Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b8b4e198d4f4f498284017d1c9696cbec5f7cf0 https://github.com/galaxyproject/galaxy/commit/2b8b4e198d4f4f498284017d1c969... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- grt - wrap every write in try-except and just fail the row if the data is crap (like {NULL, SOH, STX, ETX} and friends) Commit: f21c8caf83f6b511de6bd5b78e1aa75326823c47 https://github.com/galaxyproject/galaxy/commit/f21c8caf83f6b511de6bd5b78e1aa... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- unname the exception Commit: bde05ac88b66af597e9243d68b7ae8bb364e7653 https://github.com/galaxyproject/galaxy/commit/bde05ac88b66af597e9243d68b7ae... Author: Dannon <dannon.baker@gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6354 from martenson/superdefensive-grt [18.05] grt - wrap every write in try-except Commit: 69c8ce7e92ff41341dff855df3149ae90ca619ed https://github.com/galaxyproject/galaxy/commit/69c8ce7e92ff41341dff855df3149... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Fix size handling in legacy modal view Commit: 9f4926bd9a4f35040126cfcaa6a41c7024c3035a https://github.com/galaxyproject/galaxy/commit/9f4926bd9a4f35040126cfcaa6a41... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Limit modal body size to 67 percent of window height Commit: f6888a32d68d4f1be0b09257a390754a85319da3 https://github.com/galaxyproject/galaxy/commit/f6888a32d68d4f1be0b09257a3907... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add fasta datatype to msa viewer Commit: b0212ff45cf0bc6964278aac49cc42b0ebebdb65 https://github.com/galaxyproject/galaxy/commit/b0212ff45cf0bc6964278aac49cc4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add phylip for msa viewer Commit: 817d043f123563c77e8b430f95d347bbd482d49e https://github.com/galaxyproject/galaxy/commit/817d043f123563c77e8b430f95d34... Author: Dannon <dannon.baker@gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Merge pull request #6361 from guerler/fix_msa [18.05] Add fasta datatype to msa viewer Commit: c601a9d4915388196dc7b00d9cc4090af2b95937 https://github.com/galaxyproject/galaxy/commit/c601a9d4915388196dc7b00d9cc40... Author: John Chilton <jmchilton@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 6b8b862e4d0d6195fb85f4c91419e115dd5564ee https://github.com/galaxyproject/galaxy/commit/6b8b862e4d0d6195fb85f4c91419e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 6b7ee55bac71859c26936a7a154dad6e090047d3 https://github.com/galaxyproject/galaxy/commit/6b7ee55bac71859c26936a7a154da... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: 9e3de244d7184d059e7d19cce01386e99ad85f14 https://github.com/galaxyproject/galaxy/commit/9e3de244d7184d059e7d19cce0138... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 7cfbb032f61bbaf77be198117ba8eaa4b081c094 https://github.com/galaxyproject/galaxy/commit/7cfbb032f61bbaf77be198117ba8e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: b53d2ae3817f2c58f5e1b9f0763ee7b16cc13b81 https://github.com/galaxyproject/galaxy/commit/b53d2ae3817f2c58f5e1b9f0763ee... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: f5aec1cdf18d44d4f3dc74811f421f346fc3c0f7 https://github.com/galaxyproject/galaxy/commit/f5aec1cdf18d44d4f3dc74811f421... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: 647ba8531acdf576cfefea71bc7bb73a89ed7a0a https://github.com/galaxyproject/galaxy/commit/647ba8531acdf576cfefea71bc7bb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: 5e32d78aa7daba492ce31577481f983bd1580b68 https://github.com/galaxyproject/galaxy/commit/5e32d78aa7daba492ce31577481f9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: 333d660556129b66f0bb9e3a117f9003a4bfb368 https://github.com/galaxyproject/galaxy/commit/333d660556129b66f0bb9e3a117f9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: 128a1731e42c5eb4cdf7edf939f7a5c5b3eddbc7 https://github.com/galaxyproject/galaxy/commit/128a1731e42c5eb4cdf7edf939f7a... Author: Dannon <dannon.baker@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Merge pull request #6360 from guerler/legacy_modal_scrolling [18.05] Fix size handling in legacy modal view Commit: b8536c2005c69c42b20509b770f3888a5cbc80e8 https://github.com/galaxyproject/galaxy/commit/b8536c2005c69c42b20509b770f38... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/collection_fixes' into release_18.05 Commit: bcf105cbb37a1c16b2109192c1271b2f4d5847d8 https://github.com/galaxyproject/galaxy/commit/bcf105cbb37a1c16b2109192c1271... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/layout/modal.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Client build. Commit: f9ba72f0aecbb4cdf50a0444dcbec72cc7b8569c https://github.com/galaxyproject/galaxy/commit/f9ba72f0aecbb4cdf50a0444dcbec... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js M config/plugins/visualizations/msa/config/msa.xml M scripts/grt/export.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1c7387c53a0b...f9ba72f0aecb **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.