- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 06cc5f: Fix implicit conversion for sessionless tool API c...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: b6e9f4a6eefb53d2f3b8b415b80e1a674bd7cc8d https://github.com/galaxyproject/galaxy/commit/b6e9f4a6eefb53d2f3b8b415b80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Commit: 63e70f4f2f47f5b952bb7817e93b0e61c8614dd7 https://github.com/galaxyproject/galaxy/commit/63e70f4f2f47f5b952bb7817e93b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. Commit: 79752b5b4a0e80a6cd4b02aed8cfd93d8d61208a https://github.com/galaxyproject/galaxy/commit/79752b5b4a0e80a6cd4b02aed8cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: 24b250ab3369489b91361c22bdf51b1729861e85 https://github.com/galaxyproject/galaxy/commit/24b250ab3369489b91361c22bdf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: 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 Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa17906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: 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 Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Commit: be530a849428393ec2b16f5b0786cbe4fba148cd https://github.com/galaxyproject/galaxy/commit/be530a849428393ec2b16f5b0786… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Commit: 34458725b826fb9cd8da2d245c094abd5041345c https://github.com/galaxyproject/galaxy/commit/34458725b826fb9cd8da2d245c09… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3406 from dannon/dev Merges 16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/8041525223b2...34458725b826

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[galaxyproject/galaxy] d49e01: The /user/logout endpoint is now used for both rem...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Compare: https://github.com/galaxyproject/galaxy/compare/535dd7a5f546...b0ac7daecdda

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[galaxyproject/galaxy] aba761: Update the testing image used with ``--dockerize``...
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aba7618a3a110c3c4893d23ddb2a9d3a446c14a0 https://github.com/galaxyproject/galaxy/commit/aba7618a3a110c3c4893d23ddb2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Update the testing image used with ``--dockerize``ed tests. Should prevent Jenkins from writing files as root. Commit: 8041525223b2deeffb4b588afe6e480b62fa6c07 https://github.com/galaxyproject/galaxy/commit/8041525223b2deeffb4b588afe6e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3401 from jmchilton/testing_image_update Update the testing image used with ``--dockerize``ed tests. Compare: https://github.com/galaxyproject/galaxy/compare/1d52e9a32cec...8041525223b2

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[galaxyproject/galaxy] 2d991b: Escapes some variables
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: 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 Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa17906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: 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 Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Compare: https://github.com/galaxyproject/galaxy/compare/24b250ab3369...535dd7a5f546

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[galaxyproject/galaxy] 7a370a: Escapes some variables
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a370a4ff6bb5aa24ca9758cb9bbfadbe808e3b0 https://github.com/galaxyproject/galaxy/commit/7a370a4ff6bb5aa24ca9758cb9bb… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: 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 Log Message: ----------- Escapes some variables Commit: 1d52e9a32ceca303b12a1de84604e68069ed0e85 https://github.com/galaxyproject/galaxy/commit/1d52e9a32ceca303b12a1de84604… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: 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 Log Message: ----------- Merge pull request #3403 from yhoogstrate/visualizations_escape Escapes some variables Compare: https://github.com/galaxyproject/galaxy/compare/778bcd00451a...1d52e9a32cec

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[galaxyproject/galaxy] 8368b1: fix typo
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8368b1784356112682b4eb93692d57582f009b34 https://github.com/galaxyproject/galaxy/commit/8368b1784356112682b4eb93692d… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- fix typo Commit: 778bcd00451aa863899d520aaac38fad7b9cae35 https://github.com/galaxyproject/galaxy/commit/778bcd00451aa863899d520aaac3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Merge pull request #3402 from manabuishii/patch-3 fix typo Compare: https://github.com/galaxyproject/galaxy/compare/3c494c42e2b4...778bcd00451a

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[galaxyproject/galaxy] ca40f9: Markdown datatype support.
by GitHub 11 Jan '17

