| 2faef55 | mvdbeek | 27 February 2020, 18:42:00 UTC | Update version to 20.01 | 27 February 2020, 18:42:00 UTC |
| 703f373 | Dannon | 27 February 2020, 18:17:30 UTC | Merge pull request #9453 from mvdbeek/version-20.01 Update version to 20.01.rc1 | 27 February 2020, 18:17:30 UTC |
| a117a9a | mvdbeek | 27 February 2020, 17:09:03 UTC | Update version to 20.01.rc1 | 27 February 2020, 17:09:03 UTC |
| 63e28b6 | Dannon | 27 February 2020, 16:15:59 UTC | Merge pull request #9271 from mvdbeek/20.01_release_notes [20.01] Release notes for 20.01 | 27 February 2020, 16:15:59 UTC |
| 2bfeeec | Nicola Soranzo | 27 February 2020, 16:04:40 UTC | Drop pygithub3 dev requirement | 27 February 2020, 16:04:40 UTC |
| 4e96e3e | Nicola Soranzo | 27 February 2020, 11:49:49 UTC | Use `with` statement to open file | 27 February 2020, 11:49:49 UTC |
| b6d05e3 | mvdbeek | 26 February 2020, 15:17:08 UTC | Update for new 20.01 PRs | 26 February 2020, 15:19:32 UTC |
| aa0b883 | mvdbeek | 26 February 2020, 15:10:15 UTC | Merge branch 'release_19.09' into release_20.01 | 26 February 2020, 15:10:15 UTC |
| 07760e2 | Marius van den Beek | 26 February 2020, 15:07:57 UTC | Merge pull request #9437 from bernt-matthias/topic/searchgui_archive_meta_fix [19.09] Fix `SearchGuiArchive.set_meta()` | 26 February 2020, 15:07:57 UTC |
| 8441346 | Marius van den Beek | 26 February 2020, 15:06:54 UTC | Merge pull request #9446 from nsoranzo/release_20.01_followup_on_9432 [20.01] Fix `UserManager.get_reset_token()` after #9432 | 26 February 2020, 15:06:54 UTC |
| 865ba23 | Nicola Soranzo | 26 February 2020, 13:32:39 UTC | Fix `UserManager.get_reset_token()` after #9432 Remove `lower()` also from the right side. | 26 February 2020, 13:32:42 UTC |
| 0aa5c4b | Marius van den Beek | 26 February 2020, 13:25:10 UTC | One more version change Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 26 February 2020, 13:25:10 UTC |
| 4f0cce0 | mvdbeek | 26 February 2020, 13:06:55 UTC | Adjust docs for when we started preferring python3 | 26 February 2020, 13:06:55 UTC |
| 4066d1b | mvdbeek | 26 February 2020, 13:01:33 UTC | Restore database migration test | 26 February 2020, 13:01:36 UTC |
| 9fdbad7 | mvdbeek | 26 February 2020, 10:13:45 UTC | Mention that more distribution tools/converters need dependencies now | 26 February 2020, 10:13:45 UTC |
| 3762418 | Nicola Soranzo | 26 February 2020, 10:04:12 UTC | Merge branch 'release_19.09' into release_20.01 | 26 February 2020, 10:04:12 UTC |
| 48e015d | mvdbeek | 26 February 2020, 10:02:39 UTC | Link to Python upgrade instructions | 26 February 2020, 10:02:39 UTC |
| 1169db7 | mvdbeek | 26 February 2020, 10:02:24 UTC | Mention that database/compiled_templates needs to be removed when upgrading python | 26 February 2020, 10:02:24 UTC |
| 99bc25f | Nicola Soranzo | 19 February 2020, 16:09:12 UTC | Add more details | 26 February 2020, 09:54:56 UTC |
| 4c712f0 | Alex Ostrovsky | 18 February 2020, 20:31:29 UTC | Added conda python update | 26 February 2020, 09:54:56 UTC |
| 58ae3e4 | Nicola Soranzo | 09 February 2020, 16:03:28 UTC | Python3: decode the output of ``subprocess.check_output()`` | 26 February 2020, 09:53:49 UTC |
| 765f591 | Nicola Soranzo | 07 February 2020, 20:01:42 UTC | Create Python3 virtualenv by default - Allow specifying Python to use to create virtualenv using GALAXY_PYTHON environment variable. - Integrate Python support docs from https://galaxyproject.org/admin/python/ - Update virtualenv installation to use v16.7.9 | 26 February 2020, 09:53:43 UTC |
