November 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a58586: Cleanup SA objects between workflow invocation sch...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045 [17.09] Backport #5045 Compare: https://github.com/galaxyproject/galaxy/compare/ff3a6b084931...802c943fff71

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[galaxyproject/galaxy] b476cc: Fail job if job output collection fails
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b476cc4c57ad86c507eba22c88221584a62954a5 https://github.com/galaxyproject/galaxy/commit/b476cc4c57ad86c507eba22c8822… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fail job if job output collection fails We now set a non-zero exit code to actually set a job to failed. I belive this is a reasonable action, and it avoids green, empty datasets with log messages like: ``` galaxy.jobs.runners ERROR 2017-11-14 13:32:06,469 (19020/860246.torque6.curie.fr) Job output not returned from cluster: [Errno 2] No such file or directory: '/data/users/mvandenb/gx 124/tmp_nfs/jwd/019/19020/galaxy_19020.o' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,491 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o: [Errno 2] No suc h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,503 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e: [Errno 2] No suc h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e' galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,513 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec: [Errno 2] No su ch file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec' ``` Commit: 73454e12df8b8fe05aefc8ae120286e976985db8 https://github.com/galaxyproject/galaxy/commit/73454e12df8b8fe05aefc8ae1202… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix undefined exit_code_str problem (thx @nsoranzo) Commit: cacd6eadc5b95686173c9394f635d5a25527f503 https://github.com/galaxyproject/galaxy/commit/cacd6eadc5b95686173c9394f635… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Mark job wrapper as failed in a more direct way Commit: 13f6eeecf099316acc586282773316f3858c0549 https://github.com/galaxyproject/galaxy/commit/13f6eeecf099316acc5862827733… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py Log Message: ----------- Add new runner state for 'Job output not returned from cluster' This would allow adimns to write resubmit conditions for this specific failure. Commit: fac65894d3efd339ae0449300fba162d177efaed https://github.com/galaxyproject/galaxy/commit/fac65894d3efd339ae0449300fba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py Log Message: ----------- Merge pull request #5078 from mvdbeek/fail_if_job_output_collection_fails Fail job if job output collection fails Compare: https://github.com/galaxyproject/galaxy/compare/c6c55e1046a7...fac65894d3ef

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[galaxyproject/galaxy] 049376: Always fill `message` to avoid KeyError for sentry...
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix [17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Compare: https://github.com/galaxyproject/galaxy/compare/f6aedb0d2094...ff3a6b084931

