c8d35994bc35db8e0c7a")>
method = <selenium.webdriver.support.expected_conditions.invisibility_of_element_located object at 0x7fbb1f656450>
message = 'Timeout waiting on CSS selector [#dataset-0865882de2e81d71 .details] to become absent or hidden.'

    def until(self, method, message=''):
        """Calls the method provided with the driver as an argument until the \
        return value is not False."""
        screen = None
        stacktrace = None

        end_time = time.time() + self._timeout
        while True:
            try:
                value = method(self._driver)
                if value:
                    return value
            except self._ignored_exceptions as exc:
                screen = getattr(exc, 'screen', None)
                stacktrace = getattr(exc, 'stacktrace', None)
            time.sleep(self._poll)
            if time.time() > end_time:
                break
>       raise TimeoutException(message, screen, stacktrace)
E       selenium.common.exceptions.TimeoutException: Message: Timeout waiting on CSS selector [#dataset-0865882de2e81d71 .details] to become absent or hidden.
```
 2021-05-03 13:30:27 +02:00
Matthias Bernt 4697281406 doc 2021-05-03 12:55:23 +02:00
M BerntandMarius van den Beek 076231c3e0 rename environment variable 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-03 12:53:02 +02:00
Marius van den Beek 5964856bb4 Merge pull request #11905 from OlegZharkov/check-account-delete 
Add ``delete account`` selenium test
 2021-05-03 12:47:45 +02:00
Marius van den Beek 5e701b2bca Merge pull request #11911 from cat-bro/galaxy_interactor_encode_test_data_payload 
fix GalaxyInteractorApi get_tool_tests
 2021-05-03 12:25:12 +02:00
Marius van den Beek 728b5e6528 Merge pull request #11910 from kxk302/s3 
Fix S3 backend support in iRODS object store
 2021-05-03 12:02:44 +02:00
Marius van den Beek 5bed58f9db Merge pull request #11909 from jj-umn/datatype_toml 
Add toml datatype
 2021-05-03 11:45:45 +02:00
Dannon 1b55acccb4 Merge pull request #11895 from mvdbeek/history_switch_modal 
Implement switch to history modal for beta history panel
 2021-04-30 08:29:07 -04:00
Dannon 69b4c0a985 Merge pull request #11912 from Nerdinacan/history-menu-cosmetics 
Priority menu css tweaks
 2021-04-30 08:27:31 -04:00
Dannon 29bdf43943 Merge pull request #11884 from Nerdinacan/history-polling-since 
Optimized beta history polling by leveraging history.update_time + loading behavior bug fixes
 2021-04-29 20:17:35 -04:00
Mason Houtz 30322391ea adjusted content item css to always show 3 buttons from priority menu 2021-04-29 10:29:16 -07:00
cat-bro 0e88054792 fix other test that fails because of the the extra version of multiple_versions tool 2021-04-30 01:57:05 +10:00
Matthias Bernt 0167da6018 control uvicorn access log with env variable 2021-04-29 16:34:20 +02:00
cat-bro f2ab3f2d02 update GalaxyInteractorApi.get_tool_tests so that the version is encoded 2021-04-30 00:13:36 +10:00
cat-bro 35f341ab83 linting 2021-04-30 00:03:06 +10:00
cat-bro 58f767d296 breaking test for GalaxyInteractorApi get_tool_tests 2021-04-29 23:50:12 +10:00
Matthias Bernt e9b08f300a uvicorn: do not output access info messages 
one could also pass `log_level="warning"` but this swallows some useful
messages at startup and shutdown, ie.

```
INFO:     Started server process [1394761]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
INFO:     Uvicorn running on http://127.0.0.1:8296 (Press CTRL+C to quit)
...
INFO:     Shutting down
INFO:     Waiting for application shutdown.
INFO:     Application shutdown complete.
INFO:     Finished server process [1394761]
```
 2021-04-29 13:22:25 +02:00
Matthias Bernt 8f22fa5ab0 Revert "promote filter faiure message" 
This reverts commit 140ca7404c.
 2021-04-29 13:21:51 +02:00
Matthias BerntandDavid López 140ca7404c promote filter faiure message 
debug messages are not shown in planemo output where
the message can be really helpful.

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
 2021-04-29 13:21:08 +02:00
Mason Houtz 4649a5b8ab Added more reliable watcher test 2021-04-28 19:44:41 -07:00
Mason Houtz 3c322a876d PR 11884, corrected several scrolling errors, made polling more efficient, improved empty history and no-query results message delivery 2021-04-28 19:27:37 -07:00
Kaivan Kamali d72c767fc9 Updated push_to_irods() so it works for both S3 and disk storage 2021-04-28 16:32:35 -04:00
Jim Johnson 42c3f63994 Update datatypes_conf.xml.sample 
Add toml datatype.   MetaMorpheus proteomics application uses toml format for parameter configuration.
 2021-04-28 12:09:40 -05:00
John Chilton afa477727c Merge pull request #11899 from anvilproject/dev_subpathing_k8s 
Add subpathing to k8s_persistent_volume_claims
 2021-04-28 12:39:03 -04:00
Nicola Soranzo d8991c725f Merge pull request #11907 from natefoo/update-deps 2021-04-28 17:05:11 +01:00
Marius van den BeekandMason 3b8488a1dd Limit modal height and make it scrollable 
Thanks Mason!

Co-authored-by: Mason <nerdinacan@gmail.com>
 2021-04-28 17:37:24 +02:00
Nate Coraor f474eb2584 Dependency pins after excluding broken docutils versions. 2021-04-28 10:16:42 -04:00
Matthias Bernt 7757006fa7 improve two debug messages 
tool evaluation: for tools with many outputs its helpful to know which datasets
and collections have been created.

drmaa: for debugging its more convenient to see the command that could be copy
pasted
 2021-04-28 15:03:45 +02:00
Nate Coraor d23e81f318 Update dependencies 2021-04-27 16:58:32 -04:00
Oleg Zharkov 252ac25015 fix jslint 2021-04-27 20:12:04 +02:00
Oleg Zharkov d399fb8bc8 fix style 2021-04-27 18:02:40 +02:00
Oleg Zharkov 6563d49dbc impelemnt test_delete_account 2021-04-27 18:02:13 +02:00
Nicola Soranzo 43e59989ba Merge pull request #11901 from mvdbeek/limit_max_column_in_preview 2021-04-27 16:40:13 +01:00
mvdbeek 2b9a6a96a4 Merge branch 'release_21.01' into dev 2021-04-27 16:13:10 +02:00
Marius van den BeekandNicola Soranzo 57527efee1 Fix column count 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-27 14:01:21 +02:00
John Chilton 17b3e3851f Merge pull request #11880 from hexylena/minerva 
add minerva display app for covid
 2021-04-27 07:53:35 -04:00
mvdbeek 471a6d9fda Limit number of column in tabular preview to 50 2021-04-27 13:02:58 +02:00
Nicola Soranzo eb5b7b4230 Merge pull request #11900 from jmchilton/fix_packages 
Fix package CI.
 2021-04-27 01:08:34 +01:00
John Chilton 68fd99f6a0 Fix package CI. 2021-04-26 18:12:50 -04:00
Dannon ede2f0f6a8 Merge pull request #11896 from mvdbeek/backport_the_third 
[21.01] Backport of #11687: Expose command line if expose_dataset_path is set
 2021-04-26 15:08:37 -04:00