- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 123d9d: Additional fixes for moving to bl2
by GitHub 18 May '15

18 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 123d9d1a62c28218a4559fe5d7b90a6b2a1d2eab https://github.com/galaxyproject/usegalaxy-playbook/commit/123d9d1a62c28218… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py M stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml Log Message: ----------- Additional fixes for moving to bl2

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[galaxyproject/usegalaxy-playbook] 0d8b01: update mutable confs on production
by GitHub 18 May '15

18 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0d8b015c97b6e0a4fec8d74b3272c679d62a161c https://github.com/galaxyproject/usegalaxy-playbook/commit/0d8b015c97b6e0a4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update mutable confs on production

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[galaxyproject/usegalaxy-playbook] 4f989f: Switch Blacklight jobs to bl2.
by GitHub 18 May '15

18 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4f989fab515b0a2af8c0e384b5cda7a897a2784e https://github.com/galaxyproject/usegalaxy-playbook/commit/4f989fab515b0a2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py M stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Switch Blacklight jobs to bl2.

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[galaxyproject/usegalaxy-playbook] 878d6a: galaxyproject.org -> athena
by GitHub 18 May '15

18 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 878d6a0f4786e028b8d23836a04ddd0457890e33 https://github.com/galaxyproject/usegalaxy-playbook/commit/878d6a0f4786e028… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: M common/host_vars/athena.galaxyproject.org.yml A templates/nginx/galaxyproject.j2 Log Message: ----------- galaxyproject.org -> athena

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[galaxyproject/usegalaxy-playbook] 1afe68: Grant Enis access to ubuntu@sites1
by GitHub 18 May '15

18 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1afe68a90c997006a2f007038be150f37fd2323d https://github.com/galaxyproject/usegalaxy-playbook/commit/1afe68a90c997006… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-16 (Sat, 16 May 2015) Changed paths: M common/host_vars/sites1.yml Log Message: ----------- Grant Enis access to ubuntu@sites1 Commit: cd866505d4f68af67854b257749032ee2f55a167 https://github.com/galaxyproject/usegalaxy-playbook/commit/cd866505d4f68af6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-18 (Mon, 18 May 2015) Changed paths: A common/host_vars/athena.galaxyproject.org.yml R common/host_vars/sites1.yml M common/inventory M common/secret_vars/ssl.yml A files/ssl/athena.galaxyproject.org_cert.pem A files/ssl/wildcard_cert.pem A templates/nginx/cloudlaunch.j2 Log Message: ----------- Add athena, configs for cloudlaunch Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8dbaf4fcebd8...…

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[galaxyproject/usegalaxy-playbook] 8dbaf4: update mutable confs on Stage
by GitHub 15 May '15

15 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8dbaf4fcebd802bbe27dd2a6ef564075c4cdedf1 https://github.com/galaxyproject/usegalaxy-playbook/commit/8dbaf4fcebd802bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- update mutable confs on Stage