| 7624a4d | M Bernt | 26 February 2020, 09:52:11 UTC | add missing import | 26 February 2020, 09:52:11 UTC |
| 9748452 | mvdbeek | 26 February 2020, 09:24:49 UTC | Merge followup PR into original announcement | 26 February 2020, 09:24:52 UTC |
| 05d5fd1 | mvdbeek | 26 February 2020, 09:21:46 UTC | Update with latest PRs | 26 February 2020, 09:23:22 UTC |
| 4f8ce5e | M Bernt | 26 February 2020, 09:22:30 UTC | use TextIOWrapper instead of decode Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 26 February 2020, 09:22:30 UTC |
| 07a6922 | mvdbeek | 21 February 2020, 16:57:08 UTC | Update with new 20.01 PRs | 26 February 2020, 09:15:33 UTC |
| fe68ded | mvdbeek | 11 February 2020, 18:39:46 UTC | Pahes typo | 26 February 2020, 09:15:33 UTC |
| 6b30458 | mvdbeek | 04 February 2020, 21:04:31 UTC | Fix missing newline after section | 26 February 2020, 09:15:33 UTC |
| 3d22c72 | mvdbeek | 04 February 2020, 20:34:11 UTC | Fix RST formatting | 26 February 2020, 09:15:33 UTC |
| 090bef1 | mvdbeek | 04 February 2020, 20:32:35 UTC | Tweak image size and add 20.01_annouce to index | 26 February 2020, 09:15:33 UTC |
| b76e29a | mvdbeek | 04 February 2020, 19:29:00 UTC | Add workflow report and email button screenshots | 26 February 2020, 09:15:33 UTC |
| 722c2f2 | mvdbeek | 04 February 2020, 10:47:25 UTC | First pass at user announements | 26 February 2020, 09:15:33 UTC |
| d217b6d | mvdbeek | 29 January 2020, 09:33:45 UTC | Edit to 20.01_announce.rst | 26 February 2020, 09:15:33 UTC |
| 8619c2d | Marius van den Beek | 29 January 2020, 09:24:14 UTC | Update doc/source/releases/20.01_announce.rst Co-Authored-By: Helena Rasche <hxr@hx42.org> | 26 February 2020, 09:15:33 UTC |
| 08e9719 | mvdbeek | 28 January 2020, 18:41:06 UTC | Release notes for 20.01 | 26 February 2020, 09:15:33 UTC |
| 2dc0726 | mvdbeek | 28 January 2020, 15:28:38 UTC | Update scripts/bootstrap_history.py for python 3 / pygithub | 26 February 2020, 09:15:33 UTC |
| d5c3f93 | Marius van den Beek | 26 February 2020, 09:02:30 UTC | Merge pull request #9442 from dannon/fix-data-tables-vue [20.01] Fix data tables vue display | 26 February 2020, 09:02:30 UTC |
| 80cf8ac | Dannon Baker | 25 February 2020, 22:09:25 UTC | Fix data tables vue display | 25 February 2020, 22:09:25 UTC |
| 3851b11 | Dannon | 25 February 2020, 21:28:11 UTC | Merge pull request #9432 from mvdbeek/restore_non_lowercase_access [20.01] Fix login to accounts using different email capitalization | 25 February 2020, 21:28:11 UTC |
| 4d639f6 | Dannon | 25 February 2020, 21:26:47 UTC | Merge pull request #9441 from mvdbeek/fix_upload_tool_error [20.01] Fix to_dict for upload1 tool | 25 February 2020, 21:26:47 UTC |
| 5cac6a7 | mvdbeek | 25 February 2020, 18:16:25 UTC | Fix to_dict for upload1 tool This used to happen in tool_form.mako (https://github.com/galaxyproject/galaxy/blob/0637e0adeeafde44405f69581c3e9b2ae7123ef7/templates/webapps/galaxy/tool_form.mako#L299), where the code was: ``` # Handle calculating the redirect url for the special case where we have nginx proxy # upload and need to do url_for on the redirect portion of the tool action. try: tool_url = h.url_for(tool.action) except AttributeError: assert len(tool.action) == 2 tool_url = tool.action[0] + h.url_for(tool.action[1]) ``` Fixes