October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bd5f71: Separate endpoints for form building and attribute...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd5f711bd272dba7fc032b894a7b6c50098e1d83 https://github.com/galaxyproject/galaxy/commit/bd5f711bd272dba7fc032b894a7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Separate endpoints for form building and attribute changes Commit: e09958fd8f9a386761f6ebe520a8323e7b5e4c0c https://github.com/galaxyproject/galaxy/commit/e09958fd8f9a386761f6ebe520a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refactor form building endpoint Commit: b451c6a13741e1f7f47d759edda67e49ec4e3983 https://github.com/galaxyproject/galaxy/commit/b451c6a13741e1f7f47d759edda6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Use consistent naming for input forms Commit: d7d8817a98bc176c53c44b0110b4aa2aba01985d https://github.com/galaxyproject/galaxy/commit/d7d8817a98bc176c53c44b0110b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use consistent input appending style, remove spaces Commit: 101c9b4b355fe6903296bbc7be2ac40464b746c6 https://github.com/galaxyproject/galaxy/commit/101c9b4b355fe6903296bbc7be2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix missing role handling Commit: 14c6622cac29d0396661101154698df3e4c0f796 https://github.com/galaxyproject/galaxy/commit/14c6622cac29d039666110115469… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Show attribute editing without tabs Commit: e191991242d2c4331ae1cf22da08cdb5b30e09c6 https://github.com/galaxyproject/galaxy/commit/e191991242d2c4331ae1cf22da08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Reconnect attributes endpoint Commit: 6c321dca3fe47e474ae5f68b72c88de4cd5db712 https://github.com/galaxyproject/galaxy/commit/6c321dca3fe47e474ae5f68b72c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Fix status message handling, use consistent message format Commit: 2eeafa72abdf80d7856de6bbba5f0f031e166e57 https://github.com/galaxyproject/galaxy/commit/2eeafa72abdf80d7856de6bbba5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Add error handler, fix datatype retrieval Commit: c100667d8d1875fd9893ae41edc81bf470ae5b28 https://github.com/galaxyproject/galaxy/commit/c100667d8d1875fd9893ae41edc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove three year old comments Commit: 4bb5813800edf01ed982e65452547c7a3614c2bb https://github.com/galaxyproject/galaxy/commit/4bb5813800edf01ed982e6545254… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use one-liner for message Commit: 7b969111adc2f2cb9bcc2d70e6e134b9e0e9a52b https://github.com/galaxyproject/galaxy/commit/7b969111adc2f2cb9bcc2d70e6e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Move flush to the end of operation block Commit: 7a6786ce7f359c8e097d1f59602541139eba5b21 https://github.com/galaxyproject/galaxy/commit/7a6786ce7f359c8e097d1f596025… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix more operations, error handlers Commit: 3ab476558c73856b2e8687537a76c2e883500f00 https://github.com/galaxyproject/galaxy/commit/3ab476558c73856b2e8687537a76… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- More error handling fixes Commit: 6e3de307f11029c1de0a701bccc9b96f17a06b12 https://github.com/galaxyproject/galaxy/commit/6e3de307f11029c1de0a701bccc9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/style/blue/base.css Log Message: ----------- Fix button margin, fix autodetect operation Commit: adc183d067ca8468a75f3500ba790c680c3d9442 https://github.com/galaxyproject/galaxy/commit/adc183d067ca8468a75f3500ba79… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Remove colons from some labels, parse response to message handler Commit: bb33e65c61a68177a30779d4e690b7c4fa7be28b https://github.com/galaxyproject/galaxy/commit/bb33e65c61a68177a30779d4e690… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Reuse tab view, add area for info and annotation Commit: e45519c00ea4bf1a4901c710bfd61c483b36bad5 https://github.com/galaxyproject/galaxy/commit/e45519c00ea4bf1a4901c710bfd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix metadata name Commit: e257d0ec8a308692c92899bb8426446c151073d7 https://github.com/galaxyproject/galaxy/commit/e257d0ec8a308692c92899bb8426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Augment error handling Commit: 4b93fdf5f966251bb6c7a3eb2b8d78f5b6637263 https://github.com/galaxyproject/galaxy/commit/4b93fdf5f966251bb6c7a3eb2b8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Reduce render update to forms, do not re-render tabs Commit: 9a7150f645abe26bdeeb1d06ecfdbb177d725ae8 https://github.com/galaxyproject/galaxy/commit/9a7150f645abe26bdeeb1d06ecfd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Hide until data is available Commit: 589e83e909744ea79a78c3c6ede44f331da6a196 https://github.com/galaxyproject/galaxy/commit/589e83e909744ea79a78c3c6ede4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Restore previous appearance, use operations buttons Commit: 4b3d57579ac89dbc8141b852701d3ec2906abae5 https://github.com/galaxyproject/galaxy/commit/4b3d57579ac89dbc8141b852701d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Adjust client message handler Commit: ce6f0a7f0daa5abe0109fa522be8e7fe6c2ea5ae https://github.com/galaxyproject/galaxy/commit/ce6f0a7f0daa5abe0109fa522be8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Encode/decode role ids, add support for permission handling Commit: 591873a132ea4b1c5c25cba362656082637f15e7 https://github.com/galaxyproject/galaxy/commit/591873a132ea4b1c5c25cba36265… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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-parameters.