- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 099c15: Re-organize edge case upload options for my own cl...
by GitHub 14 Dec '17

14 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 099c1562febbcedee63a431b4314654df5e23301 https://github.com/galaxyproject/galaxy/commit/099c1562febbcedee63a431b4314… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Re-organize edge case upload options for my own clarity. I think setting each of these variables once and simplifing the context they are used in (in the case of purge_upload) makes it more clear what each variable is and how it is set. I also think one, more detailed comment for each variable helps. Note: This will break run-as-user uploads started prior to the upgrade to 18.XX and executed after the upgrade. It is a small switch to restore the old behavior but I'm not sure it is worth the complexity it adds to the file. ``` run_as_real_user = dataset.get('run_as_real_user', False) or dataset_get.('in_place', True) ``` Commit: fce9f13eba7f882025885f10c5f613772a93652e https://github.com/galaxyproject/galaxy/commit/fce9f13eba7f882025885f10c5f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-14 (Thu, 14 Dec 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5206 from jmchilton/upload_option_clarify Re-organize edge case upload options for my own understanding. Compare: https://github.com/galaxyproject/galaxy/compare/9adfa316913d...fce9f13eba7f

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[galaxyproject/galaxy] e5be2c: Fix Python3 compatibility for lib/galaxy/web/
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5be2c363a0df6d847026d584a9e79e935cb268b https://github.com/galaxyproject/galaxy/commit/e5be2c363a0df6d847026d584a9e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py Log Message: ----------- Fix Python3 compatibility for lib/galaxy/web/ Commit: 9adfa316913d348e922deb5c96e33046229034d6 https://github.com/galaxyproject/galaxy/commit/9adfa316913d348e922deb5c96e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py Log Message: ----------- Merge pull request #5200 from nsoranzo/python3 Fix Python3 compatibility for lib/galaxy/web/ Compare: https://github.com/galaxyproject/galaxy/compare/c4680394b8ac...9adfa316913d

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[galaxyproject/galaxy] 972b1c: Remove the deprecated OpenID backend of yahoo
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 972b1cbe236ce3a02d11d7864c59801bd9271ba7 https://github.com/galaxyproject/galaxy/commit/972b1cbe236ce3a02d11d7864c59… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/openid_conf.xml.sample Log Message: ----------- Remove the deprecated OpenID backend of yahoo Commit: 5d09c5e85fb3da7ca383144bf21625d51fd0cc20 https://github.com/galaxyproject/galaxy/commit/5d09c5e85fb3da7ca383144bf216… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: R openid/yahoo.xml Log Message: ----------- Deleted Yahoo openid endpoint url. Commit: c4680394b8acd71a012443f041ace33ab52723c0 https://github.com/galaxyproject/galaxy/commit/c4680394b8acd71a012443f041ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M config/openid_conf.xml.sample R openid/yahoo.xml Log Message: ----------- Merge pull request #5208 from VJalili/patch-5 Removed Yahoo OpenID support Compare: https://github.com/galaxyproject/galaxy/compare/84c069e65902...c4680394b8ac

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[galaxyproject/galaxy] 41dbb8: Remove SampleDataset and RequestType references fr...
by GitHub 13 Dec '17

13 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 41dbb88e2b1d85d9001d9ded279e1849db8328c5 https://github.com/galaxyproject/galaxy/commit/41dbb88e2b1d85d9001d9ded279e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M templates/display_common.mako Log Message: ----------- Remove SampleDataset and RequestType references from display_common; this prevents any use of this mako currently. Commit: 29c61624d67886d7d252532a24a6ddc8073f7e9f https://github.com/galaxyproject/galaxy/commit/29c61624d67886d7d252532a24a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- More request type cruft; seems to be unused and it'd blow up if tried to use Commit: 84c069e65902dbe32e53c490a0879988029a981b https://github.com/galaxyproject/galaxy/commit/84c069e65902dbe32e53c490a087… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-12-13 (Wed, 13 Dec 2017) Changed paths: M lib/galaxy/security/__init__.py M templates/display_common.mako Log Message: ----------- Merge pull request #5204 from dannon/sampletracking-removal-followup Sample tracking removal cleanup Compare: https://github.com/galaxyproject/galaxy/compare/82f9f8eb9896...84c069e65902

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[galaxyproject/galaxy] b3dc79: Python3: use collections.Mapping instead of remove...
by GitHub 12 Dec '17

12 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3dc7923dbe1b04060d9c173287d3626ce231802 https://github.com/galaxyproject/galaxy/commit/b3dc7923dbe1b04060d9c173287d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Python3: use collections.Mapping instead of removed DictMixin Commit: 82f9f8eb9896982f2f14e176a44ae6135116df30 https://github.com/galaxyproject/galaxy/commit/82f9f8eb9896982f2f14e176a44a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #5199 from nsoranzo/python3 Python3: use collections.Mapping instead of removed DictMixin Compare: https://github.com/galaxyproject/galaxy/compare/d84fd9514a54...82f9f8eb9896

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[galaxyproject/galaxy] 78a262: Fixes genome decode handling. dbkey was either un...
by GitHub 12 Dec '17

12 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78a2626d13a817c0371db665ecdbeef7a616cb32 https://github.com/galaxyproject/galaxy/commit/78a2626d13a817c0371db665ecdb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/visualization/genomes.py Log Message: ----------- Fixes genome decode handling. dbkey was either unicode or str here variously, and the previous change broke the case where it was unicode. Commit: f6fbe634465bb2305ad968ec3413e7df64fc5224 https://github.com/galaxyproject/galaxy/commit/f6fbe634465bb2305ad968ec3413… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/visualization/genomes.py Log Message: ----------- use six.string_types instead of basestring for isinstance Commit: d84fd9514a545e418cfc3335ae7669582217f40e https://github.com/galaxyproject/galaxy/commit/d84fd9514a545e418cfc3335ae76… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/visualization/genomes.py Log Message: ----------- Merge pull request #5198 from dannon/fix_genome_handling Fixes genome decode handling. Compare: https://github.com/galaxyproject/galaxy/compare/aa0334d72f4b...d84fd9514a54

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[galaxyproject/galaxy] b491a0: Fix import linting problem.
by GitHub 12 Dec '17

12 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b491a04a01036ba27913cfd108310b130ba64c53 https://github.com/galaxyproject/galaxy/commit/b491a04a01036ba27913cfd10831… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Fix import linting problem. Commit: aa0334d72f4b8fb95c1fc3f9e320c94117aae8df https://github.com/galaxyproject/galaxy/commit/aa0334d72f4b8fb95c1fc3f9e320… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-12 (Tue, 12 Dec 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Merge pull request #5197 from jmchilton/import_fix Fix import linting problem. Compare: https://github.com/galaxyproject/galaxy/compare/9f0676d7d498...aa0334d72f4b

