Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c83c38c723d76e4dd0f87b2c2fca08e88c515d87 https://github.com/galaxyproject/galaxy/commit/c83c38c723d76e4dd0f87b2c2fca0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add basic structure to support chunked file uploads Commit: 2eb4fa5e4e06455a7fa6b079211b342b85aec808 https://github.com/galaxyproject/galaxy/commit/2eb4fa5e4e06455a7fa6b079211b3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix debug statements Commit: 6de335391b9422b45b8bfc59f7d5860e6508623a https://github.com/galaxyproject/galaxy/commit/6de335391b9422b45b8bfc59f7d58... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove debugging script, submit actual data Commit: 96d3e8076d67adcfb18969ae5939e5b760f8ad6e https://github.com/galaxyproject/galaxy/commit/96d3e8076d67adcfb18969ae5939e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Modify progress handler to accomodate chunks Commit: 313f165c4a42303dbdcf795f62dfc705ffbcd4fe https://github.com/galaxyproject/galaxy/commit/313f165c4a42303dbdcf795f62dfc... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use let instead of var for for-loops Commit: afe0b6a90e8a358dafc0f0700149cfaa3f3296d8 https://github.com/galaxyproject/galaxy/commit/afe0b6a90e8a358dafc0f0700149c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use regular debug statements instead of logger Commit: d9c9482685c040a03ba954ddd89818bd1e1ca0d7 https://github.com/galaxyproject/galaxy/commit/d9c9482685c040a03ba954ddd8981... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse submission helper Commit: 309dfbf355c207b3b626076b5f9194e277bd8ec3 https://github.com/galaxyproject/galaxy/commit/309dfbf355c207b3b626076b5f919... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Remove redundant log Commit: 8805d09c07b5eb8128283f7c205106592a9a29d2 https://github.com/galaxyproject/galaxy/commit/8805d09c07b5eb8128283f7c20510... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add file data name parameter Commit: ca2382576227d078cd5e95b1f9778f121fed9e5a https://github.com/galaxyproject/galaxy/commit/ca2382576227d078cd5e95b1f9778... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix for collection handler Commit: ca2c300d943f9df45744ba3b02da23d245e0cfb4 https://github.com/galaxyproject/galaxy/commit/ca2c300d943f9df45744ba3b02da2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reduce chunk size for testing, remove debug output Commit: 09bd90845677c9b36881bbaf6f84be63049bf00a https://github.com/galaxyproject/galaxy/commit/09bd90845677c9b36881bbaf6f84b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix chunk sizes Commit: 5e26c0322a5338d0096abab1559f54227d75b6b0 https://github.com/galaxyproject/galaxy/commit/5e26c0322a5338d0096abab1559f5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix comment Commit: 975bd2f36714622b2b34e06422c9bb93ecd33e45 https://github.com/galaxyproject/galaxy/commit/975bd2f36714622b2b34e06422c9b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Submit file segments in request body, use header parameters Commit: c5337fe04a89cc6a3716469f13b0c7a5777ad5bc https://github.com/galaxyproject/galaxy/commit/c5337fe04a89cc6a3716469f13b0c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Parse file and chunk data to post helper Commit: 488ce62aa3c870c4dd524ad7d07efc9f27acbafe https://github.com/galaxyproject/galaxy/commit/488ce62aa3c870c4dd524ad7d07ef... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use template literal, fix session id parsing Commit: 0f69eafc9d7ca185a505a7c75e5ffce14cb48e49 https://github.com/galaxyproject/galaxy/commit/0f69eafc9d7ca185a505a7c75e5ff... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Rename header parameter Commit: b56bec033d111be265102deef262127cb574906e https://github.com/galaxyproject/galaxy/commit/b56bec033d111be265102deef2621... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix template string Commit: 2b18782598848f109b58efa9b5364b9afccaee7e https://github.com/galaxyproject/galaxy/commit/2b18782598848f109b58efa9b5364... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Parse nginx upload directory to client Commit: 39512626d2f35083d554d99d86030bf79f826844 https://github.com/galaxyproject/galaxy/commit/39512626d2f35083d554d99d86030... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Reuse existing request helper for whole file submission Commit: 937fe619e61023b4fe786e4a7c2bfcbb52da7cfa https://github.com/galaxyproject/galaxy/commit/937fe619e61023b4fe786e4a7c2bf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix success response parsing Commit: bd9ce253383c8833a387e3895d032ad10fd0729d https://github.com/galaxyproject/galaxy/commit/bd9ce253383c8833a387e3895d032... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comments Commit: ceedcb550fb23b045db0b1e32938df32e8d79be7 https://github.com/galaxyproject/galaxy/commit/ceedcb550fb23b045db0b1e32938d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-17 (Sat, 17 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Consolidate helpers Commit: dee0cef80f6e5e2a480a8a41a2ed6b2bcb7ca92f https://github.com/galaxyproject/galaxy/commit/dee0cef80f6e5e2a480a8a41a2ed6... 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lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/tools/tool_validator.py M scripts/common_startup.sh R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/new_tags_1.txt M test/api/test_visualizations.py M test/base/interactor.