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Add readonly support for select fields, remove custom readonly form Commit: 95200bbe4e3904f5bf8b20d77ba4128c257cf56f https://github.com/galaxyproject/galaxy/commit/95200bbe4e3904f5bf8b20d77ba4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Use hidden type and labels for input messages Commit: 7435c464b07bdc4d7947daef7e15ceb7ff54911a https://github.com/galaxyproject/galaxy/commit/7435c464b07bdc4d7947daef7e15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-view.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/form/form-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/dataset/dataset-edit-attributes.js M static/scripts/mvc/form/form-view.js Log Message: ----------- Add flag to specify editable forms Parse converter exception to client Commit: 5ecb2332ef79f8cac5c0c31e90a996d780fad3af https://github.com/galaxyproject/galaxy/commit/5ecb2332ef79f8cac5c0c31e90a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove html from error message Commit: e759b293795397ccbfb318e6244e55a166cdc30b https://github.com/galaxyproject/galaxy/commit/e759b293795397ccbfb318e6244e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix datatype form enabling Commit: 347d7805fe2e0d7e85b6edcf7aa5f8e30bdb30b3 https://github.com/galaxyproject/galaxy/commit/347d7805fe2e0d7e85b6edcf7aa5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix former edit links and targets Fix flag handling for permissions Repack Commit: 71a3158421a4430364d91e1b7ec867fd82411778 https://github.com/galaxyproject/galaxy/commit/71a3158421a4430364d91e1b7ec8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M config/error_report.yml.sample M lib/galaxy/dataset_collections/type_description.py A lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M static/maps/mvc/upload/default/default-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/upload/default/default-view.js Log Message: ----------- Merge branch 'dev' into revise_dataset_attributes Commit: 9a4c76da767c6463dfc5b82c3e6220bebb5b67c8 https://github.com/galaxyproject/galaxy/commit/9a4c76da767c6463dfc5b82c3e62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.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/dataset/dataset-edit-attributes.js Log Message: ----------- Fix names, removes space from icon cls Commit: aea59ddda12877e501141b39cf1fead83ebbf64c https://github.com/galaxyproject/galaxy/commit/aea59ddda12877e501141b39cf1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Refresh session for permissions Commit: a246510bd0cc859171f7876a141feb89b7499a03 https://github.com/galaxyproject/galaxy/commit/a246510bd0cc859171f7876a141f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix handling of multiple roles for dataset permissions Commit: 990d1aec844eca2c86188f9acc91ba0d3dbd2b8e https://github.com/galaxyproject/galaxy/commit/990d1aec844eca2c86188f9acc91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove debug message, fix spacing, remove unused library Commit: 966cc95f4030e7b9680de9ae6094f9ab84d42981 https://github.com/galaxyproject/galaxy/commit/966cc95f4030e7b9680de9ae6094… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Avoid naming conflict Commit: 470d1eee18a7508c0405ca0750deb9ab627ab7fc https://github.com/galaxyproject/galaxy/commit/470d1eee18a7508c0405ca0750de… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix anonymous access to edit attributes Commit: 90f9a50574f8e324a1b12f1100c669a3a71d6119 https://github.com/galaxyproject/galaxy/commit/90f9a50574f8e324a1b12f1100c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M static/maps/mvc/upload/upload-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/upload/upload-view.js M test/api/test_tools_upload.py M test/base/populators.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into revise_dataset_attributes Commit: dfb2cc2f363f29085e022e14b7c145c80c389d3d https://github.com/galaxyproject/galaxy/commit/dfb2cc2f363f29085e022e14b7c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4779 from guerler/revise_dataset_attributes Allow dataset attribute changes without refreshing the page Compare: https://github.com/galaxyproject/galaxy/compare/49f62e7a3577...dfb2cc2f363f

