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

[galaxyproject/galaxy] 012e26: Remove debugging warn statement.
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 012e261692a2ed8eb3e3c6ca4496b0bd48c99a84 https://github.com/galaxyproject/galaxy/commit/012e261692a2ed8eb3e3c6ca4496… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove debugging warn statement. I don't think it was meant to be here. Commit: f2e15588bfad5ad04e4f6530b9b7966e65d138ad https://github.com/galaxyproject/galaxy/commit/f2e15588bfad5ad04e4f6530b9b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #3566 from jmchilton/1701_user_warn [17.01] Remove debugging warn statement. Commit: 10b743d1d99b0a544002adf57c61a0168ca24e2a https://github.com/galaxyproject/galaxy/commit/10b743d1d99b0a544002adf57c61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 6eb735be8265e0e10d2a5bb7c3845c27dcbff6fb https://github.com/galaxyproject/galaxy/commit/6eb735be8265e0e10d2a5bb7c384… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #3575 from jmchilton/pulsar_default_fix [17.01] Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 561606621cd207c05ec4da33cb7f8c3b9f6f5bfa https://github.com/galaxyproject/galaxy/commit/561606621cd207c05ec4da33cb7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Update index.rst Commit: 884cff33fa04915f426f8c24bb53494ff43f0a36 https://github.com/galaxyproject/galaxy/commit/884cff33fa04915f426f8c24bb53… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #3577 from martenson/release-docs-menu [17.01] list new release docs Commit: 3b3bfad8e0af0d07dee1ef379560258aece3f8e6 https://github.com/galaxyproject/galaxy/commit/3b3bfad8e0af0d07dee1ef379560… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/36686199cc71...3b3bfad8e0af

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[galaxyproject/galaxy] 561606: Update index.rst
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 561606621cd207c05ec4da33cb7f8c3b9f6f5bfa https://github.com/galaxyproject/galaxy/commit/561606621cd207c05ec4da33cb7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Update index.rst Commit: 884cff33fa04915f426f8c24bb53494ff43f0a36 https://github.com/galaxyproject/galaxy/commit/884cff33fa04915f426f8c24bb53… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #3577 from martenson/release-docs-menu [17.01] list new release docs Compare: https://github.com/galaxyproject/galaxy/compare/6eb735be8265...884cff33fa04

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[galaxyproject/galaxy] 10b743: Fix default for Pulsar option "dependency_resoluti...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 10b743d1d99b0a544002adf57c61a0168ca24e2a https://github.com/galaxyproject/galaxy/commit/10b743d1d99b0a544002adf57c61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 6eb735be8265e0e10d2a5bb7c3845c27dcbff6fb https://github.com/galaxyproject/galaxy/commit/6eb735be8265e0e10d2a5bb7c384… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #3575 from jmchilton/pulsar_default_fix [17.01] Fix default for Pulsar option "dependency_resolution" to match documentation. Compare: https://github.com/galaxyproject/galaxy/compare/f2e15588bfad...6eb735be8265

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[galaxyproject/galaxy] 846e76: Update Jupyter IE name to be shorter and consisten...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 846e765fa93ebcf33c0acce2ba9a9a49366b6a3a https://github.com/galaxyproject/galaxy/commit/846e765fa93ebcf33c0acce2ba9a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Update Jupyter IE name to be shorter and consistent with other names. Makes menu entries look correct. Commit: 36686199cc7111cbf17df3ec619a5097048117e3 https://github.com/galaxyproject/galaxy/commit/36686199cc7111cbf17df3ec619a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Merge pull request #3576 from dannon/jupyter_naming Update Jupyter IE name to be shorter and consistent with other names.… Compare: https://github.com/galaxyproject/galaxy/compare/d302400b99b7...36686199cc71

