Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5ea926e4b2b5a70a408780d9fcee1b9b7e4e5e88
https://github.com/galaxyproject/galaxy/commit/5ea926e4b2b5a70a408780d9fcee…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M static/maps/mvc/ui/ui-portlet.js.map
M static/scripts/mvc/ui/ui-portlet.js
Log Message:
-----------
Insert editable title flag for portlets
Commit: 6dfc362594c83aa96f6c86acd5d7ee9a84743931
https://github.com/galaxyproject/galaxy/commit/6dfc362594c83aa96f6c86acd5d7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Add optional event handler to edit portlet title text
Commit: e96e86644ea924e21611b65e5bf8bfbf0dc23c9d
https://github.com/galaxyproject/galaxy/commit/e96e86644ea924e21611b65e5bf8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Display node type icon in portlet header for non-tool modules
Commit: 76710c4c7b5030a4cfc89d1a49339a01e0fa1d9c
https://github.com/galaxyproject/galaxy/commit/76710c4c7b5030a4cfc89d1a4933…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Disable text editing, leave feature in for future use
Commit: 7f391076b22dca78299ff9322c593ff8ea6a7510
https://github.com/galaxyproject/galaxy/commit/7f391076b22dca78299ff9322c59…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Display module type icons for tool modules too
Commit: 6e2a0db08272f32abedbbbcb3c3ad06cadaf739b
https://github.com/galaxyproject/galaxy/commit/6e2a0db08272f32abedbbbcb3c3a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use shared portlet style for both module types
Commit: 54573f02ebe7d682347e7a9df0a8360b4fad4339
https://github.com/galaxyproject/galaxy/commit/54573f02ebe7d682347e7a9df0a8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-10 (Tue, 10 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Submit label and annotation separate from other inputs to avoid future conflicts
Commit: dadd6ee2213a8c1fb4e3954b66a234dc10e81719
https://github.com/galaxyproject/galaxy/commit/dadd6ee2213a8c1fb4e3954b66a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
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-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
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-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use underscore to distinguish internal parameters, separate postchange actions
Commit: bc51f6f69fc04e07d1c0d3f7c55a15f62e9f337a
https://github.com/galaxyproject/galaxy/commit/bc51f6f69fc04e07d1c0d3f7c55a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/ui/autocom_tagging.js
M static/maps/libs/jquery/jquery.autocomplete.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/ui/autocom_tagging.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/ui/autocom_tagging.js
Log Message:
-----------
Rename custom autocomplete module to avoid interference with original jquery autocomplete, use original version to display datalists
Commit: 49e784306ba106b28e3499f054df997cfa3694fa
https://github.com/galaxyproject/galaxy/commit/49e784306ba106b28e3499f054df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack scripts
Commit: a55038067bde091be7a4edef0c7eda0400c95622
https://github.com/galaxyproject/galaxy/commit/a55038067bde091be7a4edef0c7e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Display unfiltered datalist options
Commit: e22b4bcbfc465fb46e1cd2dc314e941001ce6164
https://github.com/galaxyproject/galaxy/commit/e22b4bcbfc465fb46e1cd2dc314e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Do not attach autocomplete handler if datalist is empty
Commit: b3e161a4af6c5059338680591514efea18d553bc
https://github.com/galaxyproject/galaxy/commit/b3e161a4af6c5059338680591514…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Check datalist length before attaching autocomplete feature
Commit: dc5326ce034f6d38955fe0faa7ed6ea7fd2a4977
https://github.com/galaxyproject/galaxy/commit/dc5326ce034f6d38955fe0faa7ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Use workflow form handler options to parse tool id and version
Commit: 20c27075364996898e429936578fdfbcd9abebec
https://github.com/galaxyproject/galaxy/commit/20c27075364996898e429936578f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Attach onchange handler once, avoid overwrite
Commit: e571fce4781ca004c21f8091a46bebaecd6e3bd4
https://github.com/galaxyproject/galaxy/commit/e571fce4781ca004c21f8091a46b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.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 lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Revise label handling and duplicate check, move save controller to api for proper error response
Commit: 37501a5b8475c2c0ef65d6e5dea86cadcd3566bb
https://github.com/galaxyproject/galaxy/commit/37501a5b8475c2c0ef65d6e5dea8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Remove debug output
Commit: ddf4bad6ffa20df224c724329151e2c810af2c6a
