- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] a269a9: Fix the bug
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a269a95cf0aef62b1f1dbca8de698d7b2f61f52b https://github.com/galaxyproject/galaxy/commit/a269a95cf0aef62b1f1dbca8de69… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug

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[galaxyproject/galaxy] 83cf06: Fix the bug
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83cf06e3614b5463e3aaac74f314e3d04ad46f9a https://github.com/galaxyproject/galaxy/commit/83cf06e3614b5463e3aaac74f314… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 92826fe5e763a0938cf4710955be4d1e4e5cf967 https://github.com/galaxyproject/galaxy/commit/92826fe5e763a0938cf4710955be… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Merge pull request #5531 from bgruening/bugfix_#5522 Fix search overlay JS errors Compare: https://github.com/galaxyproject/galaxy/compare/298ef7ee1951...92826fe5e763

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[galaxyproject/galaxy] 8c941a: Fix for: https://github.com/galaxyproject/galaxy/i...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8c941ae35a37f8dd087222c6827c122ddfdcc966 https://github.com/galaxyproject/galaxy/commit/8c941ae35a37f8dd087222c6827c… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527

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[galaxyproject/galaxy] 8a721f: Fix for: https://github.com/galaxyproject/galaxy/i...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a721f6f37741d07fbe709112fa03c51b4697a49 https://github.com/galaxyproject/galaxy/commit/8a721f6f37741d07fbe709112fa0… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527 Commit: 298ef7ee1951cf64fe42b4cc44ce83b4257aace6 https://github.com/galaxyproject/galaxy/commit/298ef7ee1951cf64fe42b4cc44ce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Merge pull request #5528 from gvlproject/genomespace_18.01_bugfix Fix for GenomeSpace importer/exporter Compare: https://github.com/galaxyproject/galaxy/compare/78ee5f8451e0...298ef7ee1951

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[galaxyproject/galaxy] 7663de: Remove unused methods.
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7663de745f5df827f7873960c9ec341eb88e86a2 https://github.com/galaxyproject/galaxy/commit/7663de745f5df827f7873960c9ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Remove unused methods. Commit: aed2b4a239ebbcd4081426599023867eed94f63b https://github.com/galaxyproject/galaxy/commit/aed2b4a239ebbcd4081426599023… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- remove unused import Commit: 78ee5f8451e022515e75e9ca5888bf598d2d3414 https://github.com/galaxyproject/galaxy/commit/78ee5f8451e022515e75e9ca5888… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #5450 from jmchilton/collection_mapping_cleanup Remove unused mapping code. Compare: https://github.com/galaxyproject/galaxy/compare/41a31967540e...78ee5f8451e0

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[galaxyproject/galaxy] 283ab0: Improve performance bugs and misleading summary in...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 283ab0459fe25cc26606ccae86bdd99e1c6765b9 https://github.com/galaxyproject/galaxy/commit/283ab0459fe25cc26606ccae86bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Improve performance bugs and misleading summary info in history list. Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing. Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered. This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries. Commit: 755fb9fb21581f29ba96a1465ca73e72eb68b610 https://github.com/galaxyproject/galaxy/commit/755fb9fb21581f29ba96a1465ca7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less Log Message: ----------- style changes for history lists * include title for all state indicators * shorten title * change style of deleted indicator * comment out unused less variables Commit: 42c12c51884454c60a8b109f1ae7e814eeeaf7a4 https://github.com/galaxyproject/galaxy/commit/42c12c51884454c60a8b109f1ae7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge pull request #5533 from jmchilton/history_list_opts [18.01] Improve performance bugs and misleading summary info in history list. Compare: https://github.com/galaxyproject/galaxy/compare/1ccd55a500e5...42c12c518844

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[galaxyproject/galaxy] 712073: [18.01] Fix missing job stdout/stderr on Pulsar tr...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7120739230255c63bf9786fb735016292b57dcfd https://github.com/galaxyproject/galaxy/commit/7120739230255c63bf9786fb7350… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Shouldn't break backward compatiblity at all without it - but to get the outputs Pulsar requires an update (https://github.com/galaxyproject/pulsar/pull/159) as well. Commit: 1ccd55a500e59c98a910f783e5fcc01913beef54 https://github.com/galaxyproject/galaxy/commit/1ccd55a500e59c98a910f783e5fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/jobs/runners/pulsar.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5535 from jmchilton/pulsar_error_handling_1 [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. Compare: https://github.com/galaxyproject/galaxy/compare/296af58c3d3f...1ccd55a500e5

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[galaxyproject/galaxy] 2e51d0: Close tempfile handles.
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e51d0576a59c3400d1e107c6e85c0cecaba8c28 https://github.com/galaxyproject/galaxy/commit/2e51d0576a59c3400d1e107c6e85… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: e6535d33bfd76d18d7904ad42dabb5835ca9c5b3 https://github.com/galaxyproject/galaxy/commit/e6535d33bfd76d18d7904ad42dab… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Implement Nicola's suggestion for cleaner solution. Commit: 8fa28994fc38c82b873a295df59b937a5ad95a35 https://github.com/galaxyproject/galaxy/commit/8fa28994fc38c82b873a295df59b… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Remove unnecessary try/catch. Commit: 41a31967540e74857c25257ec8cc738900cbad6c https://github.com/galaxyproject/galaxy/commit/41a31967540e74857c25257ec8cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5506 from davebx/close_temp_files Close tempfile handles. Compare: https://github.com/galaxyproject/galaxy/compare/a35d5a535eeb...41a31967540e

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[galaxyproject/galaxy] 99e130: Rev SQLAlchemy from 1.0.15 to 1.2.2.
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 99e1305c53cde3f0244819fe495655ec61f13a9a https://github.com/galaxyproject/galaxy/commit/99e1305c53cde3f0244819fe4956… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Rev SQLAlchemy from 1.0.15 to 1.2.2. It'd be nice to use [selectinload](http://docs.sqlalchemy.org/en/latest/orm/loading_relationship… when optimizing postgres calls. xref https://github.com/galaxyproject/starforge/pull/191 Commit: a35d5a535eebb36d647353faac66c37417a8aeb7 https://github.com/galaxyproject/galaxy/commit/a35d5a535eebb36d647353faac66… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5538 from jmchilton/rev_sqlalchemy Rev SQLAlchemy from 1.0.15 to 1.2.2. Compare: https://github.com/galaxyproject/galaxy/compare/3de8593e1964...a35d5a535eeb

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[galaxyproject/galaxy] 7457ce: optimize nonadmin and nonanon library list permiss...
by GitHub 15 Feb '18

15 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7457ce426f0563464dff2313249381afa9378f28 https://github.com/galaxyproject/galaxy/commit/7457ce426f0563464dff23132493… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- optimize nonadmin and nonanon library list permission queries Before, the code would emit extra queries per each library to find out whether the current user has permissions on it. By pre-fetching all of them in one query and passing around as a dict object we should see a considerable speedup on Galaxies with many libraries. Commit: 296af58c3d3f6fdb19560f1c8ab58290c9742b8b https://github.com/galaxyproject/galaxy/commit/296af58c3d3f6fdb19560f1c8ab5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/managers/libraries.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Merge pull request #5542 from martenson/optimize-nonadmin-nonanon-datalibs [18.01] optimize nonadmin and nonanon library list permission queries Compare: https://github.com/galaxyproject/galaxy/compare/c20b68a5dd92...296af58c3d3f

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[galaxyproject/usegalaxy-playbook] 4c3876: Remove packed/ from datamanager webapp's nginx ali...
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4c38767d42c9ac7b6e882babaa780710d9eb0424 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c38767d42c9ac7b… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Remove packed/ from datamanager webapp's nginx aliases.