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[galaxyproject/galaxy] 36e0e0: Run job handlers as uWSGI mules
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 36e0e01b6b9da78ae6f37f556385befba513bc14 https://github.com/galaxyproject/galaxy/commit/36e0e01b6b9da78ae6f37f556385… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M lib/galaxy/util/handlers.py Log Message: ----------- Run job handlers as uWSGI mules Commit: 85ea2d272803e174915680be8419e3053c8f947c https://github.com/galaxyproject/galaxy/commit/85ea2d272803e174915680be8419… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: A lib/galaxy/script/__init__.py M run.sh A scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Script reusage and generate uWSGI mule args Commit: e2e3e5f7d12a2f862595b380bf9da12b3b201333 https://github.com/galaxyproject/galaxy/commit/e2e3e5f7d12a2f862595b380bf9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/model/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/uwsgi_mule/handler.py M scripts/get_uwsgi_args.py Log Message: ----------- WIP job handlers as uWSGI mules from GCC 2017 Hackathon. Commit: 092a6b49230c65bc93070d9a388105ac568058dd https://github.com/galaxyproject/galaxy/commit/092a6b49230c65bc93070d9a3881… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/script/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py R lib/galaxy/web/stack/uwsgi_mule/handler.py M run.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- WIP uWSGI mule job handlers - it works! Commit: c7663a4e2e24536f1f3257186de86144399142d2 https://github.com/galaxyproject/galaxy/commit/c7663a4e2e24536f1f3257186de8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py Log Message: ----------- WIP job handlers as uWSGI mules refactor Commit: a06d6cf6167f1ce9aee9a34a28aa50473d19cb35 https://github.com/galaxyproject/galaxy/commit/a06d6cf6167f1ce9aee9a34a28aa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/manager.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- WIP: Job handlers as UWSGI mules, attempt at unprogrammed mules. Commit: ece3f242fb857a1363a0d143fd62033de4ce9e63 https://github.com/galaxyproject/galaxy/commit/ece3f242fb857a1363a0d143fd62… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/manager.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- Abandoning unprogrammed mules (for now), fixes for programmed mules Commit: 27a0b1ba40dfdf44b3e92ec09b4733df9563103e https://github.com/galaxyproject/galaxy/commit/27a0b1ba40dfdf44b3e92ec09b47… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py A lib/galaxy/util/configdict.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- WIP: attempted to support workers shared between pools, but locking won't allow for this, since you can't wait on messages from a specific farm. Commit: d7dd9b2b6590a3ecddb2bbacec9130a3dbf9e4e2 https://github.com/galaxyproject/galaxy/commit/d7dd9b2b6590a3ecddb2bbacec91… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py R lib/galaxy/util/configdict.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M scripts/get_uwsgi_args.py Log Message: ----------- WIP: drop stack configurability, this will come later. Cleanup for WIP PR Commit: 68542b615c70c7d85885827f42ecfc8521155bbf https://github.com/galaxyproject/galaxy/commit/68542b615c70c7d85885827f42ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M scripts/galaxy-main Log Message: ----------- Remove unneeded server_name manipulation from galaxy-main script Commit: c5bd3d4729b04d30dc94a798659ecc6d34683a06 https://github.com/galaxyproject/galaxy/commit/c5bd3d4729b04d30dc94a798659e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-22 (Tue, 22 Aug 2017) Changed paths: M config/workflow_schedulers_conf.xml.sample M lib/galaxy/jobs/handler.py M lib/galaxy/web/stack/message.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Support workflow scheduling via stack messaging. Commit: 03368ef549c37f5f4e4f95f2734246930914a368 https://github.com/galaxyproject/galaxy/commit/03368ef549c37f5f4e4f95f27342… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Start job runner worker threads post fork. Commit: bb7795bcfd18c64244634418040d0b89605a8c92 https://github.com/galaxyproject/galaxy/commit/bb7795bcfd18c64244634418040d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: A lib/galaxy/util/facts.