https://github.com/galaxyproject/galaxy/commit/ddf4bad6ffa20df224c724329151…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix blank line
Commit: 6c3b4020200b52352f6a47140a6931456f2755cc
https://github.com/galaxyproject/galaxy/commit/6c3b4020200b52352f6a47140a69…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-11 (Wed, 11 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Properly attach event handler when user clicks on autocomplete selection
Commit: 6c4a4ce3e43af7488f63892420260faab7d9399f
https://github.com/galaxyproject/galaxy/commit/6c4a4ce3e43af7488f6389242026…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-14 (Sat, 14 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Revise tool model building to always provide a properly ordered array, augment model handling on front-end
Commit: 9c9c4d2d083dc9129ea257a8e0205a4ae89f371b
https://github.com/galaxyproject/galaxy/commit/9c9c4d2d083dc9129ea257a8e020…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-15 (Sun, 15 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Fix error display
Commit: 3911cb039d46f76f0548d993f4ca932204672bb2
https://github.com/galaxyproject/galaxy/commit/3911cb039d46f76f0548d993f4ca…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-24 (Tue, 24 Jan 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_galaxy.bash
M .ci/py3_sources.txt
M README.rst
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/viz/trackster/tracks.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/csg/templates/csg.mako
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/plugins/webhooks/demo/phdcomics/helper/__init__.py
M config/plugins/webhooks/demo/phdcomics/static/script.js
M doc/schema_template.md
M doc/source/admin/webhooks.rst
M doc/source/api/guidelines.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml
A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml
A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml
A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/diamond_db.dmnd
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/dependencies.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/object_wrapper.py
A lib/galaxy/util/oset.py
M lib/galaxy/util/properties.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/shed_util_common.py
M run.sh
M run_tests.sh
A scripts/manage_tool_dependencies.py
A static/maps/libs/showdown.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/libs/showdown.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/viz/trackster/tracks.js
M templates/ind_share_base.mako
M templates/webapps/galaxy/history/share.mako
A test-data/1.fastqsanger.bz2
A test-data/1.fastqsanger.gz
M test/api/test_workflows.py
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/column_param.xml
A test/functional/tools/compressed_bz2_fastq_conversion.xml
A test/functional/tools/compressed_bz2_fastq_no_conversion.xml
A test/functional/tools/compressed_gz_fastq_conversion.xml
A test/functional/tools/compressed_gz_fastq_no_conversion.xml
A test/functional/tools/explicit_conversion.xml
A test/functional/tools/implicit_conversion.xml
A test/functional/tools/legacy_r.xml
A test/functional/tools/mulled_example_conflict.xml
A test/functional/tools/param_text_option.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/integration/test_resolvers.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/unit/tools/test_tool_deps.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.xml
M tools/filters/pasteWrapper.xml
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/plotting/bar_chart.xml
M tools/stats/aggregate_binned_scores_in_intervals.xml
Log Message:
-----------
Merge branch 'dev' into fix_workflow_ui
Commit: 5bf7c46eca5c3dbad5c7009f4bb81b48503a6307
https://github.com/galaxyproject/galaxy/commit/5bf7c46eca5c3dbad5c7009f4bb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-01-31 (Tue, 31 Jan 2017)
Changed paths:
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Repack scripts
Commit: 1bb10da295fdf25855f5140f26bc7a62b278acab
https://github.com/galaxyproject/galaxy/commit/1bb10da295fdf25855f5140f26bc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Raise message exception instead of return a dictionary
Commit: f264e91cabfd29a8f385f8fbce4c8714b088fa23
https://github.com/galaxyproject/galaxy/commit/f264e91cabfd29a8f385f8fbce4c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Use update endpoint to store workflows
Commit: db47be5ad91bdd9364d5f9525941fd9a7b2c57c0
https://github.com/galaxyproject/galaxy/commit/db47be5ad91bdd9364d5f9525941…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove endpoint from routing
Commit: 284000c688724f47055a46bab4e8b377224db751
https://github.com/galaxyproject/galaxy/commit/284000c688724f47055a46bab4e8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Remove unused error variable
Commit: 5b366642019b4d69d033d916b71b5a85c3767d0f