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 15 May '15

15 May '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7c2f4457ace/ Changeset: b7c2f4457ace Branch: release_15.05 User: natefoo Date: 2015-05-15 19:21:08+00:00 Summary: Fix tags for 15.05 release. Affected #: 1 file diff -r c3cef260df887330c6da902caf8a5f068b9d29b4 -r b7c2f4457acef8bf0478170983787a2ea42eccff .hgtags --- a/.hgtags +++ b/.hgtags @@ -27,5 +27,5 @@ 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 bfd4635011e39aa210b2b1498dd65831dd2a365e latest_15.03 -31c076123a8fa32b2b6a51eb859e4cac90043333 v15.05 -31c076123a8fa32b2b6a51eb859e4cac90043333 latest_15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 latest_15.05 https://bitbucket.org/galaxy/galaxy-central/commits/46a4ef8850b5/ Changeset: 46a4ef8850b5 Branch: stable User: natefoo Date: 2015-05-15 19:21:24+00:00 Summary: Merge release_15.05 to stable Affected #: 3 files diff -r ae85e9661ccd635a08ab9e224a43fd9333fdd5c5 -r 46a4ef8850b5852390f0bf86869d889a30dffbe9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -27,5 +27,5 @@ 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 bfd4635011e39aa210b2b1498dd65831dd2a365e latest_15.03 -31c076123a8fa32b2b6a51eb859e4cac90043333 v15.05 -31c076123a8fa32b2b6a51eb859e4cac90043333 latest_15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 latest_15.05 diff -r ae85e9661ccd635a08ab9e224a43fd9333fdd5c5 -r 46a4ef8850b5852390f0bf86869d889a30dffbe9 config/auth_conf.xml.sample --- /dev/null +++ b/config/auth_conf.xml.sample @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<auth> + +  + +  + +  + +  + + + <authenticator> + <type>localdb</type> + <options> + <allow-password-change>true</allow-password-change> + </options> + </authenticator> +</auth> diff -r ae85e9661ccd635a08ab9e224a43fd9333fdd5c5 -r 46a4ef8850b5852390f0bf86869d889a30dffbe9 config/plugins/visualizations/common/templates/script_entry_point.mako --- /dev/null +++ b/config/plugins/visualizations/common/templates/script_entry_point.mako @@ -0,0 +1,10 @@ +# -*- coding: utf-8 -*- +<%inherit file="visualization_base.mako"/> + +## No stylesheets +<%def name="stylesheets()"></%def> +## No javascript libraries +<%def name="late_javascripts()"> + <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_tag_attributes.items() ]) %> + <script type="text/javascript" ${tag_attrs}></script> +</%def> https://bitbucket.org/galaxy/galaxy-central/commits/e837a68e8d14/ Changeset: e837a68e8d14 User: natefoo Date: 2015-05-15 19:21:34+00:00 Summary: Merge stable to default Affected #: 3 files diff -r 7a4e3a661a76fa8f150c11f26c2bb52b2faa0046 -r e837a68e8d149bb185d631b27e049f3edeb641d3 .hgtags --- a/.hgtags +++ b/.hgtags @@ -27,5 +27,5 @@ 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 bfd4635011e39aa210b2b1498dd65831dd2a365e latest_15.03 -31c076123a8fa32b2b6a51eb859e4cac90043333 v15.05 -31c076123a8fa32b2b6a51eb859e4cac90043333 latest_15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 v15.05 +c3cef260df887330c6da902caf8a5f068b9d29b4 latest_15.05 diff -r 7a4e3a661a76fa8f150c11f26c2bb52b2faa0046 -r e837a68e8d149bb185d631b27e049f3edeb641d3 config/auth_conf.xml.sample --- /dev/null +++ b/config/auth_conf.xml.sample @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<auth> + +  + +  + +  + +  + + + <authenticator> + <type>localdb</type> + <options> + <allow-password-change>true</allow-password-change> + </options> + </authenticator> +</auth> diff -r 7a4e3a661a76fa8f150c11f26c2bb52b2faa0046 -r e837a68e8d149bb185d631b27e049f3edeb641d3 config/plugins/visualizations/common/templates/script_entry_point.mako --- /dev/null +++ b/config/plugins/visualizations/common/templates/script_entry_point.mako @@ -0,0 +1,10 @@ +# -*- coding: utf-8 -*- +<%inherit file="visualization_base.mako"/> + +## No stylesheets +<%def name="stylesheets()"></%def> +## No javascript libraries +<%def name="late_javascripts()"> + <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_tag_attributes.items() ]) %> + <script type="text/javascript" ${tag_attrs}></script> +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add missing files excluded by .hgignore.
by commits-noreply＠bitbucket.org 15 May '15

15 May '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3cef260df88/ Changeset: c3cef260df88 Branch: release_15.05 User: natefoo Date: 2015-05-15 19:20:17+00:00 Summary: Add missing files excluded by .hgignore. Affected #: 2 files diff -r f23c513e451c2777c9cefafcf23956499a084e26 -r c3cef260df887330c6da902caf8a5f068b9d29b4 config/auth_conf.xml.sample --- /dev/null +++ b/config/auth_conf.xml.sample @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<auth> + +  + +  + +  + +  + + + <authenticator> + <type>localdb</type> + <options> + <allow-password-change>true</allow-password-change> + </options> + </authenticator> +</auth> diff -r f23c513e451c2777c9cefafcf23956499a084e26 -r c3cef260df887330c6da902caf8a5f068b9d29b4 config/plugins/visualizations/common/templates/script_entry_point.mako --- /dev/null +++ b/config/plugins/visualizations/common/templates/script_entry_point.mako @@ -0,0 +1,10 @@ +# -*- coding: utf-8 -*- +<%inherit file="visualization_base.mako"/> + +## No stylesheets +<%def name="stylesheets()"></%def> +## No javascript libraries +<%def name="late_javascripts()"> + <% tag_attrs = ' '.join([ '{0}="{1}"'.format( key, attr ) for key, attr in script_tag_attributes.items() ]) %> + <script type="text/javascript" ${tag_attrs}></script> +</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] 54aa70: Add a new EC2 instance for cloudlaunch and other s...
by GitHub 15 May '15