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[galaxyproject/galaxy] 051627: Added CloudBridge to the requirements list.
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0516279b7c5a5b6c11118017517ec06e4e3745d6 https://github.com/galaxyproject/galaxy/commit/0516279b7c5a5b6c11118017517e… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Added CloudBridge to the requirements list. Commit: aaad00162f3ea84798031de798fe99fb0fafe05b https://github.com/galaxyproject/galaxy/commit/aaad00162f3ea84798031de798fe… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Added CloudBridge to the dependencies check. Commit: 55c976cb85237bb0906379d692e212f05a327c2b https://github.com/galaxyproject/galaxy/commit/55c976cb85237bb0906379d692e2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/objectstore/cloud.py Log Message: ----------- (1) Added Cloud to ObjectStore; (2) updated CloudBridge dependencies. Commit: e4c00dd695bf23a506ffeec15f98a6f6d1a05312 https://github.com/galaxyproject/galaxy/commit/e4c00dd695bf23a506ffeec15f98… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/cloud.py Log Message: ----------- - Updated `Cloud` to account for changes in `CloudBridge` interface. - Added `Cloud` to objectstore import. Commit: ab34fc9bd92041065dd8f140194c56e0f7b2954f https://github.com/galaxyproject/galaxy/commit/ab34fc9bd92041065dd8f140194c… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated `Babel` and `requests` packages version to meet the minimum requirements of `cloudbridge` package. Commit: e8541a71a4fdd7f975b3e8d0c6b054bdc33480ab https://github.com/galaxyproject/galaxy/commit/e8541a71a4fdd7f975b3e8d0c6b0… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-26 (Wed, 26 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Reverted the changes on package versions, as these changes are requests via a different PR. Commit: cde2ff82b02233721af81936d588b6558ab3ffa5 https://github.com/galaxyproject/galaxy/commit/cde2ff82b02233721af81936d588… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/master' Commit: 7ad7d881046ddd20276998d6e1fca495d1ac9f50 https://github.com/galaxyproject/galaxy/commit/7ad7d881046ddd20276998d6e1fc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Changed boto import style. Commit: 9c57adb90481b871cc6f98f58227caca4e414467 https://github.com/galaxyproject/galaxy/commit/9c57adb90481b871cc6f98f58227… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Updated CloudBridge to its current latest version. Commit: 2589c745ae7f88ada7a08265f1238ae00274425e https://github.com/galaxyproject/galaxy/commit/2589c745ae7f88ada7a08265f123… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Commented on boto import, and removed a `use_reduced_redundancy` config. Commit: 89be432770d3cf9442f9c003ead8c6ea6a16f395 https://github.com/galaxyproject/galaxy/commit/89be432770d3cf9442f9c003ead8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed boto import, and replaced all S3-specific exception catches with a generic exception--a temporary solution till CloudBridge wraps the exceptions properly. Commit: fafb019f4be3b33ad9cab4bfd2ded6788b419592 https://github.com/galaxyproject/galaxy/commit/fafb019f4be3b33ad9cab4bfd2de… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Consolidated two upload methods, i.e., upload from file and string, because CloudBridge internally maps to appropriate functions depending on the input type. Commit: fb25495d191c2172ce22496900db2310d6fc9b69 https://github.com/galaxyproject/galaxy/commit/fb25495d191c2172ce22496900db… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed a S3-related comment, and swapped an if/else condition. Commit: 7727c0bf627af5905c6e029417602389238f120e https://github.com/galaxyproject/galaxy/commit/7727c0bf627af5905c6e02941760… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed a comment section. Commit: 37efbd03ce4215086d29e8f4e9fd977b8e1299e0 https://github.com/galaxyproject/galaxy/commit/37efbd03ce4215086d29e8f4e9fd… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-06 (Sun, 06 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Changed indentation of two lines. Commit: 9a5016fdcf4f36d5c20991f44d4b02fe7904ef66 https://github.com/galaxyproject/galaxy/commit/9a5016fdcf4f36d5c20991f44d4b… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update CloudBridge to its current latest Should use the wheel created at [this PR](https://github.com/galaxyproject/starforge/pull/139). Commit: 4e17c8e3b790d2d21bcf12c3d4a855b1226d810d https://github.com/galaxyproject/galaxy/commit/4e17c8e3b790d2d21bcf12c3d4a8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- Add Cloud configuration to object_store_conf.xml.sample Commit: 0ec02b5528e64f62b50567e79d2519a9e84e20d1 https://github.com/galaxyproject/galaxy/commit/0ec02b5528e64f62b50567e79d25… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M client/toolshed/scripts/mvc/groups/group-list-view.js M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M 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tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'remotes/upstream/dev' into CloudObjectStore Commit: a8784369e4b243856b9582f9417039bf0c6bc83a https://github.com/galaxyproject/galaxy/commit/a8784369e4b243856b9582f94170… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed white spaces. Commit: eaa5931d195d4710d939e6f8d53bfe2fed38ba2f https://github.com/galaxyproject/galaxy/commit/eaa5931d195d4710d939e6f8d53b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Updated requirements: sqlalchemy-migrate and pbr. Commit: 90c444d9a136400af608cb7fd7f8e8d59de3ba90 https://github.com/galaxyproject/galaxy/commit/90c444d9a136400af608cb7fd7f8… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Removed a white space between parenthesis and arguments Commit: f6586a8e6d861c8c6803f96340641abf6470c2fc https://github.com/galaxyproject/galaxy/commit/f6586a8e6d861c8c6803f9634064… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Surrounded CloudBridge import in a try-catch block. Commit: 26cbf04ed0f30f72c994af0ffab54eab7dd8ac0b https://github.com/galaxyproject/galaxy/commit/26cbf04ed0f30f72c994af0ffab5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Rework conditional dependency handling in galaxy.objectstore.cloud. This file may be loaded (e.g. for testing) but not used, so we shouldn't log a generic error about cloudbridge being unavailable, if someone attempts to actually use the object store and it isn't available then raise an informative exception. Commit: cf56d1d37b77b5ca18037da8a392d68199fcb4d6 https://github.com/galaxyproject/galaxy/commit/cf56d1d37b77b5ca18037da8a392… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Merge pull request #3 from jmchilton/CloudObjectStore Rework conditional dependency handling in galaxy.objectstore.cloud. Commit: 6d65e902b12b4fca9af613085b5bc828c8a6d2fc https://github.com/galaxyproject/galaxy/commit/6d65e902b12b4fca9af613085b5b… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Updated an error message. Commit: cfce6c221c3f453e75542d53262f53c7e3411f86 https://github.com/galaxyproject/galaxy/commit/cfce6c221c3f453e75542d53262f… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed `boto` logging level set. Commit: b55583701cbf33f52db88f147dda6b04499243d7 https://github.com/galaxyproject/galaxy/commit/b55583701cbf33f52db88f147dda… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed retries for getting a bucket. Commit: 5977056715a5d2e12b638012b6fc99d885ea034a https://github.com/galaxyproject/galaxy/commit/5977056715a5d2e12b638012b6fc… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Resolved a bug with uploading a dataset using Cloud (not differentiating between uploading from a file vs. string). Commit: 45ac767a4eb6ab9e15a1e46a1e9e4ae70591e188 https://github.com/galaxyproject/galaxy/commit/45ac767a4eb6ab9e15a1e46a1e9e… Author: vahid <jalili.vahid(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Removed an unused variable (i.e., mb_size) from Cloud Commit: 9f0676d7d4984fa2540c1be001f705b02d33cd8d https://github.com/galaxyproject/galaxy/commit/9f0676d7d4984fa2540c1be001f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M config/object_store_conf.xml.sample M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/cloud.py Log Message: ----------- Merge remote-tracking branch 'VJalili/CloudObjectStore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7f30028d32b5...9f0676d7d498