https://sentry.galaxyproject.org/sentry/main/issues/300358/: ``` AttributeError: 'tuple' object has no attribute 'startswith' File "galaxy/web/framework/decorators.py", line 282, in decorator rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/api/tools.py", line 124, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "galaxy/tools/__init__.py", line 2057, in to_json 'action' : self.app.url_for(self.action), File "routes/util.py", line 211, in url_for if url.startswith('/') and hasattr(config, 'environ') \ ``` | 25 February 2020, 18:20:54 UTC |
| d5be9b3 | Marius van den Beek | 25 February 2020, 15:29:32 UTC | Don't check username again Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com> | 25 February 2020, 15:29:32 UTC |
| 229e04a | M Bernt | 25 February 2020, 14:57:40 UTC | fix searchgui_archive set_meta probably with py3 reading a file from a zip file is binary. hence startswith and split fail. | 25 February 2020, 15:05:10 UTC |
| a1f9ae2 | Dannon | 25 February 2020, 14:56:16 UTC | Merge pull request #9433 from mvdbeek/fix_twobitfile_reading [20.01] Fix TwoBitFile handle not opened in binary mode | 25 February 2020, 14:56:16 UTC |
| 64aa892 | Dannon | 25 February 2020, 14:55:25 UTC | Merge pull request #9436 from mvdbeek/fix_package_installation_python_3 [19.09] Fix toolshed package installation on python 3 | 25 February 2020, 14:55:25 UTC |
| 62d4325 | Dannon | 25 February 2020, 14:04:57 UTC | Merge pull request #9430 from mvdbeek/add_additional_strip_null [20.01] Strip unicode null characters from traceback and job_messages | 25 February 2020, 14:04:57 UTC |
| 6be7ac8 | M Bernt | 24 February 2020, 13:53:15 UTC | fix two cases of opening a file binary might fix https://github.com/galaxyproject/galaxy/issues/9328 | 25 February 2020, 14:00:57 UTC |
| b57112b | Dannon | 25 February 2020, 13:49:40 UTC | Merge pull request #9434 from mvdbeek/cast_uploaded_file_content_to_unicode [20.01] Fix uploading workflow archives | 25 February 2020, 13:49:40 UTC |
| ac02dbd | Björn Grüning | 25 February 2020, 11:32:24 UTC | Merge pull request #9431 from mvdbeek/build_sites_config_fix [20.01] Build sites config fix | 25 February 2020, 11:32:24 UTC |
| 382b6a4 | mvdbeek | 25 February 2020, 11:31:16 UTC | Fix uploading workflow archives This fixes https://sentry.galaxyproject.org/sentry/main/issues/502038/: ``` TypeError: a bytes-like object is required, not 'str' File "galaxy/web/framework/decorators.py", line 282, in decorator rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/api/workflows.py", line 361, in create return self.__api_import_from_archive(trans, archive_data, "uploaded file") File "galaxy/webapps/galaxy/api/workflows.py", line 640, in __api_import_from_archive if "GalaxyWorkflow" in archive_data: ``` The actual uploaded data is still invalid, but a more meaningful message will be raised with this fix. | 25 February 2020, 11:31:18 UTC |