15 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 54aa70883002a0042939bae8c43cddfbe24f6f62 https://github.com/galaxyproject/usegalaxy-playbook/commit/54aa70883002a004… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: A common/host_vars/sites1.yml M common/inventory A ec2.yml Log Message: ----------- Add a new EC2 instance for cloudlaunch and other sites. Commit: bfb9ef0f57f7aaa84426aaff18a8ccd55f75ee92 https://github.com/galaxyproject/usegalaxy-playbook/commit/bfb9ef0f57f7aaa8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Merge branch 'master' of ssh://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ed0cc99699f9...…

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[galaxyproject/usegalaxy-playbook] ed0cc9: update mutable confs; remove Test from menu for sc...
by GitHub 15 May '15

15 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed0cc99699f93097f03b940b9a80b95aab37cf71 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed0cc99699f93097… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M stage/group_vars/galaxyservers.yml Log Message: ----------- update mutable confs; remove Test from menu for screencast purposes

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[galaxyproject/usegalaxy-playbook] fdb144: Update test to 308a8e37372abb6a25124d0782d3eef612f...
by GitHub 15 May '15

15 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fdb1445932bbbacf3e5e6f63c10a3523947dbe95 https://github.com/galaxyproject/usegalaxy-playbook/commit/fdb1445932bbbacf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to 308a8e37372abb6a25124d0782d3eef612f9bb43.

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[galaxyproject/usegalaxy-playbook] a674f4: Include the 'Test' word on the Galaxy Test masthea...
by GitHub 15 May '15

15 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a674f461bd9a3b95d21f0a4c024364f17b77b563 https://github.com/galaxyproject/usegalaxy-playbook/commit/a674f461bd9a3b95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-15 (Fri, 15 May 2015) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Include the 'Test' word on the Galaxy Test masthead to help immediate recognition

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[galaxyproject/usegalaxy-playbook] 6bda3e: Update test to 0630ae9ccfcca4ce9df7fbd2f606e1192ef...
by GitHub 14 May '15

14 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6bda3e21d5d3044b6e25d6f406ad331e454f25a3 https://github.com/galaxyproject/usegalaxy-playbook/commit/6bda3e21d5d3044b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M stage/group_vars/all.yml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update test to 0630ae9ccfcca4ce9df7fbd2f606e1192ef535fa.

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[galaxyproject/usegalaxy-playbook] 9375bb: Enable IGV gff display on test.
by GitHub 14 May '15

14 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9375bb712d96f3f76894ac0180cd8b06cb42a0a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/9375bb712d96f3f7… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Enable IGV gff display on test.

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commit/galaxy-central: natefoo: Create branch release_15.05
by commits-noreply＠bitbucket.org 14 May '15

14 May '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dcde115c0580/ Changeset: dcde115c0580 Branch: release_15.05 User: natefoo Date: 2015-05-14 17:44:41+00:00 Summary: Create branch release_15.05 Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 12 new changesets
by commits-noreply＠bitbucket.org 14 May '15