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[galaxyproject/galaxy] a54f48: Remove generic formbuilder controller redirect
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a54f4892fa1defe5e406e10a658305872f479be3 https://github.com/galaxyproject/galaxy/commit/a54f4892fa1defe5e406e10a6583… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Remove generic formbuilder controller redirect Commit: 6f2da1882a119db41adbfc766add198733522ea7 https://github.com/galaxyproject/galaxy/commit/6f2da1882a119db41adbfc766add… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: R lib/galaxy/web/framework/formbuilder.py Log Message: ----------- Remove formbuilder code file Commit: 28f7bed5ffcc85069d234724c56a6a0850f1da2c https://github.com/galaxyproject/galaxy/commit/28f7bed5ffcc85069d234724c56a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused field as html function from model Commit: 67aac2d9d9d4305f8064584366125579445cc476 https://github.com/galaxyproject/galaxy/commit/67aac2d9d9d4305f806458436612… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused html helper for address fields Commit: 372ae48a85ddf9cc5f450bba19e937e23a6a3c08 https://github.com/galaxyproject/galaxy/commit/372ae48a85ddf9cc5f450bba19e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Remove html helpers from metadata parameter inputs Commit: ec1438c9a0396cf0f370c66c14116b952bbd66a4 https://github.com/galaxyproject/galaxy/commit/ec1438c9a0396cf0f370c66c1411… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Avoid returning html in galaxy associated toolshed api Commit: c20ddb096d36f2125dee2ec9aed9ba7fde2e04d4 https://github.com/galaxyproject/galaxy/commit/c20ddb096d36f2125dee2ec9aed9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Remove html helpers from second toolshed api controller Commit: 8d41a79ba12360357aae688600963e2f4a14f524 https://github.com/galaxyproject/galaxy/commit/8d41a79ba12360357aae68860096… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove html based input doc tests Commit: 26e8d89a1a415d248aaa4c377b6587181bd77076 https://github.com/galaxyproject/galaxy/commit/26e8d89a1a415d248aaa4c377b65… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Move select builder to toolshed Commit: 9b95e7e9519467187f2a9240c47551cb74e43291 https://github.com/galaxyproject/galaxy/commit/9b95e7e9519467187f2a9240c475… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove html helpers from form builder Commit: 4f80540e89834f3092e1d9e2ba2a993130e70953 https://github.com/galaxyproject/galaxy/commit/4f80540e89834f3092e1d9e2ba2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove size handlers for html text fields Commit: a840c4792295dce538e332496e2baeba11a2f2c0 https://github.com/galaxyproject/galaxy/commit/a840c4792295dce538e332496e2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove refresh on change handler for checkbox field Commit: 96d3d27a59faa378dba4d4d9d50966b324751580 https://github.com/galaxyproject/galaxy/commit/96d3d27a59faa378dba4d4d9d509… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove html helper to disable input fields Commit: 3bc44493367cd4f6e4c4efa5551463f35238f507 https://github.com/galaxyproject/galaxy/commit/3bc44493367cd4f6e4c4efa55514… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused file field from form builder Commit: ea9d53c5d8eef6bc67ceac55c2bc8a3b6a570a66 https://github.com/galaxyproject/galaxy/commit/ea9d53c5d8eef6bc67ceac55c2bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused genome space field from form builder Commit: f77a47bf651366a259b7964658538e03f0900c73 https://github.com/galaxyproject/galaxy/commit/f77a47bf651366a259b796465853… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused hidden field wrapper from form builder Commit: 16036fbe4f4166b53c31edde9e14256a5c87b554 https://github.com/galaxyproject/galaxy/commit/16036fbe4f4166b53c31edde9e14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused params parameter from addressfield wrapper Commit: 09862dde84e0e9acbf7b09122cf22bcdc65759d5 https://github.com/galaxyproject/galaxy/commit/09862dde84e0e9acbf7b09122cf2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused params parameter from workflow fields Commit: 82f56b004a440c7b57d4103e1b2b0359756b2c1e https://github.com/galaxyproject/galaxy/commit/82f56b004a440c7b57d4103e1b2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused parameters from workflow mapping field Commit: 0147816ecf6a00472a528f7fc672c9b45888287f https://github.com/galaxyproject/galaxy/commit/0147816ecf6a00472a528f7fc672… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused parameters from history field Commit: d0565f1f5078e8e355a7f79c1f91411cd12070bb https://github.com/galaxyproject/galaxy/commit/d0565f1f5078e8e355a7f79c1f91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py Log Message: ----------- Remove checkbox special case handling, only used in toolshed Commit: f8ef4a7bc14c9ad80a0fc7a27ffb89fadefc14eb https://github.com/galaxyproject/galaxy/commit/f8ef4a7bc14c9ad80a0fc7a27ffb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove template form helper for libraries Commit: 797fd8286f2db4656a6d9ba8a720a4f1f12e0b3a https://github.com/galaxyproject/galaxy/commit/797fd8286f2db4656a6d9ba8a720… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Remove get widget helper Commit: df5a9530e0dbdf94d05bf5ee25ca722278e927d6 https://github.com/galaxyproject/galaxy/commit/df5a9530e0dbdf94d05bf5ee25ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove association for template helpers Commit: 4d1df8c4566e539e4c192867eea9cfc761191a6b https://github.com/galaxyproject/galaxy/commit/4d1df8c4566e539e4c192867eea9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused checkbox parameters Commit: 296649937ff045734480a4b673902f5921cf3ad5 https://github.com/galaxyproject/galaxy/commit/296649937ff045734480a4b67390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused on change handler for galaxy select fields Commit: 31607438e7492467e1d689060007dfaed45e5fcd https://github.com/galaxyproject/galaxy/commit/31607438e7492467e1d689060007… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused select value helper Commit: 3eed3a4df058c1674ec3d4682c8365d45f4b2386 https://github.com/galaxyproject/galaxy/commit/3eed3a4df058c1674ec3d4682c83… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: R templates/common/select_template.mako R templates/common/template_common.mako Log Message: ----------- Remove unused mako templates for custom form building Commit: 26677708e14b5e4ae23e4dfea5b105b74bc4b134 https://github.com/galaxyproject/galaxy/commit/26677708e14b5e4ae23e4dfea5b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Remove unused form template loader Commit: 07ce743b8df873a348d883e202c5f3f45315aceb https://github.com/galaxyproject/galaxy/commit/07ce743b8df873a348d883e202c5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: R templates/form.mako Log Message: ----------- Remove form.mako Commit: d489aea241a27dfc8a15875a0cb37c2f54f2eacc https://github.com/galaxyproject/galaxy/commit/d489aea241a27dfc8a15875a0cb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused refresh on change parsing for tool version selection field Commit: 91c05859b6f9fc9fefc3b4fca3f1dc12cac9a176 https://github.com/galaxyproject/galaxy/commit/91c05859b6f9fc9fefc3b4fca3f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Move remaining form builder to toolshed Commit: 8ccdee9690eac96da1b12e5b6b22c72509b90af3 https://github.com/galaxyproject/galaxy/commit/8ccdee9690eac96da1b12e5b6b22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Link toolshed form builder to repository utilites Commit: ec16aadccc9a476d5f2936953fe2975246b460ab https://github.com/galaxyproject/galaxy/commit/ec16aadccc9a476d5f2936953fe2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/grids/util.py Log Message: ----------- Link toolshed form builder with grid utilities Commit: a726eba67bd0a762346cec3cd2338481085b142d https://github.com/galaxyproject/galaxy/commit/a726eba67bd0a762346cec3cd233… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: A lib/tool_shed/util/form_util.py Log Message: ----------- Add form builder for toolshed Commit: 0dcad1a485e677de244f7483fb6210ebea47ad58 https://github.com/galaxyproject/galaxy/commit/0dcad1a485e677de244f7483fb62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/form_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Import toolshed form builder in remaining modules Commit: c1acba4a5ba63c4ef0d6e4b69e7c1840d87cae28 https://github.com/galaxyproject/galaxy/commit/c1acba4a5ba63c4ef0d6e4b69e7c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/form_util.py Log Message: ----------- Remove to dictionary helpers from toolshed form builder Commit: 2c1a9a6b7a910fb571e7b6c268ba952706e92644 https://github.com/galaxyproject/galaxy/commit/2c1a9a6b7a910fb571e7b6c268ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Use toolshed form builder for admin toolshed Commit: 0b3bcb748548dbd7bd58c54b03c273912dca96e9 https://github.com/galaxyproject/galaxy/commit/0b3bcb748548dbd7bd58c54b03c2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Avoid uninitialized variable in toolshed cloning process Commit: c2f92fdc4bcc9c440a97503f94090a748ef6c30a https://github.com/galaxyproject/galaxy/commit/c2f92fdc4bcc9c440a97503f9409… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M lib/tool_shed/util/form_util.py Log Message: ----------- Restore dict helper, some toolshed elements use the new client but the toolshed backend Commit: 87e44fbdfe1a84be77603b77043249ad73219ef6 https://github.com/galaxyproject/galaxy/commit/87e44fbdfe1a84be77603b770432… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/util/form_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Fix import order Commit: 644c108e28e3c804e2f9841d5d4ac377157be3fe https://github.com/galaxyproject/galaxy/commit/644c108e28e3c804e2f9841d5d4a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/web/__init__.py Log Message: ----------- Remove formbuilder from framework import Commit: 141a321bfe3ee35cd1a199f42f5e55d131775c0d https://github.com/galaxyproject/galaxy/commit/141a321bfe3ee35cd1a199f42f5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Remove unused panel section parsing Commit: da9d9bf61cf90dd6d3b12450bf1cdceebd2d64ea https://github.com/galaxyproject/galaxy/commit/da9d9bf61cf90dd6d3b12450bf1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Remove panel section from duplicate toolshed api endpoint Commit: c7ebf747f9fef827e89893776ee77870b996d70a https://github.com/galaxyproject/galaxy/commit/c7ebf747f9fef827e89893776ee7… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/tool_shed/util/form_util.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix the shed tool conf select field. Commit: 82b8e093fc4fe8c4e960af407824bf04308436c2 https://github.com/galaxyproject/galaxy/commit/82b8e093fc4fe8c4e960af407824… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Merge branch 'remove_formbuilder' of ssh://github.com/guerler/galaxy into remove_formbuilder Commit: 47a91eae67b2d66ed8beb45893577dc1e101b7a5 https://github.com/galaxyproject/galaxy/commit/47a91eae67b2d66ed8beb4589357… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py M templates/user/register.mako Log Message: ----------- Build subscribe checkbox in register mako without html backend helper Commit: 9fb40508fdf4c4c8ab4dafcec38185b28574eb6d https://github.com/galaxyproject/galaxy/commit/9fb40508fdf4c4c8ab4dafcec381… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/tool_shed/util/form_util.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Merge branch 'remove_formbuilder' of https://github.com/guerler/galaxy into remove_formbuilder Commit: 969f3d7e2ea3e39f52e5e5f0d5c4dd0ca769291a https://github.com/galaxyproject/galaxy/commit/969f3d7e2ea3e39f52e5e5f0d5c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: R client/galaxy/scripts/apps/admin-toolshed.js A client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/apps/library.js R client/galaxy/scripts/apps/masthead.js R client/galaxy/scripts/apps/viz.js R client/galaxy/scripts/apps/workflow.