1 0

[galaxyproject/galaxy] e06b44: Add labels to collection flattening operation to a...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e06b44437b46a82402e43c8e4c26d21af765fb3f https://github.com/galaxyproject/galaxy/commit/e06b44437b46a82402e43c8e4c26… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/tools/flatten_collection.xml Log Message: ----------- Add labels to collection flattening operation to avoid confusion Commit: 49f62e7a3577c214bcfc16e7f2c21c594e387162 https://github.com/galaxyproject/galaxy/commit/49f62e7a3577c214bcfc16e7f2c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/tools/flatten_collection.xml Log Message: ----------- Merge pull request #4791 from guerler/fix_flatten_label Add labels to selection options of the collection flattening tool Compare: https://github.com/galaxyproject/galaxy/compare/e02faa35f918...49f62e7a3577

1 0

[galaxyproject/galaxy] bce4da: Add another upload test this time with no dbkey pa...
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bce4da7bc8837b35854e08b7ffbd9258219c709f https://github.com/galaxyproject/galaxy/commit/bce4da7bc8837b35854e08b7ffbd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Add another upload test this time with no dbkey param. Works fine... Commit: e02faa35f918b3417680eb27e8a2aae8a84d7b8c https://github.com/galaxyproject/galaxy/commit/e02faa35f918b3417680eb27e8a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge pull request #4790 from jmchilton/upload_test_no_dbkey Add another upload test this time with no dbkey param. Compare: https://github.com/galaxyproject/galaxy/compare/643be6463ddf...e02faa35f918

1 0

[galaxyproject/galaxy] 4a2aa7: Always send dbkey during upload.
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a2aa7cab51c81023cf04b3575e47a2f06f4f165 https://github.com/galaxyproject/galaxy/commit/4a2aa7cab51c81023cf04b3575e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-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/upload/upload-view.js Log Message: ----------- Always send dbkey during upload. Seems to be needed on test.galaxyproject.org and for Selenium tests but not just running on my local laptop. This does seem to fix the problems though: A passing selenium suite with this change: https://jenkins.galaxyproject.org/view/All/job/jmchilton-selenium/172/. Commit: 82f671d3eeb64f9afc3ca79edee5a859b5b9cbe4 https://github.com/galaxyproject/galaxy/commit/82f671d3eeb64f9afc3ca79edee5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use initial dbkey and file_type to specify defaults Commit: 32e10a2e30dd5ab6b9159212ae8dd96d881a156d https://github.com/galaxyproject/galaxy/commit/32e10a2e30dd5ab6b9159212ae8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-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/upload/upload-view.js Log Message: ----------- Use ? and auto as defaults Commit: 627fb407ed90bebb714e12b400b85fe7bd06d495 https://github.com/galaxyproject/galaxy/commit/627fb407ed90bebb714e12b400b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-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/upload/upload-view.js Log Message: ----------- Merge pull request #59 from guerler/selenium_fix_000 Use initial dbkey and file_type to specify defaults Commit: 643be6463ddf0489936b1f0e7882e36fd1932d22 https://github.com/galaxyproject/galaxy/commit/643be6463ddf0489936b1f0e7882… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-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/upload/upload-view.js Log Message: ----------- Merge pull request #4789 from jmchilton/selenium_fix Always send dbkey during upload from UI. Compare: https://github.com/galaxyproject/galaxy/compare/5bf08cf01765...643be6463ddf

1 0

[galaxyproject/galaxy] 500a7a: test case to fix mothur.freq sniffer
by GitHub 12 Oct '17