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[galaxyproject/galaxy] b87d57: Make galaxy compatible with pysam 0.14
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b87d57aac7c15c0455e0936c0325a1a0b326407e https://github.com/galaxyproject/galaxy/commit/b87d57aac7c15c0455e0936c0325… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Make galaxy compatible with pysam 0.14 Commit: 349b25b74ae4de51ab567a0215054d854af9a934 https://github.com/galaxyproject/galaxy/commit/349b25b74ae4de51ab567a021505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minimize duplication of BAM set_meta code Commit: 3b8a2f9edc93c45e5153896035f321bd23c7ec1a https://github.com/galaxyproject/galaxy/commit/3b8a2f9edc93c45e5153896035f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin pysam to 0.14 Commit: 321cd78ad82b2c686e515567c15062cc2ef92aec https://github.com/galaxyproject/galaxy/commit/321cd78ad82b2c686e515567c150… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5512 from mvdbeek/fix_new_pysam [18.01] Make galaxy compatible with pysam 0.14 Commit: e73731f5528a08735a6b65bf419a6f7986c1c771 https://github.com/galaxyproject/galaxy/commit/e73731f5528a08735a6b65bf419a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Optimize database interaction for user workflow list. Don't LEFT OUTER JOIN workflow against its steps to produce step count - this causes a lot of duplicated workflow data and fetches step data not needed to just produce a step count. Tweak pre-fetching for workflows shared with user also. Commit: b9ddec71a4632942534048069f7d0d474b2c8982 https://github.com/galaxyproject/galaxy/commit/b9ddec71a4632942534048069f7d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- disable loading of webhooks in TS and reports apps Commit: 80a41f32744d2d76b74973663cd6d751daf8e8a5 https://github.com/galaxyproject/galaxy/commit/80a41f32744d2d76b74973663cd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Optimize public grid database interactions. For all four grid types (histories, viz, workflows, and pages), this computes rating average on the server and prefetches any annotations. This eliminates at least two extra queries for response element in the grid. See comment in the history controller for why I am fairly confident this is a good idea for annotations but tags are less obvious - these grids still go back to the postgres server multiple times per rendered item to render tags. I'm confident we should either subqueryload, joinedload, or upgrade to sqlalchemy 2.2 and selectinload (http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalch…) the tags as well - but I'm not sure which without being able to hack on a usegalaxy.org. This also brings in less of the user model (only username instead of all of it) to reduce over-the-wire transmission of unneeded data from postgres to Galaxy. For workflows we were LEFT OUTER JOIN-ing on the steps of the latest workflow - so we were bringing back a lot of extra rows for data that was completely unused. In light of this, it makes perfect sense to me why published workflows were the slowest of these and I suspect they will all be equally performant after this change (modulo the number of rows in the tables and the number of rows rendered). Commit: fd1ac05cdfb1dff01e17edcdfd7304803ece2201 https://github.com/galaxyproject/galaxy/commit/fd1ac05cdfb1dff01e17edcdfd73… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5515 from jmchilton/optimize_workflow_list [18.01] Optimize database interaction for user workflow list. Commit: ed23cc652df321371ef6d66d32e7812406577f30 https://github.com/galaxyproject/galaxy/commit/ed23cc652df321371ef6d66d32e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5514 from jmchilton/optimize_public_grids [18.01] Optimize public grid database interactions. Commit: adaacbc66508d1bb57376c5b43cac21b3d7c28bb https://github.com/galaxyproject/galaxy/commit/adaacbc66508d1bb57376c5b43ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Merge pull request #5521 from martenson/webhooks-galaxy-only [18.01] disable loading of webhooks in TS and reports apps Commit: 5ff6be93ed074485a60e567309247e9dbf02db09 https://github.com/galaxyproject/galaxy/commit/5ff6be93ed074485a60e56730924… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Use profile="18.01" for BamNative converters This is because samtools writes to stderr when sorting/merging large files. Part of https://github.com/galaxyproject/galaxy/issues/5496#issuecomment-365458089. Commit: c20b68a5dd92e29c0e1a985f46fccae89efcac18 https://github.com/galaxyproject/galaxy/commit/c20b68a5dd92e29c0e1a985f46fc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Merge pull request #5532 from mvdbeek/bam_native_converter_fix [18.01] Use profile="18.01" for BamNative converters Commit: 043fe35e9521c20987cd995de90aaf1f01e94e63 https://github.com/galaxyproject/galaxy/commit/043fe35e9521c20987cd995de90a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_18.01' into dev_merge_0 Commit: 3de8593e19641ad1078dbb53a870876ec32c80e1 https://github.com/galaxyproject/galaxy/commit/3de8593e19641ad1078dbb53a870… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5540 from jmchilton/dev_merge_0 Merge release_18.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/0b137669d7d2...3de8593e1964