| d649338 | mvdbeek | 25 February 2020, 11:13:14 UTC | Fix TwoBitFile handle not opened in binary mode Fixes https://sentry.galaxyproject.org/sentry/main/issues/501741/: ``` UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd7 in position 77: invalid continuation byte File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 34, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 143, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 222, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 57, in call_and_format rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/api/genomes.py", line 41, in show region = self.app.genomes.reference(trans, dbkey=id, chrom=chrom, low=low, high=high) File "galaxy/visualization/genomes.py", line 395, in reference twobit = TwoBitFile(open(twobit_file_name)) File "bx/seq/twobit.py", line 56, in __init__ strng = file.read(TWOBIT_MAGIC_SIZE) File "python3.6/codecs.py", line 321, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) ``` | 25 February 2020, 11:13:17 UTC |
| c86c75c | mvdbeek | 25 February 2020, 10:31:58 UTC | Fix login to accounts using different email capitalization https://github.com/galaxyproject/galaxy/pull/8631 added case-insensitive matches to user emails. If two accounts with different email capitalizations exist one of them will be picked at random for login. To fix this we first check for exact match and only if there is no direct match we lowercase the comparison. | 25 February 2020, 11:02:59 UTC |
| 24a97be | Sergey Golitsynskiy | 24 February 2020, 20:45:48 UTC | Check sample config for build_sites | 25 February 2020, 09:01:14 UTC |
| c54836e | Sergey Golitsynskiy | 24 February 2020, 19:36:24 UTC | Remove '.sample' from default value; rebuild schema | 25 February 2020, 09:01:10 UTC |
| ead6bb4 | mvdbeek | 25 February 2020, 08:48:00 UTC | Strip unicode null characters from traceback and job_messages May or may not help with https://github.com/galaxyproject/galaxy/issues/9428. | 25 February 2020, 08:48:07 UTC |
| 41876b0 | Marius van den Beek | 24 February 2020, 15:12:34 UTC | Merge pull request #9415 from mvdbeek/interval_viewport_fixes [20.01] Fixes for get_estimated_display_viewport | 24 February 2020, 15:12:34 UTC |
| 4d98745 | Nicola Soranzo | 24 February 2020, 13:03:06 UTC | Use explicit for loop instead of `list(map())` when used exclusively as a shorthand, with no return value. | 24 February 2020, 13:03:09 UTC |
| 16b2eec | Nicola Soranzo | 24 February 2020, 13:01:21 UTC | Use a list comprehension instead of `list(map())` with a lambda function | 24 February 2020, 13:01:59 UTC |
| 2c4da06 | Marius van den Beek | 24 February 2020, 09:51:08 UTC | Merge pull request #9411 from dannon/fix_shed_image_resolution [20.01] Fix shed image resolution | 24 February 2020, 09:51:08 UTC |
| 0bf308d | mvdbeek | 24 February 2020, 09:48:59 UTC | Restore map unpacking, skip list casting | 24 February 2020, 09:48:59 UTC |
| 5f945a3 | mvdbeek | 21 February 2020, 11:01:36 UTC | Fixes for get_estimated_display_viewport Map objects cannot be unpacked, decrease log level, use context managers for opening files. Silences https://sentry.galaxyproject.org/sentry/main/issues/517474/: ``` line (##sequence-regionSL4.0ch07 1 67883646 ) uses an unsupported ##sequence-region definition. ``` and similar. | 24 February 2020, 09:46:44 UTC |
| a2b8f48 | Marius van den Beek | 24 February 2020, 09:39:03 UTC | Merge pull request #9421 from nsoranzo/release_20.01_conda_startup_fixes [20.01] Conda startup fixes | 24 February 2020, 09:39:03 UTC |
| acb0674 | Nicola Soranzo | 24 February 2020, 02:11:02 UTC | Upgrade Checkout GitHub Action | 24 February 2020, 02:11:41 UTC |