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/plugins/visualizations/charts/static/client/app.js M config/plugins/visualizations/charts/static/client/components/model.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/client/views/description.js M config/plugins/visualizations/charts/static/client/views/editor.js M config/plugins/visualizations/charts/static/client/views/groups.js M config/plugins/visualizations/charts/static/client/views/settings.js M config/plugins/visualizations/charts/static/client/views/viewer.js M config/plugins/visualizations/charts/static/client/views/viewport.js M config/plugins/visualizations/charts/webpack.config.js R config/plugins/visualizations/scatterplot/Gruntfile.js R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js R config/plugins/visualizations/scatterplot/src/scatterplot-display.js R config/plugins/visualizations/scatterplot/src/scatterplot-model.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js M config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A config/plugins/visualizations/scatterplot/webpack.config.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js A static/scripts/bundled/extended.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into remove_formbuilder Commit: aba0d3d0156a58d6b9301cdd9fcf440400f87e71 https://github.com/galaxyproject/galaxy/commit/aba0d3d0156a58d6b9301cdd9fcf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Remove debug output Commit: 49783c21e853467e18d997bfde869ac4bbfbb2af https://github.com/galaxyproject/galaxy/commit/49783c21e853467e18d997bfde86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Make client Commit: c49a184952c2ab6fa15b906d9726cfe3f36ecce8 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templates/webapps/tool_shed/user/manage_email_alerts.mako Log Message: ----------- Revise checkbox in manage emails mako Commit: 0e14da24feb002e6885cae5cba05e75f80feb033 https://github.com/galaxyproject/galaxy/commit/0e14da24feb002e6885cae5cba05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Revise malicious checkbox in repository manager Commit: efc0135fc5d4ed2267e8516c3ec3a17504e4e6bc https://github.com/galaxyproject/galaxy/commit/efc0135fc5d4ed2267e8516c3ec3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Replace select field for alerts Commit: 41eb44961f7553689c677dae39e18620f8a5d89f https://github.com/galaxyproject/galaxy/commit/41eb44961f7553689c677dae39e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Transform checkboxes in find workflows and tools Commit: 27d738192fed9eb66882e35e838499360a9f9522 https://github.com/galaxyproject/galaxy/commit/27d738192fed9eb66882e35e8384… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M templates/user/register.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Add shared checkbox and select field helper to common makos Commit: 7583c2be55ac74e9747351f58056c020b1d6a623 https://github.com/galaxyproject/galaxy/commit/7583c2be55ac74e9747351f58056… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Adjust previously revised checkboxes Commit: a32f8349d47741e6f960084da4e6eef88cc189ed https://github.com/galaxyproject/galaxy/commit/a32f8349d47741e6f960084da4e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako Log Message: ----------- Adjust mako templates Commit: 84ea08973acc16960bfa1e96530d68b8f341a8d4 https://github.com/galaxyproject/galaxy/commit/84ea08973acc16960bfa1e96530d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Revise alerts checkbox in manage repositories Commit: 9fc4817518516f0527e6c62dacf2e6dce91de0a8 https://github.com/galaxyproject/galaxy/commit/9fc4817518516f0527e6c62dacf2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository_review/edit_review.mako Log Message: ----------- Edit review Commit: 662e01a3a251f4edc9c540b534e2eee912f77bc2 https://github.com/galaxyproject/galaxy/commit/662e01a3a251f4edc9c540b534e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/repository_review/browse_review.mako Log Message: ----------- Fix review editing Commit: 8965d85607cd146a9d57789f107e7e99d0c3062c 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----------- Remove last get_html caller from toolshed backend library Commit: 4fd96359395632f00277a03b59d69644af148b9c https://github.com/galaxyproject/galaxy/commit/4fd96359395632f00277a03b59d6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R lib/tool_shed/util/form_util.py Log Message: ----------- Remove toolshed form builder Commit: c20277dbb25316d79cadad24591a48303de708c8 https://github.com/galaxyproject/galaxy/commit/c20277dbb25316d79cadad24591a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_types/util.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Remove form util helper from use cases Commit: 4a66364fb19374468bc5ef322730f881ac172fb1 https://github.com/galaxyproject/galaxy/commit/4a66364fb19374468bc5ef322730… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add field id to select field handler Commit: 48012b6c98b49e89b7d6291f08d84d0a5e874aae https://github.com/galaxyproject/galaxy/commit/48012b6c98b49e89b7d6291f08d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Remove get html use cases in makos Commit: 5bfb5196788c286c9ea88f0dd59b142055000490 https://github.com/galaxyproject/galaxy/commit/5bfb5196788c286c9ea88f0dd59b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako Log Message: ----------- Remove get html calls from remaining makos Commit: c6fc1a82824c58c4e241aa78f4b313dbbb0d10e9 https://github.com/galaxyproject/galaxy/commit/c6fc1a82824c58c4e241aa78f4b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Regress form mako preview Commit: b6e520902fe59ea8695e23f6689f67ddbb1ef8a5 https://github.com/galaxyproject/galaxy/commit/b6e520902fe59ea8695e23f6689f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix push list handler Commit: 4e2e2eb59af873038c979602c8d108d96fb43e1a https://github.com/galaxyproject/galaxy/commit/4e2e2eb59af873038c979602c8d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add multiple handler to mako Commit: fcbd540eede33d013ebdabab914d263314b53b55 https://github.com/galaxyproject/galaxy/commit/fcbd540eede33d013ebdabab914d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add refresh on change flag to select Commit: 819225500218157ff7c0bd3a1c37ed23c61cb41b https://github.com/galaxyproject/galaxy/commit/819225500218157ff7c0bd3a1c37… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add escape handler Commit: 5aba71c84a1e83327f3769f165bbb44804aa7b07 https://github.com/galaxyproject/galaxy/commit/5aba71c84a1e83327f3769f165bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako Log Message: ----------- Restore checkbox view for toolshed makos Commit: 3f43fadd53dd5a9937e2e1dd7a5dee6df7a29151 https://github.com/galaxyproject/galaxy/commit/3f43fadd53dd5a9937e2e1dd7a5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Insert import into mako caller, escape labels Commit: 3b16a39dc873aa41c7c35e83e6d7f4c2de0e1b41 https://github.com/galaxyproject/galaxy/commit/3b16a39dc873aa41c7c35e83e6d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Escape values and labels Commit: 790a0b9e2cd0b3a62c851b30cf4474ecdaba3a35 https://github.com/galaxyproject/galaxy/commit/790a0b9e2cd0b3a62c851b30cf44… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository_review.py Log Message: ----------- Avoid uninitialized parameter Commit: db5cf7204a825c8beac97afee3d1bf693611cfc3 https://github.com/galaxyproject/galaxy/commit/db5cf7204a825c8beac97afee3d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix value parsing to checkbox field Commit: ecbe7878655f95d63896f4a70a6993c4acf3f0b1 https://github.com/galaxyproject/galaxy/commit/ecbe7878655f95d63896f4a70a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Fix allow push, switch to select field Commit: c814e09563a29f998749e91338f7cf237c5e0070 https://github.com/galaxyproject/galaxy/commit/c814e09563a29f998749e91338f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Remove input element preview from tool preview Commit: d746f8bd9e8fe506534d0332589db245ef9dcb5d https://github.com/galaxyproject/galaxy/commit/d746f8bd9e8fe506534d0332589d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Fix multiple handler Commit: faf1c4f3224aba16cd7124f8f5fc1181f7e95b70 https://github.com/galaxyproject/galaxy/commit/faf1c4f3224aba16cd7124f8f5fc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add value selection to select field Commit: c9a9cb5e24dce19ff9283d72568003c1e5c2dcf8 https://github.com/galaxyproject/galaxy/commit/c9a9cb5e24dce19ff9283d725680… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Add value support for checkboxes Commit: 701cdad4393310b67aa563a957ed3191ff9ecead https://github.com/galaxyproject/galaxy/commit/701cdad4393310b67aa563a957ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/tool_shed/common/common.mako Log Message: ----------- Revise onchange attribute Commit: c1e29a2cc2ba65ab926b5d032088b2dc6108ce2a https://github.com/galaxyproject/galaxy/commit/c1e29a2cc2ba65ab926b5d032088… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository_review.py Log Message: ----------- Restore previous behavior Commit: 0444aa6ae68ae6b9f860f997c9bacd6aa02a9538 https://github.com/galaxyproject/galaxy/commit/0444aa6ae68ae6b9f860f997c9ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository_review/browse_review.mako Log Message: ----------- Fix checked value setting for private mode Commit: 319205a57242ca8fb475dde0a67e21cf23fab420 https://github.com/galaxyproject/galaxy/commit/319205a57242ca8fb475dde0a67e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M templates/webapps/tool_shed/repository_review/edit_review.mako Log Message: ----------- Handle checkbox flag for private settings, component name encoded in checkbox name Commit: fa793bd637705b56f7cbb69b41a08843a9000ac1 https://github.com/galaxyproject/galaxy/commit/fa793bd637705b56f7cbb69b41a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M 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client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M 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client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M config/plugins/webhooks/demo/tour_generator/static/script.js A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/repositories.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/onload.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Merge branch 'dev' into remove_formbuilder Commit: 98319803c0d63913a62bd620377090d7314174e2 https://github.com/galaxyproject/galaxy/commit/98319803c0d63913a62bd6203770… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M templates/webapps/tool_shed/repository_review/edit_review.mako Log Message: ----------- Restore behavior, adjust for missing checkbox field value Commit: 2686299ac9c2bff79429c2d2615f9d1ac1a9edbf https://github.com/galaxyproject/galaxy/commit/2686299ac9c2bff79429c2d2615f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M test/shed_functional/base/twilltestcase.py Log Message: ----------- Fix value setting in test case Commit: 066d94b43482e3ee95a70b4a69a49a8fb99bcf58 https://github.com/galaxyproject/galaxy/commit/066d94b43482e3ee95a70b4a69a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix truthness detection for test cases Commit: 34a71af9e1bd955bde43b91ea682af164988a339 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test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into remove_formbuilder Commit: 7f30028d32b56eeeaacc6a874f8f1f2e312b9b49 https://github.com/galaxyproject/galaxy/commit/7f30028d32b56eeeaacc6a874f8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/__init__.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/libs/bibtex.js M static/scripts/mvc/toolshed/repository-view.js M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/form.mako M templates/user/register.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #5114 from guerler/remove_formbuilder Remove html formbuilder from backend Compare: https://github.com/galaxyproject/galaxy/compare/1e8c15b3ba36...7f30028d32b5