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[galaxyproject/usegalaxy-playbook] f0af13: Update Test
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f0af13e742903cbb73fac7e82d2904fccb3dd327 https://github.com/galaxyproject/usegalaxy-playbook/commit/f0af13e742903cbb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M common_roles M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] ca6688: Move charts client to core
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca66882fcec96ff29c6dc147146f20c6584670a6 https://github.com/galaxyproject/galaxy/commit/ca66882fcec96ff29c6dc147146f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A client/galaxy/scripts/mvc/visualization/client/components/model.js A client/galaxy/scripts/mvc/visualization/client/components/screenshot.js A client/galaxy/scripts/mvc/visualization/client/views/description.js A client/galaxy/scripts/mvc/visualization/client/views/editor.js A client/galaxy/scripts/mvc/visualization/client/views/groups.js A client/galaxy/scripts/mvc/visualization/client/views/settings.js A client/galaxy/scripts/mvc/visualization/client/views/viewer.js A client/galaxy/scripts/mvc/visualization/client/views/viewport.js A client/galaxy/scripts/mvc/visualization/visualization-client.js A client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Move charts client to core Commit: daf500f80cfa2bdb36b74acadca6a9eb7a61975c https://github.com/galaxyproject/galaxy/commit/daf500f80cfa2bdb36b74acadca6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Add routes to analysis app Commit: 80ee52b2d12f361f58cc2724372ec88fad3d9a76 https://github.com/galaxyproject/galaxy/commit/80ee52b2d12f361f58cc2724372e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Redirect link in history panel to visualization client Commit: bc5eecf6a8efe0f299b740046a5e5ab77ab95b5b https://github.com/galaxyproject/galaxy/commit/bc5eecf6a8efe0f299b740046a5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less Log Message: ----------- Augment thumbnail styles for default icon Commit: c7bf80599e19f2a165a4406b00391e64035ad116 https://github.com/galaxyproject/galaxy/commit/c7bf80599e19f2a165a4406b0039… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Check for visualization logo to be displayed in thumbnail selector Commit: 26f72481aaa20c0a57d491c6086d573b82dbeeec https://github.com/galaxyproject/galaxy/commit/26f72481aaa20c0a57d491c6086d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py R static/scripts/packed M static/style/blue/base.css Log Message: ----------- Augment registry response Commit: feab8314b0bf309804e23de61de4a5e550c55a71 https://github.com/galaxyproject/galaxy/commit/feab8314b0bf309804e23de61de4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes to build app Commit: 0049d5a760ec19383fa97f2ca72afa6352486d3c https://github.com/galaxyproject/galaxy/commit/0049d5a760ec19383fa97f2ca72a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Augment thumbnail viewer Commit: b16c6027dfdff5208adaeae760062cffa2aaad0a https://github.com/galaxyproject/galaxy/commit/b16c6027dfdff5208adaeae76006… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml Log Message: ----------- Augment xmls Commit: 39c0eb37ba73b127e36260279491bc1408943c3c https://github.com/galaxyproject/galaxy/commit/39c0eb37ba73b127e36260279491… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add regular attribute to config parser Commit: b6db962284d06918a1ff1dc61b73b534712f2821 https://github.com/galaxyproject/galaxy/commit/b6db962284d06918a1ff1dc61b73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Revise initial viewer, fix logo display Commit: 1829c4a8bcb0a428593530cf901645f01ef2b056 https://github.com/galaxyproject/galaxy/commit/1829c4a8bcb0a428593530cf9016… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/visualizations.py Log Message: ----------- Move dictionary generator from registry to plugin Commit: 33ae04a04fca19f9c251efb2acac36fb521a93a0 https://github.com/galaxyproject/galaxy/commit/33ae04a04fca19f9c251efb2acac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add static url to response Commit: 80222ba4116476c04a7a4c08c4af76e43374b97a https://github.com/galaxyproject/galaxy/commit/80222ba4116476c04a7a4c08c4af… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-client.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Parse entry point in dictionary Commit: 9b6b757503efd1877e5addc185cdf12c03eacde2 https://github.com/galaxyproject/galaxy/commit/9b6b757503efd1877e5addc185cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/mvc/visualization/client/components/model.js R client/galaxy/scripts/mvc/visualization/client/components/screenshot.js R client/galaxy/scripts/mvc/visualization/client/views/description.js R client/galaxy/scripts/mvc/visualization/client/views/editor.js R client/galaxy/scripts/mvc/visualization/client/views/groups.js R client/galaxy/scripts/mvc/visualization/client/views/settings.js R client/galaxy/scripts/mvc/visualization/client/views/viewer.js R client/galaxy/scripts/mvc/visualization/client/views/viewport.js R client/galaxy/scripts/mvc/visualization/visualization-client.js M client/webpack.config.js M config/plugins/visualizations/charts/config/charts.xml A config/plugins/visualizations/common/templates/chart_entry_point.mako M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add chart type common mako and bundle to visualization framework Commit: 6ec649c04d4200a38066fb8cca951dda5de22a92 https://github.com/galaxyproject/galaxy/commit/6ec649c04d4200a38066fb8cca95… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/chart/views/viewport.js Log Message: ----------- Add shared chart client Commit: 48518d84f7d06903e2f2ad22ce24ebb617de82ae https://github.com/galaxyproject/galaxy/commit/48518d84f7d06903e2f2ad22ce24… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Load dataset for chart visualization plugin Commit: 76fac9181f1a9f85913be6e6daea72da0ced549a https://github.com/galaxyproject/galaxy/commit/76fac9181f1a9f85913be6e6daea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Add name to response dictionary Commit: 9be959396ec4c401e2ee8af83a600a8b7cfac3bf https://github.com/galaxyproject/galaxy/commit/9be959396ec4c401e2ee8af83a60… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M config/plugins/visualizations/common/templates/chart_entry_point.mako A config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M static/style/blue/base.css Log Message: ----------- Move json config to xml Commit: 123e9febb856731df4a0d990349adfbf1288b923 https://github.com/galaxyproject/galaxy/commit/123e9febb856731df4a0d990349a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml Log Message: ----------- Fix support for data groups form in client Commit: 1c30571677865173452478dfb429792e580051f3 https://github.com/galaxyproject/galaxy/commit/1c30571677865173452478dfb429… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add conditional parameters to visualizations xml config Commit: fd9ac30d890a179e7184ceb62d9d8d0c333f8ad5 https://github.com/galaxyproject/galaxy/commit/fd9ac30d890a179e7184ceb62d9d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add optional specifiers Commit: 664bf8bba5a4954926fba840aea43a06019ef163 https://github.com/galaxyproject/galaxy/commit/664bf8bba5a4954926fba840aea4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js Log Message: ----------- More client side cleanup, revise import styles Commit: 1eccb2a6434fc6e098626066b739f2fa7c5f56a4 https://github.com/galaxyproject/galaxy/commit/1eccb2a6434fc6e098626066b739… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js Log Message: ----------- Use plugin object instead of chart definition Use plugin instead of definition Commit: 911b667f383b801ac22f8fb87bae81bd52051b19 https://github.com/galaxyproject/galaxy/commit/911b667f383b801ac22f8fb87bae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Fix conditional parameter description in xml Commit: 4bcc9e6c2e79110bfde3c472debe427ca3097f21 https://github.com/galaxyproject/galaxy/commit/4bcc9e6c2e79110bfde3c472debe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Remove unused split function Commit: d1798f376d2633d6d25955b238b38a7de1fb4d5e https://github.com/galaxyproject/galaxy/commit/d1798f376d2633d6d25955b238b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R 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config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/nvd3/package.json A config/plugins/visualizations/nvd3/static/bundle.js A config/plugins/visualizations/nvd3/static/bundle.js.map A config/plugins/visualizations/nvd3/static/entry.js A config/plugins/visualizations/nvd3/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3/static/utilities/jobs.js A config/plugins/visualizations/nvd3/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3/static/utilities/utils.js A config/plugins/visualizations/nvd3/webpack.config.js Log Message: ----------- Add bundle for nvd3 Commit: 964c82329c3a8bdc2c47ab5f2412e8c23be12ef6 https://github.com/galaxyproject/galaxy/commit/964c82329c3a8bdc2c47ab5f2412… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3/package.json R config/plugins/visualizations/nvd3/static/bundle.js R config/plugins/visualizations/nvd3/static/bundle.js.map R config/plugins/visualizations/nvd3/static/entry.js R config/plugins/visualizations/nvd3/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3/static/utilities/jobs.js R config/plugins/visualizations/nvd3/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3/static/utilities/utils.js R config/plugins/visualizations/nvd3/webpack.config.js Log Message: ----------- Fix entry name Commit: 778f92155ca6e19a3755fac7423dec9ac5a033cb https://github.com/galaxyproject/galaxy/commit/778f92155ca6e19a3755fac7423d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3bar/package.json A config/plugins/visualizations/nvd3bar/static/bundle.js A config/plugins/visualizations/nvd3bar/static/bundle.js.map A config/plugins/visualizations/nvd3bar/static/logo.png A config/plugins/visualizations/nvd3bar/static/nvd3.js A config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3bar/static/utilities/jobs.js A config/plugins/visualizations/nvd3bar/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3bar/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3bar/static/utilities/utils.js A config/plugins/visualizations/nvd3bar/webpack.config.js Log Message: ----------- Add webpack config and bundle files Commit: 4b158e3f7a39f8019fc1af81e88e32b2e2adeb7d https://github.com/galaxyproject/galaxy/commit/4b158e3f7a39f8019fc1af81e88e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add macro