June 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 14cfb2: Give NO_REPLACEMENT constant object a str value.
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14cfb26ca1b888156ae517dc33ebeefc099bac6f https://github.com/galaxyproject/galaxy/commit/14cfb26ca1b888156ae517dc33eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Give NO_REPLACEMENT constant object a str value. Shows up in logging a lot and such - make it more clear. Commit: 95962d9e5aa2b3b8e60755767b0dbc06ef341782 https://github.com/galaxyproject/galaxy/commit/95962d9e5aa2b3b8e60755767b0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M test/base/populators.py Log Message: ----------- More correct file_data handling in populators.py. Any of file_N|file_data fields can have attached data. Commit: 31640840e310f76dc38e24f4147c0d4d1959f178 https://github.com/galaxyproject/galaxy/commit/31640840e310f76dc38e24f4147c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Fix consumption of macro paths from tool spec. Commit: 5551611aff92f55c7b1e00f573c44473b6b2823a https://github.com/galaxyproject/galaxy/commit/5551611aff92f55c7b1e00f573c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Drop old comment, we use this variable now and have for some time. Commit: b50ae948368abae7f91af8e2d4f3cbc69418ab92 https://github.com/galaxyproject/galaxy/commit/b50ae948368abae7f91af8e2d4f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-15 (Tue, 15 May 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Move workflow api test helpers into base class for more reuse. Commit: 5a27b0cf4d4105f61c7660b63de97d812346df13 https://github.com/galaxyproject/galaxy/commit/5a27b0cf4d4105f61c7660b63de9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/populators.py Log Message: ----------- Merge pull request #6148 from jmchilton/cwl-small-stuff-2 Small fixes and small refactorings toward reuse in CWL branch (retry) Compare: https://github.com/galaxyproject/galaxy/compare/d514ebce3bfe...5a27b0cf4d41 **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.

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[galaxyproject/galaxy] 6e78a4: Add impersonate to main user grid when it's enable...
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e78a440b308a0a0df541b6d98891d17b99a2a46 https://github.com/galaxyproject/galaxy/commit/6e78a440b308a0a0df541b6d9889… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add impersonate to main user grid when it's enabled Commit: 96b4532e9999b816df3dcc5de6e7c2d7607b5ec6 https://github.com/galaxyproject/galaxy/commit/96b4532e9999b816df3dcc5de6e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M templates/admin/impersonate.mako Log Message: ----------- Drop emails query we weren't actually even using... Commit: 3bd8b3b18b6032e8844795fae488e501074cd573 https://github.com/galaxyproject/galaxy/commit/3bd8b3b18b6032e8844795fae488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/impersonate.mako M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Impersonation refactoring, condense functionality into user grid, optimize some stuff. Commit: ce2893d50d1e2914fa2193aea26d563258a11bc9 https://github.com/galaxyproject/galaxy/commit/ce2893d50d1e2914fa2193aea26d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add APIKey generation operation to user grid. Commit: 5e9cd276ebbef84a0091ef3b531d4b5553874bff https://github.com/galaxyproject/galaxy/commit/5e9cd276ebbef84a0091ef3b531d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Match existing formatting. Commit: c3d01f0505a42903f4fd2bc42d8e5bdce13315d3 https://github.com/galaxyproject/galaxy/commit/c3d01f0505a42903f4fd2bc42d8e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Actually include new_key in msgstring Commit: fb199c5f8c8083e78cc50d62b1c77c9fec21f249 https://github.com/galaxyproject/galaxy/commit/fb199c5f8c8083e78cc50d62b1c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Slight safeguarding of user selection, respond with a more contextualized message Commit: 61e2e82a09047b5b1d4194259012178bc8dfd7f8 https://github.com/galaxyproject/galaxy/commit/61e2e82a09047b5b1d4194259012… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/apps/admin.js R client/galaxy/scripts/components/admin/UserAPIKeys.vue Log Message: ----------- Drop individual UserAPIKeys.vue; this functionality is included in the standard user grid now. Commit: 9dcb1019c5afe76c864cb4e361509b4f47f215c2 https://github.com/galaxyproject/galaxy/commit/9dcb1019c5afe76c864cb4e36150… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Drop separate APIKeys blurb Commit: d514ebce3bfe936091f57d22bbafbca48d419fa8 https://github.com/galaxyproject/galaxy/commit/d514ebce3bfe936091f57d22bbaf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js R client/galaxy/scripts/components/admin/UserAPIKeys.vue M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/impersonate.mako M templates/webapps/galaxy/admin/center.mako Log Message: ----------- Merge pull request #6176 from dannon/user_grid_impersonate Add impersonate to main user grid when it's enabled Compare: https://github.com/galaxyproject/galaxy/compare/542dbe63e896...d514ebce3bfe **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.