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Generalize the collection of system/application "facts" usable for string templating. Commit: 14e9dddadec856a1a8aa916b4a4459f5fb487a06 https://github.com/galaxyproject/galaxy/commit/14e9dddadec856a1a8aa916b4a44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main Log Message: ----------- WIP: support log configuration from yaml/json app config with logging.config.dictConfig. Still working on yaml/json config loading in the webless app. Commit: aff0a7460e69b59cba67769040d761ac768032c3 https://github.com/galaxyproject/galaxy/commit/aff0a7460e69b59cba67769040d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Finish dictConfig logging feature Commit: ea70bafa0cf5b4b68a09ea62aeabb24b9ef62878 https://github.com/galaxyproject/galaxy/commit/ea70bafa0cf5b4b68a09ea62aeab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix mule starting under uWSGI with --ini-paste Commit: 17ea3d671facb06ec9a1101f80505c5c64758fe7 https://github.com/galaxyproject/galaxy/commit/17ea3d671facb06ec9a1101f8050… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M run.sh M scripts/get_uwsgi_args.py Log Message: ----------- Improve automatic uWSGI startup options interaction with [uwsgi] section in config file Commit: 1326a4d67107206babd4acd457734511f24a8996 https://github.com/galaxyproject/galaxy/commit/1326a4d67107206babd4acd45773… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/scheduling_manager.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Cleaning, lint and test fixes. Commit: 4d962d4ad29bfdad7c6f108d0300c79354d01a01 https://github.com/galaxyproject/galaxy/commit/4d962d4ad29bfdad7c6f108d0300… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Only include --paste-logger in uWSGI args if logging is configured in the PasteDeploy config Commit: bcfa874158bb82b7c45f8ff51d0701cb7b734f06 https://github.com/galaxyproject/galaxy/commit/bcfa874158bb82b7c45f8ff51d07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Fix for job_handler_count = 0 Commit: 9da850289f0d403ccba565ab88123c942db5b491 https://github.com/galaxyproject/galaxy/commit/9da850289f0d403ccba565ab8812… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Allow test framework to run uwsgi tests. Commit: 5c01c1cc3b71dbc069e03639c4804f084bdb37dc https://github.com/galaxyproject/galaxy/commit/5c01c1cc3b71dbc069e03639c480… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py M test/base/integration_util.py A test/integration/test_mules_as_job_handlers.py Log Message: ----------- Add mules integration test and integration test framework updates to support uwsgi. Commit: ac4d8477177e94b858519d7873beba352aec0431 https://github.com/galaxyproject/galaxy/commit/ac4d8477177e94b858519d7873be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix connection rejected errors for linux when waiting for uwsgi servers in test framework. Commit: 27e34d5ad93aa1f62ae5d55d3ceed98d2da3dd7b https://github.com/galaxyproject/galaxy/commit/27e34d5ad93aa1f62ae5d55d3cee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Do a better job cleaning up uwsgi processes for tests. Commit: 8fb47a0a2c211b83e31e64557ec04a05dea17f2b https://github.com/galaxyproject/galaxy/commit/8fb47a0a2c211b83e31e64557ec0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Fix mules test to not require ``app`` in test's memory. Just run a simple upload using a DatasetPopulator instead of running a tool test that requires the tool be in memory. Commit: 1fe9883774f53f0a03418021eebd78c86978e8b6 https://github.com/galaxyproject/galaxy/commit/1fe9883774f53f0a03418021eebd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Be a more forceful about cleaning uwsgi during tests. Commit: 00b8574404dd79e112b22f13ec72043a7b09ab09 https://github.com/galaxyproject/galaxy/commit/00b8574404dd79e112b22f13ec72… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix a segfault in uWSGI mules caused by trying to access invalid memory post-fork. There may be more cases like this that we'll have to handle in the mule fixup function. Context ======= uWSGI mules don't fork()/exec(), they fork() and then (as documented) run supplied code[1]. In order to read the URL parameter for IGV builds in the default tool_data_table_conf.xml, Galaxy imports urlopen() from six.moves.urllib.request. In Python 2.7, this imports the same function from urllib2. urllib2 uses (and reuses) a module global "opener" object[2]. This is initialized during the prefork application startup when used for the IGV data table, and then the same object is used postfork for the mule to load the same data table. It was discovered when attempting to run the mule job handler test under macOS, it does not occur in testing on Linux, nor does it occur on macOS with the default tool_conf.xml.sample and datatypes_conf.xml.sample. Whether or not the segfault was encountered seemed to depend on which tools or datatypes were loaded, but not in any clear pattern. The cause is presumably due to differences in memory allocation schemes between macOS and Linux, and perhaps garbage collection differences depending on different config file sizes? Regardless, it seems to be a classical case of holding on to references to memory that has been deallocated elsewhere. The