12 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 500a7aee64708717a187ee87b4351d1295c48a6a https://github.com/galaxyproject/galaxy/commit/500a7aee64708717a187ee87b435… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq Log Message: ----------- test case to fix mothur.freq sniffer Commit: 787c3e575371b0969f57592a6f522d7d2634e2bc https://github.com/galaxyproject/galaxy/commit/787c3e575371b0969f57592a6f52… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- test case to fix mothur.freq sniffer Commit: 6dd59d9d2dcf6241506cf7720729145874e66121 https://github.com/galaxyproject/galaxy/commit/6dd59d9d2dcf6241506cf7720729… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- flake Commit: 03fe2a9779dfe51659f021b6856a74cac6c44ba3 https://github.com/galaxyproject/galaxy/commit/03fe2a9779dfe51659f021b6856a… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- addresses comments Commit: 5bf08cf017659de3026d9ca17c7ebeb0f7257ccb https://github.com/galaxyproject/galaxy/commit/5bf08cf017659de3026d9ca17c7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-12 (Thu, 12 Oct 2017) Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq Log Message: ----------- Merge pull request #4781 from yhoogstrate/mothur_freq_fix Mothur.freq sniffer more stringent Compare: https://github.com/galaxyproject/galaxy/compare/d3345d9feedf...5bf08cf01765

1 0

[galaxyproject/galaxy] d5b714: Remove unused concept of dataset children.
by GitHub 11 Oct '17

11 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5b71415f62d97487ef898934875da65a2b29c47 https://github.com/galaxyproject/galaxy/commit/d5b71415f62d97487ef898934875… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove unused concept of dataset children. We didn't really have any corresponding to active tools, we know if they are present they break multiple different parts of Galaxy. Lots of database loads and complexity we are not using and that is broken. Commit: d3345d9feedff9469239d7e0e6cec647f934a4d1 https://github.com/galaxyproject/galaxy/commit/d3345d9feedff9469239d7e0e6ce… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-11 (Wed, 11 Oct 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4771 from jmchilton/copy_children Remove unused concept of dataset children. Compare: https://github.com/galaxyproject/galaxy/compare/490dea3d267c...d3345d9feedf

1 0

[galaxyproject/galaxy] fb7015: Bug fix for XML warning during tool loads.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: fb7015bf70aaf3468b34f9d5a464df18edcae7ac https://github.com/galaxyproject/galaxy/commit/fb7015bf70aaf3468b34f9d5a464… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Bug fix for XML warning during tool loads. Commit: fd8e2e1927f0c6248e6d7ae4c5338015328bf9a0 https://github.com/galaxyproject/galaxy/commit/fd8e2e1927f0c6248e6d7ae4c533… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #4784 from jmchilton/tool_xml_warning [17.09] Bug fix for XML warning during tool loads. Compare: https://github.com/galaxyproject/galaxy/compare/2b18a0b8d5f7...fd8e2e1927f0

1 0

[galaxyproject/galaxy] cbb119: pin flake and pydocstyle in tox
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cbb119ebcd7bccc390eaae3874759b5e1091a86e https://github.com/galaxyproject/galaxy/commit/cbb119ebcd7bccc390eaae387475… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- pin flake and pydocstyle in tox Commit: 490dea3d267c1f5f7f5cc87cda759e31d3e4524b https://github.com/galaxyproject/galaxy/commit/490dea3d267c1f5f7f5cc87cda75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4787 from martenson/pin-tox pin flake and pydocstyle in tox Compare: https://github.com/galaxyproject/galaxy/compare/eab8f8e43f70...490dea3d267c

1 0

[galaxyproject/usegalaxy-playbook] 0e5105: Removed PEAR from test and main.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e510520722c7dd8ff5675f4dc123976c32b5412 https://github.com/galaxyproject/usegalaxy-playbook/commit/0e510520722c7dd8… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Removed PEAR from test and main.

1 0

[galaxyproject/galaxy] 065c08: Bugfix - do not initiate empty FTP uploads.
by GitHub 10 Oct '17

10 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 065c08dd903211e73b9cb90e9061a0959b31fa13 https://github.com/galaxyproject/galaxy/commit/065c08dd903211e73b9cb90e9061… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-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/upload/default/default-view.js Log Message: ----------- Bugfix - do not initiate empty FTP uploads. Broken with #4513. Commit: eab8f8e43f702898ca22f27e33ecdec0894d5aeb https://github.com/galaxyproject/galaxy/commit/eab8f8e43f702898ca22f27e33ec… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-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/upload/default/default-view.js Log Message: ----------- Merge pull request #4778 from jmchilton/no_empty_upload Bugfix - do not initiate empty FTP uploads. Compare: https://github.com/galaxyproject/galaxy/compare/f608753e2add...eab8f8e43f70

1 0