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[galaxyproject/galaxy] 098e3d: Remove sample tracking controller from reports
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 098e3d8c9e89c8ee64041c36489d0da601f55874 https://github.com/galaxyproject/galaxy/commit/098e3d8c9e89c8ee64041c36489d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: R lib/galaxy/webapps/reports/controllers/sample_tracking.py Log Message: ----------- Remove sample tracking controller from reports Commit: 47b89b3540eeb92e5dfd61cf59a5d3f12b3cbe8d https://github.com/galaxyproject/galaxy/commit/47b89b3540eeb92e5dfd61cf59a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove unused legacy flag in config Commit: af7b6af268b2ea547cd7029862985014aaf279cb https://github.com/galaxyproject/galaxy/commit/af7b6af268b2ea547cd702986298… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M templates/webapps/reports/index.mako Log Message: ----------- Remove sample tracking option from reports panel Commit: a0e355559419929dccd6cb93f3172d3114789f02 https://github.com/galaxyproject/galaxy/commit/a0e355559419929dccd6cb93f317… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: R templates/common/select_template.mako R templates/common/template_common.mako Log Message: ----------- Remove unused common mako templates Commit: 410646c9799ef0409964a0b4c5ea76c76d8c609f https://github.com/galaxyproject/galaxy/commit/410646c9799ef0409964a0b4c5ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako Log Message: ----------- Remove unused sequencing request makos in reports Commit: 1e8c15b3ba36d7b190b39530cceb5772f1908079 https://github.com/galaxyproject/galaxy/commit/1e8c15b3ba36d7b190b39530cceb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M lib/galaxy/config.py R lib/galaxy/webapps/reports/controllers/sample_tracking.py R templates/common/select_template.mako R templates/common/template_common.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako Log Message: ----------- Merge pull request #5182 from guerler/clear_sample_tracking Remove legacy request controller from reports app Compare: https://github.com/galaxyproject/galaxy/compare/3d989243a9fb...1e8c15b3ba36

