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

[galaxyproject/galaxy] 24dfba: add new API endpoint which reads a new config file...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 24dfbafe4381406f2028af9076f37d30241536f1 https://github.com/galaxyproject/galaxy/commit/24dfbafe4381406f2028af9076f3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add new API endpoint which reads a new config file for new user-preferences Commit: 7426693830e90501225aa0af2e150880c0fa0a67 https://github.com/galaxyproject/galaxy/commit/7426693830e90501225aa0af2e15… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: A config/user_preferences_extra_conf.xml.sample Log Message: ----------- add new config file Commit: 910044e77370bfa4d6a6637d665624949dee7e38 https://github.com/galaxyproject/galaxy/commit/910044e77370bfa4d6a6637d6656… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/extra-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Adding extra information page for the User Preferences Commit: d2caf4ce33b8f33806c3915adde87fb0f7b1b711 https://github.com/galaxyproject/galaxy/commit/d2caf4ce33b8f33806c3915adde8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- change comment Commit: 8a52c3ae89aaf17b28b2e98afc18543c33fce1ec https://github.com/galaxyproject/galaxy/commit/8a52c3ae89aaf17b28b2e98afc18… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample 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 Log Message: ----------- Updates Commit: 93d97d83239dcaa71c48d556a75d600efeadba55 https://github.com/galaxyproject/galaxy/commit/93d97d83239dcaa71c48d556a75d… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- add save button and boilerplate Commit: 4268d61b6f32e1910a8a9f063ca801ee84bfb46b https://github.com/galaxyproject/galaxy/commit/4268d61b6f32e1910a8a9f063ca8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py 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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Adding save feature for extra user preferences Commit: 320f17be6ab29e668ec6f278b88c92dca2baf14c https://github.com/galaxyproject/galaxy/commit/320f17be6ab29e668ec6f278b88c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding serialization-deserialization to save dynamic user preferences Commit: ff9f39aa4181323aca1844953c633c9909215662 https://github.com/galaxyproject/galaxy/commit/ff9f39aa4181323aca1844953c63… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- fix if we don't have a prefilled user objecte Commit: 85fde4c16d9fb5ca60a93c05c9c4248c463c5273 https://github.com/galaxyproject/galaxy/commit/85fde4c16d9fb5ca60a93c05c9c4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- fixing bugs related to empty data or config Commit: 4b53ae0b54790664732700b2b1dd1d45934afc92 https://github.com/galaxyproject/galaxy/commit/4b53ae0b54790664732700b2b1dd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- removing name from the plugin config Commit: b3d7a027243dd1143d98b341f06cc03494412e40 https://github.com/galaxyproject/galaxy/commit/b3d7a027243dd1143d98b341f06c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- bugfix in the json implementation Commit: aaa641b49cc229ea6a654fc8e22c071d7fb78240 https://github.com/galaxyproject/galaxy/commit/aaa641b49cc229ea6a654fc8e22c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-08-13 (Sat, 13 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/extra-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- adding a stable jQuery selector Commit: 81b8f60b00e143e06dadf5f645cdf3ceccb312df https://github.com/galaxyproject/galaxy/commit/81b8f60b00e143e06dadf5f645cd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt A .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/bower.json M 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static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- Adding edit and save extra user preferences if present to manage info screen in User Preferences and merging base.css file in the static folder Commit: cc96000ba0a109dcb31300ca56927e5f07e3e775 https://github.com/galaxyproject/galaxy/commit/cc96000ba0a109dcb31300ca5692… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Updating databse object of extra preferences to take dict() and not list() Commit: 9a114393a539cc4f9256784f852dffb4a94beb41 https://github.com/galaxyproject/galaxy/commit/9a114393a539cc4f9256784f852d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Adding error message for empty required fields for additional user preferences Commit: 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tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merging with dev Commit: 748f85e700f6a23d681edc74f2e375130e4b38e8 https://github.com/galaxyproject/galaxy/commit/748f85e700f6a23d681edc74f2e3… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Handling malformed additional preferences config xml Commit: 0c95a7a2b281f3399e2bf7a8c6dd2c35fb781b0b https://github.com/galaxyproject/galaxy/commit/0c95a7a2b281f3399e2bf7a8c6dd… Author: anuprulez <anup.rulez(a)gmail.com> Date: 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tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into extra_user_preferences Commit: 24d52054adf43b55d50d0fca10c6cbab0a041983 https://github.com/galaxyproject/galaxy/commit/24d52054adf43b55d50d0fca10c6… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample M lib/galaxy/webapps/galaxy/api/users.py 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 Log Message: ----------- Merge branch 'extra_user_preferences' of https://github.com/bgruening/galaxy into extra_user_preferences Commit: 22dba016be3ca3753a1b2ee8769e506864f8770b https://github.com/galaxyproject/galaxy/commit/22dba016be3ca3753a1b2ee8769e… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-04 (Wed, 04 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/libs.bundled.js.map Log Message: ----------- static build Commit: 5a86e3c5ca09932a67957afe44d9444dff8474f0 https://github.com/galaxyproject/galaxy/commit/5a86e3c5ca09932a67957afe44d9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- linting fixes Commit: 94b2184f897cf19ab5d884708fe484451d199219 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test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/wc_gnu.