support to visualization xmls Commit: 8c3babfd1823137879797ce8af932c45741b8b18 https://github.com/galaxyproject/galaxy/commit/8c3babfd1823137879797ce8af93… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml A config/plugins/visualizations/nvd3bar/config/nvd3shared.xml Log Message: ----------- Add shared parameters Commit: 0451024aa08cbd7d4b96b01c9ef35d72554290fd https://github.com/galaxyproject/galaxy/commit/0451024aa08cbd7d4b96b01c9ef3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M config/plugins/visualizations/nvd3bar/config/nvd3shared.xml M lib/galaxy/util/xml_macros.py Log Message: ----------- Disable base name sanitization of macro imports for now Commit: 2b50fe94af3d12649ed76251cf1ec3ca4cc3a147 https://github.com/galaxyproject/galaxy/commit/2b50fe94af3d12649ed76251cf1e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M config/plugins/visualizations/nvd3bar/config/nvd3shared.xml A config/plugins/visualizations/nvd3scatter/config/nvd3scatter.xml A config/plugins/visualizations/nvd3scatter/static/logo.png Log Message: ----------- Add scatter plot configuration Commit: f56cb32fb722640fa63b943293eb146b819070c4 https://github.com/galaxyproject/galaxy/commit/f56cb32fb722640fa63b943293eb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3_bar/static/utilities/jobs.js A config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3_bar/static/utilities/utils.js A config/plugins/visualizations/nvd3_bar/webpack.config.js A config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3_horizontal_stacked/config.js A config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3_scatter/static/logo.png R config/plugins/visualizations/nvd3bar/config/nvd3bar.xml R config/plugins/visualizations/nvd3bar/config/nvd3shared.xml R config/plugins/visualizations/nvd3bar/package.json R config/plugins/visualizations/nvd3bar/static/bundle.js R config/plugins/visualizations/nvd3bar/static/bundle.js.map R config/plugins/visualizations/nvd3bar/static/logo.png R config/plugins/visualizations/nvd3bar/static/nvd3.js R config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3bar/static/utilities/jobs.js R config/plugins/visualizations/nvd3bar/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3bar/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3bar/static/utilities/utils.js R config/plugins/visualizations/nvd3bar/webpack.config.js R config/plugins/visualizations/nvd3scatter/config/nvd3scatter.xml R config/plugins/visualizations/nvd3scatter/static/logo.png Log Message: ----------- Use underscores to specify nvd3 types Commit: d871196c5e70ee089d357a0c252321bd6e06f920 https://github.com/galaxyproject/galaxy/commit/d871196c5e70ee089d357a0c2523… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3_bar_stacked/static/logo.png R config/plugins/visualizations/nvd3_horizontal_stacked/config.js Log Message: ----------- Add config for stacked bars Commit: 5e8bd49b126b91cdbf2b2c29988e1395bb4a6670 https://github.com/galaxyproject/galaxy/commit/5e8bd49b126b91cdbf2b2c29988e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3_stackedarea_stream/static/logo.png Log Message: ----------- Add remaining configuration files for nvd3 visualizations Commit: 83c27b629a2e6d17a8ce955f3de1586fce6581da https://github.com/galaxyproject/galaxy/commit/83c27b629a2e6d17a8ce955f3de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Fix chart entry point mako Commit: e011371096401673c2774ac6e3201323ab7c0baf https://github.com/galaxyproject/galaxy/commit/e011371096401673c2774ac6e320… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml Log Message: ----------- Fix indention Commit: a0fa19048a49c662afa0a6e068aeeebe322c8a6d https://github.com/galaxyproject/galaxy/commit/a0fa19048a49c662afa0a6e068ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Fix bug with non-static-serving viz urls that was causing a browser crash Commit: 2b0fbe80ebc8814d2d6bba8bae0dcab9922a418d https://github.com/galaxyproject/galaxy/commit/2b0fbe80ebc8814d2d6bba8bae0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Client formatting. Commit: 73486849e03f3bbe6daaebd7953b39a6b3a65d67 https://github.com/galaxyproject/galaxy/commit/73486849e03f3bbe6daaebd7953b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix scratchbook link click function, remove some unused vars. Commit: 1e9c8cf57a7f9a3978416bc0ba706f0cd7a858fd https://github.com/galaxyproject/galaxy/commit/1e9c8cf57a7f9a3978416bc0ba70… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js Log Message: ----------- Extend instead of overwrite window.bundleEntries Commit: 2b0074be26c725a708aa4150ac7e723b86889ee9 https://github.com/galaxyproject/galaxy/commit/2b0074be26c725a708aa4150ac7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Remove unused imports, vars, some minor refactoring for clarity. Commit: 039bdfb2d460fc3dc0b01d1cf2d601e9270e8378 https://github.com/galaxyproject/galaxy/commit/039bdfb2d460fc3dc0b01d1cf2d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Minor var cleanup in ui-thumbnails Commit: 172f9317d2c25246a04f0297347d1ce08a9420b6 https://github.com/galaxyproject/galaxy/commit/172f9317d2c25246a04f0297347d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/editor.js Log Message: ----------- Minor refactoring trying to fix chart viz launch Commit: 660df78c7cb2d4e8858686191d54788e43bfa7aa https://github.com/galaxyproject/galaxy/commit/660df78c7cb2d4e8858686191d54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- Grunt is not used here Commit: 04c71f33e3f802233da60ae1eab333c82bb5ba42 https://github.com/galaxyproject/galaxy/commit/04c71f33e3f802233da60ae1eab3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json R config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3_bar/webpack.config.js Log Message: ----------- Incremental step swapping to parcel for viz building -- simpler, faster, zero config (ish). Commit: 65590f1350245753f04fcc132775fef54d86b172 https://github.com/galaxyproject/galaxy/commit/65590f1350245753f04fcc132775… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- nvd3 formatting Commit: 939bbff6d81fcde264323819f548efcadac9b463 https://github.com/galaxyproject/galaxy/commit/939bbff6d81fcde264323819f548… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/dist/nvd3.js A config/plugins/visualizations/nvd3_bar/package-lock.json M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add a few package dependencies, convert to es6 imports, and build to dist. Commit: ae0da08047a06231578de3ec98e8e7662c7c03a5 https://github.com/galaxyproject/galaxy/commit/ae0da08047a06231578de3ec98e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3_bar/package-lock.json Log Message: ----------- Remove package-lock Commit: d9c445796f43dc1a2d1d811c21d50915eac40f78 https://github.com/galaxyproject/galaxy/commit/d9c445796f43dc1a2d1d811c21d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- transpile es6 for nvd3 Commit: 5848c991caf5dd271d16cb346d286b6c1e1f0a58 https://github.com/galaxyproject/galaxy/commit/5848c991caf5dd271d16cb346d28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/.babelrc Log Message: ----------- Add .babelrc with env preset. Commit: 3329bf8907410b7eb8fec45a40fa5ce3072d0c38 https://github.com/galaxyproject/galaxy/commit/3329bf8907410b7eb8fec45a40fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add d3 for correct imports in nvd3 chart Commit: f65d42d4fd298ed34110425f88523d868b94b834 https://github.com/galaxyproject/galaxy/commit/f65d42d4fd298ed34110425f8852… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Initial parcel building for scatterplot Commit: b6b31e0853bc486065fd3d7b917aa80fdbde18ff https://github.com/galaxyproject/galaxy/commit/b6b31e0853bc486065fd3d7b917a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Remove unused webpack config Commit: 16405ce19aa14c5a2a744fc3d0d15cd03bc5c385 https://github.com/galaxyproject/galaxy/commit/16405ce19aa14c5a2a744fc3d0d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Directly export charts client as view Commit: 8518432e265ed90b377409d621b5b64170fd86d3 https://github.com/galaxyproject/galaxy/commit/8518432e265ed90b377409d621b5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- Move packed nvd3 build to static directory Commit: 49618cf061f1873d2e5c83f4771ef1b7951aa33b https://github.com/galaxyproject/galaxy/commit/49618cf061f1873d2e5c83f4771e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Remove require libs from common mako endpoint Commit: a0ad05494cbe109a58932b1a51cfc814719093e1 https://github.com/galaxyproject/galaxy/commit/a0ad05494cbe109a58932b1a51cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js M config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js M config/plugins/visualizations/nvd3_bar/static/utilities/utils.js M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Load nvd3 plugins into bundle Commit: be3d22215c6b91d8d1111a525663c32eb7b1bdd1 https://github.com/galaxyproject/galaxy/commit/be3d22215c6b91d8d1111a525663… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml Log Message: ----------- Fix Commit: ebb8f05c6d99ecb6d151c5b83b470f7b7bea5f8c https://github.com/galaxyproject/galaxy/commit/ebb8f05c6d99ecb6d151c5b83b47… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/src/utilities/datasets.js A config/plugins/visualizations/nvd3_bar/src/utilities/helpers.js A config/plugins/visualizations/nvd3_bar/src/utilities/jobs.js A config/plugins/visualizations/nvd3_bar/src/utilities/utils.js R config/plugins/visualizations/nvd3_bar/static/utilities/jobs.js R config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3_bar/static/utilities/utils.js Log Message: ----------- Fixes for nvd3 viewer, import styles, link entry function Commit: f9107934b8373aac40673bcfe91233f1c48677c5 https://github.com/galaxyproject/galaxy/commit/f9107934b8373aac40673bcfe912… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/utils.js R config/plugins/visualizations/nvd3_bar/src/utilities/datasets.js R config/plugins/visualizations/nvd3_bar/src/utilities/helpers.js R config/plugins/visualizations/nvd3_bar/src/utilities/jobs.js R config/plugins/visualizations/nvd3_bar/src/utilities/utils.js Log Message: ----------- Prepare shared chart utility features Commit: 21e065052e714acc4708c94cc0b8923ab55160ca https://github.com/galaxyproject/galaxy/commit/21e065052e714acc4708c94cc0b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R client/galaxy/scripts/mvc/visualization/chart/utilities/utils.js Log Message: ----------- Remove unused utils helper Commit: 2b3c517161f701bfcf2a549ee3dbf03c5a7e4598 https://github.com/galaxyproject/galaxy/commit/2b3c517161f701bfcf2a549ee3db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- D3 / NVD3 compatability changes, use from node_modules. Still need to add zoom customization. Commit: dea41ef60c245f8bc4dbe25a8f85c9d03c95c586 https://github.com/galaxyproject/galaxy/commit/dea41ef60c245f8bc4dbe25a8f85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Drop d3 from inline chart_entry_point libs; we should look at the rest of these, too, probably. Commit: 2683cc527550dfc27fae0885efc4ac9615302772 https://github.com/galaxyproject/galaxy/commit/2683cc527550dfc27fae0885efc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/static/nvd3.css Log Message: ----------- Add bundled nvd3 css; this got dropped during rebases. Commit: df90cc78addf1b2adc711347c54c399373f241c2 https://github.com/galaxyproject/galaxy/commit/df90cc78addf1b2adc711347c54c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js Log Message: ----------- Fix tooltips to use new nvd3 chart generator. Commit: 62e4e0da8664490b20e3b090bd211d1cc3fe40d4 https://github.com/galaxyproject/galaxy/commit/62e4e0da8664490b20e3b090bd21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Client cleanup, no functional change. Commit: fa3d12a33cb6185cd9988a9e9d74d16993510995 https://github.com/galaxyproject/galaxy/commit/fa3d12a33cb6185cd9988a9e9d74… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Build final nvd3.js with included deps Commit: 719383fbea2d7cadf347967fb40e344a6be46e94 https://github.com/galaxyproject/galaxy/commit/719383fbea2d7cadf347967fb40e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Fix y-axis label for nvd3, fix duration Commit: 525bc13d8dadbf5164f60967bdd2f01c2fc13ef6 https://github.com/galaxyproject/galaxy/commit/525bc13d8dadbf5164f60967bdd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml Log Message: ----------- Add entry function for scatter plot Commit: 171dcc1e24f84c2f7818105ec29788d767ce1aac https://github.com/galaxyproject/galaxy/commit/171dcc1e24f84c2f7818105ec297… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add zooming feature Commit: 21fb51782cc38e8ead0833417cf4bf0f6d091b73 https://github.com/galaxyproject/galaxy/commit/21fb51782cc38e8ead0833417cf4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Remove duration, interference with zooming Commit: 159a8c72bc69c8c19d4dd6e039d801a6740d4921 https://github.com/galaxyproject/galaxy/commit/159a8c72bc69c8c19d4dd6e039d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js Log Message: ----------- Add another fallback value for tooltips Commit: de7cac90537b4bd9fa9500cb55b314408a5a1f06 https://github.com/galaxyproject/galaxy/commit/de7cac90537b4bd9fa9500cb55b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml Log Message: ----------- Remove zoomable flag for barcharts Commit: 00a105ef6a28add188b9356572e89392b3517099 https://github.com/galaxyproject/galaxy/commit/00a105ef6a28add188b9356572e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js R client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Revise shared utilities Commit: 91c4641c886c1f1015218abb34f541aff7a82bdd https://github.com/galaxyproject/galaxy/commit/91c4641c886c1f1015218abb34f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png R config/plugins/visualizations/nvd3_bar/.babelrc R config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml R config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml R config/plugins/visualizations/nvd3_bar/package.json R config/plugins/visualizations/nvd3_bar/src/nvd3.js R config/plugins/visualizations/nvd3_bar/static/logo.png R config/plugins/visualizations/nvd3_bar/static/nvd3.css R config/plugins/visualizations/nvd3_bar/static/nvd3.js R config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml R config/plugins/visualizations/nvd3_bar_stacked/static/logo.png M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Allow plugins to be placed into first level sub directories Commit: 055e0fa167d77c94c03166bea65fe432867af226 https://github.com/galaxyproject/galaxy/commit/055e0fa167d77c94c03166bea65f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png R config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml R config/plugins/visualizations/nvd3_histogram/static/logo.png R config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml R config/plugins/visualizations/nvd3_histogram_discrete/static/logo.png R config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml R config/plugins/visualizations/nvd3_horizontal/static/logo.png R config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml R config/plugins/visualizations/nvd3_horizontal_stacked/static/logo.png R config/plugins/visualizations/nvd3_line/config/nvd3_line.xml R config/plugins/visualizations/nvd3_line/static/logo.png R config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml R config/plugins/visualizations/nvd3_line_focus/static/logo.png R config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml R config/plugins/visualizations/nvd3_pie/static/logo.png R config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml R config/plugins/visualizations/nvd3_scatter/static/logo.png R config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml R config/plugins/visualizations/nvd3_stackedarea/static/logo.png R config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml R config/plugins/visualizations/nvd3_stackedarea_full/static/logo.png R config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml R config/plugins/visualizations/nvd3_stackedarea_stream/static/logo.png Log Message: ----------- Move nvd3 plugins into subdirectory Commit: 83467ca9efa5266c9968be5a598fb5fdd5c3c82e https://github.com/galaxyproject/galaxy/commit/83467ca9efa5266c9968be5a598f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix remaining nvd3 plugins Commit: 1014b5d5d31232212946e781fd92745133fe5865 https://github.com/galaxyproject/galaxy/commit/1014b5d5d31232212946e781fd92… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js Log Message: ----------- Add ngl viewer Commit: b33ec3b3ca9cf346ae07673d60178d5fff2e7c79 https://github.com/galaxyproject/galaxy/commit/b33ec3b3ca9cf346ae07673d6017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js Log Message: ----------- Add pv protein viewer Commit: 43d45dfee465e55657cbd3c4058541146b03aadf https://github.com/galaxyproject/galaxy/commit/43d45dfee465e55657cbd3c40585… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js Log Message: ----------- Add venn diagram Commit: 97cab84b0846342f7d723203172f9c697af6066b https://github.com/galaxyproject/galaxy/commit/97cab84b0846342f7d723203172f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js Log Message: ----------- Add biojs msa Commit: 820d0b4135e528ce3127daae6fc5d45b0e55dee3 https://github.com/galaxyproject/galaxy/commit/820d0b4135e528ce3127daae6fc5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js Log Message: ----------- Add drawrna, with existing code until npm dependency works Commit: c4ca8aba1ff56a540662eba7cefb3c25c9718180 https://github.com/galaxyproject/galaxy/commit/c4ca8aba1ff56a540662eba7cefb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js Log Message: ----------- Add phylocanvas, using npm module Commit: d834a3c96865a6b74e1a4c2ce9b692e22d0b65aa https://github.com/galaxyproject/galaxy/commit/d834a3c96865a6b74e1a4c2ce9b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js Log Message: ----------- Add cytoscape Commit: bedbd06a3983b27e9dc44ab07c5df3cfbd5cfc94 https://github.com/galaxyproject/galaxy/commit/bedbd06a3983b27e9dc44ab07c5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js Log Message: ----------- Add jqplot bar Commit: a19088a68c8d361d39f9b1f9df46de96139ca477 https://github.com/galaxyproject/galaxy/commit/a19088a68c8d361d39f9b1f9df46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml Log Message: ----------- Remove color picker for jqplot Commit: 4f9e0d92394d4b7b5a3e39505a0e52ffc6a7464e https://github.com/galaxyproject/galaxy/commit/4f9e0d92394d4b7b5a3e39505a0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml Log Message: ----------- Add legend option to tabular plugins Commit: a770cbcea305aa98d5d4d0583fa5d4de537a580b https://github.com/galaxyproject/galaxy/commit/a770cbcea305aa98d5d4d0583fa5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png Log Message: ----------- Add remaining jqplot plugins Commit: 35ac99bfe5bccb103965f4f2d73a670a2b04dd80 https://github.com/galaxyproject/galaxy/commit/35ac99bfe5bccb103965f4f2d73a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js Log Message: ----------- Add heatmap plugin Commit: 7f896c84d76ef9879aa70227e15dea6c9390f573 https://github.com/galaxyproject/galaxy/commit/7f896c84d76ef9879aa70227e15d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/package.json Log Message: ----------- Use version 3 of d3 for heatmap Commit: e829579be3e34e6f0ff1c15327959e818f34cad8 https://github.com/galaxyproject/galaxy/commit/e829579be3e34e6f0ff1c1532795… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/example/config/config.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js Log Message: ----------- Add example plugin Commit: adea33ad935e641ac8acca1646c1e035fd0b9ed8 https://github.com/galaxyproject/galaxy/commit/adea33ad935e641ac8acca1646c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/example/config/config.js M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/example/package.json M config/plugins/visualizations/example/src/script.js M config/plugins/visualizations/example/static/script.js Log Message: ----------- Fix example Commit: a64b0835a23019995617f4c8679e4d293777b24c https://github.com/galaxyproject/galaxy/commit/a64b0835a23019995617f4c8679e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Fix vis saving Commit: 75b9d5f00487c124327ab73c1e7051e8f4a2d1cf https://github.com/galaxyproject/galaxy/commit/75b9d5f00487c124327ab73c1e70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Load visualization with default values into the viewer before displaying editor Commit: 3df3f6fe02916f310a901e5dda7b16d64c65ee72 https://github.com/galaxyproject/galaxy/commit/3df3f6fe02916f310a901e5dda7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/style/less/ui.less Log Message: ----------- Load visualization on single click, highlight on hover, add series module Commit: 0f3aacdd919dd2a3d12702d522ed62e652e5ffe3 https://github.com/galaxyproject/galaxy/commit/0f3aacdd919dd2a3d12702d522ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix highlighting for suggested thumbnails Commit: 67e911b4be3b5d6b1fee686bab3928fd71332ea4 https://github.com/galaxyproject/galaxy/commit/67e911b4be3b5d6b1fee686bab39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less Log Message: ----------- Remove highlighting Commit: ff84aa42706621fee4a6658745bb0fa1a19c19e1 https://github.com/galaxyproject/galaxy/commit/ff84aa42706621fee4a6658745bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/cytoscape/src/script.js M config/plugins/visualizations/drawrna/src/script.js M static/style/blue/base.css Log Message: ----------- Use default load function for chart plugins Commit: 77340dded76f75148450c1bdcf47f356a770d330 https://github.com/galaxyproject/galaxy/commit/77340dded76f75148450c1bdcf47… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/cytoscape/static/script.js M config/plugins/visualizations/drawrna/static/script.js M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/ngl/src/ngl.js M config/plugins/visualizations/ngl/static/ngl.js M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/phylocanvas/src/script.js M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/pv/src/pv.js M config/plugins/visualizations/pv/static/pv.js M config/plugins/visualizations/venn/config/venn.