11 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca40f984b0dfda58af1aa55d167edf615582192a https://github.com/galaxyproject/galaxy/commit/ca40f984b0dfda58af1aa55d167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Markdown datatype support. With test tools demonstrating HTML and Markdown outputs from tools. Implements #3396 as part of the Qiime hackathon. Commit: 3c494c42e2b42da7e934b38954df910d20bf286d https://github.com/galaxyproject/galaxy/commit/3c494c42e2b42da7e934b38954df… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3399 from jmchilton/markdown Markdown datatype support. Compare: https://github.com/galaxyproject/galaxy/compare/6c4dff3f4604...3c494c42e2b4

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[galaxyproject/infrastructure-playbook] 87ea9a: Change jenkins access lists
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 87ea9ab3b08a743504e6cefc41078f8e4a460eb7 https://github.com/galaxyproject/infrastructure-playbook/commit/87ea9ab3b08… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M galaxyenv/secret_group_vars/jenkinsslaves.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Change jenkins access lists

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[galaxyproject/galaxy] 09f027: Document how to create Docker testing images.
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09f0272ede3a17a5445956179acded53e213a1c4 https://github.com/galaxyproject/galaxy/commit/09f0272ede3a17a5445956179acd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Document how to create Docker testing images. With fix noted by @martenson. Commit: 6c4dff3f4604857f5c067c87a7a568a2e3acf0a5 https://github.com/galaxyproject/galaxy/commit/6c4dff3f4604857f5c067c87a7a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Merge pull request #3400 from jmchilton/document_docker_testing_image Document how to create Docker testing images. Compare: https://github.com/galaxyproject/galaxy/compare/542dc4077f35...6c4dff3f4604

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[galaxyproject/usegalaxy-playbook] 37566d: Update Test and Main
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37566d989afac47f68666393c3c26732460eb8c2 https://github.com/galaxyproject/usegalaxy-playbook/commit/37566d989afac47f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/galaxy_version.yml M stage/galaxy_version.yml M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Test and Main

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[galaxyproject/usegalaxy-playbook] ebee65: Remove job limits on Bridges
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ebee6544642ee65d3126e294be92bfc41026d381 https://github.com/galaxyproject/usegalaxy-playbook/commit/ebee6544642ee65d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Remove job limits on Bridges Commit: 3ef2b14e2f3706da505d32575919f1c5e8809a74 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ef2b14e2f3706da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test Commit: fa36467433c88244fdb44b9135c1f807121fd08a https://github.com/galaxyproject/usegalaxy-playbook/commit/fa36467433c88244… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M files/galaxy/usegalaxy.org/config/tool_conf.xml Log Message: ----------- Reenable disabled tools Commit: 53c51d53699cfa25603dd7c46f8fa289eecc97c6 https://github.com/galaxyproject/usegalaxy-playbook/commit/53c51d53699cfa25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Updated Main (a while ago, forgot to commit) Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1e7c06ad0d53...…

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[galaxyproject/galaxy] 79752b: Do not allow recursive replacements in PJA.
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 79752b5b4a0e80a6cd4b02aed8cfd93d8d61208a https://github.com/galaxyproject/galaxy/commit/79752b5b4a0e80a6cd4b02aed8cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: 24b250ab3369489b91361c22bdf51b1729861e85 https://github.com/galaxyproject/galaxy/commit/24b250ab3369489b91361c22bdf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 Compare: https://github.com/galaxyproject/galaxy/compare/63e70f4f2f47...24b250ab3369

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[galaxyproject/galaxy] caf9bf: Refactor DependencyManager to walk dependencies re...
by GitHub 10 Jan '17

