Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 959e6f0d55a7647ae096d996d91e18f8755ce2f2 https://github.com/galaxyproject/galaxy/commit/959e6f0d55a7647ae096d996d91e1... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: A tools/cloud/download.xml Log Message: ----------- Add a wrapper for the download-to-cloud tool. Commit: 21602ba426ce2363f54529c0f3069b86ea163a50 https://github.com/galaxyproject/galaxy/commit/21602ba426ce2363f54529c0f3069... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: A tools/cloud/download.py Log Message: ----------- Draft download-to-cloud tool. Commit: 90e879c5d773f79c2e0544ba9bb58ecdc1a6bc39 https://github.com/galaxyproject/galaxy/commit/90e879c5d773f79c2e0544ba9bb58... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- Add entries in tool config samples pointing to the cloud download tool. Commit: 1d1b72999a0022644a22b99c5db10dc7acb4ba49 https://github.com/galaxyproject/galaxy/commit/1d1b72999a0022644a22b99c5db10... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud download manager to leverage the cloud download tool. Commit: 5567d5121f640c3b314a4be3a37cf3d1d470bd4b https://github.com/galaxyproject/galaxy/commit/5567d5121f640c3b314a4be3a37cf... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Define two variables to store the cloud download tool name and version. Commit: 335c79cc972e6265bb764f69b5e0cf402ebd0d5a https://github.com/galaxyproject/galaxy/commit/335c79cc972e6265bb764f69b5e0c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update xml file of the cloud download tool match new input setup. Commit: ad6a4334f42ca36b677adc0e93aa2c19f5ddd0c1 https://github.com/galaxyproject/galaxy/commit/ad6a4334f42ca36b677adc0e93aa2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an unused import. Commit: 06371f3e84408124469e80f8b7a60b88f27275fa https://github.com/galaxyproject/galaxy/commit/06371f3e84408124469e80f8b7a60... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor the _configure_provider method in cloud manager. Commit: 114b9bde8baccc6512ab7bfc5a9e142b1878adf5 https://github.com/galaxyproject/galaxy/commit/114b9bde8baccc6512ab7bfc5a9e1... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Implement download function in the download-to-cloud tool. Commit: d6a9c202b103c65f77f8105ca9e4481cc8740167 https://github.com/galaxyproject/galaxy/commit/d6a9c202b103c65f77f8105ca9e44... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update the argument parser in the download-to-cloud tool. Commit: f21e1b18eed88bbe5dd70d2831cd3ec6ea11578c https://github.com/galaxyproject/galaxy/commit/f21e1b18eed88bbe5dd70d2831cd3... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update the required arguments list in the download-to-cloud tool. Commit: 2ce272484a2fce1ab3bac3f16739d2e21a5b0cff https://github.com/galaxyproject/galaxy/commit/2ce272484a2fce1ab3bac3f16739d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Fix a bug in the config file of the Download-to-cloud tool. Commit: aa4f8d7cf9dcf9a65f8d90cdedaa5c5df0848c8c https://github.com/galaxyproject/galaxy/commit/aa4f8d7cf9dcf9a65f8d90cdedaa5... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add the download_to_cloud tool to GALAXY_LIB_TOOLS_UNVERSIONED array. Commit: 82d6a80d9e7f4f93ab65a3994d427fd67b2a30f7 https://github.com/galaxyproject/galaxy/commit/82d6a80d9e7f4f93ab65a3994d427... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Fix some bugs in the download-to-cloud tool and its wrapper. Commit: 2419c7107739a1894d8ce6be45d437abcfacc586 https://github.com/galaxyproject/galaxy/commit/2419c7107739a1894d8ce6be45d43... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in the cloud storage manager class. Commit: 880d0bcd69669b8f31f81b4c6e5328643d7fa35e https://github.com/galaxyproject/galaxy/commit/880d0bcd69669b8f31f81b4c6e532... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Cloud download skips deleted, purged, or non-OK datasets. Commit: 244638690c9b587c660f0ec65506cf496cec1f00 https://github.com/galaxyproject/galaxy/commit/244638690c9b587c660f0ec65506c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Write user credentials 2 a file & pass the path 2 file 2 download tool. Commit: 264796eddf7ee689c9a2746f3891453d032dff13 https://github.com/galaxyproject/galaxy/commit/264796eddf7ee689c9a2746f38914... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Cloud download tool now reads user credentials from a file. Commit: ac40ad52035fa3ef4856fa31c7281ca42b902f2f https://github.com/galaxyproject/galaxy/commit/ac40ad52035fa3ef4856fa31c7281... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Delete the temporary credentials file after it is read. Commit: 72cd57d0114c4d90f7eb146247f0592bc36a8f99 https://github.com/galaxyproject/galaxy/commit/72cd57d0114c4d90f7eb146247f05... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Refactor the `credentials` argument to `credentials_file`. Commit: ce5b05853aa86f054d5ed9e910c0bd06dee5a388 https://github.com/galaxyproject/galaxy/commit/ce5b05853aa86f054d5ed9e910c0b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Fix a bug naming variable/argument credentials_file (missing _file). Commit: 999f3b07aff9c65f46576314e5e241bc709ed440 https://github.com/galaxyproject/galaxy/commit/999f3b07aff9c65f46576314e5e24... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Convert bool in string type to Boolean type in Download-to-cloud tool. Commit: 0a2f838352634aba28fbd62f937024c9641ca59d https://github.com/galaxyproject/galaxy/commit/0a2f838352634aba28fbd62f93702... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Throw an err if the file of the dataset to be downloaded, doesn't exist. Commit: ffc8d42daf36451ebf1aebd95b4d4baaa63846fe https://github.com/galaxyproject/galaxy/commit/ffc8d42daf36451ebf1aebd95b4d4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace: (_ <- space) in HDA name when downloading to cloud, cos space is the delimiter for tools cli args. Commit: 35459b23c9c107e1c9f5820103ea4a025a071603 https://github.com/galaxyproject/galaxy/commit/35459b23c9c107e1c9f5820103ea4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not download if tool id is the download tool id. Commit: 94d14567847141ea18763870fd11b5109136b348 https://github.com/galaxyproject/galaxy/commit/94d14567847141ea18763870fd11b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug determining the job created for downloading data to cloud. Commit: 2d6ed38e6fb7e580a5a3d15f4f7304e5eb5ded3e https://github.com/galaxyproject/galaxy/commit/2d6ed38e6fb7e580a5a3d15f4f730... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Cloud download API now returns the job id for each queued download job. Commit: cbca243eb70c1bcc2d4d523450b0bd7254f9a090 https://github.com/galaxyproject/galaxy/commit/cbca243eb70c1bcc2d4d523450b0b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Variable rename: uploaded -> downloaded. Commit: 275953be06073e83a9711f06d8fa22581ecb2d8b https://github.com/galaxyproject/galaxy/commit/275953be06073e83a9711f06d8fa2... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update docs. Commit: 73b32652c3e02d9d8635cde9c11456116e084c2e https://github.com/galaxyproject/galaxy/commit/73b32652c3e02d9d8635cde9c1145... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the Download tool xml, define provider param as a `select` type param Commit: df283962bb829b78da5fe4758e280430cdd2404e https://github.com/galaxyproject/galaxy/commit/df283962bb829b78da5fe4758e280... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Replace `filename` with `input` in the download-to-cloud tool. Commit: 4b7615e98d18c2657c25ab8254ba5157f0bfbf06 https://github.com/galaxyproject/galaxy/commit/4b7615e98d18c2657c25ab8254ba5... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py M tools/cloud/download.xml Log Message: ----------- Refactor `input` back to `filename` as it causes issues in cloud API. Commit: b6196323d878c84bc9b4c744659035d152de0ccf https://github.com/galaxyproject/galaxy/commit/b6196323d878c84bc9b4c74465903... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Fix a bug in variable naming. Commit: fc8ae7eeefffc88124aeeb7b7076aa14e3d52506 https://github.com/galaxyproject/galaxy/commit/fc8ae7eeefffc88124aeeb7b7076a... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Change the type of `overwrite_existing` key to boolean. Commit: a9dc89e5aa0e5e54c34748966859da00957e8df4 https://github.com/galaxyproject/galaxy/commit/a9dc89e5aa0e5e54c34748966859d... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Download tool wrapper now takes provider-specific credentials. Commit: b60246c8e12fd469a2e248c1770e407639a832c2 https://github.com/galaxyproject/galaxy/commit/b60246c8e12fd469a2e248c1770e4... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Pass credentials args based on the selected provider. Commit: f8ee1c161434d9cdc77422f4360fde52f76aef9f https://github.com/galaxyproject/galaxy/commit/f8ee1c161434d9cdc77422f4360fd... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update args list in the download.py. Commit: ef0dbb293165c8290833592927334eeb94867ac1 https://github.com/galaxyproject/galaxy/commit/ef0dbb293165c8290833592927334... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Implement a args parser function in the download-to-cloud tool. Commit: 6c62cc57eb5ea337b0889a3f6bad6003557dc531 https://github.com/galaxyproject/galaxy/commit/6c62cc57eb5ea337b0889a3f6bad6... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Refactor the parser function in the download-to-cloud tool. Commit: f2d1db9c23c10c8299ea2786e9420db17fc361df https://github.com/galaxyproject/galaxy/commit/f2d1db9c23c10c8299ea2786e9420... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor a variable. Commit: 4d83b83c22014580e373e36abb8b056ff6042b15 https://github.com/galaxyproject/galaxy/commit/4d83b83c22014580e373e36abb8b0... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Replace `provider` arg with connection, reflecting related conditional arg defined in the download-to-cloud tool wrapper. Commit: ab7741548475319006ef65d232b78f032f2a754b https://github.com/galaxyproject/galaxy/commit/ab7741548475319006ef65d232b78... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Instead of filename, cloud manager sends HDA to the download tool. Commit: 9d15ce4b21396b13e2a9a42373289451604a3525 https://github.com/galaxyproject/galaxy/commit/9d15ce4b21396b13e2a9a42373289... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Convert SUPPORTED_PROVIDERS to a dict reflecting their order in wrapper. Commit: 13aa6be72090dcd056f96b93db6c6cde896ee1fb https://github.com/galaxyproject/galaxy/commit/13aa6be72090dcd056f96b93db6c6... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Add a comment. Commit: b4950a9678251ceb065add2f0cc3c666393c06e4 https://github.com/galaxyproject/galaxy/commit/b4950a9678251ceb065add2f0cc3c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- The Download-to-cloud tool now reads provider-specific credential args. Commit: 6c710ed85f444e3672c8aaf12e26c536c4060656 https://github.com/galaxyproject/galaxy/commit/6c710ed85f444e3672c8aaf12e26c... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-05 (Sun, 05 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Fix a bug defining provider credentials in the download-to-cloud tool. Commit: 35eabd5543379702b92c439d7239e60f52f181f8 https://github.com/galaxyproject/galaxy/commit/35eabd5543379702b92c439d7239e... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the download-to-cloud tool, set `object_label` to hda.name. Commit: 8502dc5b6138133319301ae926a4238031e7699f https://github.com/galaxyproject/galaxy/commit/8502dc5b6138133319301ae926a42... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the wrapper of download-to-cloud tool, hide `object_label`. Commit: 0aae0505951b7a0a33bebd263c100f624d50270e https://github.com/galaxyproject/galaxy/commit/0aae0505951b7a0a33bebd263c100... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- In the download-to-cloud tool, replace blank space in hda name with `_`. Commit: 1dd62afa7f16cee7b20c4b87ba705713d852da0f https://github.com/galaxyproject/galaxy/commit/1dd62afa7f16cee7b20c4b87ba705... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.py Log Message: ----------- Fix some lint issues. Commit: b5cbaaecbc3bc30e34c0700345eab0a6759cb7c1 https://github.com/galaxyproject/galaxy/commit/b5cbaaecbc3bc30e34c0700345eab... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Fix some lint issues. Commit: 9de5927b5bbe9c3baddef22ea89d85cf6d79cd50 https://github.com/galaxyproject/galaxy/commit/9de5927b5bbe9c3baddef22ea89d8... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Rename the label of the output of the download-to-cloud. Commit: 2528c83bf2bc3483779fd509f5a8bab95e3e3690 https://github.com/galaxyproject/galaxy/commit/2528c83bf2bc3483779fd509f5a8b... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add docs to the download-to-cloud tool. Commit: 909c7a72d6fb9fce30844cee30909f017294fa89 https://github.com/galaxyproject/galaxy/commit/909c7a72d6fb9fce30844cee30909... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add storage account and resource group as required args for Azure. Commit: 4d73ea6a6e61563d6f02787f7a851f5491345b58 https://github.com/galaxyproject/galaxy/commit/4d73ea6a6e61563d6f02787f7a851... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Add azure storage account & resource group to the download tool wrapper. Commit: 897d024ef7301403ec1ead14452493b2fda62bc1 https://github.com/galaxyproject/galaxy/commit/897d024ef7301403ec1ead1445249... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add Azure storage account and resource group to cloud manager. Commit: 8413f778294cc2e45ec15f8d03d0a8f80ac2a83c https://github.com/galaxyproject/galaxy/commit/8413f778294cc2e45ec15f8d03d0a... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .ci/jenkins/toolshed/run_tests.sh M .coveragerc M .gitignore M .travis.yml M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/galaxy.pages.js M 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test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py M test/unit/test_objectstore.py M test/unit/test_rule_utils.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/ucsc_tablebrowser_test.xml M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloud_download_tool # Conflicts: # lib/galaxy/managers/cloud.py # lib/galaxy/webapps/galaxy/api/cloud.py Commit: 5c35813e302eab21db4f9c8e1e7c55e39339a9d3 https://github.com/galaxyproject/galaxy/commit/5c35813e302eab21db4f9c8e1e7c5... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace credentials with authz_id in the payload of cloud download api. Commit: 8198b336bdbcf71264962b1eda7b5309ddb597ca https://github.com/galaxyproject/galaxy/commit/8198b336bdbcf71264962b1eda7b5... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Use cloudauthz to get cloud credentials in cloud download manager. Commit: 08703ec87750e11bf41ceb1e68649670c6238c6a https://github.com/galaxyproject/galaxy/commit/08703ec87750e11bf41ceb1e68649... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Decode authz_id in cloud download api before sending it to the manager. Commit: 0e4045755f90f3d997e9200f036acc9408c32716 https://github.com/galaxyproject/galaxy/commit/0e4045755f90f3d997e9200f036ac... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace the provider in cloud api with authz.provider. Commit: f3ebdae0ce05b1543839a15dd6000826e304d9c8 https://github.com/galaxyproject/galaxy/commit/f3ebdae0ce05b1543839a15dd6000... Author: vahid <jalili.vahid@gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Fix incorrect argument and function naming in cloud api & manager. Commit: 5f8c0dfa342e12f10e06273a90c9034f96f617ca https://github.com/galaxyproject/galaxy/commit/5f8c0dfa342e12f10e06273a90c90... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-03 (Wed, 03 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Replace trans with sa_session and user_id in try_get_authz_config. Commit: 1babfdfda9ae7f95221b3992178fb25ee52e5161 https://github.com/galaxyproject/galaxy/commit/1babfdfda9ae7f95221b3992178fb... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/README.md M client/galaxy/scripts/components/DisplayStructured.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M 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lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/slurm.py A lib/galaxy/jobs/runners/util/cli/job/lsf.py M lib/galaxy/managers/base.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M 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lib/galaxy/webapps/galaxy/controllers/data_manager.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/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/groups.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/tool_shed/managers/groups.py M lib/tool_shed/util/repository_util.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M static/style/blue/base.css M templates/galaxy_client_app.mako M templates/ind_share_base.mako M templates/show_params.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/share.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/common/repository_actions_menu.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/role/role.mako M templates/webapps/tool_shed/user/username.mako A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar M test/api/test_api_batch.py M test/api/test_dataset_collections.py M test/api/test_histories.