14 May '15

12 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cfd4ff7e3972/ Changeset: cfd4ff7e3972 Branch: release_15.03 User: guerler Date: 2015-04-23 20:05:00+00:00 Summary: Fix base url tool parameter Affected #: 1 file diff -r d7a9896af111d6f86735eb4f2295eee67f7e3527 -r cfd4ff7e397264336ccafd0c6086c91bd2d3a533 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -689,7 +689,7 @@ return form_builder.HiddenField( self.name, self.get_value( trans ) ) def get_initial_value( self, trans, context, history=None ): - return self.value + return self.get_value( trans ) def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters https://bitbucket.org/galaxy/galaxy-central/commits/a5400c7f61d8/ Changeset: a5400c7f61d8 Branch: release_15.03 User: natefoo Date: 2015-04-27 19:56:30+00:00 Summary: Make the `enable_tool_shed_check` option perform as advertised in the sample config file. Also disables checks at startup. Affected #: 2 files diff -r cfd4ff7e397264336ccafd0c6086c91bd2d3a533 -r a5400c7f61d8ccae54e8f72502b4117c9ce82076 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -121,6 +121,7 @@ self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) + self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) if isinstance( self.hours_between_check, basestring ): self.hours_between_check = float( self.hours_between_check ) try: diff -r cfd4ff7e397264336ccafd0c6086c91bd2d3a533 -r a5400c7f61d8ccae54e8f72502b4117c9ce82076 lib/tool_shed/galaxy_install/update_repository_manager.py --- a/lib/tool_shed/galaxy_install/update_repository_manager.py +++ b/lib/tool_shed/galaxy_install/update_repository_manager.py @@ -16,12 +16,13 @@ self.app = app self.context = self.app.install_model.context # Ideally only one Galaxy server process should be able to check for repository updates. - self.running = True - self.sleeper = Sleeper() - self.restarter = threading.Thread( target=self.__restarter ) - self.restarter.daemon = True - self.restarter.start() - self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) + if self.app.config.enable_tool_shed_check: + self.running = True + self.sleeper = Sleeper() + self.restarter = threading.Thread( target=self.__restarter ) + self.restarter.daemon = True + self.restarter.start() + self.seconds_to_sleep = int( app.config.hours_between_check * 3600 ) def get_update_to_changeset_revision_and_ctx_rev( self, repository ): """Return the changeset revision hash to which the repository can be updated.""" @@ -94,8 +95,9 @@ log.info( 'Update repository manager restarter shutting down...' ) def shutdown( self ): - self.running = False - self.sleeper.wake() + if self.app.config.enable_tool_shed_check: + self.running = False + self.sleeper.wake() def update_repository_record( self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): """ https://bitbucket.org/galaxy/galaxy-central/commits/41d7ef6d0d64/ Changeset: 41d7ef6d0d64 Branch: release_15.03 User: natefoo Date: 2015-04-28 16:43:18+00:00 Summary: Fix job stopping under some conditions: 1. track_jobs_in_database is False 2. Jobs being stopped were in the local runner 3. Jobs were deleted with the deleted state and not deleted_new Affected #: 2 files diff -r a5400c7f61d8ccae54e8f72502b4117c9ce82076 -r 41d7ef6d0d6488feb987c573a363b0468b16d6b3 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -680,7 +680,10 @@ except Empty: pass for job, error_msg in jobs_to_check: - if job.state != job.states.DELETED_NEW and job.finished: + if ( job.state not in ( job.states.DELETED_NEW, + job.states.DELETED ) + and job.finished ): + # terminated before it got here log.debug('Job %s already finished, not deleting or stopping', job.id) continue final_state = job.states.DELETED @@ -695,7 +698,8 @@ self.dispatcher.stop( job ) def put( self, job_id, error_msg=None ): - self.queue.put( ( job_id, error_msg ) ) + if not self.app.config.track_jobs_in_database: + self.queue.put( ( job_id, error_msg ) ) def shutdown( self ): """Attempts to gracefully shut down the worker thread""" diff -r a5400c7f61d8ccae54e8f72502b4117c9ce82076 -r 41d7ef6d0d6488feb987c573a363b0468b16d6b3 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -134,9 +134,11 @@ def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished job_ext_output_metadata = job.get_external_output_metadata() - if job_ext_output_metadata: + try: pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them - else: + assert pid not in [ None, '' ] + except: + # metadata internal or job not complete yet pid = job.get_job_runner_external_id() if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.get_id() ) https://bitbucket.org/galaxy/galaxy-central/commits/aceedb22b312/ Changeset: aceedb22b312 Branch: release_15.03 User: natefoo Date: 2015-04-28 20:26:29+00:00 Summary: Don't use a bare except Affected #: 1 file diff -r 41d7ef6d0d6488feb987c573a363b0468b16d6b3 -r aceedb22b31220f9a388935d8ac2cdd5b0dee406 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -137,7 +137,7 @@ try: pid = job_ext_output_metadata[0].job_runner_external_pid # every JobExternalOutputMetadata has a pid set, we just need to take from one of them assert