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 M tox.ini Log Message: ----------- merge with master Commit: 045039da95cf0cb86160e2da18450209ee7409c5 https://github.com/galaxyproject/galaxy/commit/045039da95cf0cb86160e2da1845… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- merge with master, address Aysams comments Commit: c0a00890551f3241a17ebd280c71a58880907589 https://github.com/galaxyproject/galaxy/commit/c0a00890551f3241a17ebd280c71… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Log Message: ----------- merge with master Commit: 82ce70ee67f139cfa1775c9a7be58d1d88c13830 https://github.com/galaxyproject/galaxy/commit/82ce70ee67f139cfa1775c9a7be5… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample Log Message: ----------- address Erics comments Commit: 913bf293dba532cae696c4c1fbeea27307e686e3 https://github.com/galaxyproject/galaxy/commit/913bf293dba532cae696c4c1fbee… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.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 Log Message: ----------- update client Commit: 40071e2949bb4217e10f225d0d9cbf976f76c67f https://github.com/galaxyproject/galaxy/commit/40071e2949bb4217e10f225d0d9c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M config/user_preferences_extra_conf.xml.sample Log Message: ----------- remove another password field Commit: 4aa8d631d97e3c253d6f4c1398a599039aa52acf https://github.com/galaxyproject/galaxy/commit/4aa8d631d97e3c253d6f4c1398a5… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- register user_preference config file Commit: 54fb8487d25e2964ca9f7ad02b3b2fc45ed591fb https://github.com/galaxyproject/galaxy/commit/54fb8487d25e2964ca9f7ad02b3b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: R config/user_preferences_extra_conf.xml.sample A config/user_preferences_extra_conf.yml.sample Log Message: ----------- rename config file Commit: 1ca8f2c927c91d467d160af81081a89073a36b5a https://github.com/galaxyproject/galaxy/commit/1ca8f2c927c91d467d160af81081… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- use yml instead of XML and reorder the preference panels Commit: dc9c71f7575450f5100ae538000ac0232e4ead52 https://github.com/galaxyproject/galaxy/commit/dc9c71f7575450f5100ae538000a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- rename the config files from XML to YML Commit: 03bbbe96a9df6fdfd6ea7599b3cc7a8484a22660 https://github.com/galaxyproject/galaxy/commit/03bbbe96a9df6fdfd6ea7599b3cc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- fix linting error Commit: 305f9f94c04579a8414e0034e0ec90311119431b https://github.com/galaxyproject/galaxy/commit/305f9f94c04579a8414e0034e0ec… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.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 Log Message: ----------- revert static files Commit: a06ec3e58dc1c53a8bcf515f38c89976eae1a074 https://github.com/galaxyproject/galaxy/commit/a06ec3e58dc1c53a8bcf515f38c8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- change xml to yml Commit: a71f64c8da2427b6f5808b9f4e91612fe82efe10 https://github.com/galaxyproject/galaxy/commit/a71f64c8da2427b6f5808b9f4e91… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M config/user_preferences_extra_conf.yml.sample Log Message: ----------- fix apollo spelling Commit: 338fffad0bcaea709cc552dcab5310e4b73ea4c7 https://github.com/galaxyproject/galaxy/commit/338fffad0bcaea709cc552dcab53… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove user_preferences_extra_conf.yml sample file from the default list Commit: eb8f7f0da328b0fd440f67bdf0c6f9c5e366a32d https://github.com/galaxyproject/galaxy/commit/eb8f7f0da328b0fd440f67bdf0c6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- remove debug statement Commit: 196a2bbcf50c4f9fa41588d8e087e5b5cee9da65 https://github.com/galaxyproject/galaxy/commit/196a2bbcf50c4f9fa41588d8e087… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: A config/user_preferences_extra_conf.yml.sample M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3383 from bgruening/extra_user_preferences Add extension point for user preferences Compare: https://github.com/galaxyproject/galaxy/compare/4a35bd3532ce...196a2bbcf50c

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[galaxyproject/infrastructure-playbook] 3e18d5: Increase max walltime for Jetstream jobs for Du No...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e18d57835e51c48d17366fed93027a536d41e05 https://github.com/galaxyproject/infrastructure-playbook/commit/3e18d57835e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M jetstream_common/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase max walltime for Jetstream jobs for Du Novo: Align Families (how did this work before)?