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflow_fixtures.py R test/base/workflows_format_2/README.txt R test/base/workflows_format_2/__init__.py R test/base/workflows_format_2/converter.py R test/base/workflows_format_2/interface.py R test/base/workflows_format_2/main.py M test/functional/tools/disambiguate_cond.xml A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_job_wrapper.py A test/unit/test_compression_util.py M test/unit/test_galaxy_mapping.py A test/unit/test_utils.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_toolbox_filters.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge and resolve conflicts. Commit: 9cf7cf6b1ea45478424bad81ffa2907bf12f8b01 https://github.com/galaxyproject/galaxy/commit/9cf7cf6b1ea45478424bad81ffa29... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- In the cloud download tool, accept credentials via a tmp file only. Commit: cf919d7befb7ef1c76e6afc710939e032da7dac4 https://github.com/galaxyproject/galaxy/commit/cf919d7befb7ef1c76e6afc710939... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Do not assert provider name in cloud download tool. Commit: 81eabec6e6517d9ef40b9880925bbcbffe95b6f6 https://github.com/galaxyproject/galaxy/commit/81eabec6e6517d9ef40b9880925bb... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update cloud download to adhere with cloudbridge v1 interface changes. Commit: b3a12919cab11f9a174b723cc2d686982a52924c https://github.com/galaxyproject/galaxy/commit/b3a12919cab11f9a174b723cc2d68... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Update download tool wrapper to leverage tmp credentials in tmp file. Commit: 68251722e346fc8fa4d9cec1860809688a5b4d74 https://github.com/galaxyproject/galaxy/commit/68251722e346fc8fa4d9cec186080... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- In authnz manager, user_id can be string & should be casted to int. Commit: 171b1dd26ea58f666e37672d73084b5ce4aa4dac https://github.com/galaxyproject/galaxy/commit/171b1dd26ea58f666e37672d73084... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Define a new func in authnz manager to write tmp cred. to a tmp file. Commit: 90f0a8615d927f1343bc1bc12519c96c04165280 https://github.com/galaxyproject/galaxy/commit/90f0a8615d927f1343bc1bc12519c... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug in calling get_cloud_access_credentials: missing args. Commit: 1b3855cc88cee647f70676f54c82c2174cae3f4d https://github.com/galaxyproject/galaxy/commit/1b3855cc88cee647f70676f54c82c... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Inform user if a given decoded history to download from does not exist. Commit: 8d0b4e0c04cc003b02d9b9d5e089134f9b0bef64 https://github.com/galaxyproject/galaxy/commit/8d0b4e0c04cc003b02d9b9d5e0891... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Pass authz_id from cloud download manager to the download tool wrapper. Commit: 4bcd3366ef5eabea4f89571c845b1f5667247ad9 https://github.com/galaxyproject/galaxy/commit/4bcd3366ef5eabea4f89571c845b1... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Send bucket_name instead of bucket obj from cloud download mgr. to tool. Commit: e31c7768fb49966961fc8630672f3127b7df6e12 https://github.com/galaxyproject/galaxy/commit/e31c7768fb49966961fc8630672f3... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove `connection` and `bucket` from cloud download manager. Commit: d9baf394d528586b44308f41cfa7041e3b8ab1d8 https://github.com/galaxyproject/galaxy/commit/d9baf394d528586b44308f41cfa70... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Cloud download tool: don't create cred. files if manager has provided. Commit: 5821fc1f1e932962f92bbabd9c7c3476e5770d61 https://github.com/galaxyproject/galaxy/commit/5821fc1f1e932962f92bbabd9c7c3... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Leverage authnz manager to create and write tmp cred. to a tmp file. Commit: 9a8daa5e746203cd5fd537015aeaf53451f0a074 https://github.com/galaxyproject/galaxy/commit/9a8daa5e746203cd5fd537015aeaf... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround cloud download in try-catch and record failed datasets. Commit: 93a5a22b61f4cbea9a5def0928be134d6c25f5f4 https://github.com/galaxyproject/galaxy/commit/93a5a22b61f4cbea9a5def0928be1... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Return & report a list of fails to create download job. Commit: 8cd1b0e118062555cdb7bc41c29b95f173deb5da https://github.com/galaxyproject/galaxy/commit/8cd1b0e118062555cdb7bc41c29b9... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Remove hidden credentials_file arg from download tool wrapper. Commit: 1efa29419840425072d42db783afd456d7d126fe https://github.com/galaxyproject/galaxy/commit/1efa29419840425072d42db783afd... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Encode and decode authnz id in download tool wrapper & manager. Commit: 9eabf5c6c61f18c0a91407c748e93c00e4d7022b https://github.com/galaxyproject/galaxy/commit/9eabf5c6c61f18c0a91407c748e93... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M tools/cloud/download.xml Log Message: ----------- Only download tool wrapper creates tmp credentials tmp file. Commit: 8d68e8e5d33ca1c91c1f5b424d6045ece29946a4 https://github.com/galaxyproject/galaxy/commit/8d68e8e5d33ca1c91c1f5b424d604... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove unused imports from managers/cloud.py. Commit: 0061562bd8c112827c7cd0fd3a6ac4e8b92bd7ce https://github.com/galaxyproject/galaxy/commit/0061562bd8c112827c7cd0fd3a6ac... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud download API documentation. Commit: 7c599f8a8d762d5783e2534f91588e88e96b2510 https://github.com/galaxyproject/galaxy/commit/7c599f8a8d762d5783e2534f91588... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Provide more insights for errors occurring queuing cloud download jobs. Commit: 081e4eb96de77200322d4fb2998b950e8e789e0e https://github.com/galaxyproject/galaxy/commit/081e4eb96de77200322d4fb2998b9... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud download api docs w.r.t to updates to error reports. Commit: d316b9d7656c60a2888423790c9cf7ffd07dc666 https://github.com/galaxyproject/galaxy/commit/d316b9d7656c60a2888423790c9cf... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add docstring to get_cloud_access_credentials_in_file. Commit: 6504fe6ef1a15d379e8fad68dfe42d2e50dcb8e5 https://github.com/galaxyproject/galaxy/commit/6504fe6ef1a15d379e8fad68dfe42... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M tools/cloud/download.xml Log Message: ----------- Always pass user_id as int to authnz/managers so to avoid check & cast. Commit: 010c512855ea83a94a27d9ce754b053e6121c2ae https://github.com/galaxyproject/galaxy/commit/010c512855ea83a94a27d9ce754b0... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an extra space (lint issue). Commit: be34b7501829bdbadf13f502651ceb4d6697a7ab https://github.com/galaxyproject/galaxy/commit/be34b7501829bdbadf13f502651ce... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove openstack from cloud manager's supported providers list. Commit: bd4023f521ed33cdaf9975e517b90cbe2b00e15b https://github.com/galaxyproject/galaxy/commit/bd4023f521ed33cdaf9975e517b90... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add some logging to cloudauthz and cloud download api. Commit: 4305e2c56cc92a8cc67a29640897e92cc69a81e6 https://github.com/galaxyproject/galaxy/commit/4305e2c56cc92a8cc67a29640897e... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Add some logging steps in the cloud download tool. Commit: 847f66340d1346fe7cd405b614c29c529ef7ddbb https://github.com/galaxyproject/galaxy/commit/847f66340d1346fe7cd405b614c29... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Remove a comment from download tool wrapper. Commit: 3ce2a3564799595fef08e5692a951757e853bf72 https://github.com/galaxyproject/galaxy/commit/3ce2a3564799595fef08e5692a951... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M tools/cloud/download.py Log Message: ----------- Update print func syntax in cloud download tool to adhere with py3 req. Commit: e943ec2bb48c6cbd693e0981d6134c4443f5ed70 https://github.com/galaxyproject/galaxy/commit/e943ec2bb48c6cbd693e0981d6134... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M tools/cloud/download.xml Log Message: ----------- Rename cloud download tool log dataset. Commit: 01a124314db553c2b9f646addc18aea3669905de https://github.com/galaxyproject/galaxy/commit/01a124314db553c2b9f646addc18a... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py R tools/cloud/download.py R tools/cloud/download.xml A tools/cloud/send.py A tools/cloud/send.xml Log Message: ----------- Rename cloud/download.