pid not in [ None, '' ] - except: + except Exception: # metadata internal or job not complete yet pid = job.get_job_runner_external_id() if pid in [ None, '' ]: https://bitbucket.org/galaxy/galaxy-central/commits/832a82ca1937/ Changeset: 832a82ca1937 Branch: release_15.03 User: natefoo Date: 2015-05-01 16:48:04+00:00 Summary: Ensure JobWrapper.galaxy_lib_dir is set, necessary for locally setting metadata externally with Pulsar, which (sometimes?) does not call the wrapper's prepare() method. Affected #: 1 file diff -r aceedb22b31220f9a388935d8ac2cdd5b0dee406 -r 832a82ca19379381894d82c7e2683d2506ec2a2c lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -720,7 +720,7 @@ # Tool versioning variables self.write_version_cmd = None self.version_string = "" - self.galaxy_lib_dir = None + self.__galaxy_lib_dir = None # With job outputs in the working directory, we need the working # directory to be set before prepare is run, or else premature deletion # and job recovery fail. @@ -769,6 +769,12 @@ def commands_in_new_shell(self): return self.app.config.commands_in_new_shell + @property + def galaxy_lib_dir(self): + if self.__galaxy_lib_dir is None: + self.__galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root + return self.__galaxy_lib_dir + # legacy naming get_job_runner = get_job_runner_url @@ -830,8 +836,8 @@ self.sa_session.flush() self.command_line, self.extra_filenames = tool_evaluator.build() - # FIXME: for now, tools get Galaxy's lib dir in their path - self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root + # Ensure galaxy_lib_dir is set in case there are any later chdirs + self.galaxy_lib_dir # Shell fragment to inject dependencies self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job @@ -1631,9 +1637,8 @@ self.command_line, self.extra_filenames = tool_evaluator.build() - # FIXME: for now, tools get Galaxy's lib dir in their path - if self.command_line and self.command_line.startswith( 'python' ): - self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root + # Ensure galaxy_lib_dir is set in case there are any later chdirs + self.galaxy_lib_dir # Shell fragment to inject dependencies self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job https://bitbucket.org/galaxy/galaxy-central/commits/21fed755993a/ Changeset: 21fed755993a Branch: release_15.03 User: BjoernGruening Date: 2015-05-02 01:54:53+00:00 Summary: Bind the IPython IE to a fixed Docker Image Affected #: 1 file diff -r 832a82ca19379381894d82c7e2683d2506ec2a2c -r 21fed755993a6f6f6e834b0e787785c2c3edd7f1 config/plugins/interactive_environments/ipython/config/ipython.ini.sample --- a/config/plugins/interactive_environments/ipython/config/ipython.ini.sample +++ b/config/plugins/interactive_environments/ipython/config/ipython.ini.sample @@ -8,7 +8,7 @@ [docker] command = docker -image = bgruening/docker-ipython-notebook +image = bgruening/docker-ipython-notebook:0.2 # URL to access the Galaxy API with from the spawn Docker containter, if empty # this falls back to galaxy.ini's galaxy_infrastructure_url and finally to the https://bitbucket.org/galaxy/galaxy-central/commits/73c4d3c6689c/ Changeset: 73c4d3c6689c Branch: release_15.03 User: mvdbeek Date: 2015-05-01 00:39:23+00:00 Summary: Import safe_dumps from galaxy_utils to properly set metadata for interval files. Affected #: 1 file diff -r 21fed755993a6f6f6e834b0e787785c2c3edd7f1 -r 73c4d3c6689ce8ba96a6c8c9f7a693d1a32dbe32 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -24,6 +24,7 @@ from galaxy.util import stringify_dictionary_keys from galaxy.util import string_as_bool from galaxy.util import in_directory +from galaxy.util.json import safe_dumps from galaxy.util.odict import odict from galaxy.web import form_builder @@ -486,7 +487,7 @@ def to_safe_string( self, value ): # We do not sanitize json dicts - return json.safe_dumps( value ) + return safe_dumps( value ) class PythonObjectParameter( MetadataParameter ): https://bitbucket.org/galaxy/galaxy-central/commits/720bf46e134e/ Changeset: 720bf46e134e Branch: release_15.03 User: jmchilton Date: 2015-05-05 13:22:45+00:00 Summary: Fix job files API for case when nginx upload not being used. Fixes regressions introduced with PR #110. Affected #: 2 files diff -r 73c4d3c6689ce8ba96a6c8c9f7a693d1a32dbe32 -r 720bf46e134e16ab3a1af84a67f57cc81715dae9 lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -342,7 +342,7 @@ encoded_job_id = self.app.security.encode_id(job_id) job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) - endpoint_base = "%s/api/jobs/%s?job_key=%s" + endpoint_base = "%s/api/jobs/%s/files?job_key=%s" if self.app.config.nginx_upload_job_files_path: endpoint_base = "%s" + \ self.app.config.nginx_upload_job_files_path + \ diff -r 73c4d3c6689ce8ba96a6c8c9f7a693d1a32dbe32 -r 720bf46e134e16ab3a1af84a67f57cc81715dae9 lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -99,7 +99,12 @@ try: shutil.move( input_file.name, path ) finally: - input_file.close() + try: + input_file.close() + except OSError: + # Fails to close file if not using nginx upload because the + # tempfile has moved and Python wants to