- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 355b48: Make handler assignment configurable in preparatio...
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 355b48c361e68a7d9fbe9fe86de7aa2313e5d608 https://github.com/galaxyproject/galaxy/commit/355b48c361e68a7d9fbe9fe86de7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Make handler assignment configurable in preparation for new assignment methods. Commit: 10c45705bca081c336214b08fcc84d209b19b345 https://github.com/galaxyproject/galaxy/commit/10c45705bca081c336214b08fcc8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Unit tests and fixes for bugs discovered while testing. Commit: 1fb8203a0c1f6f941e0b13fa6357ec04ea677ffb https://github.com/galaxyproject/galaxy/commit/1fb8203a0c1f6f941e0b13fa6357… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-10 (Mon, 10 Dec 2018) Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/jobs/manager.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Handler assignment documentation. Commit: 40f776afde460759b5d682c19ef698fefd2d4388 https://github.com/galaxyproject/galaxy/commit/40f776afde460759b5d682c19ef6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/manager.py M lib/galaxy/util/handlers.py M test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py Log Message: ----------- Fix tests broken with changes to job_conf.xml.sample_advanced, fix the broken direct handler assignment method, document the new handler assignment methods for future method authors. Ensure that enqueue does its best to return a handler (if known). Commit: 4a006335ac4ac84a69b5cb1f851e3e63400443ae https://github.com/galaxyproject/galaxy/commit/4a006335ac4ac84a69b5cb1f851e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix default job config (no job_conf.xml). Commit: e9aec176fac8bb3681ea533be6178ffd43c3bf4d https://github.com/galaxyproject/galaxy/commit/e9aec176fac8bb3681ea533be617… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Fixes for workflow scheduling tests. Commit: 7bed9f03180826f7c7f99b12b08bcb265867217b https://github.com/galaxyproject/galaxy/commit/7bed9f03180826f7c7f99b12b08b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/workflow_schedulers_conf.xml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/scaling.md M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/manager.py M lib/galaxy/managers/datasets.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/scheduling_manager.py A test/unit/jobs/handler_template_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_actions.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7091 from natefoo/handler-assignment-fixes Configurable job/workflow handler assignment methods Compare: https://github.com/galaxyproject/galaxy/compare/1fd3fccb216b...7bed9f031808 **NOTE:** This service has 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] 0c145b: Updated Neo4j IE to 3.1.9
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c145b3326f2476b05ed8ca7ee66d754099a452f https://github.com/galaxyproject/galaxy/commit/0c145b3326f2476b05ed8ca7ee66… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated Neo4j IE to 3.1.9 Commit: 2da38803a3bc12a19e1fa53a1e8cc9e9448eb1b6 https://github.com/galaxyproject/galaxy/commit/2da38803a3bc12a19e1fa53a1e8c… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-18 (Thu, 18 Oct 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Catering for shlex.split(cmd_inject) behaviour Commit: 1fd3fccb216bcfab298e2cfd812f2ec3b3e45afe https://github.com/galaxyproject/galaxy/commit/1fd3fccb216bcfab298e2cfd812f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6897 from thobalose/neo4j-ie Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9 Compare: https://github.com/galaxyproject/galaxy/compare/bf550da2afe9...1fd3fccb216b **NOTE:** This service has 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] 952fda: Remove unused and broken tool
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952fdac419e9b4123c158fd088f90a9a09bc7fd3 https://github.com/galaxyproject/galaxy/commit/952fdac419e9b4123c158fd088f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: R tools/data_source/bed_convert.xml Log Message: ----------- Remove unused and broken tool Commit: f865e8359fa6c8d599011edcea61a2a728afb9ea https://github.com/galaxyproject/galaxy/commit/f865e8359fa6c8d599011edcea61… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Deprecate `size` attribute of `<param/>` and remove it from tools Also: - dos2unix test/functional/tools/for_workflows/head.xml - Single-quote text and data params in `<command/>` - Remove deprecated `interpreter` attribute of `<command />` Commit: bf550da2afe94ad53aae71e3d930a49cb98558a4 https://github.com/galaxyproject/galaxy/commit/bf550da2afe94ad53aae71e3d930… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M config/job_resource_params_conf.xml.sample M config/workflow_resource_params_conf.xml.sample M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/for_workflows/head.xml M test/unit/tools/test_wrappers.py R tools/data_source/bed_convert.xml M tools/data_source/genbank.xml M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/CreateInterval.xml M tools/filters/bed_to_bigbed.xml M tools/filters/changeCase.xml M tools/filters/fileGrep.xml M tools/filters/fixedValueColumn.