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/test_saved_histories.py M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: d95337bde017cf15eceee8b989aee01c9707fca4 https://github.com/galaxyproject/galaxy/commit/d95337bde017cf15eceee8b989aee... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/tools/parameters/grouping.py M static/style/blue/base.css Log Message: ----------- Add tool submission request Commit: c04bb8c2479a739d7bfeec2fd9ec7bec2b91a79a https://github.com/galaxyproject/galaxy/commit/c04bb8c2479a739d7bfeec2fd9ec7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Increase chunksize Commit: afd5c8d1c5b9e34fd7861b40c6ca78cbe4804490 https://github.com/galaxyproject/galaxy/commit/afd5c8d1c5b9e34fd7861b40c6ca7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Add warning notification Commit: ba859bf603240caa385358e05529beca323a30a8 https://github.com/galaxyproject/galaxy/commit/ba859bf603240caa385358e05529b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix state handling, show warning message Commit: 42e7cebe43eaa57a9538a689dbe7f4700e52cfee https://github.com/galaxyproject/galaxy/commit/42e7cebe43eaa57a9538a689dbe7f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix function declarations Commit: ecac866a26d80f32d329fb0c2be345caac62a2a0 https://github.com/galaxyproject/galaxy/commit/ecac866a26d80f32d329fb0c2be34... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix debug statement, increase chunk size to 50MB Commit: 99d20ae69f637ac9f0483c457c43c8aa0b707c8c https://github.com/galaxyproject/galaxy/commit/99d20ae69f637ac9f0483c457c43c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Resume uploads if server or nginx proxy reload Commit: 4ac01cd50b6470a7641b009f857f04fc8f0099ff https://github.com/galaxyproject/galaxy/commit/4ac01cd50b6470a7641b009f857f0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove/fix debug statements Commit: b50ca79fe8b7bcb9066ce710eba9c43649d504e5 https://github.com/galaxyproject/galaxy/commit/b50ca79fe8b7bcb9066ce710eba9c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/webapps/galaxy/api/remote_files.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add separate api endpoint to handle uploads Commit: 093f33232d6e328e5ac528a6328b45031fe0c698 https://github.com/galaxyproject/galaxy/commit/093f33232d6e328e5ac528a6328b4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Use api endpoint to store chunks Commit: 11e0fde5f86fa39363ae92b397011058ac8eba26 https://github.com/galaxyproject/galaxy/commit/11e0fde5f86fa39363ae92b397011... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Fix chunk size, close files properly Commit: f4ae4b766bd0932bb40b2e5366953137fc1404bc https://github.com/galaxyproject/galaxy/commit/f4ae4b766bd0932bb40b2e5366953... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Fix lint Commit: 1a536ee77cb93ba0fef08709867b5589c6f1e3a5 https://github.com/galaxyproject/galaxy/commit/1a536ee77cb93ba0fef08709867b5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove unused nginx specifiers Commit: b0a4cb499b8ed139659f7173b5f75e277cd96ef8 https://github.com/galaxyproject/galaxy/commit/b0a4cb499b8ed139659f7173b5f75... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Properly handle error response Commit: ad5c8a38f20dce9a0a65c346b76805493f1a07c4 https://github.com/galaxyproject/galaxy/commit/ad5c8a38f20dce9a0a65c346b7680... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove unused import Commit: c6b4d2e8a460731b5523372e4c40d2d7554be0d4 https://github.com/galaxyproject/galaxy/commit/c6b4d2e8a460731b5523372e4c40d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/managers/configuration.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove dependency from nginx variables, only pass session id Commit: 789c41c550e406b2d9cc27f33df49e2da647d208 https://github.com/galaxyproject/galaxy/commit/789c41c550e406b2d9cc27f33df49... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Raise proper value error if session id is invalid Commit: 97f0530a866ad3160d4e35f75721087fda55ce1c https://github.com/galaxyproject/galaxy/commit/97f0530a866ad3160d4e35f757210... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M lib/galaxy/managers/configuration.py Log Message: ----------- Fix naming conflict between regular upload path and nginx path Commit: 5047e92d385b4b2fca042428bafe05eb3790e117 https://github.com/galaxyproject/galaxy/commit/5047e92d385b4b2fca042428bafe0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix session condition, use literal templates Commit: 9bd911275619b6740877c5c25f9ba408d5c254ad https://github.com/galaxyproject/galaxy/commit/9bd911275619b6740877c5c25f9ba... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Use literal template for tool panel Commit: 19cffb57d86a4cd8682feb5111900022e644bebc https://github.com/galaxyproject/galaxy/commit/19cffb57d86a4cd8682feb5111900... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/workflow.py M run_tests.sh M test/base/populators.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/galaxy_selenium/navigation.yml M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_jupyter.