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js Log Message: ----------- Use default load handler Commit: 1afea3eec0c94d0d4bac660ac5674f7d6855b102 https://github.com/galaxyproject/galaxy/commit/1afea3eec0c94d0d4bac660ac567… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/drawrna/config/drawrna.xml Log Message: ----------- Fix drawrnajs caller Commit: a6529c51d3ca0b0554e1bc4cebf7fdd8383288c7 https://github.com/galaxyproject/galaxy/commit/a6529c51d3ca0b0554e1bc4cebf7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Show viewer before initiating load process Commit: 3a0c8b5634f1af656ad5c87a1181d030cae33a8c https://github.com/galaxyproject/galaxy/commit/3a0c8b5634f1af656ad5c87a1181… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Check len of tree elements Commit: 82a1f6e49e016372aa1a5a615f305900953bdd88 https://github.com/galaxyproject/galaxy/commit/82a1f6e49e016372aa1a5a615f30… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Improve resilience of dataset loader Commit: cea4db4a53ca25d4d92a9bed2b181cee65d838d7 https://github.com/galaxyproject/galaxy/commit/cea4db4a53ca25d4d92a9bed2b18… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Fix visualization name parsing when saving visualizations Commit: 4af913f7dfb55e1ddc028296063d1cab046cf956 https://github.com/galaxyproject/galaxy/commit/4af913f7dfb55e1ddc028296063d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M test/api/test_visualizations.py Log Message: ----------- Fix visualization type Commit: 3c7b621b3b320d98025caa7981c70afe864c472f https://github.com/galaxyproject/galaxy/commit/3c7b621b3b320d98025caa7981c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml Log Message: ----------- Fix entry function specifier for heatmaps Commit: 2507034e936db38024a8b9f70a359d3f28c94e1c https://github.com/galaxyproject/galaxy/commit/2507034e936db38024a8b9f70a35… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused components from config parser Commit: a77cf155e66cecaf2aaa3bcdf87a6c2bae236b63 https://github.com/galaxyproject/galaxy/commit/a77cf155e66cecaf2aaa3bcdf87a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix spacing Commit: e2d339936cb229096ab7e502831a2e90187cdd25 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https://github.com/galaxyproject/galaxy/commit/a109ca9e9bc9b77738acb0438406… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js Log Message: ----------- Fix panel hiding options Commit: 50c8cb382618f4ac587439154c7f2bd8afb9d161 https://github.com/galaxyproject/galaxy/commit/50c8cb382618f4ac587439154c7f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Parse panel hiding options for scratchbook embedding Commit: 3ba5b2816ca2c33874c52dc48dfceaf32530e6b0 https://github.com/galaxyproject/galaxy/commit/3ba5b2816ca2c33874c52dc48dfc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Fix scratchbook parameter parsing Commit: cb5c30c32ae42ff6d122c395d8fe50fac559aa88 https://github.com/galaxyproject/galaxy/commit/cb5c30c32ae42ff6d122c395d8fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml Log Message: ----------- Sort visualizations alphabetically Commit: c09d9c81b46e60a65b08840ac1cd52287c1cea9d https://github.com/galaxyproject/galaxy/commit/c09d9c81b46e60a65b08840ac1cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml Log Message: ----------- Fix horizontal bar diagram settings Commit: c132eb1c325802134cb40bd7b3f02811679b7671 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<aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Add export options and message view Commit: b098ba7952d7db9028b2af503ddd9482ff99425f https://github.com/galaxyproject/galaxy/commit/b098ba7952d7db9028b2af503ddd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix styles and naming Commit: 2257c2ff172f665ebf5dd0e9b2343b0eb1ac9bfe 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----------- Fix description style Commit: 4fa486082c2ee231fe09b584ed62a11d9146bdcd https://github.com/galaxyproject/galaxy/commit/4fa486082c2ee231fe09b584ed62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix margin style Commit: f2335fe46192187316458d785918b920b61cf293 https://github.com/galaxyproject/galaxy/commit/f2335fe46192187316458d785918… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js Log Message: ----------- Instantly refresh visualizations on setting changes Commit: 9ae6cb1c6e91ed6903b5955df859529ad9ea0a8f https://github.com/galaxyproject/galaxy/commit/9ae6cb1c6e91ed6903b5955df859… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Fix config parser Commit: 0ff4f7419e7dfbd77c36fd2c362d9e3e8c5a4e89 https://github.com/galaxyproject/galaxy/commit/0ff4f7419e7dfbd77c36fd2c362d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Add label to scratchbook Commit: bd9167400e243392d29cefc235db3bde9bc8a2d8 https://github.com/galaxyproject/galaxy/commit/bd9167400e243392d29cefc235db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Reduce top padding Commit: 0b30336c213207d58a8e4d24ec871da7289012b6 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config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/venn/config/venn.xml Log Message: ----------- Show list for all visualization types Commit: 39ad58066b6ebabc00657f7b0421f787c93a6570 https://github.com/galaxyproject/galaxy/commit/39ad58066b6ebabc00657f7b0421… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Repack style sheets Commit: 54659b085f78dabfc987d8292e6d4750ecc83dd7 https://github.com/galaxyproject/galaxy/commit/54659b085f78dabfc987d8292e6d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Client format Commit: be7f503448a6ffd5f5a63d27e6c54601dd558271 https://github.com/galaxyproject/galaxy/commit/be7f503448a6ffd5f5a63d27e6c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/example/package.json M config/plugins/visualizations/example/src/script.js M config/plugins/visualizations/example/static/script.js Log Message: ----------- Fix example plugin imports Commit: 6c68e8e980c7155dee8389e25d90b25864aa2bd7 https://github.com/galaxyproject/galaxy/commit/6c68e8e980c7155dee8389e25d90… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Graphviz cleanup Commit: 5d4301ab3c73de38125a43f3a5f3e0c38a0d28cd https://github.com/galaxyproject/galaxy/commit/5d4301ab3c73de38125a43f3a5f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js Log Message: ----------- Fix imports in nvd3.js, include underscore in package bundle Commit: fafcfbb5774033098ca5a6745b86d97d7cc5e177 https://github.com/galaxyproject/galaxy/commit/fafcfbb5774033098ca5a6745b86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js Log Message: ----------- Remove duplicate key for nvd3_line lineChart. Commit: a82f4a1ae10457071ffad01956f27dd74a8b5574 https://github.com/galaxyproject/galaxy/commit/a82f4a1ae10457071ffad01956f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Document jquery entanglement Commit: 320f1fccac8daac11b5411d36c947b707857575b https://github.com/galaxyproject/galaxy/commit/320f1fccac8daac11b5411d36c94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/src/script.js Log Message: ----------- Incremental cleanup in heatmap default viz Commit: 997e31b88100ef38294632bf138c5994fd006316 https://github.com/galaxyproject/galaxy/commit/997e31b88100ef38294632bf138c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/src/script.js Log Message: ----------- More heatmap cleanup, trying to fix heatmap_cluster Commit: 15d8afeddd3d7b1cd19595a1af2e7c3d275cc24c https://github.com/galaxyproject/galaxy/commit/15d8afeddd3d7b1cd19595a1af2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/package.json M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js Log Message: ----------- Swap d3-3 back to d3 with a version pin. Commit: d5c089acc7467d9dd218485acb9f8c02594f9cff https://github.com/galaxyproject/galaxy/commit/d5c089acc7467d9dd218485acb9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Remove unused import, add required backbone import, document $, Galaxy globals Commit: cd1ed9bb56ecaff61b09e48f183f3bf3f93595b9 https://github.com/galaxyproject/galaxy/commit/cd1ed9bb56ecaff61b09e48f183f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Add backbone import to components/model in viz Commit: c18eafce90fd247e914c922561017198f6ab3a0c https://github.com/galaxyproject/galaxy/commit/c18eafce90fd247e914c92256101… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js Log Message: ----------- Fix some conflicting var defs (use let for scope control) in chart utils Commit: 13c40b1cffaf26b05468a00baa36f7e5b35df0a8 https://github.com/galaxyproject/galaxy/commit/13c40b1cffaf26b05468a00baa36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Cleanup in viz/utils/jobs, clarify scope in a few places and remove unused vars Commit: e9b26b4bd00052d8b75578a30f1aee7cc2f6be1a https://github.com/galaxyproject/galaxy/commit/e9b26b4bd00052d8b75578a30f1a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js Log Message: ----------- Document conflicting global d3 in series, minor refactoring. Commit: 5b66429cb44836b1a56fb76c5e644b814ef5fd5c https://github.com/galaxyproject/galaxy/commit/5b66429cb44836b1a56fb76c5e64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Rebuild heatmap, nvd3 after refactoring. 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config/plugins/visualizations/heatmap/heatmap_default/static/script.js A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M test/api/test_visualizations.py Log Message: ----------- Merge pull request #5505 from guerler/revise_charts_ui Integration of charts into the generic visualization framework Compare: https://github.com/galaxyproject/galaxy/compare/39fd5fdc05e8...0b137669d7d2