segfault is specifically on the socket_getaddrinfo function in the _socket C module that provides functionality for the socket module in the standard Python lib. socket.getaddrinfo() is called by urlopen() by way of httplib. uWSGI mule debugging -------------------- I ultimately figured out the cause of the segfault with lldb. To make that experience better, I used a debug build of both Python and uWSGI (uWSGI was probably less important to do but that process is explained here anyway). Python with debugging is not ABI compatible with non-debug Python, so building all of Galaxy's C Extension wheels was necessary. In many cases, pip will do this for you (using the standard pip invocation in scripts/common_startup.sh), but not all will be successful. To build debug Python and debug uWSGI and run Galaxy under them, I used the following steps: 1. You will need a newer version OpenSSL than the one that ships with Sierra, I used the one from Brew: CFLAGS=-I/usr/local/opt/openssl/include \ LDFLAGS=-L/usr/local/opt/openssl/lib \ MACOSX_DEPLOYMENT_TARGET=10.12 \ ./configure --prefix=$HOME/pydebug --with-pydebug Be sure to set $MACOSX_DEPLOYMENT_TARGET. If you do not, the `getaddrinfo` function will utilize locking around `getaddrinfo` that should not be used[3]. 2. After intsalling Python, `virtualenv -p ~/pydebug .venv` in the Galaxy root. 3. In the uWSGI source, copy buildconf/default.ini to buildconf/debug.ini, set `debug = true` in debug.ini and then (with .venv activated) run: UWSGI_PROFILE=buildconf/debug.ini python setup.py install 4. Manually install a few problematic dependencies: - Use the Starforge recipe for building pysam[4], which mainly means grabbing a tarball of @dannon's fork, fixing the version number, and running `python setup.py install`. The ssdist tarball for this verison on wheels.galaxyproject.org is broken (files are missing from its manifest) and I need to fix that. Dannon is also currently working on upstreaming his changes and updating Galaxy for the latest version of pysam so this shouldn't be a problem in the future. - The mercurial sdist tarball on wheels.galaxyproject.org is also broken, download the correct version tarball directly from the mercurial release distribution site and `python setup.py install` it. I need to fix this as well. - Install numpy before bx-python (if it's not installed before bx is, bx will be missing needed features): pip install -i https://wheels.galaxyproject.org --no-binary :all: \ $(grep -i numpy= requirements.txt) 5. Install remaining requirements, iirc the rest should be ok: pip install -i https://wheels.galaxyproject.org --no-binary :all: \ -r requirements.txt --no-binary :all: is necessary because there are numerous macOS wheels in PyPI with a `none` SOABI tag, meaning these wheels will install but will not work for the debug Python ABI. When you run Galaxy under the debugger, you won't be able to directly control the fork()ed mules. Instead, you'll need to fire up a second debugger to catch the mule[5]: 1. Start up Galaxy under lldb, set a breakpoint on fork Be sure that your virtualenv is *NOT* activated before starting lldb, or it will fail miserably at loading its own python module. % lldb .venv/bin/uwsgi (lldb) b fork 2. Run Galaxy, e.g.: (lldb) r --virtualenv /Users/nate/galaxy/.venv --module galaxy.webapps.galaxy.buildapp:uwsgi_app_factory() --yaml config/galaxy.yml --processes 1 --threads 4 --http localhost:8080 --pythonpath lib --master --static-map /static/style=/Users/nate/galaxy/static/style/blue --static-map /static=/Users/nate/galaxy/static --die-on-term --enable-threads --py-call-osafterfork --mule=lib/galaxy/main.py --farm=job-handlers:1 3. The first fork() is for the workers, so you'll want to skip this: (lldb) n 4. The second fork is for the mule. At this point, start a second lldb in another terminal, set a breakpoint on something interesting, and attach it to the process that is about to start: % lldb (lldb) b socket_getaddrinfo (lldb) pro at -n uwsgi -w 5. Continue the fork in the original lldb: (lldb) n 6. Continue debugging in the second lldb, which is now attached to the mule. [1]: https://github.com/unbit/uwsgi/blob/5039a4b679735348422638baa7cff7a8116762e… [2]: https://github.com/python/cpython/blob/20958e6d91d11a80d6c664ce6346791259b1… [3]: https://emptysqua.re/blog/getaddrinfo-deadlock/ [4]: https://github.com/galaxyproject/starforge/blob/f1013ddf6119381ffba6df06e8d… [5]: https://stackoverflow.com/questions/14746315/how-to-attach-to-child-process… Commit: e91db56f0e377f94574f80c833182e79a43156fb https://github.com/galaxyproject/galaxy/commit/e91db56f0e377f94574f80c83318… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Use fancy uWSGI log messages when running tests under uWSGI, or you can