pulsar-galaxy-lib 0.15.6

Description:

pulsargalaxylib 0.15.6

This project is a Python server application that allows a Galaxy server to run jobs on remote systems (including
Windows) without requiring a shared mounted file systems. Unlike traditional
Galaxy job runners - input files, scripts, and config files may be transferred
to the remote system, the job is executed, and the results are transferred back
to the Galaxy server - eliminating the need for a shared file system.
Full documentation for the project can be found on Read The Docs.

Configuring Galaxy
Galaxy job runners are configured in Galaxy’s job_conf.xml file. Some small
examples of how to configure this can be found here, but be sure
to check out job_conf.xml.sample_advanced in your Galaxy code base or on
Github
for complete information.


Quickstart
Full details on different ways to install Pulsar can be found in the install
section of the
documentaiton, but if your machine has the proper Python dependencies
available it can be quickly download and a test job run with:
$ mkdir pulsar
$ cd pulsar
$ python3 -m venv venv
$ . venv/bin/activate # venv\Scripts\activate.bat on Windows
$ pip install 'pulsar-app[web]'
$ pulsar-config
$ pulsar --daemon # just `pulsar` on Windows
$ pulsar-check # runs a test job
Please note that as of the 0.14.0 release, Pulsar no longer supports any version
of Python 2. The minimum supported Python version is 3.5.
The configuration documentation
has many details on securing your Pulsar server and enabling advanced features
such as cluster integration and message queue communication.


Development and Testing
The recommended approach to setting up a development environment for Pulsar on
Linux or macOS is rougly as follows:
$ git clone https://github.com/galaxyproject/pulsar
$ cd pulsar
$ python3 -m venv .venv
$ . .venv/bin/activate # .venv\Scripts\activate on Windows
$ pip install -e '.[web]'
$ pip install -r dev-requirements.txt
The -e flag to pip installs Pulsar in “editable” mode, meaning that
changes you make to the source code will be reflected when running the pulsar
commands installed in the virtual environment.
This project is distributed with unit and integration tests (many of which will
not run under Windows), the following command will install the needed python
components to run these tests. The following command will then run these tests:
$ make tests
The following command will then produce a coverage report corresponding to this
test and place it in the coverage_html_report subdirectory of this
project.:
$ coverage html
Check out the Contributing documentation
for many more details on developing and contributing to Pulsar.
Please note that this project is released with a Contributor Code of Conduct. By participating
in this project you agree to abide by its terms.


Support
This documentation is an incomplete work in progress. There are more ways to
configure and use Pulsar than are documented, and a growing number of Pulsar
experts who would be more than happy to answer your questions and help with any
problems you may run in to while setting up a Pulsar deployment. Please do not
hesitate to reach out on the Galaxy Admins Gitter Channel

History



0.15.6 (2024-01-15)

Allow tus uploads to Galaxy.
Pull Request 351



0.15.5 (2023-09-15)

Add catchall OSError to recoverable exceptions (thanks to @mvdbeek).
Pull Request 338



0.15.4 (2023-08-29)

Add .readthedocs.yaml (thanks to @natefoo). Pull Request 332
Add explicit TimeoutError catching (thanks to @mvdbeek). Pull Request 337
Update galaxy-job-metrics requirement (thanks to @cat-bro). Pull Request 334



0.15.3 (2023-07-20)

Fix Pulsar consumer state after ConnectionResetError. Pull Request 331
User auth plugins (thanks to @SergeyYakubov). Pull Request 321



0.15.2 (2023-05-02)

Fix Pulsar and Pulsar client reconnection to AMQP server. Pull Request 324
Reduce verbosity of timeout exception catching. Pull Request 325



0.15.1 (2023-04-13)

No changes, working around pypi isssue.



0.15.0 (2023-04-13)

Updated Galaxy+Pulsar container. Pull Request 306
Rework container execution - generalize Kubernetes execution to allow it to work without a
message queue and to allow TES execution based on pydantic-tes (https://github.com/jmchilton/pydantic-tes). Pull Request 302
Add documentation and diagrams for container execution scenarios. Pull Request 302
Rework integration tests to use pytest more aggressively.
Fixes to CI to run more tests that weren’t being executed because Tox was not sending
environment variables through to pytest.
Add option amqp_key_prefix to direct task queue naming while retaining simple
default manager names and such in container scheduling deployments. Pull Request 315
Various typing and CI fixes. Pull Request 312, Pull Request 319
Fixes for extra_file handling. Pull Request 318
Separate tool_stdio and job_stdio handling. Pull Request 318
Re-import MEMORY_STATEMENT.sh from Galaxy. Pull Request 297
Add support for logging to sentry. Pull Request 322



0.14.16 (2022-10-04)

Fix small regression related to building URLs for client action mapping.