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[galaxyproject/usegalaxy-playbook] 7e2309: Mutable config changes
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7e2309669b568de8860058c1d90d2422301beb13 https://github.com/galaxyproject/usegalaxy-playbook/commit/7e2309669b568de8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable config changes Commit: b61e885c80ff6903060fba9337b29df67f8f51dd https://github.com/galaxyproject/usegalaxy-playbook/commit/b61e885c80ff6903… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Add a banner to Main about post-update issues Commit: 5f810bc6116f576a219f198d4510df62f6d9380e https://github.com/galaxyproject/usegalaxy-playbook/commit/5f810bc6116f576a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: A env/common/files/galaxy/config/dependency_resolvers_conf.xml A env/main/files/galaxy/config/dependency_resolvers_conf.xml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/galaxy/config/dependency_resolvers_conf.xml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Test/Main: Change dependency resolution from default to prefer conda over Galaxy packages. This fixes issues where galaxy package dependencies existed for tools where other requirements were installed via conda, meaning they would not have a single mulled environment for all dependencies. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/41c84e4b7b85...…

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[galaxyproject/galaxy] 5ff6be: Use profile="18.01" for BamNative converters
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 5ff6be93ed074485a60e567309247e9dbf02db09 https://github.com/galaxyproject/galaxy/commit/5ff6be93ed074485a60e56730924… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Use profile="18.01" for BamNative converters This is because samtools writes to stderr when sorting/merging large files. Part of https://github.com/galaxyproject/galaxy/issues/5496#issuecomment-365458089. Commit: c20b68a5dd92e29c0e1a985f46fccae89efcac18 https://github.com/galaxyproject/galaxy/commit/c20b68a5dd92e29c0e1a985f46fc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- Merge pull request #5532 from mvdbeek/bam_native_converter_fix [18.01] Use profile="18.01" for BamNative converters Compare: https://github.com/galaxyproject/galaxy/compare/adaacbc66508...c20b68a5dd92