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[galaxyproject/galaxy] 83ab84: change hicexplorer image name
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83ab849f3886e163ee4ab7267cc3949081994b57 https://github.com/galaxyproject/galaxy/commit/83ab849f3886e163ee4ab7267cc3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-09 (Sat, 09 Dec 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample Log Message: ----------- change hicexplorer image name Commit: 3d989243a9fb2228a434b729044b2428bd514cec https://github.com/galaxyproject/galaxy/commit/3d989243a9fb2228a434b729044b… Author: Enis Afgan <afgane(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #5177 from bgruening/hic_img_name change hicexplorer image name Compare: https://github.com/galaxyproject/galaxy/compare/477ab4eeb8c5...3d989243a9fb

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[galaxyproject/galaxy] f67682: don't copy subworkflows
by GitHub 11 Dec '17

11 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f676823c7a0e57d3346192eef935febde5a30e77 https://github.com/galaxyproject/galaxy/commit/f676823c7a0e57d3346192eef935… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- don't copy subworkflows Commit: 477ab4eeb8c5feefd70dde96f7573750c08a1306 https://github.com/galaxyproject/galaxy/commit/477ab4eeb8c5feefd70dde96f757… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-11 (Mon, 11 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/scripts/bundled/extended.bundled.js A static/scripts/libs/bibtex.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #5185 from anatskiy/workflow_step_cloning_fix Don't clone subworkflows Compare: https://github.com/galaxyproject/galaxy/compare/e198dd75782c...477ab4eeb8c5

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[galaxyproject/galaxy] 3fa608: Use pysam.merge instead of samtools merge
by GitHub 10 Dec '17

