[galaxy-commits] [galaxyproject/galaxy] 24dfba: add new API endpoint which reads a new config file...

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 24dfbafe4381406f2028af9076f37d30241536f1 https://github.com/galaxyproject/galaxy/commit/24dfbafe4381406f2028af9076f37... Author: Bjoern Gruening <bjoern.gruening@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/7426693830e90501225aa0af2e150... Author: Bjoern Gruening <bjoern.gruening@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/910044e77370bfa4d6a6637d66562... Author: anuprulez <anup.rulez@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/d2caf4ce33b8f33806c3915adde87... Author: anuprulez <anup.rulez@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/8a52c3ae89aaf17b28b2e98afc185... Author: Bjoern Gruening <bjoern.gruening@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/93d97d83239dcaa71c48d556a75d6... Author: Bjoern Gruening <bjoern.gruening@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/4268d61b6f32e1910a8a9f063ca80... Author: anuprulez <anup.rulez@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/320f17be6ab29e668ec6f278b88c9... Author: anuprulez <anup.rulez@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/ff9f39aa4181323aca1844953c633... Author: Bjoern Gruening <bjoern.gruening@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/85fde4c16d9fb5ca60a93c05c9c42... Author: anuprulez <anup.rulez@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/4b53ae0b54790664732700b2b1dd1... Author: anuprulez <anup.rulez@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/b3d7a027243dd1143d98b341f06cc... Author: Bjoern Gruening <bjoern.gruening@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/aaa641b49cc229ea6a654fc8e22c0... Author: anuprulez <anup.rulez@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/81b8f60b00e143e06dadf5f645cdf... 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client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M 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tox.ini Log Message: ----------- Merging with remove_mako_user_pref Commit: 22e465899029de9c2156d13b3f4325a83ff9e023 https://github.com/galaxyproject/galaxy/commit/22e465899029de9c2156d13b3f432... 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Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: 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 M static/scripts/bundled/login.bundled.js M 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/cc96000ba0a109dcb31300ca56927... 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M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M 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/748f85e700f6a23d681edc74f2e37... Author: anuprulez <anup.rulez@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/0c95a7a2b281f3399e2bf7a8c6dd2... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Updating a for loop Commit: 6d70e92c9c71d40cccbefb69466afca1188e40a3 https://github.com/galaxyproject/galaxy/commit/6d70e92c9c71d40cccbefb69466af... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- revert style changes Commit: 4b43a1fb68bc5ed49e4c46ee231337f800fbe2e4 https://github.com/galaxyproject/galaxy/commit/4b43a1fb68bc5ed49e4c46ee23133... 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tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M 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/24d52054adf43b55d50d0fca10c6c... Author: Bjoern Gruening <bjoern.gruening@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/22dba016be3ca3753a1b2ee8769e5... Author: Bjoern Gruening <bjoern.gruening@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/5a86e3c5ca09932a67957afe44d94... Author: Björn Grüning <bjoern@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 https://github.com/galaxyproject/galaxy/commit/94b2184f897cf19ab5d884708fe48... 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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/045039da95cf0cb86160e2da18450... Author: Bjoern Gruening <bjoern.gruening@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/c0a00890551f3241a17ebd280c71a... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Log Message: ----------- merge with master Commit: 82ce70ee67f139cfa1775c9a7be58d1d88c13830 https://github.com/galaxyproject/galaxy/commit/82ce70ee67f139cfa1775c9a7be58... Author: Bjoern Gruening <bjoern.gruening@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/913bf293dba532cae696c4c1fbeea... Author: Bjoern Gruening <bjoern.gruening@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/40071e2949bb4217e10f225d0d9cb... Author: Bjoern Gruening <bjoern.gruening@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/4aa8d631d97e3c253d6f4c1398a59... Author: Bjoern Gruening <bjoern.gruening@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/54fb8487d25e2964ca9f7ad02b3b2... Author: Bjoern Gruening <bjoern.gruening@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/1ca8f2c927c91d467d160af81081a... Author: Bjoern Gruening <bjoern.gruening@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/dc9c71f7575450f5100ae538000ac... Author: Bjoern Gruening <bjoern.gruening@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/03bbbe96a9df6fdfd6ea7599b3cc7... Author: Bjoern Gruening <bjoern.gruening@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/305f9f94c04579a8414e0034e0ec9... Author: Bjoern Gruening <bjoern.gruening@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/a06ec3e58dc1c53a8bcf515f38c89... Author: Björn Grüning <bjoern@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/a71f64c8da2427b6f5808b9f4e916... Author: Björn Grüning <bjoern@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/338fffad0bcaea709cc552dcab531... Author: Björn Grüning <bjoern@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/eb8f7f0da328b0fd440f67bdf0c6f... Author: Björn Grüning <bjoern@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/196a2bbcf50c4f9fa41588d8e087e... Author: Eric Rasche <hxr@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