| da25657 | Nicola Soranzo | 23 February 2020, 01:21:05 UTC | Source the full path of conda activate script Otherwise, if a virtualenv is active on top of conda base env (e.g. when running py37-first_startup tox test in TravisCI), the wrong `activate` script is sourced. Also fix `CONDA_PREFIX` environment variable definition when using a shell not supported by conda. | 23 February 2020, 23:06:01 UTC |
| f61ae2c | Nicola Soranzo | 22 February 2020, 02:22:17 UTC | Don't check if python is from conda when `CONDA_EXE` env var is set Since at least version 3.7.4 of the `python` package from the `defaults` conda channel, `python -V` doesn't reveal its origin any more. Also some fixes suggested by `shellcheck`. | 23 February 2020, 23:05:52 UTC |
| a5050fe | John Chilton | 23 February 2020, 15:14:43 UTC | Merge pull request #9416 from mvdbeek/fix_wrong_map_use [20.01] Fix wrong map use in many places | 23 February 2020, 15:14:43 UTC |
| 4b1fe09 | John Chilton | 23 February 2020, 15:12:47 UTC | Merge pull request #9406 from mvdbeek/fix_discovered_datasets_always_being_ok [20.01] Make dataset discovery respect final_job_state | 23 February 2020, 15:12:47 UTC |
| f3fd660 | Pablo Moreno | 23 February 2020, 12:53:33 UTC | Handles floats correctly in ByteSize | 23 February 2020, 15:10:10 UTC |
| 35b5a27 | mvdbeek | 21 February 2020, 12:46:04 UTC | Fix many places where map use is wrong on python 3 | 21 February 2020, 12:46:04 UTC |
| 32dc205 | mvdbeek | 21 February 2020, 12:19:35 UTC | Fix get_keys_from_dict | 21 February 2020, 12:19:35 UTC |
| 8564095 | Marius van den Beek | 21 February 2020, 09:08:33 UTC | Merge pull request #9413 from blankenberg/igv-20.01 [20.01] Fixes for IGV GEDA handling of genomes | 21 February 2020, 09:08:33 UTC |
| 66856d2 | Daniel Blankenberg | 21 February 2020, 01:53:45 UTC | missing igv genbank geda | 21 February 2020, 01:53:45 UTC |
| f012b30 | Daniel Blankenberg | 21 February 2020, 01:49:55 UTC | IGV GEDAs only set genome if dbkey is set | 21 February 2020, 01:49:55 UTC |
| 4d27d83 | Daniel Blankenberg | 21 February 2020, 01:25:34 UTC | add igv genbank GEDA | 21 February 2020, 01:25:34 UTC |
| ef5e04d | Daniel Blankenberg | 21 February 2020, 01:23:55 UTC | quote plus dbkeys in igv GEDAs | 21 February 2020, 01:23:55 UTC |
| 2f05741 | Nicola Soranzo | 20 February 2020, 23:07:02 UTC | Merge branch 'release_19.09' into release_20.01 | 20 February 2020, 23:07:02 UTC |
| 259d51e | Nicola Soranzo | 20 February 2020, 23:05:06 UTC | Merge branch 'release_19.05' into release_19.09 | 20 February 2020, 23:05:06 UTC |
| 4d0bae3 | Nicola Soranzo | 20 February 2020, 23:03:11 UTC | Merge branch 'release_19.01' into release_19.05 | 20 February 2020, 23:03:11 UTC |
| 6ed152d | Dannon Baker | 20 February 2020, 22:50:46 UTC | Throw exception for invalid requested image instead of just returning nothing, so we can catch these in sentry. | 20 February 2020, 22:50:46 UTC |
| 90a6e55 | Dannon | 20 February 2020, 22:07:30 UTC | Merge pull request #9408 from nsoranzo/release_19.01_update_bleach [19.01] Update bleach to 3.1.1 | 20 February 2020, 22:07:30 UTC |
| b43236d | Dannon Baker | 20 February 2020, 21:44:37 UTC | Fix shed image resolution to actually test base-path images as intended (and then fail through to static/images) | 20 February 2020, 21:44:37 UTC |
| 7e8c851 | Martin Cech | 15 July 2019, 17:57:00 UTC | remove libpython requirement for uwsgi building | 20 February 2020, 15:16:14 UTC |
| cc0a71b | mvdbeek | 20 February 2020, 12:22:14 UTC | Make dataset discovery respect final_job_state Fixes https://github.com/galaxyproject/galaxy/issues/9394 | 20 February 2020, 14:31:49 UTC |