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/grep.xml M tools/filters/headWrapper.xml M tools/filters/randomlines.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/wig_to_bigwig.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/blat_wrapper.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper.xml M tools/sr_mapping/PerM.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.xml M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups Log Message: ----------- Merge pull request #6684 from nsoranzo/deprecate_param_size Deprecate `size` attribute of `<param/>` and remove it from tools Compare: https://github.com/galaxyproject/galaxy/compare/d06718ef2420...bf550da2afe9 **NOTE:** This service has 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] 7b027d: improved grouping
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b027d8a1fbed0b5471f774fe3d3a3cab123093f https://github.com/galaxyproject/galaxy/commit/7b027d8a1fbed0b5471f774fe3d3… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- improved grouping - replaces non 'floatable' values to a user supplied default value - do not strip lines because this removes empty cells at the ends - added some comments to python code Commit: d06718ef24202d2fcaf3d6e8bfaa9a862044f90f https://github.com/galaxyproject/galaxy/commit/d06718ef24202d2fcaf3d6e8bfaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- Merge pull request #6577 from bernt-matthias/topic/grouping-wreplace improved grouping tool Compare: https://github.com/galaxyproject/galaxy/compare/c6fc4dc83a6a...d06718ef2420 **NOTE:** This service has 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] e5c9d9: Fix ``size_to_bytes`` for some float values
by GitHub 12 Dec '18

12 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e5c9d9673d6d92291b7911f4255cbbafebceed0e https://github.com/galaxyproject/galaxy/commit/e5c9d9673d6d92291b7911f4255c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix ``size_to_bytes`` for some float values Values like `.01` and `1.` were broken in commit 26a6b1c83381d1c75131f330d8b8f4c23680f1dd . The new regexp allows also scientific notation like `1.2E2` . Commit: c6fc4dc83a6ac46244ff05d560864cba1de8bf55 https://github.com/galaxyproject/galaxy/commit/c6fc4dc83a6ac46244ff05d56086… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-12 (Wed, 12 Dec 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #7096 from nsoranzo/followup_on_7067 Fix ``size_to_bytes`` for some float values Compare: https://github.com/galaxyproject/galaxy/compare/0b0c0084198d...c6fc4dc83a6a **NOTE:** This service has 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] c4ab2a: Add workaround for https://github.com/travis-ci/tr...
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround [18.09] boto cfg workaround Commit: 0b0c0084198d59e5767decb9b79580cc2a3932b2 https://github.com/galaxyproject/galaxy/commit/0b0c0084198d59e5767decb9b795… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-12 (Wed, 12 Dec 2018) Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/10aa953a40e1...0b0c0084198d **NOTE:** This service has 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] c4ab2a: Add workaround for https://github.com/travis-ci/tr...
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround [18.09] boto cfg workaround Compare: https://github.com/galaxyproject/galaxy/compare/57459954de18...3a1bdd0ea688 **NOTE:** This service has 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] 55bd75: Update TTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55bd75a7ce10d1088e75a799b5ec6e025c9a67df https://github.com/galaxyproject/usegalaxy-playbook/commit/55bd75a7ce10d108… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS **NOTE:** This service has 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] 2de4a0: Remove legacy job handling hacks.
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2de4a0f72e5d51661318e1abeb727fdaa10f7444 https://github.com/galaxyproject/galaxy/commit/2de4a0f72e5d51661318e1abeb72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Remove legacy job handling hacks. These were left in to let Galaxy jobs complete after version upgrades, but the plan was always to remove them eventually. Commit: 10aa953a40e171246bdd1804c74e8019da8e8200 https://github.com/galaxyproject/galaxy/commit/10aa953a40e171246bdd1804c74e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7082 from jmchilton/legacy_hacks Remove legacy job handling hacks. Compare: https://github.com/galaxyproject/galaxy/compare/11428a03b819...10aa953a40e1 **NOTE:** This service has 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] 3ae75e: Update MTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ae75e93d54584e6d250f745f6d1a176cf73ba22 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ae75e93d54584e6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS **NOTE:** This service has 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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