10 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: caf9bf21de894312a3a3d164ae4ac3be37e487e1 https://github.com/galaxyproject/galaxy/commit/caf9bf21de894312a3a3d164ae4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Refactor DependencyManager to walk dependencies resolvers first, then requirements. Invert previous loop to give resolvers a chance to resolve everything at once in subsequent commits. Commit: 0a280e7d48c64d0a9daed6514eafe0314a6aa940 https://github.com/galaxyproject/galaxy/commit/0a280e7d48c64d0a9daed6514eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Give dependency resolvers a shot at resolving all dependencies at once. Commit: c2ac19275064b4c5b07685133f28bb509fd6be7d https://github.com/galaxyproject/galaxy/commit/c2ac19275064b4c5b07685133f28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement resolve_all on Conda dependency resolver. This is a somewhat substantial reversal in the typical way that the Conda resolver works. Everything related to caching, copying, linking, and building environments on the fly should now only apply if both of the following conditions are met (1) there is more than one requirement tag in a tool and (2) not all of them are resolvable exactly by the Conda resolver. For recipes that don't meet both of these two criteria - the normal case I would suspect going forward - Galaxy will just look for a hashed environment for these requirements built for all the requirements at once whenever the requirements are installed. The new 90% case, such environments should be much less buggy for two primary reasons. - #3299 is solved - in other words Conda is deferred to and if packages have potential conflicts - Conda can choose the right combination of build specifiers to resolve things correctly. - Environments are no longer built on a per-job basis - this means file system problems related to linking and copying aren't really an issue and complexity related to caching can be safely ignored. My guess is we should re-write all the Conda docs to make the other use case seem like a corner case - because hopefully it is now. This commit includes a test tool that wouldn't work without the rewrite I believe. Commit: 0e509a98ed79daf250fdd486f827d14335e88486 https://github.com/galaxyproject/galaxy/commit/0e509a98ed79daf250fdd486f827… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Create merged environments at install time Currently tested with UI only Commit: ad92bbf9bebafed22395e0199efd35a838ac1f4a https://github.com/galaxyproject/galaxy/commit/ad92bbf9bebafed22395e0199efd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Restore the cached environments for now ... better to completely eliminate them later Commit: fd8243b3d3a6ac0fcaea5f7ccfd7d5ec472b083b https://github.com/galaxyproject/galaxy/commit/fd8243b3d3a6ac0fcaea5f7ccfd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #52 from mvdbeek/install_time_improvements Create merged environments at install time Commit: 48a22d6e53c08de37a8a39cc5bb0228789a19033 https://github.com/galaxyproject/galaxy/commit/48a22d6e53c08de37a8a39cc5bb0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Revert "Restore the cached environments for now ... better to completely eliminate them later" This reverts commit ad92bbf9bebafed22395e0199efd35a838ac1f4a. Commit: 50bee381d35b97c951982ddbed442f8068574a46 https://github.com/galaxyproject/galaxy/commit/50bee381d35b97c951982ddbed44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Revert "Create merged environments at install time" This reverts commit 0e509a98ed79daf250fdd486f827d14335e88486. Commit: eea89de19adffe3a18f562cac7c97087e8a2e604 https://github.com/galaxyproject/galaxy/commit/eea89de19adffe3a18f562cac7c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Use resolver to explicitly install dependencies This avoids replicating the resolver logic when installing dependencies and should be better than https://github.com/jmchilton/galaxy/pull/52 Commit: 5c325236189ce17344ffedc1d821e94c6fb33483 https://github.com/galaxyproject/galaxy/commit/5c325236189ce17344ffedc1d821… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #53 from mvdbeek/install_time_2 Install time 2 Commit: 542dc4077f35d3760d3a8b51716acffce2574bef https://github.com/galaxyproject/galaxy/commit/542dc4077f35d3760d3a8b51716a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3391 from jmchilton/resolve_all_at_once Resolve Conda Dependencies All at Once Compare: https://github.com/galaxyproject/galaxy/compare/1082385b0b8b...542dc4077f35

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[galaxyproject/galaxy] d1cf0d: Do not allow recursive replacements in PJA.
by GitHub 09 Jan '17