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[galaxyproject/usegalaxy-playbook] 4d11e2: Main integrated tool panel
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4d11e2dadd455daba11c24eae5a039d7e488717a https://github.com/galaxyproject/usegalaxy-playbook/commit/4d11e2dadd455dab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Main integrated tool panel Commit: 2d2db24e8d099282666f5acda432305aeb887a04 https://github.com/galaxyproject/usegalaxy-playbook/commit/2d2db24e8d099282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/common/stack.yml M env/main/_inc_config_post_tasks.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/nginx/tacc-protected/index.html M env/test/group_vars/webservers/vars.yml M env/test/group_vars/webservers/vault.yml A env/test/templates/nginx/nginx_galaxy.pam.j2 M env/test/templates/nginx/tacc_protected.j2 Log Message: ----------- Fix Main impersonation and other protected stuff Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f0726c237e5c...…

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[galaxyproject/galaxy] bf6896: Fix get_tool returning list when it shouldn't.
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf68966accd18af2da1e4fa518d01119f5a696f2 https://github.com/galaxyproject/galaxy/commit/bf68966accd18af2da1e4fa518d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix get_tool returning list when it shouldn't. Commit: 4a35bd3532ce3a9e0af84c3a86ee33585e9e0ba3 https://github.com/galaxyproject/galaxy/commit/4a35bd3532ce3a9e0af84c3a86ee… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4390 from jmchilton/toollist Fix get_tool returning list when it shouldn't. Compare: https://github.com/galaxyproject/galaxy/compare/d53a5424967e...4a35bd3532ce

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[galaxyproject/galaxy] ecad39: Refactor ToolOutputCollectionStructure to allow it...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ecad3996f1f4715db5ff326f9f6ae5067cd2e0fc https://github.com/galaxyproject/galaxy/commit/ecad3996f1f4715db5ff326f9f6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Refactor ToolOutputCollectionStructure to allow it be more easily consumed. Make complex arguments optional. Commit: e8112210429d710a9eb9702f541cfaed6e219454 https://github.com/galaxyproject/galaxy/commit/e8112210429d710a9eb9702f541c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection. Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection. Commit: d53a5424967e46d683f7baafe06cb53703e86adf https://github.com/galaxyproject/galaxy/commit/d53a5424967e46d683f7baafe06c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #4389 from jmchilton/output_collect_refactor Refactor ToolOutputCollectionStructure... Compare: https://github.com/galaxyproject/galaxy/compare/d2394aa172e2...d53a5424967e

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[galaxyproject/galaxy] 15cc6e: Async update 20170615
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15cc6e461a9d921c9762a54a112f74abc9353309 https://github.com/galaxyproject/galaxy/commit/15cc6e461a9d921c9762a54a112f… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Async update 20170615 The asynchronous procedure expects that only one output is defined in the tool XML schema. This improvement permits to define also collections. This feature is useful in conjunction with tools like [galaxy-json-collect-data-source](https://github.com/fabio-cumbo/galaxy- json-collect-data-source) (please see the README of the tool for more information). It does not affect the behaviour of the asynchronous data sources previously developed. Commit: b4fdc27f533a0a204f9eedfcd265a15ef0fb469e https://github.com/galaxyproject/galaxy/commit/b4fdc27f533a0a204f9eedfcd265… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Blank line contains whitespace: fixed Commit: d5409500aebe1c5798ae632977be64b8f71a85a8 https://github.com/galaxyproject/galaxy/commit/d5409500aebe1c5798ae632977be… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- minor update 20170711 if GALAXY_TYPE is provided, we do not need to loop over tool.outputs.values() Commit: e516ba738ecbb13f29d072fd0ad707f8470369de https://github.com/galaxyproject/galaxy/commit/e516ba738ecbb13f29d072fd0ad7… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- except Exception: fixed Commit: 835e4fb0ae09c12a8db80ca6f3d339275f3881f0 https://github.com/galaxyproject/galaxy/commit/835e4fb0ae09c12a8db80ca6f3d3… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- outputs count: fixed Commit: d2394aa172e2030c301f7b50863fb3d96664a2db https://github.com/galaxyproject/galaxy/commit/d2394aa172e2030c301f7b50863f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Merge pull request #4198 from fabio-cumbo/data-source-async Async update: support to collections Compare: https://github.com/galaxyproject/galaxy/compare/6e37bc05c1d5...d2394aa172e2