10 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fa608f54850d9a93e910cdc55fa1f87c4c87c7c https://github.com/galaxyproject/galaxy/commit/3fa608f54850d9a93e910cdc55fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Use pysam.merge instead of samtools merge Commit: 16d0d3ecafb47ca8f112e8fa339f492446f9e80c https://github.com/galaxyproject/galaxy/commit/16d0d3ecafb47ca8f112e8fa339f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/1.unsorted.bam Log Message: ----------- Add unsorted test bam Commit: 3c9999d89acfdd7aa1f56969ca7e03da3d83e655 https://github.com/galaxyproject/galaxy/commit/3c9999d89acfdd7aa1f56969ca7e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/test/1.bam M lib/galaxy/datatypes/test/1.unsorted.bam Log Message: ----------- Use pysam for metadata setting and grooming There are also some noteworthy changes here: - We do always respect the sort-order specified in the header - If the sort order is not mentioned in the header or no header exists we coordinate-sort the file. - We do not use indexing to determine if a file is coordinate sorted, because this does not work reliably with samtools/pysam > 1.X, since arbitrarily sorted files can be indexed now. This also fixes advanced metadata setting (sort_order, bam_version and more), which appears to have been broken. This probably went by unnoticed because of the catch-all try-except-pass. The downside to fixing this is that I had to (temporarilly, hopefully) comment out the reference_names, reference_lengths, bam_header and readgroups attributes, because they led to the following error: ``` galaxy.model.metadata DEBUG 2017-11-19 14:47:30,540 loading metadata from file for: HistoryDatasetAssociation 582 galaxy.jobs.runners.local ERROR 2017-11-19 14:47:30,636 Job wrapper finish method failed Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 130, in queue_job job_wrapper.finish(stdout, stderr, exit_code) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1357, in finish self.sa_session.flush() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 157, in do return getattr(self.registry(), name)(*args, **kwargs) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2019, in flush self._flush(objects) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2137, in _flush transaction.rollback(_capture_exception=True) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2101, in _flush flush_context.execute() File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 706, in _emit_update_statements execute(statement, multiparams) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1341, in _handle_dbapi_exception exc_info File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 202, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) index row size 7208 exceeds maximum 2712 for index "ix_history_dataset_association_metadata" HINT: Values larger than 1/3 of a buffer page cannot be indexed. Consider a function index of an MD5 hash of the value, or use full text indexing. [SQL: 'UPDATE history_dataset_association SET update_time=%(update_time)s, blurb=%(blurb)s, peek=%(peek)s, metadata=%(_metadata)s WHERE history_dataset_association.id = %(history_dataset_association_id)s'] [parameters: {'_metadata': <psycopg2.extensions.Binary object at 0x119ed8990>, 'update_time': datetime.datetime(2017, 11, 19, 13, 47, 30, 598058), 'history_dataset_association_id': 582, 'blurb': '3.5 KB', 'peek': 'Binary bam alignments file'}] ``` Commit: 369485a43ad50a877dc68324c1a2b6ab876030ea https://github.com/galaxyproject/galaxy/commit/369485a43ad50a877dc68324c1a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py A test/unit/datatypes/test_bam.py Log Message: ----------- Move Bam doctests to unittests Commit: ae72e5668364f6f72861c21a62a641f9f65636e1 https://github.com/galaxyproject/galaxy/commit/ae72e5668364f6f72861c21a62a6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M test/unit/datatypes/test_bam.py Log Message: ----------- Use subprocess to check if pysam.index succeeds Checking if pysam.index succeeds tests whether a file is coordinate sorted. If pysam.index fails to index htslib writes to stderr and this fails set meta tool. To prevent this we run this in a subprocess and discard stderr. Commit: 836aea072e84411fb4a24e37fb306b5ec72044c6 https://github.com/galaxyproject/galaxy/commit/836aea072e84411fb4a24e37fb30… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/2.shuffled.bam Log Message: ----------- Add test file with random order Commit: bac56d6b27068d3744e84eb9756bc28bf392f718 https://github.com/galaxyproject/galaxy/commit/bac56d6b27068d3744e84eb9756b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M tools/data_source/upload.xml Log Message: ----------- Drop samtools from metadata and upload tools We only need samtools for the dataproviders, which shouldn't be used by these tools. Commit: df35d089e3ea8c15330afaeedfa24e9c2f0fa7b2 https://github.com/galaxyproject/galaxy/commit/df35d089e3ea8c15330afaeedfa2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py Log Message: ----------- Add more unittests for CRAM, bcf and vcf Commit: 3f6a59e85ff8acf2fb0b39670f450a523ea11f38 https://github.com/galaxyproject/galaxy/commit/3f6a59e85ff8acf2fb0b39670f45… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Replace bcftools index with pysam.bcftools.index or pysam.tabix_index Commit: 8e580ec7ac599993ae082732b5c80f2b9bcce493 https://github.com/galaxyproject/galaxy/commit/8e580ec7ac599993ae082732b5c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Metadata fixes for VcfGz Commit: 0ac77ad7fd5c6d6660521d69f6010cb61d4947ac https://github.com/galaxyproject/galaxy/commit/0ac77ad7fd5c6d6660521d69f601… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/unit/datatypes/test_vcf.py M test/unit/datatypes/util.py Log Message: ----------- Fix Vcf index generation and test Commit: 6ca896ff9b199ac097f408e35e37a3365ff2ec46 https://github.com/galaxyproject/galaxy/commit/6ca896ff9b199ac097f408e35e37… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/unit/datatypes/test_bcf.py M test/unit/datatypes/test_cram.py M test/unit/datatypes/test_vcf.py M test/unit/datatypes/util.py Log Message: ----------- Fix index file syntax and fix linting problems Commit: 9c4a2f70ea6a62f35b3c736730fcc71bddf6dce9 https://github.com/galaxyproject/galaxy/commit/9c4a2f70ea6a62f35b3c736730fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py Log Message: ----------- Tabix indexing fixes. Upstream used 'index' instead of 'index_filename', and 'force' is now required since we precreate the destination location. Commit: 2a6e00dd001ea4f27cd7d9a12cddfcf9649da7ef https://github.com/galaxyproject/galaxy/commit/2a6e00dd001ea4f27cd7d9a12cdd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M test/unit/datatypes/test_cram.py Log Message: ----------- one more linting fix Commit: 07158e03308e026ee013bd6a50708167918c2d27 https://github.com/galaxyproject/galaxy/commit/07158e03308e026ee013bd6a5070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Need force=True in pysam.tabix_index because the index file path exists in the object store Commit: 64deb4f935ac7969a0e81024297d84d9831a8cfd https://github.com/galaxyproject/galaxy/commit/64deb4f935ac7969a0e81024297d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/cram_to_bam.py Log Message: ----------- We can use multiple threads when converting cram to bam files Commit: 90a56aea3f19df6943dfc648474d161e5c8f6d66 https://github.com/galaxyproject/galaxy/commit/90a56aea3f19df6943dfc648474d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Use more threads when sorting BAM files and GALAXY_SLOTS is set Commit: eb636c11361ef8f6cf85c8750f0a37608dcbee1a https://github.com/galaxyproject/galaxy/commit/eb636c11361ef8f6cf85c8750f0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/test_bam.py M test/unit/datatypes/util.py Log Message: ----------- Make sure files don't change in-place Commit: 1195183ea63c3916e1b8e163b2cc0839bd18d8c4 https://github.com/galaxyproject/galaxy/commit/1195183ea63c3916e1b8e163b2cc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Symlink tbi index to work around pysam limitation Before https://github.com/pysam-developers/pysam/pull/586 is merged and a new release is out we create a symlink to the tbi file, which is required for creating TabixFile instances. Since we want to cleanup the symlinks I turned `get_data_file` into a contextmanager. Along the way I also changed many open()/close() calls to `with` statements. Commit: 4795e490636e9a9234cb2d61c0a14508472a297d https://github.com/galaxyproject/galaxy/commit/4795e490636e9a9234cb2d61c0a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Detect if index symlink hack is necessary Commit: 46371d1251ed80b740956dc7111708aa93041092 https://github.com/galaxyproject/galaxy/commit/46371d1251ed80b740956dc71117… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/util.py Log Message: ----------- Decompose interval_to_tabix converter script This renames some variables to make it clearer what files they reflect. Also adds a very basic test that this works as intended. Commit: 309b71720e3b5615fac6abd028aa66735fa94eef https://github.com/galaxyproject/galaxy/commit/309b71720e3b5615fac6abd028aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/1.unsorted.bam M lib/galaxy/visualization/data_providers/genome.py M test/unit/datatypes/util.py Log Message: ----------- Improvements to datatypes suggested by @nsoranzo Commit: e198dd75782ce5b2a9619a5283e77a026393e149 https://github.com/galaxyproject/galaxy/commit/e198dd75782ce5b2a9619a5283e7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam M lib/galaxy/visualization/data_providers/genome.py A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5037 from mvdbeek/samtools_to_pysam Samtools to pysam Compare: https://github.com/galaxyproject/galaxy/compare/5ad4f57a63b0...e198dd75782c

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[galaxyproject/galaxy] 4b0a4d: Another fix for 404 on /workflow.
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b0a4d3d7d44fa6efd416ee168e484ba8da50dab https://github.com/galaxyproject/galaxy/commit/4b0a4d3d7d44fa6efd416ee168e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Another fix for 404 on /workflow. Similar to 82f44479fcc92fae0507c50aad19b2f2776ccadc. Commit: 5ad4f57a63b00cf6f27a6852e13d87d7902cac4a https://github.com/galaxyproject/galaxy/commit/5ad4f57a63b00cf6f27a6852e13d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #5170 from jmchilton/workflow_list Another fix for 404 on /workflow. Compare: https://github.com/galaxyproject/galaxy/compare/b99180c5a23c...5ad4f57a63b0

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[galaxyproject/galaxy] 5602f9: Fix inputFilled logic in workflow editor w/ collec...
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5602f911e757e2c08485166e61c39d7c854a7446 https://github.com/galaxyproject/galaxy/commit/5602f911e757e2c08485166e61c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix inputFilled logic in workflow editor w/ collections. Commit: 30bada4c4a96eeb78a43aefa85a48fbcb6966eeb https://github.com/galaxyproject/galaxy/commit/30bada4c4a96eeb78a43aefa85a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix another undefined collection type var. Commit: d3d6658160684211fda02c92ed1fb54d018a7471 https://github.com/galaxyproject/galaxy/commit/d3d6658160684211fda02c92ed1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Some misc cleanup in workflow-terminals.js Commit: 7a1e8c67627866b431917ecee0f974e9a0cdc418 https://github.com/galaxyproject/galaxy/commit/7a1e8c67627866b431917ecee0f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Client formatting. Commit: fd3a558895feeea9e50835e3ddfbcf88a38db40e https://github.com/galaxyproject/galaxy/commit/fd3a558895feeea9e50835e3ddfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Client build. Commit: b99180c5a23cd7477b5a630a7a6d7ee994b67b9a https://github.com/galaxyproject/galaxy/commit/b99180c5a23cd7477b5a630a7a6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/scripts/bundled/extended.bundled.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #5166 from dannon/fix_workflow_collections Fix workflow collection attachments Compare: https://github.com/galaxyproject/galaxy/compare/db317b6341e9...b99180c5a23c

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[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Compare: https://github.com/galaxyproject/galaxy/compare/e9f05cb1b11d...42c572f34469