set whatever log format string you want with `$GALAXY_TEST_LOG_FORMAT`. If unset, and not running under uWSGI, galaxy.config.logging (the logging.config.dictConfig dict) will not be set and the default logging config will be used. Commit: 3477906dc556ce17223bafbc470f1d809f6196cb https://github.com/galaxyproject/galaxy/commit/3477906dc556ce17223bafbc470f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Provide failure reason when tool configs fail to load due to system errors (ENOENT, EPERM, etc.). Commit: 3f0082515af630bd095ee5fc57bac044369c8f0e https://github.com/galaxyproject/galaxy/commit/3f0082515af630bd095ee5fc57ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/driver_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Improvements for mule job handler testing. Ensure that the server running the job is a mule. Added a test tool that will write Galaxy app.config attributes to the output dataset. Commit: 09feaf6f4d46509c7401970013b5a8097a5d4c4e https://github.com/galaxyproject/galaxy/commit/09feaf6f4d46509c7401970013b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/script/__init__.py M lib/galaxy/util/__init__.py A lib/galaxy/util/path.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/util/commit_util.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M test/base/driver_util.py Log Message: ----------- - Do all logging configuration other than paste fileConfig logging from dictConfig. Default log message format varies by stack. - Refactor a lot of file extension handling in to galaxy.util.path. - Simplify and improve config file finding. - Simplify and improve native app creation. - Integrate uWSGI argument generation with @jmchilton's improvements to the startup scripts. - Fix starting without a config file under uWSGI Commit: 11857db011f4814a4aa0feb151a8a838f91b8c88 https://github.com/galaxyproject/galaxy/commit/11857db011f4814a4aa0feb151a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Attempt uWSGI restarts when running for testing. It's not able to detect if it failed due to port binding, but it'll retry if uwsgi exits non-zero. Commit: 318bf0bd01ffe6a2bd08fbbfffd8be88e95ae8f7 https://github.com/galaxyproject/galaxy/commit/318bf0bd01ffe6a2bd08fbbfffd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Rework cleanup of uwsgi in tests... This looks cleaner and was closer to what I originally wanted - undoes some stuff @natefoo did hopefully he isn't mad. Commit: 37738b94fbcad6e5aefe410f0c01af4dbac17281 https://github.com/galaxyproject/galaxy/commit/37738b94fbcad6e5aefe410f0c01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- More mule testing. Commit: 1e6080e1bf6d410a617079af93e85a29cad21243 https://github.com/galaxyproject/galaxy/commit/1e6080e1bf6d410a617079af93e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-02 (Sat, 02 Sep 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Don't require integration tests to use the same port for every Galaxy instance. The previous logic would pick a port at random if one wasn't explicitly defined and then set an environment variable requiring each instance to re-use that. This new logic doesn't reuse randomly assigned ports that way by tracking if a port was randomly assigned or not. Commit: 32a280bf3100f359e1d046206d47a36e0d92db62 https://github.com/galaxyproject/galaxy/commit/32a280bf3100f359e1d046206d47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Just skip the mule tests on Jenkins. They work locally alone or ran together, they work locally in the same Docker container as Jenkins, I don't understand. Commit: d7aec7e04dc064fd9e133d9a592e1cb5ef486037 https://github.com/galaxyproject/galaxy/commit/d7aec7e04dc064fd9e133d9a592e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Revert "Just skip the mule tests on Jenkins." This reverts commit 32a280bf3100f359e1d046206d47a36e0d92db62. Commit: 30266c522127d4b9b13fd0a7433473747cec023c https://github.com/galaxyproject/galaxy/commit/30266c522127d4b9b13fd0a74334… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M Makefile M README.rst A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M 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tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into job-handler-mules Commit: 4eface7e722ff46276225457da0dcacc537fb10e https://github.com/galaxyproject/galaxy/commit/4eface7e722ff46276225457da0d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: R lib/galaxy/util/path.