09 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d1cf0def31b9060f5fe4b4f116ae8a8f47d0633e https://github.com/galaxyproject/galaxy/commit/d1cf0def31b9060f5fe4b4f116ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: d1eeafcc8f647fda2362b20c8625224b49520493 https://github.com/galaxyproject/galaxy/commit/d1eeafcc8f647fda2362b20c8625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case d1cf0def31b9060f5fe4b4f116ae8a8f47d0633e. Commit: 1082385b0b8b343482d7c06056473cf80b568779 https://github.com/galaxyproject/galaxy/commit/1082385b0b8b343482d7c0605647… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3395 from jmchilton/pja_infinite_loop Do not allow recursive replacements in PJA renames. Compare: https://github.com/galaxyproject/galaxy/compare/f358d14670cc...1082385b0b8b

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[galaxyproject/galaxy] 5f0a41: Add diamond database
by GitHub 09 Jan '17

09 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f0a4131dfdba219a0298f1ad3f8e7270b499a17 https://github.com/galaxyproject/galaxy/commit/5f0a4131dfdba219a0298f1ad3f8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add diamond database Commit: 0518cbf02e5541514dbbca6178213dcc046b7bc4 https://github.com/galaxyproject/galaxy/commit/0518cbf02e5541514dbbca617821… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add sniffer for dmnd extension Commit: 87000dca9ef49d7d6e068cf50313dec43dd10a3c https://github.com/galaxyproject/galaxy/commit/87000dca9ef49d7d6e068cf50313… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add dmnd class Commit: 8cfbfcdaff4cfdeefe4e11733ac1530eebb80da2 https://github.com/galaxyproject/galaxy/commit/8cfbfcdaff4cfdeefe4e11733ac1… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Add test to dmnd Commit: 275f2fb84beffb89c7a8a22d14a176455d9bf328 https://github.com/galaxyproject/galaxy/commit/275f2fb84beffb89c7a8a22d14a1… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Add test data for diamond datatype Commit: 34471bbc47b5bd428099c8f5518c0329b3c86582 https://github.com/galaxyproject/galaxy/commit/34471bbc47b5bd428099c8f5518c… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Correct the header Commit: 5dcb2f317bc3a3f07e30e1fce070ed012f0e7379 https://github.com/galaxyproject/galaxy/commit/5dcb2f317bc3a3f07e30e1fce070… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Change the header to find for dmnd Commit: 50f9f74884068690f7c5e125b4aae10fd48bf41e https://github.com/galaxyproject/galaxy/commit/50f9f74884068690f7c5e125b4aa… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add extra line to fix flake8 Commit: f50272be0dee7d63ba452bc033ce6b5970a27e4a https://github.com/galaxyproject/galaxy/commit/f50272be0dee7d63ba452bc033ce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Merge pull request #33 from ASaiM/dmnddb Add sniffer for dmnd files Commit: f358d14670cc0e4974bfdda1db96d5c63e553ee0 https://github.com/galaxyproject/galaxy/commit/f358d14670cc0e4974bfdda1db96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Merge pull request #3379 from bgruening/dmnddb Add diamond database as datatype Compare: https://github.com/galaxyproject/galaxy/compare/dd9aa82db691...f358d14670cc

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[galaxyproject/galaxy] b6e9f4: Fix workflow extraction of dataset/collections nam...
by GitHub 09 Jan '17

09 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: b6e9f4a6eefb53d2f3b8b415b80e1a674bd7cc8d https://github.com/galaxyproject/galaxy/commit/b6e9f4a6eefb53d2f3b8b415b80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. Commit: 63e70f4f2f47f5b952bb7817e93b0e61c8614dd7 https://github.com/galaxyproject/galaxy/commit/63e70f4f2f47f5b952bb7817e93b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. Compare: https://github.com/galaxyproject/galaxy/compare/41f5ff48ed84...63e70f4f2f47