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[galaxyproject/galaxy] 82f444: Resolve broken link in for all workflows
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82f44479fcc92fae0507c50aad19b2f2776ccadc https://github.com/galaxyproject/galaxy/commit/82f44479fcc92fae0507c50aad19… Author: Milad Miladi <mmiladi(a)users.noreply.github.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Resolve broken link in for all workflows The docker galaxy flavors built on dev branch have a broken link in tool panel, href in "All workflows" section. This should fix it. Commit: eab3c32cfad9b3acebeceb56e3d948320558d0b9 https://github.com/galaxyproject/galaxy/commit/eab3c32cfad9b3acebeceb56e3d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Merge branch 'toolpanel-fixlink' into dev Commit: db317b6341e9267371a048131fb95a9387c31842 https://github.com/galaxyproject/galaxy/commit/db317b6341e9267371a048131fb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Client build w/ merge of mmiladi:toolpanel-fixlink Compare: https://github.com/galaxyproject/galaxy/compare/044dcfbb216a...db317b6341e9

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[galaxyproject/galaxy] 3dcf95: Test resubmit for completely dynamic JobDestinatio...
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dcf9549f6bb4a3d0a5420185c2e7dedb78cc4d5 https://github.com/galaxyproject/galaxy/commit/3dcf9549f6bb4a3d0a5420185c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Test resubmit for completely dynamic JobDestination structures. Commit: 044dcfbb216ad1b2fb46933c6b21597828e42a91 https://github.com/galaxyproject/galaxy/commit/044dcfbb216ad1b2fb46933c6b21… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #5139 from jmchilton/resubmit_dynamic Test resubmit for dynamic JobDestination structures. Compare: https://github.com/galaxyproject/galaxy/compare/fe0fdeb4ce35...044dcfbb216a

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[galaxyproject/galaxy] 3dfbbc: Provide Galaxy.config var to indicate whether onlo...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dfbbc7e081cae0c8b95b727e3791915afcc47ec https://github.com/galaxyproject/galaxy/commit/3dfbbc7e081cae0c8b95b727e379… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Provide Galaxy.config var to indicate whether onload webhooks should kick off; use it. Fixes shed/reports use of them. Commit: 6f80bed294e99abbc5f880ea7ee0b781e60f7e2a https://github.com/galaxyproject/galaxy/commit/6f80bed294e99abbc5f880ea7ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Minor onload.js cleanup. Commit: 7f1b77ff16c2678327130f3d7282cd900130def8 https://github.com/galaxyproject/galaxy/commit/7f1b77ff16c2678327130f3d7282… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js Log Message: ----------- Move tours kicker out of onload.js; just use the import. Commit: 8858b5511cdaf282eb5a1e75eda42ce7dde25b42 https://github.com/galaxyproject/galaxy/commit/8858b5511cdaf282eb5a1e75eda4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Standardize import naming a little. Commit: d87e5755c73c59c3dfc4291b76da059fe8a81675 https://github.com/galaxyproject/galaxy/commit/d87e5755c73c59c3dfc4291b76da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tours import/export cleanup. tour_opts is internal only. Commit: 3f5aabbf150bd126b8bfa209214874a42399c666 https://github.com/galaxyproject/galaxy/commit/3f5aabbf150bd126b8bfa2092148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tour launching refactoring. Commit: a2cf121e34dc4cdb556ffb47337199d1e8a15f1b https://github.com/galaxyproject/galaxy/commit/a2cf121e34dc4cdb556ffb473371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Reduce tour launch duplication, refine module interface. Commit: d68dd305d86ae5767b00a0dbd7b2736101500e0a https://github.com/galaxyproject/galaxy/commit/d68dd305d86ae5767b00a0dbd7b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Run client-format. Commit: 03062992cfe037ea6d190c8587de39e66070fc55 https://github.com/galaxyproject/galaxy/commit/03062992cfe037ea6d190c8587de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Actually add /config to the commit... Commit: afae7c5dbd05bd4e69f4278902b8a0d1e3fde900 https://github.com/galaxyproject/galaxy/commit/afae7c5dbd05bd4e69f4278902b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Slight reorg in tours.js; internal stuff first, exports at the end. Commit: 2a7daaaefb605e7567cdafb71d49903e3db3389d https://github.com/galaxyproject/galaxy/commit/2a7daaaefb605e7567cdafb71d49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Rebuild client. Commit: fe0fdeb4ce35dc1de9fa2ce26ffffab6276552e0 https://github.com/galaxyproject/galaxy/commit/fe0fdeb4ce35dc1de9fa2ce26fff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #5116 from dannon/onload_webhook_segmentation Onload webhook toggles. Compare: https://github.com/galaxyproject/galaxy/compare/30196f5941df...fe0fdeb4ce35

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[galaxyproject/galaxy] 688128: Minor tweak; use dot notation in history-list.js
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 688128feed6147e359969f19775630d11a5281c1 https://github.com/galaxyproject/galaxy/commit/688128feed6147e359969f197756… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Minor tweak; use dot notation in history-list.js Commit: 12da37bb9ab1fbf35b13a36ba808d23f054a738c https://github.com/galaxyproject/galaxy/commit/12da37bb9ab1fbf35b13a36ba808… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Grid-view cleanup. Commit: 35d854b8c13d951692e9f0bc9564031d1dc790e0 https://github.com/galaxyproject/galaxy/commit/35d854b8c13d951692e9f0bc9564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Fixes in grid-template. A couple redefined vars, one used out of scope, and some general cleanup. Commit: f296d1f3334098481f56ac82ea861554cb48ab38 https://github.com/galaxyproject/galaxy/commit/f296d1f3334098481f56ac82ea86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Minor formatting. Commit: 53bcd063bce83257546a46918d73074491693324 https://github.com/galaxyproject/galaxy/commit/53bcd063bce83257546a46918d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Started refactoring more dramatically, but I think we probably want to do a bigger rewrite of this stuff with Vue grid components, Vuex, etc., so this simple subclassing should fix the problems we're seeing for now. Commit: cb6bbe3a0fbf5fb12507ddc391366b24177724c0 https://github.com/galaxyproject/galaxy/commit/cb6bbe3a0fbf5fb12507ddc39136… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Client format. Commit: 556c17d154e2efe496484b917f25acacaaba7c87 https://github.com/galaxyproject/galaxy/commit/556c17d154e2efe496484b917f25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Convert a bunch of iterables to use 'of' syntax instead of 'in'. Commit: eca993539a2e00895e32316e939e09fdfb79b84d https://github.com/galaxyproject/galaxy/commit/eca993539a2e00895e32316e939e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/repositories.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M test/api/test_workflows.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix-history-copy Commit: a92da1c109c3e5cbc530d17cd148a5877098a676 https://github.com/galaxyproject/galaxy/commit/a92da1c109c3e5cbc530d17cd148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- use encoded ids for popup anchor identifiers instead of sequence; this is more robust Commit: e08a3d0ffd01a7d58ad7445ef19050e6fbbefae3 https://github.com/galaxyproject/galaxy/commit/e08a3d0ffd01a7d58ad7445ef190… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Make client Commit: 30196f5941df704f6bb0a2a215315db08ffc92bf https://github.com/galaxyproject/galaxy/commit/30196f5941df704f6bb0a2a21531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Merge pull request #5144 from dannon/fix-history-copy Fix history copy Compare: https://github.com/galaxyproject/galaxy/compare/ef13e2857851...30196f5941df

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Commit: ef13e28578513f94014a705127585a42aba1c470 https://github.com/galaxyproject/galaxy/commit/ef13e28578513f94014a70512758… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/228623a133fd...ef13e2857851

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 228623a133fd05f0a310fe0ab063b48fa748c3b5 https://github.com/galaxyproject/galaxy/commit/228623a133fd05f0a310fe0ab063… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6055de286d6c...228623a133fd

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/cd1454c40a43...a0eae9510c9e

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

1 0