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix path module divergence Commit: b75583ea26269101f12cb29df76a23eeecf68ab5 https://github.com/galaxyproject/galaxy/commit/b75583ea26269101f12cb29df76a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Fix post-merge lint issues Commit: bf9e2b6a9696a7b3ecc0b369424c9b805ac64a11 https://github.com/galaxyproject/galaxy/commit/bf9e2b6a9696a7b3ecc0b369424c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-09 (Thu, 09 Nov 2017) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Fix call to __listify. Commit: e97de138e32d350d4fc7593498130ca9cd3c9d06 https://github.com/galaxyproject/galaxy/commit/e97de138e32d350d4fc759349813… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M test/base/integration_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Revert "Revert "Just skip the mule tests on Jenkins."" This reverts commit d7aec7e04dc064fd9e133d9a592e1cb5ef486037. Commit: b96a8476899aef2dfe1e1b6cde5048afae8e3428 https://github.com/galaxyproject/galaxy/commit/b96a8476899aef2dfe1e1b6cde50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/util/properties.py Log Message: ----------- Fix an iterator bug with find_config_file() when using include_samples and write a doctest for it. Commit: df6a1dedc0c68c8b743b63a6fddaaac71c2b56bc https://github.com/galaxyproject/galaxy/commit/df6a1dedc0c68c8b743b63a6fdda… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix config file finding in the orm scripts utility and make its doctest clean up after itself Commit: b8df770bfd3d0e3bd2d5cb26db3cf159ed4e8d3a https://github.com/galaxyproject/galaxy/commit/b8df770bfd3d0e3bd2d5cb26db3c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix import linting errors Commit: cf9ba1e0cc88f695a27d74c96895b3d6b093e583 https://github.com/galaxyproject/galaxy/commit/cf9ba1e0cc88f695a27d74c96895… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/util/properties.py Log Message: ----------- Clarifications/fixes from @nsoranzo's comments Commit: b805fa5945e1f6799e6cf28097155e7b1d434b4e https://github.com/galaxyproject/galaxy/commit/b805fa5945e1f6799e6cf2809715… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Undo changes unrelated to uWSGI mule work Commit: 806438edc9b3b407b9cb259f7cdaa8a85fe97f64 https://github.com/galaxyproject/galaxy/commit/806438edc9b3b407b9cb259f7cda… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: R lib/galaxy/script/__init__.py A lib/galaxy/util/script.py M scripts/get_uwsgi_args.py M scripts/manage_tool_dependencies.py Log Message: ----------- Revert script changes unrelated to uWSGI mule work. Includes galaxy.util.script so that get_uwsgi_args.py still works, but that will be PR'd separately and merged later. Commit: 1062c705a2a7a8e4cb1b8c6899941474a620885d https://github.com/galaxyproject/galaxy/commit/1062c705a2a7a8e4cb1b8c689994… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix typo in facts module Commit: c340d4ebecd56583d7b524e380dedf460e5a7175 https://github.com/galaxyproject/galaxy/commit/c340d4ebecd56583d7b524e380de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/model/orm/scripts.py M lib/tool_shed/galaxy_install/migrate/check.py R manage_tools.sh R scripts/manage_tools.py Log Message: ----------- Fix tool migrations with config file changes, do everything from manage_db.sh. Commit: 418fd53739800b639924455722618b7172e23168 https://github.com/galaxyproject/galaxy/commit/418fd53739800b63992445572261… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh M .ci/jenkins/selenium/run_tests.sh M .travis.yml M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/utils/ajax-queue.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/releases/17.09_announce.rst A lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/converters/bgzip.py A lib/galaxy/datatypes/converters/cram_to_bam.py A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M 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test/base/driver_util.py M test/base/populators.py M test/base/testcase.py M test/functional/test_toolbox.py A test/functional/tools/cat_data_and_sleep.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/test_local_job_cancellation.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_contents.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_describing_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_objectstore.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/phenotype_association/senatag.