delete it. + pass return {"message": "ok"} def __authorize_job_access(self, trans, encoded_job_id, **kwargs): https://bitbucket.org/galaxy/galaxy-central/commits/f1c47e6554eb/ Changeset: f1c47e6554eb Branch: release_15.03 User: dannon Date: 2015-04-10 16:23:46+00:00 Summary: Check to see if toolshed install is actually bound prior to disposing (exact same functionality here, but it's less chatty this way, since it might not be bound) Affected #: 1 file diff -r 720bf46e134e16ab3a1af84a67f57cc81715dae9 -r f1c47e6554ebc5fe79e697c1959da335ca18a8a5 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -110,7 +110,9 @@ except: log.exception("Unable to dispose of pooled galaxy model database connections.") try: - galaxy.model.tool_shed_install.mapping.metadata.bind.dispose() + # This model may not actually be bound. + if galaxy.model.tool_shed_install.mapping.metadata.bind: + galaxy.model.tool_shed_install.mapping.metadata.bind.dispose() except: log.exception("Unable to dispose of pooled toolshed install model database connections.") https://bitbucket.org/galaxy/galaxy-central/commits/f6e636fe4269/ Changeset: f6e636fe4269 Branch: release_15.03 User: jmchilton Date: 2015-04-21 14:29:50+00:00 Summary: Bugfix: Resolve metadata dependencies for task runner. Also deduplicates code for next fix. Affected #: 1 file diff -r f1c47e6554ebc5fe79e697c1959da335ca18a8a5 -r f6e636fe42692e5e8d1c7aef95e4f2a7d6d11111 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -124,19 +124,7 @@ #run the metadata setting script here #this is terminate-able when output dataset/job is deleted #so that long running set_meta()s can be canceled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: - external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(), - set_extension=True, - kwds={ 'overwrite' : False } ) # we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) - external_metadata_proc = subprocess.Popen( args=external_metadata_script, - shell=True, - env=os.environ, - preexec_fn=os.setpgrp ) - job_wrapper.external_output_metadata.set_job_runner_external_pid( external_metadata_proc.pid, self.sa_session ) - external_metadata_proc.wait() - log.debug( 'execution of external set_meta finished for job %d' % job_wrapper.job_id ) - + self._handle_metadata_externally(job_wrapper, resolve_requirements=True ) # Finish the job try: job_wrapper.finish( stdout, stderr, job_exit_code ) https://bitbucket.org/galaxy/galaxy-central/commits/d03588c4c3ed/ Changeset: d03588c4c3ed Branch: release_15.03 User: jmchilton Date: 2015-04-21 14:36:44+00:00 Summary: Bugfix: Fix metadata python path when using _handle_metadata_externally. This is used by lwr, pulsar, and task runners and possibly by the local job runner in some configurations. Broken with PR #22 which was merged into 15.03. Affected #: 1 file diff -r f6e636fe42692e5e8d1c7aef95e4f2a7d6d11111 -r d03588c4c3ed222ba0c4f40aa813b9bf5cec65d4 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -34,6 +34,8 @@ JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = "Job runner parameter '%s' value '%s' could not be converted to the correct type" JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE = "Job runner parameter %s failed validation" +GALAXY_LIB_ADJUST_TEMPLATE = """GALAXY_LIB="%s"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi;""" + class RunnerParams( ParamsWithSpecs ): @@ -250,11 +252,13 @@ #this is terminate-able when output dataset/job is deleted #so that long running set_meta()s can be canceled without having to reboot the server if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and job_wrapper.output_paths: + lib_adjust = GALAXY_LIB_ADJUST_TEMPLATE % job_wrapper.galaxy_lib_dir external_metadata_script = job_wrapper.setup_external_metadata( output_fnames=job_wrapper.get_output_fnames(), set_extension=True, tmp_dir=job_wrapper.working_directory, #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) + external_metadata_script = "%s %s" % (lib_adjust, external_metadata_script) if resolve_requirements: dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() if dependency_shell_commands: https://bitbucket.org/galaxy/galaxy-central/commits/a9d766325bd8/ Changeset: a9d766325bd8 Branch: release_15.03 User: guerler Date: 2015-04-22 17:21:24+00:00 Summary: Fix default values for nested conditional test parameters Affected #: 1 file diff -r d03588c4c3ed222ba0c4f40aa813b9bf5cec65d4 -r a9d766325bd8b659482b5c15f37ca7ffef323859 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2446,7 +2446,8 @@ elif input.type == 'conditional': if 'test_param' in tool_dict: test_param = tool_dict['test_param'] - test_param['value'] = jsonify(group_state.get(test_param['name'], None)) + test_param['default_value'] = jsonify(input.test_param.get_initial_value(trans, other_values)) + test_param['value'] = jsonify(group_state.get(test_param['name'], test_param['default_value'])) for i in range (len ( tool_dict['cases'] ) ): current_state = {} if i == group_state.get('__current_case__', None): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] 1f7ffa: Updated integrated tool panel on Test
by GitHub 14 May '15