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[galaxyproject/galaxy] b9ddec: disable loading of webhooks in TS and reports apps
by GitHub 14 Feb '18

14 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b9ddec71a4632942534048069f7d0d474b2c8982 https://github.com/galaxyproject/galaxy/commit/b9ddec71a4632942534048069f7d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- disable loading of webhooks in TS and reports apps Commit: adaacbc66508d1bb57376c5b43cac21b3d7c28bb https://github.com/galaxyproject/galaxy/commit/adaacbc66508d1bb57376c5b43ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Merge pull request #5521 from martenson/webhooks-galaxy-only [18.01] disable loading of webhooks in TS and reports apps Compare: https://github.com/galaxyproject/galaxy/compare/ed23cc652df3...adaacbc66508

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[galaxyproject/galaxy] 80a41f: Optimize public grid database interactions.
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 80a41f32744d2d76b74973663cd6d751daf8e8a5 https://github.com/galaxyproject/galaxy/commit/80a41f32744d2d76b74973663cd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Optimize public grid database interactions. For all four grid types (histories, viz, workflows, and pages), this computes rating average on the server and prefetches any annotations. This eliminates at least two extra queries for response element in the grid. See comment in the history controller for why I am fairly confident this is a good idea for annotations but tags are less obvious - these grids still go back to the postgres server multiple times per rendered item to render tags. I'm confident we should either subqueryload, joinedload, or upgrade to sqlalchemy 2.2 and selectinload (http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalch…) the tags as well - but I'm not sure which without being able to hack on a usegalaxy.org. This also brings in less of the user model (only username instead of all of it) to reduce over-the-wire transmission of unneeded data from postgres to Galaxy. For workflows we were LEFT OUTER JOIN-ing on the steps of the latest workflow - so we were bringing back a lot of extra rows for data that was completely unused. In light of this, it makes perfect sense to me why published workflows were the slowest of these and I suspect they will all be equally performant after this change (modulo the number of rows in the tables and the number of rows rendered). Commit: ed23cc652df321371ef6d66d32e7812406577f30 https://github.com/galaxyproject/galaxy/commit/ed23cc652df321371ef6d66d32e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5514 from jmchilton/optimize_public_grids [18.01] Optimize public grid database interactions. Compare: https://github.com/galaxyproject/galaxy/compare/fd1ac05cdfb1...ed23cc652df3

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[galaxyproject/galaxy] e73731: Optimize database interaction for user workflow li...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: e73731f5528a08735a6b65bf419a6f7986c1c771 https://github.com/galaxyproject/galaxy/commit/e73731f5528a08735a6b65bf419a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Optimize database interaction for user workflow list. Don't LEFT OUTER JOIN workflow against its steps to produce step count - this causes a lot of duplicated workflow data and fetches step data not needed to just produce a step count. Tweak pre-fetching for workflows shared with user also. Commit: fd1ac05cdfb1dff01e17edcdfd7304803ece2201 https://github.com/galaxyproject/galaxy/commit/fd1ac05cdfb1dff01e17edcdfd73… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #5515 from jmchilton/optimize_workflow_list [18.01] Optimize database interaction for user workflow list. Compare: https://github.com/galaxyproject/galaxy/compare/321cd78ad82b...fd1ac05cdfb1

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[galaxyproject/usegalaxy-playbook] d7d51f: Use the sha1 hash filter for supervisor passwords ...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7d51f525b4d4eccf23572c180175b150767729c https://github.com/galaxyproject/usegalaxy-playbook/commit/d7d51f525b4d4ecc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M common_roles M env/common/group_vars/toolshedservers/common_vars.yml M env/common/group_vars/toolshedservers/common_vault.yml M env/main/group_vars/supervisorservers/vars.yml M env/main/group_vars/supervisorservers/vault.yml M env/test/group_vars/supervisorservers/vars.yml M env/test/group_vars/supervisorservers/vault.yml Log Message: ----------- Use the sha1 hash filter for supervisor passwords rather than requiring the admin to hash it themselves Commit: 41c84e4b7b851700448c785e479a319ac565c5ad https://github.com/galaxyproject/usegalaxy-playbook/commit/41c84e4b7b851700… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M env/common/stack.yml M env/common/update_shed.yml A env/testtoolshed/stack_extras.yml A env/testtoolshed/templates/toolshed/shedctl.j2 A env/testtoolshed/templates/toolshed/supervisorctl.j2 A env/testtoolshed/templates/toolshed/supervisord.conf.j2 M roles/usegalaxy_admin/tasks/main.yml Log Message: ----------- Shed stack missing pieces Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/526019280e50...…

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[galaxyproject/usegalaxy-playbook] 07fc7a: Update roles
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 07fc7a99e5b717cc9d0fc6b22b253e746e5acc73 https://github.com/galaxyproject/usegalaxy-playbook/commit/07fc7a99e5b717cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M roles/galaxyproject.galaxy/meta/.galaxy_install_info M roles/galaxyproject.galaxy/tasks/dependencies.yml M roles/galaxyproject.galaxy_toolshed/meta/.galaxy_install_info M roles/galaxyproject.galaxy_toolshed/tasks/database.yml Log Message: ----------- Update roles Commit: 526019280e502f8b430a6b0002eabe5c3ff0a507 https://github.com/galaxyproject/usegalaxy-playbook/commit/526019280e502f8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: A env/common/_inc_client_build.yml M env/common/update_shed.yml A env/testtoolshed/_inc_client_build.yml Log Message: ----------- TTS client build support Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/10df88a24d90...…

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[galaxyproject/ansible-galaxy]
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/tags/0.7.5 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 8e8a95: Include PyPI in conditional dependency sources.
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 8e8a950d11fe42bcc1d98ee3cbe06b4688359aae https://github.com/galaxyproject/ansible-galaxy/commit/8e8a950d11fe42bcc1d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Include PyPI in conditional dependency sources.

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[galaxyproject/usegalaxy-playbook] 10df88: Fix automatic (Python) dependency installation on ...
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 10df88a24d903a2f0a1bbadd6d95992f67358f9b https://github.com/galaxyproject/usegalaxy-playbook/commit/10df88a24d903a2f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M env/common/update_shed.yml Log Message: ----------- Fix automatic (Python) dependency installation on TS updates

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[galaxyproject/galaxy] b87d57: Make galaxy compatible with pysam 0.14
by GitHub 13 Feb '18

13 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b87d57aac7c15c0455e0936c0325a1a0b326407e https://github.com/galaxyproject/galaxy/commit/b87d57aac7c15c0455e0936c0325… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Make galaxy compatible with pysam 0.14 Commit: 349b25b74ae4de51ab567a0215054d854af9a934 https://github.com/galaxyproject/galaxy/commit/349b25b74ae4de51ab567a021505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minimize duplication of BAM set_meta code Commit: 3b8a2f9edc93c45e5153896035f321bd23c7ec1a https://github.com/galaxyproject/galaxy/commit/3b8a2f9edc93c45e5153896035f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Pin pysam to 0.14 Commit: 321cd78ad82b2c686e515567c15062cc2ef92aec https://github.com/galaxyproject/galaxy/commit/321cd78ad82b2c686e515567c150… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5512 from mvdbeek/fix_new_pysam [18.01] Make galaxy compatible with pysam 0.14 Compare: https://github.com/galaxyproject/galaxy/compare/aefe0e14498d...321cd78ad82b

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