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[galaxyproject/galaxy] 5ea926: Insert editable title flag for portlets
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ea926e4b2b5a70a408780d9fcee1b9b7e4e5e88 https://github.com/galaxyproject/galaxy/commit/5ea926e4b2b5a70a408780d9fcee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/mvc/ui/ui-portlet.js Log Message: ----------- Insert editable title flag for portlets Commit: 6dfc362594c83aa96f6c86acd5d7ee9a84743931 https://github.com/galaxyproject/galaxy/commit/6dfc362594c83aa96f6c86acd5d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add optional event handler to edit portlet title text Commit: e96e86644ea924e21611b65e5bf8bfbf0dc23c9d https://github.com/galaxyproject/galaxy/commit/e96e86644ea924e21611b65e5bf8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Display node type icon in portlet header for non-tool modules Commit: 76710c4c7b5030a4cfc89d1a49339a01e0fa1d9c https://github.com/galaxyproject/galaxy/commit/76710c4c7b5030a4cfc89d1a4933… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Disable text editing, leave feature in for future use Commit: 7f391076b22dca78299ff9322c593ff8ea6a7510 https://github.com/galaxyproject/galaxy/commit/7f391076b22dca78299ff9322c59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Display module type icons for tool modules too Commit: 6e2a0db08272f32abedbbbcb3c3ad06cadaf739b https://github.com/galaxyproject/galaxy/commit/6e2a0db08272f32abedbbbcb3c3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared portlet style for both module types Commit: 54573f02ebe7d682347e7a9df0a8360b4fad4339 https://github.com/galaxyproject/galaxy/commit/54573f02ebe7d682347e7a9df0a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Submit label and annotation separate from other inputs to avoid future conflicts Commit: dadd6ee2213a8c1fb4e3954b66a234dc10e81719 https://github.com/galaxyproject/galaxy/commit/dadd6ee2213a8c1fb4e3954b66a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use underscore to distinguish internal parameters, separate postchange actions Commit: bc51f6f69fc04e07d1c0d3f7c55a15f62e9f337a https://github.com/galaxyproject/galaxy/commit/bc51f6f69fc04e07d1c0d3f7c55a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/ui/autocom_tagging.js M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/ui/autocom_tagging.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/ui/autocom_tagging.js Log Message: ----------- Rename custom autocomplete module to avoid interference with original jquery autocomplete, use original version to display datalists Commit: 49e784306ba106b28e3499f054df997cfa3694fa https://github.com/galaxyproject/galaxy/commit/49e784306ba106b28e3499f054df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: a55038067bde091be7a4edef0c7eda0400c95622 https://github.com/galaxyproject/galaxy/commit/a55038067bde091be7a4edef0c7e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Display unfiltered datalist options Commit: e22b4bcbfc465fb46e1cd2dc314e941001ce6164 https://github.com/galaxyproject/galaxy/commit/e22b4bcbfc465fb46e1cd2dc314e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Do not attach autocomplete handler if datalist is empty Commit: b3e161a4af6c5059338680591514efea18d553bc https://github.com/galaxyproject/galaxy/commit/b3e161a4af6c5059338680591514… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Check datalist length before attaching autocomplete feature Commit: dc5326ce034f6d38955fe0faa7ed6ea7fd2a4977 https://github.com/galaxyproject/galaxy/commit/dc5326ce034f6d38955fe0faa7ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Use workflow form handler options to parse tool id and version Commit: 20c27075364996898e429936578fdfbcd9abebec https://github.com/galaxyproject/galaxy/commit/20c27075364996898e429936578f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Attach onchange handler once, avoid overwrite Commit: e571fce4781ca004c21f8091a46bebaecd6e3bd4 https://github.com/galaxyproject/galaxy/commit/e571fce4781ca004c21f8091a46b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Revise label handling and duplicate check, move save controller to api for proper error response Commit: 37501a5b8475c2c0ef65d6e5dea86cadcd3566bb https://github.com/galaxyproject/galaxy/commit/37501a5b8475c2c0ef65d6e5dea8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove debug output Commit: ddf4bad6ffa20df224c724329151e2c810af2c6a https://github.com/galaxyproject/galaxy/commit/ddf4bad6ffa20df224c724329151… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix blank line Commit: 6c3b4020200b52352f6a47140a6931456f2755cc https://github.com/galaxyproject/galaxy/commit/6c3b4020200b52352f6a47140a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Properly attach event handler when user clicks on autocomplete selection Commit: 6c4a4ce3e43af7488f63892420260faab7d9399f https://github.com/galaxyproject/galaxy/commit/6c4a4ce3e43af7488f6389242026… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise tool model building to always provide a properly ordered array, augment model handling on front-end Commit: 9c9c4d2d083dc9129ea257a8e0205a4ae89f371b https://github.com/galaxyproject/galaxy/commit/9c9c4d2d083dc9129ea257a8e020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix error display Commit: 3911cb039d46f76f0548d993f4ca932204672bb2 https://github.com/galaxyproject/galaxy/commit/3911cb039d46f76f0548d993f4ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/viz/trackster/tracks.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/schema_template.md M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A 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test/functional/tools/explicit_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/param_text_option.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.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/unit/tools/test_tool_deps.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_ui Commit: 5bf7c46eca5c3dbad5c7009f4bb81b48503a6307 https://github.com/galaxyproject/galaxy/commit/5bf7c46eca5c3dbad5c7009f4bb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Repack scripts Commit: 1bb10da295fdf25855f5140f26bc7a62b278acab https://github.com/galaxyproject/galaxy/commit/1bb10da295fdf25855f5140f26bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Raise message exception instead of return a dictionary Commit: f264e91cabfd29a8f385f8fbce4c8714b088fa23 https://github.com/galaxyproject/galaxy/commit/f264e91cabfd29a8f385f8fbce4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use update endpoint to store workflows Commit: db47be5ad91bdd9364d5f9525941fd9a7b2c57c0 https://github.com/galaxyproject/galaxy/commit/db47be5ad91bdd9364d5f9525941… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove endpoint from routing Commit: 284000c688724f47055a46bab4e8b377224db751 https://github.com/galaxyproject/galaxy/commit/284000c688724f47055a46bab4e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused error variable Commit: 5b366642019b4d69d033d916b71b5a85c3767d0f https://github.com/galaxyproject/galaxy/commit/5b366642019b4d69d033d916b71b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M test/qunit/tests/form_tests.js Log Message: ----------- Fix qunit tests Commit: 6a8dc6e26cf92d0c54a35e76c978dba8d6cd9864 https://github.com/galaxyproject/galaxy/commit/6a8dc6e26cf92d0c54a35e76c978… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/steps.py Log Message: ----------- Evaluate cyclic workflows on the fly when loading the run workflow form Commit: afb024819917535ba4820405c31f00d16224f453 https://github.com/galaxyproject/galaxy/commit/afb024819917535ba4820405c31f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Remove blank line Commit: d302400b99b7ae32a2d3f09266b15380b81d83b3 https://github.com/galaxyproject/galaxy/commit/d302400b99b7ae32a2d3f09266b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/ui/autocom_tagging.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/ui/autocom_tagging.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #3407 from guerler/fix_workflow_ui Workflow editor UI touch up Compare: https://github.com/galaxyproject/galaxy/compare/7411aa52fd9c...d302400b99b7