0.14.15 (2022-10-03)

Fix small regressions bugs in 0.14.14 - updating runner util code was bigger swap over
than it seemed.



0.14.14 (2022-10-30)

Bring in updated Galaxy runner util code. Pull Request 303
Fix recovering “lost” jobs where the job directory does not exist at
startup/recovery time (thanks to @natefoo). Pull Request 301
Use urlencode to encode path (thanks to @mvdbeek). Pull Request 299
Support the k8s_job_ttl_secs_after_finished option as in the Galaxy
Kubernetes runner (thanks to @natefoo). Pull Request 287



0.14.13 (2021-12-06)

Don’t pass all environment variables to jobs launched by Manager (thanks
to @nsoranzo).
Pull Request 295
Drop legacy job conf for Galaxy framework tests, test against
metadata_strategy: extended (thanks to @mvdbeek).
Pull Request 294



0.14.12 (2021-11-10)

Fixes to bring HOME and temp directory handling closer to Galaxy native runners.
Enable globbed from_work_dir outputs for remote metadata.



0.14.11 (2021-07-19)

Fix and test for returncode handling in certain cases. Pull Request 274
Modernize tox. Pull Request 271



0.14.10 (2021-07-17)

Don’t error out if annotated galaxy.json is absent. Pull Request 270



0.14.9 (2021-07-16)

Implement dynamic file sources abstraction for parsing files to transfer
from galaxy.json files. Pull Request 269
Use tool classes to only test remote Galaxy tools. Pull Request 266
Run Galaxy framework tests against dev and master branches of Galaxy (thanks
to @mvdbeek). Pull Request 264



0.14.8 (2021-07-14)

Fix Galaxy composite input references. Pull Request 262
Run galaxy’s tool framework tests against this repo’s pulsar (thanks to
@mvdbeek). Pull Request 259



0.14.7 (2021-07-13)

Accept description of tool files to transfer from Galaxy.
Pull Request 261
Support globs in from_work_dir outputs (thanks to @natefoo).
Pull Request 257
Fix loading the Galaxy dependency resolvers config, plus additional config
directory fixes (thanks to @natefoo). Pull Request 256



0.14.6 (2021-05-24)

Fix for newer Galaxy tool profiles having isolated home directories.



0.14.5 (2021-04-15)

Potential fix for setting file actions via job destination parameters.



0.14.4 (2021-04-14)

Re-attempt release process - published wrong branch with 0.14.3.



0.14.3 (2021-04-13)

Allow transferring fewer files from Pulsar when using extended metadata with
Galaxy.



0.14.2 (2021-02-15)

Fix the use of requests, limits, and walltime with coexecution pods. Pull Request 246



0.14.1 (2021-02-02)

Fix the use of named managers with coexecution pods. Pull Request 242



0.14.0 (2020-09-17)

fix the PyYAML “load() deprecation” warning (thanks to @gmauro). Pull
Request 232
Set the DRMAA workingDirectory to the job’s working directory
Pull Request 230
Fix a unicode issue and polish a bit of variables (thanks to @gmauro).
Pull Request 229
Respond to MQ messages requesting status updates. Pull Request 228
Fix REST connections broken with Py3 using standard transport Issue 227
Pull Request 231
Drop Python 2.7 support in standard transport, drop Python 2.7 tests and fix
Python 3.7 wheel install test, general test debugging enhancements.
Pull Request 231
drop python 2.6 and add 3.7 and update the testing infrastructure to a more
recent Ubuntu setup (thanks to @bgruening). Pull Request 226
Use is_alive in favour of isAlive for Python 3.9 compatibility (thanks to
@tirkarthi). Issue 224 Pull Request 225
Request and register ports for Galaxy ITs when using Kubernetes.
Pull Request 223
Implement killing k8s jobs. Pull Request 221
Respond to MQ messages requesting status updates.
Pull Request 228
Drop python 2.6 and add 3.7 and update the testing infrastructure to a more
recent Ubuntu setup (thanks to @bgruening). Pull Request 226
Add a more descriptive message in case of error parsing an external id
(thanks to @gmauro). Pull Request 213
Use requests (thanks to @mvdbeek). Pull Request 216
Use is_alive in favour of isAlive for Python 3.9 compatibility (thanks to
@tirkarthi). Pull Request 225
Debug connection string for AMQP.
Pull Request 217
Various small Kubernetes fixes and enhancements.
Pull Request 218, Pull Request 219
Improvements and fixes to container handling.
Pull Request 202
Fix a typo in exception logging thanks to @erasche.
Pull Request 203
Cleanup config file handling a bit by removing branch for very
old Pulsar servers likely no longer supported.
Pull Request 201