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[galaxyproject/galaxy] b19640: Stop loading tools that require a newer galaxy
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b19640b81a83af2759666717ae658940103588fe https://github.com/galaxyproject/galaxy/commit/b19640b81a83af2759666717ae65… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Stop loading tools that require a newer galaxy We look at a tools profile attribute, and if it is too new we will not load the tool. This is a first step towards https://github.com/galaxyproject/galaxy/issues/2086 Commit: 6e37bc05c1d5ce247c0f371799a69e9f064168b4 https://github.com/galaxyproject/galaxy/commit/6e37bc05c1d5ce247c0f371799a6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4382 from mvdbeek/enforce_tool_profiles Stop loading tools that require a newer galaxy Compare: https://github.com/galaxyproject/galaxy/compare/5be7768047f4...6e37bc05c1d5

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[galaxyproject/galaxy] 6943c7: Allow import of history archives via siple file up...
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6943c74556858f89703567c4558e885291d95c57 https://github.com/galaxyproject/galaxy/commit/6943c74556858f89703567c4558e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Allow import of history archives via siple file upload Commit: 5be7768047f471d49a85525bd0aa9bd814b081aa https://github.com/galaxyproject/galaxy/commit/5be7768047f471d49a85525bd0aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #4326 from mvdbeek/history_import_from_file Allow import of history archives via simple file upload Compare: https://github.com/galaxyproject/galaxy/compare/31f68edbbaf9...5be7768047f4

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[galaxyproject/galaxy] 1f2fa3: Reuse Shell objects after initialization
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f2fa31963b56c79072ae36a09ddf6a31a5e9683 https://github.com/galaxyproject/galaxy/commit/1f2fa31963b56c79072ae36a09dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py A test/unit/test_remote_shell.py Log Message: ----------- Reuse Shell objects after initialization Commit: 330fe392096f68d34c964ae2cb62d454f609fc3c https://github.com/galaxyproject/galaxy/commit/330fe392096f68d34c964ae2cb62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Sleep 100 ms before polling process This should be long enough for most shell commands and speed up the average time to check a job's status. Commit: 5a37bc263feeb7be2411d555ebb3e03359c488aa https://github.com/galaxyproject/galaxy/commit/5a37bc263feeb7be2411d555ebb3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- Add a new Paramiko-based shell runner and tests This allows a single ssh connection to be reused. The unit test also tests the current SecureShell class. The unit tests require [mock-ssh-server](https://github.com/carletes/mock-ssh-server). These tests are being skipped if this library is not importable. Commit: 69365e49eaeea173f3ecaad17d1f4bcefa65c316 https://github.com/galaxyproject/galaxy/commit/69365e49eaeea173f3ecaad17d1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M tox.ini Log Message: ----------- Install mock-ssh-server or unit testing Commit: 31f68edbbaf9fdccd3582bde5b20b43728251755 https://github.com/galaxyproject/galaxy/commit/31f68edbbaf9fdccd3582bde5b20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py A test/unit/test_remote_shell.py M tox.ini Log Message: ----------- Merge pull request #4358 from mvdbeek/paramiko_based_shell_runner Paramiko based shell runner Compare: https://github.com/galaxyproject/galaxy/compare/3e1b46fe42ad...31f68edbbaf9

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[galaxyproject/galaxy] 2e31a5: Add test tool for API tests
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e31a5b6d18c62411cc419fb5dfd3008bd7a14df https://github.com/galaxyproject/galaxy/commit/2e31a5b6d18c62411cc419fb5dfd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: A test/functional/tools/identifier_source.xml Log Message: ----------- Add test tool for API tests Commit: b4c72eaccf07c9ee0d7e93de21311f0c6d9cc6c4 https://github.com/galaxyproject/galaxy/commit/b4c72eaccf07c9ee0d7e93de2131… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M test/functional/tools/identifier_source.xml Log Message: ----------- Fix the command section (thx @nsoranzo) Commit: 3e1b46fe42ad57aa8a1f8c2d0752cfd4bed47ad4 https://github.com/galaxyproject/galaxy/commit/3e1b46fe42ad57aa8a1f8c2d0752… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: A test/functional/tools/identifier_source.xml Log Message: ----------- Merge pull request #4380 from mvdbeek/tie_down_collection_matcher Add test tool for API tests Compare: https://github.com/galaxyproject/galaxy/compare/e92a15a18523...3e1b46fe42ad

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