https://github.com/galaxyproject/galaxy/commit/5b366642019b4d69d033d916b71b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M static/maps/mvc/form/form-input.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Fix qunit tests
Commit: 6a8dc6e26cf92d0c54a35e76c978dba8d6cd9864
https://github.com/galaxyproject/galaxy/commit/6a8dc6e26cf92d0c54a35e76c978…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Evaluate cyclic workflows on the fly when loading the run workflow form
Commit: afb024819917535ba4820405c31f00d16224f453
https://github.com/galaxyproject/galaxy/commit/afb024819917535ba4820405c31f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/workflow/steps.py
Log Message:
-----------
Remove blank line
Commit: d302400b99b7ae32a2d3f09266b15380b81d83b3
https://github.com/galaxyproject/galaxy/commit/d302400b99b7ae32a2d3f09266b1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-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-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.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/ui/autocom_tagging.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/steps.py
M static/maps/libs/jquery/jquery.autocomplete.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/ui/autocom_tagging.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-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-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.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/ui/autocom_tagging.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge pull request #3407 from guerler/fix_workflow_ui
Workflow editor UI touch up
Compare: https://github.com/galaxyproject/galaxy/compare/7411aa52fd9c...d302400b99b7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 417d119df9151b0462aa1c802108fa63f46e3f09
https://github.com/galaxyproject/galaxy/commit/417d119df9151b0462aa1c802108…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Avoid stringification of tool state root dictionary
Commit: ee6063ec5b88308b2fbc2da9a47c3549f6a5c37b
https://github.com/galaxyproject/galaxy/commit/ee6063ec5b88308b2fbc2da9a47c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-01 (Wed, 01 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Adjust export for backward compatibility
Commit: fa93c6bbc8449555b1d59dbe9cfaab3ddd3fa45e
https://github.com/galaxyproject/galaxy/commit/fa93c6bbc8449555b1d59dbe9cfa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Remove state handling from tool shed mako
Commit: 26a18440304c8b637dc5e0ffe7d3835026087903
https://github.com/galaxyproject/galaxy/commit/26a18440304c8b637dc5e0ffe7d3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Attempt to use dicts also for module parameter value storage
Commit: 6acbafee8a60b03faae9906bfce44d67abfe54b1
https://github.com/galaxyproject/galaxy/commit/6acbafee8a60b03faae9906bfce4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-04 (Sat, 04 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Use basic parameter handler to ensure proper text type value decoding
Commit: 09f9396eab2c511013c0b637997191bc4f0e74ba
https://github.com/galaxyproject/galaxy/commit/09f9396eab2c511013c0b6379971…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-02-06 (Mon, 06 Feb 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Use number library to identify numeric values
Commit: 7411aa52fd9cdaa1874a773fbfd440866f909e65
https://github.com/galaxyproject/galaxy/commit/7411aa52fd9cdaa1874a773fbfd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/modules.py
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Merge pull request #3522 from guerler/store_step_json_000
Store module step states as nested dictionaries, fix export for backward compatibility
Compare: https://github.com/galaxyproject/galaxy/compare/68752b7db0c6...7411aa52fd9c
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0d21f657ca4115ce3e309394cff8bdb084de6ef3
https://github.com/galaxyproject/galaxy/commit/0d21f657ca4115ce3e309394cff8…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Consolidate exception logging in db migrations
Also:
- align engine_true() and engine_false() methods
- remove unused 'now' variables
Commit: cb4fbe7a1caba8195ac8ec4965c702a58378f592
https://github.com/galaxyproject/galaxy/commit/cb4fbe7a1caba8195ac8ec4965c7…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
Log Message:
-----------
Fix a bunch of database migration bugs
Commit: 68752b7db0c6328d1d88e657ad21b2e4312f4401
https://github.com/galaxyproject/galaxy/commit/68752b7db0c6328d1d88e657ad21…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-07 (Tue, 07 Feb 2017)
Changed paths:
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Merge pull request #3570 from nsoranzo/database_migrations
Database migrations: improvements and fixes
Compare: https://github.com/galaxyproject/galaxy/compare/27d871f20edc...68752b7db0c6