0.13.1 (2020-09-16)

Pinned all listed requirements. This is the final version of Pulsar to support Python 2.



0.13.0 (2019-06-25)

Various improvements and simplifications to Kubernetes job execution.



0.12.1 (2019-06-03)

Retry botched release that didn’t include all relevant commits.



0.12.0 (2019-06-03)

Revise Python Galaxy dependencies to use newer style Galaxy decomposition.
galaxy-lib can no longer be installed in Pulsar’s environment, so you will
likely need to rebuild your Pulsar virtualenv for this release.
Pull Request 187
Add a Dockerfile for Pulsar with CVMFS (thanks to @nuwang and @afgane).
Pull Request 166
Various small improvements to Kubernetes pod execution environment.
Pull Request 190
Improve readme linting.
Pull Request 186
Update example docs for Condor (thanks to @bgruening).
Pull Request 189



0.11.0 (2019-05-16)

Implement staging Galaxy metadata input files in the client.
39de377
Fix ‘amqp_ack_republish_time’ in sample (thanks to @dannon).
Pull Request 185
Updated amqp_url in job_conf_sample_mq_rsync.xml (thanks to @AndreasSko).
Pull Request 184
Use wildcard char for pulsar version (thanks to @VJalili).
Pull Request 181
Refactor toward more structured inputs. f477bc4
Refactor toward passing objectstore identifying information around.
Pull Request 180
Rework imports for new Galaxy library structure. da086c9
Revert empty input testing, it really probably should cause a failure
to transfer a non-existent file.
8bd5511
Better client mapper documentation. b6278b4



0.10.0 (2019-05-06)

Implement support for Kubernetes two container pod jobs - staging and
tool execution as separate containers in the same job’s pod.
Pull Request 176, Pull Request 178



0.9.1 (2019-05-01)

Fix duplicate inputs being a problem when staging Galaxy files.
Pull Request 175
Fix deprecated assertEquals() (thanks to @nsoranzo). Pull Request 173
Fix a method missing problem. Pull Request 174
Sync “recent” galaxy runner util changes. Pull Request 177



0.9.0 (2019-04-12)

Add configuration parameter to limit stream size read from disk. Pull
Request 157
Pass full job status for failed and lost jobs. Pull Request 159
Improve message handling if problems occur during job setup/staging. Pull
Request 160
Rework preprocessing job state to improve restartability and reduce job loss.
This change should be applied while no jobs are running.
Pull Request 164
Add support for overriding config through environment variables (thanks to
@nuwang). Pull Request 165
Minor docs updates (thanks to @afgane). Pull Request 170
Python 3 fixes in Pulsar client (thanks to @mvdbeek). Pull Request 172



0.8.3 (2018-02-08)

Create universal wheels to enable Python 3 support when installing from PyPI
(thanks to @nsoranzo).
Pull Request 156



0.8.1 (2018-02-08)

Update link for logo image. Pull Request 145
Minor error and log message typos (thanks to @blankenberg).
Pull Request 146, Pull Request 153
Fixes/improvements for catching quoted tool files. Pull Request 148
Fix config sample parsing so run.sh works out of the box.
Pull Request 149



0.8.0 (2017-09-21)

Support new features in Galaxy job running/scripting so that Pulsar respects
$GALAXY_VIRTUAL_ENV and $PRESERVE_GALAXY_ENVIRONMENT. Fix remote
metadata in cases where the tool environment changes the python on
$PATH. Pull Request 137
Precreate Galaxy tool outputs on the remote before executing (fixes a bug
related to missing output files on stage out). Pull Request 141
Support the remote_transfer file action without setting the
jobs_directory destination param Pull Request 136
Fix invalid character in job managers documentation (thanks to @mapa17).
Pull Request 130
Fix conda_auto_* option resolution and include a sample
dependency_resolvers_conf.xml (thanks to @mapa17). Pull Request 132
Fix tox/Travis tests. Pull Request 138, Pull Request 139,
Pull Request 140
Fix a bug with AMQP acknowledgement. Pull Request 143