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[galaxyproject/galaxy] d3291c: fix PHD Comics plugin
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3291c15f96c05d17900606ca670acc4f9c90391 https://github.com/galaxyproject/galaxy/commit/d3291c15f96c05d17900606ca670… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js Log Message: ----------- fix PHD Comics plugin Commit: dd9aa82db69167e26b31d4f12da851c95ff2ee64 https://github.com/galaxyproject/galaxy/commit/dd9aa82db69167e26b31d4f12da8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js Log Message: ----------- Merge pull request #3392 from anatskiy/phdcomics_fix Fix PHD Comics plugin Compare: https://github.com/galaxyproject/galaxy/compare/64faeece93c1...dd9aa82db691

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[galaxyproject/galaxy] 433b99: Slim down testing ``Dockerfile``.
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 433b993ecae7d306d4222ca5d91a4a31cd907e52 https://github.com/galaxyproject/galaxy/commit/433b993ecae7d306d4222ca5d91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Slim down testing ``Dockerfile``. - Remove broken CasperJS from testing Dockerfile. - Remove multi-process mode. Multi-process mode was difficult to maintain and the last time I did testing at scale I found docker-galaxy-stable to be much more useful and easy to use. The test framework now supports GALAXY_TEST_EXTERNAL again so it should be easy enough to rig something up with docker-compose that actually uses a best practice container for scaling tests such as those in ``test/manual``. Commit: 64faeece93c1ecb59ff4d10b7664660e7886d419 https://github.com/galaxyproject/galaxy/commit/64faeece93c1ecb59ff4d10b7664… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3286 from jmchilton/slim_test_dockerfile Slim down testing ``Dockerfile``. Compare: https://github.com/galaxyproject/galaxy/compare/e1fbdc6808d3...64faeece93c1

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[galaxyproject/galaxy] e260c8: Fix UX problem when sharing objects with users.
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e260c8eb05b7e7ca9d39d136041d84314f13d1d8 https://github.com/galaxyproject/galaxy/commit/e260c8eb05b7e7ca9d39d136041d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Fix UX problem when sharing objects with users. The problem is that by default Galaxy doesn't expose usernames and user e-mails via this form but a select2 + search is used anyway making it appear that any selection matches an actual user. It is confusing. Fixes #3250 reported by @peterjc. xref #1111 Commit: e1fbdc6808d3cf5b20870c07b39326bb13836ef1 https://github.com/galaxyproject/galaxy/commit/e1fbdc6808d3cf5b20870c07b393… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Merge pull request #3373 from jmchilton/remove_unused_select2 Fix UX problem when sharing objects with users. Compare: https://github.com/galaxyproject/galaxy/compare/dcf3b2175207...e1fbdc6808d3