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[galaxyproject/galaxy] 417d11: Avoid stringification of tool state root dictionar...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 417d119df9151b0462aa1c802108fa63f46e3f09 https://github.com/galaxyproject/galaxy/commit/417d119df9151b0462aa1c802108… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid stringification of tool state root dictionary Commit: ee6063ec5b88308b2fbc2da9a47c3549f6a5c37b https://github.com/galaxyproject/galaxy/commit/ee6063ec5b88308b2fbc2da9a47c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Adjust export for backward compatibility Commit: fa93c6bbc8449555b1d59dbe9cfaab3ddd3fa45e https://github.com/galaxyproject/galaxy/commit/fa93c6bbc8449555b1d59dbe9cfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Remove state handling from tool shed mako Commit: 26a18440304c8b637dc5e0ffe7d3835026087903 https://github.com/galaxyproject/galaxy/commit/26a18440304c8b637dc5e0ffe7d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use dicts also for module parameter value storage Commit: 6acbafee8a60b03faae9906bfce44d67abfe54b1 https://github.com/galaxyproject/galaxy/commit/6acbafee8a60b03faae9906bfce4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use basic parameter handler to ensure proper text type value decoding Commit: 09f9396eab2c511013c0b637997191bc4f0e74ba https://github.com/galaxyproject/galaxy/commit/09f9396eab2c511013c0b6379971… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use number library to identify numeric values Commit: 7411aa52fd9cdaa1874a773fbfd440866f909e65 https://github.com/galaxyproject/galaxy/commit/7411aa52fd9cdaa1874a773fbfd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #3522 from guerler/store_step_json_000 Store module step states as nested dictionaries, fix export for backward compatibility Compare: https://github.com/galaxyproject/galaxy/compare/68752b7db0c6...7411aa52fd9c