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: 688923259033f64758e6d1076ec6748a31505d04 https://github.com/galaxyproject/galaxy/commit/688923259033f64758e6d1076ec67... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Remove duplicate slash Commit: be504071a961a09d6b72c4e225ec3dfbdfeb96e3 https://github.com/galaxyproject/galaxy/commit/be504071a961a09d6b72c4e225ec3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Escape workflow name Commit: 2cae71a2dd258c12b4b77315df2609132653a7b1 https://github.com/galaxyproject/galaxy/commit/2cae71a2dd258c12b4b77315df260... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py Log Message: ----------- Add upload chunk size setting to configuration Commit: cc64f5879e4d6ca5cdc961fabcde22ceb1199b2f https://github.com/galaxyproject/galaxy/commit/cc64f5879e4d6ca5cdc961fabcde2... 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client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/data/__init__.py M 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lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/migrate_tools/migrate_tools.py M static/style/blue/base.css R templates/webapps/galaxy/history/display_structured.mako R templates/webapps/galaxy/history/view.mako A test-data/qname_sorted.bam M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/tools/multi_output_recurse.xml M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'dev' into chunk_uploads Commit: ecc6ac5dbf58c351e71a10835641c988ec1d0d48 https://github.com/galaxyproject/galaxy/commit/ecc6ac5dbf58c351e71a10835641c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/managers/configuration.py Log Message: ----------- Default to 100 in configuration manager Commit: d6a3964c5b41f0a9a268a1c5182fa23798526a55 https://github.com/galaxyproject/galaxy/commit/d6a3964c5b41f0a9a268a1c5182fa... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Add additional checks, use join Commit: 3f56aeb3cf1e2d5f6eba961f1a6925b35e836cb4 https://github.com/galaxyproject/galaxy/commit/3f56aeb3cf1e2d5f6eba961f1a692... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Re-use regex to validate session id Commit: 51a135bbaaee7a65619a802e5506ecd1fd27df8b https://github.com/galaxyproject/galaxy/commit/51a135bbaaee7a65619a802e5506e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Read chunks of chunks when writing target file Commit: 529e98ef04e67a5068b55efd54d946aca126527f https://github.com/galaxyproject/galaxy/commit/529e98ef04e67a5068b55efd54d94... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Rely on automated file closing, add new line Commit: a4287f1212050c7ff068ad161ce2d17cd65bd7cb https://github.com/galaxyproject/galaxy/commit/a4287f1212050c7ff068ad161ce2d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-12 (Mon, 12 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M lib/galaxy/config.py M test/base/driver_util.py Log Message: ----------- Test chunked uploads Commit: a137420c42206fdf9482615ff292ba3d1546f22f https://github.com/galaxyproject/galaxy/commit/a137420c42206fdf9482615ff292b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Use ceil instead of floor Commit: 2dba72fb2f850c9fb7ab940be7ae7bef5626acd9 https://github.com/galaxyproject/galaxy/commit/2dba72fb2f850c9fb7ab940be7ae7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Align chunk size check Commit: 22dd4a8a64820711abe91b6e1f75d2da52144b8a https://github.com/galaxyproject/galaxy/commit/22dd4a8a64820711abe91b6e1f75d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Fix lint Commit: 7589bbbb4dd556e41988ff6a6327e004b53e5ef9 https://github.com/galaxyproject/galaxy/commit/7589bbbb4dd556e41988ff6a6327e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/uploads.py M test/base/driver_util.py Log Message: ----------- Specify chunk size in bytes instead of megabytes Commit: 71c88092c0a4fcd3ccb02e652c024591e004e7f8 https://github.com/galaxyproject/galaxy/commit/71c88092c0a4fcd3ccb02e652c024... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- Remove unused import Commit: 8d1e0fccc2f116674250a1b977168beef2cbd238 https://github.com/galaxyproject/galaxy/commit/8d1e0fccc2f116674250a1b977168... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add chunk size config option to schema Commit: 941017b04a3092556d525130e40c8e242860d828 https://github.com/galaxyproject/galaxy/commit/941017b04a3092556d525130e40c8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-13 (Tue, 13 Mar 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Moderate chunk size for upload tests Commit: 759511479f86b95575ca8b5f3bcf06d6acecf56f https://github.com/galaxyproject/galaxy/commit/759511479f86b95575ca8b5f3bcf0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix typo Commit: fcd00166e279cdd216deee8921449070192b19b9 https://github.com/galaxyproject/galaxy/commit/fcd00166e279cdd216deee8921449... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Client format Commit: c6993caabff5aa0dcdbb2150a2f18fb9566aae84 https://github.com/galaxyproject/galaxy/commit/c6993caabff5aa0dcdbb2150a2f18... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/decorators.py A lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/root.py M test/base/driver_util.py Log Message: ----------- Merge branch 'chunk_uploads' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5f73d7fbbd2c...c6993caabff5