0.7.4 (2017-02-07)

Fix Conda resolution and add a test case. 11ce744
Style fixes for updated flake8 libraries. 93ab8a1, 3573341
Remove unused script. 929bffa
Fixup README. 629fdea



0.7.3 (2016-10-31)

Fix “AttributeError” when submitting a job as a real user.
Pull Request 124, Issue 123



0.7.2 (2016-08-31)

Fix bug causing loops on in response to preprocessing error conditions.



0.7.1 (2016-08-29)

Do a release to circumvent a tool version logic error in Galaxy (
released Galaxy versions think 0.7.0 < 0.7.0.dev3).



0.7.0 (2016-08-26)

Update Makefile to allow release pulsar as an application and a library
for Galaxy at the same time.
Small update to test scripts for TravisCI changes.
Improvements for embedded Galaxy runner. (TODO: fill this out)
Remove support for Python 2.6. 60bf962
Update docs to describe project goverance and reuse Galaxy’s
Code of Conduct. 7e23d43, dc47140
Updated cluster slots detection for SLURM from Galaxy. cadfc5a
Various changes to allow usage within Galaxy as a library. ce9d4f9
Various changes to allow embedded Pulsar managers within Galaxy.
ce9d4f9, d262323, 8f7c04a
Introduce a separate working and metadata directory as required for
Galaxy 16.04 that requires this separation. 6f4328e
Improve logging and comments. 38953f3, a985107, ad33cb9
Add Tox target for Python 2.7 unit testing. d7c524e
Add Makefile command for setup.py develop. fd82d00



0.6.1 (2015-12-23)

Tweak release process that left 0.6.0 with an incorrect PyPI description page.



0.6.0 (2015-12-23)

Pulsar now depends on the new galaxy-lib Python package instead of
manually synchronizing Python files across Pulsar and Galaxy.
Numerous build and testing improvements.
Fixed a documentation bug in the code (thanks to @erasche). e8814ae
Remove galaxy.eggs stuff from Pulsar client (thanks to @natefoo). 00197f2
Add new logo to README (thanks to @martenson). abbba40
Implement an optional awknowledgement system on top of the message queue
system (thanks to @natefoo). Pull Request 82 431088c
Documentation fixes thanks to @remimarenco. Pull Request 78, Pull Request 80
Fix project script bug introduced this cycle (thanks to @nsoranzo). 140a069
Fix config.py on Windows (thanks to @ssorgatem). Pull Request 84
Add a job manager for XSEDE jobs (thanks to @natefoo). 1017bc5
Fix pip dependency installation (thanks to @afgane) Pull Request 73



0.5.0 (2015-05-08)

Allow cURL downloader to resume transfers during staging in (thanks to
@natefoo). 0c61bd9
Fix to cURL downloaders status code handling (thanks to @natefoo). 86f95ce
Fix non-wheel installs from PyPI. Issue 72
Fix mesos imports for newer versions of mesos (thanks to @kellrott). fe3e919
More, better logging. 2b3942d, fa2b6dc



0.4.0 (2015-04-20)

Python 3 support. Pull Request 62
Fix bug encountered when running pulsar-main and pulsar-config commands as scripts. 9d43ae0
Add pulsar-run script for issues commands against a Pulsar server (experimental). 3cc7f74



0.3.0 (2015-04-12)

Changed the name of project to Pulsar, moved to Github.
New RESTful web services interface.
SCP and Rsync file staging options added by E. Rasche. Pull
Request
Allow YAML based configuration.
Support for more traditional pip/setup.py-style
installs.
Dozens of smaller bugfixes and documentation updates.



0.2.0

Last version named the LWR - found on BitBucket.
Still supported in Galaxy as of 15.03 the release.
Introduced support for submitting to various queueing systems,
operation as a Mesos framework, Docker support, and
various other advanced deployment options.
Message queue support.
Framework for configurable file actions introduced.



0.1.0

Simple support for running jobs managed by the Python LWR
web process.
https://bitbucket.org/jmchilton/lwr/branch/0.1



0.0.1

See the original announcement
and initial commit.