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[galaxyproject/galaxy] 0d21f6: Consolidate exception logging in db migrations
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0d21f657ca4115ce3e309394cff8bdb084de6ef3 https://github.com/galaxyproject/galaxy/commit/0d21f657ca4115ce3e309394cff8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Consolidate exception logging in db migrations Also: - align engine_true() and engine_false() methods - remove unused 'now' variables Commit: cb4fbe7a1caba8195ac8ec4965c702a58378f592 https://github.com/galaxyproject/galaxy/commit/cb4fbe7a1caba8195ac8ec4965c7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- Fix a bunch of database migration bugs Commit: 68752b7db0c6328d1d88e657ad21b2e4312f4401 https://github.com/galaxyproject/galaxy/commit/68752b7db0c6328d1d88e657ad21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Merge pull request #3570 from nsoranzo/database_migrations Database migrations: improvements and fixes Compare: https://github.com/galaxyproject/galaxy/compare/27d871f20edc...68752b7db0c6

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[galaxyproject/galaxy] 5657a8: Display the genbank file type in upload
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5657a8b809e5938d3d996a77c826811e1176c108 https://github.com/galaxyproject/galaxy/commit/5657a8b809e5938d3d996a77c826… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Display the genbank file type in upload Commit: 27d871f20edc8bc45a8b7b9d54ef88e48d3cb154 https://github.com/galaxyproject/galaxy/commit/27d871f20edc8bc45a8b7b9d54ef… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3569 from natefoo/genbank-upload Display the genbank file type in upload Compare: https://github.com/galaxyproject/galaxy/compare/6fc64f6f46f1...27d871f20edc

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[galaxyproject/galaxy] 012e26: Remove debugging warn statement.
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 012e261692a2ed8eb3e3c6ca4496b0bd48c99a84 https://github.com/galaxyproject/galaxy/commit/012e261692a2ed8eb3e3c6ca4496… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove debugging warn statement. I don't think it was meant to be here. Commit: f2e15588bfad5ad04e4f6530b9b7966e65d138ad https://github.com/galaxyproject/galaxy/commit/f2e15588bfad5ad04e4f6530b9b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #3566 from jmchilton/1701_user_warn [17.01] Remove debugging warn statement. Compare: https://github.com/galaxyproject/galaxy/compare/9feb8b3f0203...f2e15588bfad

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[galaxyproject/usegalaxy-playbook] 4254ea: Update main.
by GitHub 06 Feb '17

06 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4254ea1892437f3025aa856a821243b93fc76042 https://github.com/galaxyproject/usegalaxy-playbook/commit/4254ea1892437f30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update main.

1 0