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into job-handler-mules Commit: e68b8a312e3051b9378e59340ef42dd91302c1c0 https://github.com/galaxyproject/galaxy/commit/e68b8a312e3051b9378e59340ef4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py Log Message: ----------- Fix use of configure_logging() by scripts that pass the config as a dict rather than a galaxy configuration object Commit: c270614fac007c35eefe473a9023964d7feafe89 https://github.com/galaxyproject/galaxy/commit/c270614fac007c35eefe473a9023… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/history_contents.py M templates/user/register.mako M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/create_2.xml M test/integration/test_data_manager_table_reload.py M tools/data_source/microbial_import.xml Log Message: ----------- Merge remote-tracking branch 'origin/dev' into job-handler-mules Commit: 43138be11f8194dabc4645d20d58bb156f9bdb3c https://github.com/galaxyproject/galaxy/commit/43138be11f8194dabc4645d20d58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Reenable automatic silencing of chatty loggers by default. This is needed when Paste is used but PasteDeploy is not, e.g. with tests. Commit: f78436bba0209d5d886387f81020d3383e08c327 https://github.com/galaxyproject/galaxy/commit/f78436bba0209d5d886387f81020… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/util/facts.py Log Message: ----------- Fix None server_name when using the default under uWSGI Commit: c18521d7f774febb75a715e4de7926ff957daab9 https://github.com/galaxyproject/galaxy/commit/c18521d7f774febb75a715e4de79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Move signal handling from uWSGI stack to main Commit: 1ec960bcf66769c682135901cbd4623b6719fdf8 https://github.com/galaxyproject/galaxy/commit/1ec960bcf66769c682135901cbd4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/galaxy-main M scripts/get_uwsgi_args.py Log Message: ----------- Improve shutdown cleanliness under uWSGI. Commit: b4863b2df8214972b5e14b0b318591e1ded613f6 https://github.com/galaxyproject/galaxy/commit/b4863b2df8214972b5e14b0b3185… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/app.py M scripts/galaxy-main Log Message: ----------- Fix lint errors Commit: eda29c81c16c4422167c7d22f7a79980f7799baa https://github.com/galaxyproject/galaxy/commit/eda29c81c16c4422167c7d22f7a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/tool_shed/config.py M test/base/driver_util.py M test/shed_functional/functional_tests.py Log Message: ----------- Remove deprecated job runner URL config options Commit: e858ceb84a340c658c682d33e350eb7c19649978 https://github.com/galaxyproject/galaxy/commit/e858ceb84a340c658c682d33e350… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M config/galaxy.ini.sample M scripts/get_uwsgi_args.py Log Message: ----------- Do not autostart uWSGI mules Commit: 47473cb85d38a4c7c4ccc9c03186787693f28efb https://github.com/galaxyproject/galaxy/commit/47473cb85d38a4c7c4ccc9c03186… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Postfork thread start fixes Commit: e8a22447fd6b9d5f077e2d6b8a0d1144b2cb20db https://github.com/galaxyproject/galaxy/commit/e8a22447fd6b9d5f077e2d6b8a0d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/util/handlers.py Log Message: ----------- Run jobs in web workers if no job-handlers farm is configured and using a default job conf (no job_conf.xml) Commit: 49158ba38ba7204a078f2da22ddd6bad75c25f23 https://github.com/galaxyproject/galaxy/commit/49158ba38ba7204a078f2da22ddd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/web/stack/__init__.py M scripts/galaxy-main Log Message: ----------- Add multi-farm support to the main script Commit: 2764fe0b5cb73087f76c701a6faf1e71b3c96394 https://github.com/galaxyproject/galaxy/commit/2764fe0b5cb73087f76c701a6faf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/facts.py M lib/galaxy/web/stack/__init__.py Log Message: ----------- Fix/improve server name manipulation Commit: 4b2c177ae504af7d290d1a6ed436ce0ed4207400 https://github.com/galaxyproject/galaxy/commit/4b2c177ae504af7d290d1a6ed436… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/manager.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Attempt to deal with job_conf.xml handlers in a backwards-compatible way. Commit: a3346e2fb7c8cc4d800684f36bb3ca5ae82ced72 https://github.com/galaxyproject/galaxy/commit/a3346e2fb7c8cc4d800684f36bb3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix unit tests Commit: c6c55e1046a74686d58f5de8010b6654b70e2421 https://github.com/galaxyproject/galaxy/commit/c6c55e1046a74686d58f5de8010b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/workflow_schedulers_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py A lib/galaxy/web/stack/message.py A lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/util/commit_util.py R manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh M scripts/galaxy-main A scripts/get_uwsgi_args.py R scripts/manage_tools.py M test/base/driver_util.py M test/base/integration_util.py A test/functional/tools/config_vars.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_mules_as_job_handlers.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_job_configuration.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #4475 from natefoo/job-handler-mules Run Galaxy fully under uWSGI, including job handlers Compare: https://github.com/galaxyproject/galaxy/compare/d82933d410f6...c6c55e1046a7