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[galaxyproject/galaxy] f59b13: Replace non-existent `tab` format with `tabular` i...
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f59b13c1cdb8e688d6738463ce54027e53d61cb7 https://github.com/galaxyproject/galaxy/commit/f59b13c1cdb8e688d6738463ce54… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Replace non-existent `tab` format with `tabular` in 2 tools Also: - Remove deprecated `interpreter` attribute of `<command>` - Single-quote text and data parameters inside the command - Fix wrong `name` attribute of `output` in 3 tests - Linting and cleanups Commit: b454bef75de0730b80820326eb53c2501b8baa05 https://github.com/galaxyproject/galaxy/commit/b454bef75de0730b80820326eb53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Fix indentation Commit: 542dbe63e89689daec88ab0d075ad7f1f77bf0b0 https://github.com/galaxyproject/galaxy/commit/542dbe63e89689daec88ab0d075a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Merge pull request #6269 from nsoranzo/phenotype_association_tools Fixes for phenotype association tools Compare: https://github.com/galaxyproject/galaxy/compare/9b9ab6a1cf44...542dbe63e896 **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.

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[galaxyproject/galaxy] 713bca: Allow #if $datasets #end if patern for file lists
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 713bca04f63f464ccbb47ced90d971624ed075b6 https://github.com/galaxyproject/galaxy/commit/713bca04f63f464ccbb47ced90d9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow #if $datasets #end if patern for file lists Otherwise the following exception occurs: ``` Traceback (most recent call last): File "/home/wolffj/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job job_wrapper.prepare() File "/home/wolffj/src/galaxy/lib/galaxy/jobs/__init__.py", line 858, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/wolffj/src/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build raise e AttributeError: 'DatasetListWrapper' object has no attribute 'value' ``` This is because DatasetListWrapper inherits `__bool__` from ToolParameterValueWrapper which defines bool as ``` def __bool__(self): return bool(self.value) __nonzero__ = __bool__ ``` while DatasetListWrapper has no `value` attribute. Fixes https://github.com/galaxyproject/galaxy/issues/6314 reported by @joachimwolff (many thanks for the detailed report!). Commit: 0a29e533d3362e3a0dd7bfc202e8fff799a9e6ee https://github.com/galaxyproject/galaxy/commit/0a29e533d3362e3a0dd7bfc202e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Use #if $datasets #end if pattern in test tool Commit: 6f213b36975b5b8f66b0b02f8920744a5e2d0064 https://github.com/galaxyproject/galaxy/commit/6f213b36975b5b8f66b0b02f8920… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix __bool__ for empty optional multidata parameters Commit: 550eb882100a3a9210689dbe789b67a1eb2ba5c2 https://github.com/galaxyproject/galaxy/commit/550eb882100a3a9210689dbe789b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Add a test for not providing an optional input Commit: 9b9ab6a1cf4485920c88b252d27642f6f20c3525 https://github.com/galaxyproject/galaxy/commit/9b9ab6a1cf4485920c88b252d276… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/multi_data_optional.xml Log Message: ----------- Merge pull request #6317 from mvdbeek/fix_6314 Allow #if $datasets #end if pattern for file lists Compare: https://github.com/galaxyproject/galaxy/compare/c08f7c9a4cfd...9b9ab6a1cf44 **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.

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[galaxyproject/galaxy] 6ad419: Fix undefined success_message
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ad41928093c033568eeb3e530f32a813accb24e https://github.com/galaxyproject/galaxy/commit/6ad41928093c033568eeb3e530f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Fix undefined success_message Commit: c08f7c9a4cfdf4da4771b7f891892ea1332666dc https://github.com/galaxyproject/galaxy/commit/c08f7c9a4cfdf4da4771b7f89189… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Merge pull request #6316 from mvdbeek/success_message_fix Fix undefined success_message Compare: https://github.com/galaxyproject/galaxy/compare/254a6bc8d793...c08f7c9a4cfd **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.

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[galaxyproject/galaxy] b46ab9: Fix typo (UnitializedTree -> UninitializedTree)
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b46ab962adcaef54b75b8e9bf3e5647b59b128cc https://github.com/galaxyproject/galaxy/commit/b46ab962adcaef54b75b8e9bf3e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix typo (UnitializedTree -> UninitializedTree) Commit: 254a6bc8d7939a385783795aba6f1fb4a7c4677d https://github.com/galaxyproject/galaxy/commit/254a6bc8d7939a385783795aba6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6315 from mvdbeek/fix_uninitialized_typo Fix typo (UnitializedTree -> UninitializedTree) Compare: https://github.com/galaxyproject/galaxy/compare/1b50504678dc...254a6bc8d793 **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.