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[galaxyproject/galaxy] de35c8: Refactor API helpers for re-use in rest of test fr...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de35c85b655e7de0e5f349a2d61e4f11d73ef23e https://github.com/galaxyproject/galaxy/commit/de35c85b655e7de0e5f349a2d61e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py M test/manual/workflows_scaling.py Log Message: ----------- Refactor API helpers for re-use in rest of test framework. - Move api.helpers to base.populators. - Refactor helper subclasses adapted to use bioblend instead of test framework stuff into base.populators for greater visibility. - Refactor workflow format 2 testing stuff for reuse by Selenium. Commit: a0177fe2f4cfa0f02e835788c3f036a17786da37 https://github.com/galaxyproject/galaxy/commit/a0177fe2f4cfa0f02e835788c3f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/base/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Add ability to import workflows without Galaxy modifying tool version. Needed to test workflow tool upgrades when loading workflows, but I think it is good to have a way to preserve the original tool state as well for the sake of absolute reproducibility/tracibility. Commit: 76b8a69c37093e1b222b4f264370934ee8c04bb7 https://github.com/galaxyproject/galaxy/commit/76b8a69c37093e1b222b4f264370… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Capture page source and DOM of top-level frame on Selenium errors. Dump to the same directory as the last screenshot related to the error. Commit: 78b099f3a78520412a63a0c6353fe4ef09c9f4e3 https://github.com/galaxyproject/galaxy/commit/78b099f3a78520412a63a0c6353f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py Log Message: ----------- Expand selenium test coverage for workflows. Expand and then break out workflow management tests into its own file since these aren't related to the workflow editor per se. Includes new tests of workflow "viewing" and "renaming". Add a new file for testing workflow execution. This currently contains tests for simple execution with a single input and a test for running workflows with tool version upgrades. This includes a refactoring of some existing tests related to checking various things in the history panel - as part of building up good history panel abstractions. The previous constructs were ported fairly literally from older CasperJS tests. These abstractions therefore referred to everything has "hda"s instead of history items. The newer abstractions therefore allow for collections and are built around HIDs (a visual thing exposed to the user) instead of HDA IDs. I think this is higher-level and more appropriate for a web functional test. Rebase into workflow GUI tests. Commit: dcf3b21752070c8a2b2747cc921db91fdd3ab42d https://github.com/galaxyproject/galaxy/commit/dcf3b21752070c8a2b2747cc921d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #3371 from jmchilton/selenium_workflow Expand selenium test coverage for workflows. Compare: https://github.com/galaxyproject/galaxy/compare/627fafafdfb1...dcf3b2175207

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[galaxyproject/galaxy] dfcd8e: Rework display of inputs for workflow form.
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dfcd8e4bf69cccd50a5482b5440937e11e569b84 https://github.com/galaxyproject/galaxy/commit/dfcd8e4bf69cccd50a5482b54409… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) 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/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py Log Message: ----------- Rework display of inputs for workflow form. - If steps have labels, use them. - Use workflow icon from workflow editor in step bar. - Eliminate "Step Index" from display of workflow steps. Commit: cd0387f7ba0da51806cea4224da20f908faadc97 https://github.com/galaxyproject/galaxy/commit/cd0387f7ba0da51806cea4224da2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack client scripts. Commit: c8ef41f1f1212457c2040ba4f14d7403c3f2aeb9 https://github.com/galaxyproject/galaxy/commit/c8ef41f1f1212457c2040ba4f14d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js 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/bundled/login.bundled.js.map Log Message: ----------- Undo changes label handling adjustments to form-input and form-section modules Commit: 69e6ff724fd69fe6fec976667b22b0a717328379 https://github.com/galaxyproject/galaxy/commit/69e6ff724fd69fe6fec976667b22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js 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/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #51 from guerler/workflow_inputs_display_000 Undo changes label handling adjustments to form-input and form-section modules Commit: ccdf09b099c1201aa1e4b5d0537547cf162998cf https://github.com/galaxyproject/galaxy/commit/ccdf09b099c1201aa1e4b5d05375… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused local variable Commit: e846b517c16014d5b32ffef4d23998d5cd2170d2 https://github.com/galaxyproject/galaxy/commit/e846b517c16014d5b32ffef4d239… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rely on backend to specify label Commit: 71b64472c645cacbba3674f5a0f48c675b29437d https://github.com/galaxyproject/galaxy/commit/71b64472c645cacbba3674f5a0f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Repack scripts Commit: d84221ea47719049c5415f7edc88736d22955f44 https://github.com/galaxyproject/galaxy/commit/d84221ea47719049c5415f7edc88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.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-section.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Add label hiding option without need to overwrite actual label Commit: bcd660c9f0d27e7da87f8c124d09526882382f13 https://github.com/galaxyproject/galaxy/commit/bcd660c9f0d27e7da87f8c124d09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Refine workflow step title display in run form. - Go back to prefixing with the step number as discussed on #3369. - Use the label regardless of step type - don't ignore tool labels. Commit: a24ce4c61f6899d13bd2197144fa0a3ea379af5a https://github.com/galaxyproject/galaxy/commit/a24ce4c61f6899d13bd2197144fa… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'workflow_inputs_display' of https://github.com/jmchilton/galaxy into jmchilton-workflow_inputs_display Commit: 5bfffac06965136c970f3ddfd20ff770dc092324 https://github.com/galaxyproject/galaxy/commit/5bfffac06965136c970f3ddfd20f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: 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/login.bundled.js.map Log Message: ----------- repack Commit: 627fafafdfb1fea1cc5c456f11752c090129336f https://github.com/galaxyproject/galaxy/commit/627fafafdfb1fea1cc5c456f1175… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'jmchilton-workflow_inputs_display' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dad4c60d852d...627fafafdfb1