| 324c0b9 | Nicola Soranzo | 20 February 2020, 14:17:22 UTC | Update bleach to 3.1.1 due to security fixes explained in https://github.com/mozilla/bleach/blob/master/CHANGES | 20 February 2020, 14:17:24 UTC |
| 9d788cb | Dannon | 20 February 2020, 12:17:40 UTC | Merge pull request #9400 from dannon/fix-email-notification-anon [20.01] Prevent anonymous users from being able to request email notification on job completion | 20 February 2020, 12:17:40 UTC |
| 5a36e9d | Dannon | 20 February 2020, 12:17:03 UTC | Merge pull request #9404 from mvdbeek/fix_anonymous_exception_resend_verification [20.01] Don't raise exception if anon goes to <galaxy_url>/user/resend_verification | 20 February 2020, 12:17:03 UTC |
| 0809b63 | mvdbeek | 20 February 2020, 09:41:42 UTC | Don't raise exception if anon goes to <galaxy_url>/user/resend_verification Cosmetic fix for https://sentry.galaxyproject.org/sentry/main/issues/298051/ which is mostly triggered by web crawlers. | 20 February 2020, 09:44:27 UTC |
| 48e3433 | Nicola Soranzo | 20 February 2020, 00:21:34 UTC | Merge branch 'release_19.09' into release_20.01 | 20 February 2020, 00:21:34 UTC |
| 450c9b0 | Marius van den Beek | 19 February 2020, 19:29:47 UTC | Merge pull request #9349 from jmchilton/entryports [20.01] Allow remote jobs to configure entry points. | 19 February 2020, 19:29:47 UTC |
| b43c090 | Marius van den Beek | 19 February 2020, 19:26:22 UTC | Merge pull request #9389 from mvdbeek/fix_tar_to_directory_dependency [20.01] Fix dependency for CONVERTER_tar_to_directory | 19 February 2020, 19:26:22 UTC |
| 8665316 | Marius van den Beek | 19 February 2020, 19:25:58 UTC | Merge pull request #9393 from mvdbeek/fix_maf_tools [20.01] Fix maf tools | 19 February 2020, 19:25:58 UTC |
| b10fe39 | Marius van den Beek | 19 February 2020, 19:25:20 UTC | Merge pull request #9397 from mvdbeek/backport_citation_fixes [20.01] Backport citation fixes | 19 February 2020, 19:25:20 UTC |
| 24a01e7 | Marius van den Beek | 19 February 2020, 19:24:58 UTC | Merge pull request #9395 from mvdbeek/make_set_metdata_exec_after_process_more_robust [20.01] Make set metadata exec after process more robust | 19 February 2020, 19:24:58 UTC |
| e0bba3a | Marius van den Beek | 19 February 2020, 19:23:05 UTC | Merge pull request #9399 from jmchilton/fix_joiner [20.01] XML fix for joiner.xml. | 19 February 2020, 19:23:05 UTC |
| 39f5fe9 | Dannon Baker | 19 February 2020, 19:21:43 UTC | Wrap entire email action execute method -- regardless of what happens here we don't want an exception to bubble up. | 19 February 2020, 19:21:43 UTC |
| 77a4c6d | Dannon Baker | 19 February 2020, 18:51:56 UTC | Raise an exception if an anonymous user tries to use email notification (which, of course, can't work anonymously...) | 19 February 2020, 18:51:56 UTC |
| 50959d2 | John Chilton | 19 February 2020, 18:31:24 UTC | Merge pull request #9398 from mvdbeek/fix_comparison_failing_with_hdas_without_hid [20.01] Fix hid comparison failing with hdas without hid | 19 February 2020, 18:31:24 UTC |
| 594fbb8 | John Chilton | 19 February 2020, 18:13:08 UTC | XML fix for joiner.xml. | 19 February 2020, 18:13:08 UTC |
| 15016b9 | John Chilton | 19 February 2020, 15:09:32 UTC | Cleanup remote job port mapping based on PR comments. | 19 February 2020, 18:04:03 UTC |
