Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2515267ca5a058d2029c589357f518b1cfb372b8
https://github.com/galaxyproject/galaxy/commit/2515267ca5a058d2029c589357f5…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/wig_to_bigwig.xml
Log Message:
-----------
Add `version` attribute to tool requirements
instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` .
Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 .
See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for
an explanation why that's preferrable for future-proof reproducibility.
Also, small fixes to `tools/evolution/codingSnps.xml` .
Commit: 1624b6ce7d382c5ad1a883a5ca7f86106460e96c
https://github.com/galaxyproject/galaxy/commit/1624b6ce7d382c5ad1a883a5ca7f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/wig_to_bigwig.xml
Log Message:
-----------
Merge pull request #5973 from nsoranzo/followup_on_5544
Add `version` attribute to some tool requirements
Compare: https://github.com/galaxyproject/galaxy/compare/e7158658d026...1624b6ce7d38
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d9904bf595c3815c4827bb0852004d036600936e
https://github.com/galaxyproject/galaxy/commit/d9904bf595c3815c4827bb085200…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Fix for split columns rule definition.
Commit: 8af243c176fd9c261277327750aaa71806add4ef
https://github.com/galaxyproject/galaxy/commit/8af243c176fd9c261277327750aa…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
A client/galaxy/scripts/components/RulesDisplay.vue
M client/galaxy/scripts/mocha/tests/rules_tests.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tool/tool-form.js
A client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M config/tool_conf.xml.main
M lib/galaxy/app.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
A lib/galaxy/tools/apply_rules.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
A lib/galaxy/util/rules_dsl.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/data/rules_dsl_spec.yml
A test/base/rules_test_data.py
M test/base/workflow_fixtures.py
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
A test/unit/test_rule_utils.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Allow rule based operations on existing collections.
Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions.
For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules".
This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions.
This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running.
Commit: c225c5dbd651b048b3354e97a8821d8148b559fe
https://github.com/galaxyproject/galaxy/commit/c225c5dbd651b048b3354e97a882…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M lib/galaxy/tools/apply_rules.xml
Log Message:
-----------
Add simple help for apply rules tool.
Commit: d2b8ad9105e5c06c8ab3685672c1a6dc64b31406
https://github.com/galaxyproject/galaxy/commit/d2b8ad9105e5c06c8ab3685672c1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
RuleBuilder tool param fix for to_dict.
An exception in generating a "text representation" of a None value was preventing the rest of to_dict from running properly for that parameter value. This restores the rule preview table in the tool form.
Commit: a6d052a6819d2bc277744b3e2633785c31c844fb
https://github.com/galaxyproject/galaxy/commit/a6d052a6819d2bc277744b3e2633…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
Log Message:
-----------
Fix modal title for apply_rules branch changes.
Commit: 383eb0d2736269d24d595ed5b8aa730908812be3
https://github.com/galaxyproject/galaxy/commit/383eb0d2736269d24d595ed5b8aa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M config/tool_conf.xml.sample
Log Message:
-----------
Add apply rules tool to standard tool xml sample
Commit: f4eda4fd173b64d782a39da97d7a2b224a7637c3
https://github.com/galaxyproject/galaxy/commit/f4eda4fd173b64d782a39da97d7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M lib/galaxy/tools/apply_rules.xml
Log Message:
-----------
Fix up help language in apply_rules tool.
Commit: cf2f6d7dcf2dba76dc02f1fe6ab0abd360584ef4
https://github.com/galaxyproject/galaxy/commit/cf2f6d7dcf2dba76dc02f1fe6ab0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Fix selenium tests failing because APPLY_RULES appears twice in panel.
Commit: dbd86642d514badcc0fedf3f822f19d7b4dd9d15
https://github.com/galaxyproject/galaxy/commit/dbd86642d514badcc0fedf3f822f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Merge other recent rule PRs into apply_rules branch.
Commit: e7158658d026b7559adb173cea1ac0a26852bca8
https://github.com/galaxyproject/galaxy/commit/e7158658d026b7559adb173cea1a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-04-25 (Wed, 25 Apr 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
A client/galaxy/scripts/components/RulesDisplay.vue
M client/galaxy/scripts/mocha/tests/rules_tests.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/scripts/mvc/tool/tool-form.js
A client/galaxy/scripts/mvc/ui/ui-rules-edit.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M lib/galaxy/app.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/managers/collections.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
A lib/galaxy/tools/apply_rules.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
A lib/galaxy/util/rules_dsl.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/data/rules_dsl_spec.yml
A test/base/rules_test_data.py
M test/base/workflow_fixtures.py
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_run.py
A test/unit/test_rule_utils.py
M test/unit/tools/test_parsing.py
Log Message:
-----------
Merge pull request #5819 from jmchilton/apply_rules
Allow rule based operations on existing collections.
Compare: https://github.com/galaxyproject/galaxy/compare/8f8dc08a4cbe...e7158658d026
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4b09027ebbad5058af4aa882ae6b2fe520c386f9
https://github.com/galaxyproject/galaxy/commit/4b09027ebbad5058af4aa882ae6b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-02-15 (Thu, 15 Feb 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/wig_to_bigwig.xml
Log Message:
-----------
Update all tools/converters using UCSC binaries to depend only on the
binary they are using.
Commit: 7712f69b69d90def8fba5c961b11ecf2169f72df
https://github.com/galaxyproject/galaxy/commit/7712f69b69d90def8fba5c961b11…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/wig_to_bigwig.xml
Log Message:
-----------
Rev tool versions for tools with updated ucsc tool requirements.
Commit: 34016542d9e6987bd615f6e0051d2c6cd1d4dd95
https://github.com/galaxyproject/galaxy/commit/34016542d9e6987bd615f6e0051d…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/wig_to_bigwig.xml
Log Message:
-----------
Merge pull request #5544 from natefoo/split-ucsc-requirements
Update all tools/converters using UCSC binaries to depend only on the binary they are using
Compare: https://github.com/galaxyproject/galaxy/compare/1d5d83feac99...34016542d9e6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2fcfec1bd3b8b31e39c2ae67816c723d96ebf177
https://github.com/galaxyproject/galaxy/commit/2fcfec1bd3b8b31e39c2ae67816c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Data Libary -> Rule Builder fixes.
- Missed allowing collection name in library mode - I told Martin this possible because I thought it was and the library collection type text states it is possible but I didn't fix the switch in rule-definitions.js and notice the problems in createCollection associated with that.
- Fix to drop file type and genome selector when coming from libraries because this targets existing datasets - think this might have slipped back in a bad merge.
- Fix modal title when coming from data library folders.
- Improve text instructions when coming from a library.
Fixes #5967.
Commit: 1d5d83feac999797a127aee7d3b64a0811d1ed49
https://github.com/galaxyproject/galaxy/commit/1d5d83feac999797a127aee7d3b6…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-04-24 (Tue, 24 Apr 2018)
Changed paths:
M client/galaxy/scripts/components/RuleCollectionBuilder.vue
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Merge pull request #5969 from jmchilton/rule_fixes_1
Data Library -> Rule Builder fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/f3455f5276d1...1d5d83feac99