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[galaxyproject/galaxy] f854a8: Fix upload to respect explicit name override on pa...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f854a8b01cef74369bd3049dfb5d981a5310d21a https://github.com/galaxyproject/galaxy/commit/f854a8b01cef74369bd3049dfb5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: d9ffbc433ef417c08d5d040b27a6d3d626d54872 https://github.com/galaxyproject/galaxy/commit/d9ffbc433ef417c08d5d040b27a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test cases for renaming datasets based on tool input datasets. Includes test cases for #3197 and #662. Commit: a18b24e0679016da159703a4e6b873f0ae95cf4e https://github.com/galaxyproject/galaxy/commit/a18b24e0679016da159703a4e6b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py M test/functional/tools/for_workflows/mapper2.xml Log Message: ----------- Allow rename PJA to target input collections. Implements #2346 w/test case. Commit: dad4c60d852d3c2cd06d4327c20f2b2ee516c9cf https://github.com/galaxyproject/galaxy/commit/dad4c60d852d3c2cd06d4327c20f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3381 from jmchilton/rename_improvements Test cases & small enhancement to workflow renaming PJAs. Compare: https://github.com/galaxyproject/galaxy/compare/690b512dbded...dad4c60d852d

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[galaxyproject/galaxy] eefd71: Migrate more CasperJS API tests to the API test fr...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eefd716f1f86e8c964f54d133b91db2a0a575b44 https://github.com/galaxyproject/galaxy/commit/eefd716f1f86e8c964f54d133b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Migrate more CasperJS API tests to the API test framework. - Replace visualization tests (api-visualizations-tests.js -> test_visualizations.py). - Replace dataset API tests (api-dataset-tests.js -> test_datasets.py). - Start work on migrating history dataset API tests (api-hda-tests.js -> test_history_contents.py). Commit: 690b512dbded1989fa3c98af3b7733d258ec3f97 https://github.com/galaxyproject/galaxy/commit/690b512dbded1989fa3c98af3b77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Merge pull request #3288 from jmchilton/casper2api_0 Migrate more CasperJS API tests to the API test framework. Compare: https://github.com/galaxyproject/galaxy/compare/bb5d450b32af...690b512dbded

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[galaxyproject/galaxy] 50257a: Add re-submission info to job_conf.xml.sample_adva...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50257aac80c7aedf41ad436d475640d586ca732c https://github.com/galaxyproject/galaxy/commit/50257aac80c7aedf41ad436d4756… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add re-submission info to job_conf.xml.sample_advanced. Commit: 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c https://github.com/galaxyproject/galaxy/commit/34f0b0fe8911c01562c7dfc0e83e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Implement a Galaxy config option for default job re-submission conditions. Commit: bb5d450b32afca22b666095e9ea4482f08647e3d https://github.com/galaxyproject/galaxy/commit/bb5d450b32afca22b666095e9ea4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #3319 from jmchilton/job_resubmission_refinement_0 Make it easier to use job re-submission conditions. Compare: https://github.com/galaxyproject/galaxy/compare/9843e404b70b...bb5d450b32af

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[galaxyproject/galaxy] 06cc5f: Fix implicit conversion for sessionless tool API c...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Compare: https://github.com/galaxyproject/galaxy/compare/4d73dfc2e03d...41f5ff48ed84

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