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[galaxyproject/galaxy] 1cfdf8: add ICM datatype for glimmer
by GitHub 28 Nov '17

28 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add ICM datatype for glimmer Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- copy paste mistake... Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't read too much Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt [17.09] Add ICM datatype for glimmer Compare: https://github.com/galaxyproject/galaxy/compare/ed162d5a69a3...f6aedb0d2094

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[galaxyproject/galaxy] adfb62: Fix metadata setting for Otu datatypes
by GitHub 27 Nov '17

27 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix metadata setting for Otu datatypes I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard. Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation [BUG][17.09] Fix metadata setting for Otu datatypes Compare: https://github.com/galaxyproject/galaxy/compare/f16491cd6506...ed162d5a69a3

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[galaxyproject/galaxy] d868ff: Improved qunit testing options.
by GitHub 26 Nov '17

26 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d868ffd08b8a5b539ba7977172e7c5a5c7be49a3 https://github.com/galaxyproject/galaxy/commit/d868ffd08b8a5b539ba7977172e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/test.js M client/karma.config.js M client/package.json Log Message: ----------- Improved qunit testing options. - Speed up qunit testing but not re-building production bundles that aren't used anyway. - Add a watch option for qunit. - Add option to speed up running all tests by building tests as single bundle instead of many bundles. (May be future default for ``make client-test``.) This is as close as I think we are going to get to closing #4843. Commit: d82933d410f61fc703b5191d235f13f6b370a936 https://github.com/galaxyproject/galaxy/commit/d82933d410f61fc703b5191d235f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-26 (Sun, 26 Nov 2017) Changed paths: M Makefile A client/galaxy/scripts/qunit/test.js M client/karma.config.js M client/package.json Log Message: ----------- Merge pull request #5066 from jmchilton/qunit_improvements Improved Karma configuration and options. Compare: https://github.com/galaxyproject/galaxy/compare/52eb970d1804...d82933d410f6

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[galaxyproject/galaxy] c28b36: Re-enable qunit tests.
by GitHub 25 Nov '17

25 Nov '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c28b3681abe0f15b40b709471a625f816df1923a https://github.com/galaxyproject/galaxy/commit/c28b3681abe0f15b40b709471a62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M .travis.yml Log Message: ----------- Re-enable qunit tests. Commit: 4b20acbed1d082c24e766da33588c049622ff7f9 https://github.com/galaxyproject/galaxy/commit/4b20acbed1d082c24e766da33588… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-23 (Thu, 23 Nov 2017) Changed paths: M Makefile Log Message: ----------- Fix client-test Makefile target. Commit: f2b6af6ef9167cd859dd4790d56d13eb38bf5e26 https://github.com/galaxyproject/galaxy/commit/f2b6af6ef9167cd859dd4790d56d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M Makefile Log Message: ----------- Guess we need to build full client before webpack for qunit? Commit: 52eb970d180424654d380b9997ab345de8e49417 https://github.com/galaxyproject/galaxy/commit/52eb970d180424654d380b9997ab… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-25 (Sat, 25 Nov 2017) Changed paths: M .travis.yml M Makefile Log Message: ----------- Merge pull request #5063 from jmchilton/reenable_qunit Re-enable qunit testing. Compare: https://github.com/galaxyproject/galaxy/compare/3303fab75b90...52eb970d1804

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[galaxyproject/galaxy] 8db428: Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Closes https://github.com/galaxyproject/galaxy/issues/2645. Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade [BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Compare: https://github.com/galaxyproject/galaxy/compare/a71d5aa2db41...f16491cd6506

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[galaxyproject/galaxy] cbc74f: Ignore OSError when chmod'ing integrated_tool_pane...
by GitHub 24 Nov '17

24 Nov '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ``` Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes [BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/a7c8edbaa448...a71d5aa2db41

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