14 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1f7ffaa415b993da4589bea18be6854a27c04826 https://github.com/galaxyproject/usegalaxy-playbook/commit/1f7ffaa415b993da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- Updated integrated tool panel on Test

1 0

[galaxyproject/usegalaxy-playbook] adf1c3: Update Test
by GitHub 14 May '15

14 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: adf1c31d7beb8af10a337307558339e3da24bbf7 https://github.com/galaxyproject/usegalaxy-playbook/commit/adf1c31d7beb8af1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-14 (Thu, 14 May 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

1 0

[galaxyproject/usegalaxy-playbook] 466a2e: Mutable configs on Test
by GitHub 14 May '15

14 May '15

1 0

[galaxyproject/usegalaxy-playbook] ba06c7: Install tophat wrapper version 0.9
by GitHub 13 May '15

13 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ba06c706bace89c87e89eb89ec4198d4db0acdcb https://github.com/galaxyproject/usegalaxy-playbook/commit/ba06c706bace89c8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-05-13 (Wed, 13 May 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Install tophat wrapper version 0.9

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[galaxyproject/usegalaxy-playbook] 6eaf76: update prod mutable confs (hide sam_merge)
by GitHub 12 May '15

12 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6eaf767df8f319496b2f8b2dee41eff93a6e7333 https://github.com/galaxyproject/usegalaxy-playbook/commit/6eaf767df8f31949… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-12 (Tue, 12 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml Log Message: ----------- update prod mutable confs (hide sam_merge)

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[galaxyproject/usegalaxy-playbook] 2c1d5b: Update Test and Main
by GitHub 12 May '15

12 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2c1d5b6893aa0dd1d00cd27a5c24e367f346e12c https://github.com/galaxyproject/usegalaxy-playbook/commit/2c1d5b6893aa0dd1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-05-12 (Tue, 12 May 2015) Changed paths: M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main

1 0

[galaxyproject/usegalaxy-playbook] 2f30a7: update prod integrated conf
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f30a780d9bd107e31677fe7633fa3b6e88ff5d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/2f30a780d9bd107e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- update prod integrated conf move samtools section up form beta section and rename

1 0

[galaxyproject/usegalaxy-playbook] d552eb: update prod mutable configs after samtools 1.2 ins...
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d552eb56ebc171fd86e6781f1658262f3d7b4cd9 https://github.com/galaxyproject/usegalaxy-playbook/commit/d552eb56ebc171fd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update prod mutable configs after samtools 1.2 installation

1 0

[galaxyproject/usegalaxy-playbook] 61ec7e: update prod mutable confs
by GitHub 11 May '15

11 May '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 61ec7ea2421984ae78c29fc6515a47b66c344d69 https://github.com/galaxyproject/usegalaxy-playbook/commit/61ec7ea2421984ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-05-11 (Mon, 11 May 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update prod mutable confs

1 0