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[galaxyproject/galaxy] 6c2f19: Rules - test case and bug fixes for adding cols fo...
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c2f1957a9c49943182b8b971097f9a8ef511bab https://github.com/galaxyproject/galaxy/commit/6c2f1957a9c49943182b8b971097… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: 898e73eca1eccfb9fb707cdb5af75ee72c3d7565 https://github.com/galaxyproject/galaxy/commit/898e73eca1eccfb9fb707cdb5af7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: ec723829bf788b3100bfb56f72c22dd4981e3fdf https://github.com/galaxyproject/galaxy/commit/ec723829bf788b3100bfb56f72c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Rules - fix poor name for Apply Rules output collection. Commit: 050c9e99c6c981518f160d99aeaa2f395a84e4b5 https://github.com/galaxyproject/galaxy/commit/050c9e99c6c981518f160d99aeaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Rules - test case for apply rules tutorial. Demonstrates using the Apply Rules collection operation tool against existing collections to: - Use grouping to build nested lists from flat ones. - Invert nested collections. - Filter collections. - Filter while also grouping to build nested collections. Based on count data used in the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq…) originally from the Bioconductor Pasilla package (http://bioconductor.org/packages/release/data/experiment/html/pasilla.html) Citation: Huber W, Reyes A (2018). pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.. R package version 1.8.0. Commit: 1b50504678dc5c84fa292236ac58697591611aa4 https://github.com/galaxyproject/galaxy/commit/1b50504678dc5c84fa292236ac58… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6066 from jmchilton/apply_rules_tutorials Rules - test case for apply rules tutorial. Compare: https://github.com/galaxyproject/galaxy/compare/178486b840b6...1b50504678dc **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.

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[galaxyproject/galaxy] 940ed5: Break test by adding "list" to collection_type
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 940ed5f5dd1f34456d81513db8bbf0a66476e683 https://github.com/galaxyproject/galaxy/commit/940ed5f5dd1f34456d81513db8bb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 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: cb97f89d129cf7f0b7cf7146c0c15309b3dcb0c7 https://github.com/galaxyproject/galaxy/commit/cb97f89d129cf7f0b7cf7146c0c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 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: 9b19d5c267900409b5aace9f2c554b2da13ce8e7 https://github.com/galaxyproject/galaxy/commit/9b19d5c267900409b5aace9f2c55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: fd16302d65193f13eb04456b610044343ca54adb https://github.com/galaxyproject/galaxy/commit/fd16302d65193f13eb04456b6100… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: 258ccb89bd5190e703f9d1705ec888b65ce77724 https://github.com/galaxyproject/galaxy/commit/258ccb89bd5190e703f9d1705ec8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: fc06a7a168d5d36fabb3f6f420a4ef0b12363f2c https://github.com/galaxyproject/galaxy/commit/fc06a7a168d5d36fabb3f6f420a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: 178486b840b64c2bfb1b4cffefd44c945a8ccb3e https://github.com/galaxyproject/galaxy/commit/178486b840b64c2bfb1b4cffefd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/history_query.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 pull request #6278 from mvdbeek/fix_paired_mapping_over Various fixes for mapping over collections Compare: https://github.com/galaxyproject/galaxy/compare/cd2feb7dcb81...178486b840b6 **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.

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[galaxyproject/usegalaxy-playbook] 1b5edc: Updated RNAStar on test and main to version 2.6.0b
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1b5edc4e15bcbd5db7e8774e0a5504413c365f5a https://github.com/galaxyproject/usegalaxy-playbook/commit/1b5edc4e15bcbd5d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Updated RNAStar on test and main to version 2.6.0b **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.

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[galaxyproject/galaxy] 39dc8c: Revise job success message
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39dc8cfac9a9f090e433ef94e01025329ba421e7 https://github.com/galaxyproject/galaxy/commit/39dc8cfac9a9f090e433ef94e010… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise job success message Commit: 8e55b22542ff4a7118294efeab296ccc5849db84 https://github.com/galaxyproject/galaxy/commit/8e55b22542ff4a7118294efeab29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Sort history items by history id in success message Commit: 086bf43eeb3362a775a62420f430156b19b1df19 https://github.com/galaxyproject/galaxy/commit/086bf43eeb3362a775a62420f430… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Hide inputs for tools without inputs Commit: 106dda140f322734c6c4917a54b137c418840a99 https://github.com/galaxyproject/galaxy/commit/106dda140f322734c6c4917a54b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Missing semicolon. Commit: 80e1590869527627ede01954d0a4271ca05304bf https://github.com/galaxyproject/galaxy/commit/80e1590869527627ede01954d0a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client format Commit: cd2feb7dcb81424e753ef371879c3f4b397555b6 https://github.com/galaxyproject/galaxy/commit/cd2feb7dcb81424e753ef371879c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge branch 'job_success_message' into dev Compare: https://github.com/galaxyproject/galaxy/compare/99c1da2f6273...cd2feb7dcb81 **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.

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