* to cloud/send.* Commit: b62e0476be4e27064efffd56a9516860a25e486e https://github.com/galaxyproject/galaxy/commit/b62e0476be4e27064efffd56a9516... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M tools/cloud/send.xml Log Message: ----------- cloud Download > Send refactoring in tool wrapper, & related places. Commit: 8f11f78aa2b9e1e342b03a7b3a8e3f47779eab12 https://github.com/galaxyproject/galaxy/commit/8f11f78aa2b9e1e342b03a7b3a8e3... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- download > send refactoring in the tool. Commit: d304068161dce41eba53a5ec2c4710a203fdf27a https://github.com/galaxyproject/galaxy/commit/d304068161dce41eba53a5ec2c471... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Cloud download > send refactoring in the related api. Commit: 24ed804ab40c931716c5f2f15b76f35160034c56 https://github.com/galaxyproject/galaxy/commit/24ed804ab40c931716c5f2f15b76f... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Cloud download > send refactoring in cloud manager. Commit: a35b686dfda36439dd7bdfe632cefb242c383fac https://github.com/galaxyproject/galaxy/commit/a35b686dfda36439dd7bdfe632cef... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Assert if toolbox returns `send` tool before using it. Commit: 4e0b09499ec58cb90449ef15fb3fea424e58dd3f https://github.com/galaxyproject/galaxy/commit/4e0b09499ec58cb90449ef15fb3fe... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample Log Message: ----------- Refactor cloud download > send in tool config. Commit: 47b41d1bb058244bcb06b88a5c612a4371d45e1f https://github.com/galaxyproject/galaxy/commit/47b41d1bb058244bcb06b88a5c612... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Add timestamp, and transfer ET & rate to the Send to cloud tool's log. Commit: b01ff7c2289bbfe7e6e9e543f0a98fd18f9a05f2 https://github.com/galaxyproject/galaxy/commit/b01ff7c2289bbfe7e6e9e543f0a98... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Log cloudauthz exceptions as `info`, not as an `exception`. Commit: b9771b7ccc417b9e4326151058f0fd221a21ff80 https://github.com/galaxyproject/galaxy/commit/b9771b7ccc417b9e4326151058f0f... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Log entire cloudauthz exception, not just its message. Commit: 8543231b401bf3eec4d44d63f41c68e7b4ad8e02 https://github.com/galaxyproject/galaxy/commit/8543231b401bf3eec4d44d63f41c6... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Surround getting cloudauthz cred. in Send tool in a try-catch block. Commit: 8c95f174ba0d61c9632a03e9bec243509ca63a19 https://github.com/galaxyproject/galaxy/commit/8c95f174ba0d61c9632a03e9bec24... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Fix lint issues. Commit: d4d659a85191bbf8e7683c8840c716a96c09d85b https://github.com/galaxyproject/galaxy/commit/d4d659a85191bbf8e7683c8840c71... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Replace the hardcoded msg with the exception msg in the cloud send tool. Commit: b72e08e8b8f1d5c47aee6bc42a9bb292ff304ab5 https://github.com/galaxyproject/galaxy/commit/b72e08e8b8f1d5c47aee6bc42a9bb... 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lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/xml_util.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/pgcleanup.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M static/style/blue/base.css A static/style/blue/info_icon.svg M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/history/share.mako A test-data/MTBLS6.zip M test/api/test_tools.py M test/api/test_tools_upload.py M test/base/populators.py A test/base/ssh_util.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigation.yml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py M test/unit/test_remote_shell.py M test/unit/tools/test_actions.py M tools/data_source/upload.py Log Message: ----------- Merge and resolve conflicts. Commit: a236c64ea79ac45ed8bcde67c586f16d92e7e70a https://github.com/galaxyproject/galaxy/commit/a236c64ea79ac45ed8bcde67c586f... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Repalce "sys.exc_info" with "Exception as e" in cloud Send tool wrapper. Commit: e30460049ff2ab7ec64b703fca590dab88db3ec7 https://github.com/galaxyproject/galaxy/commit/e30460049ff2ab7ec64b703fca590... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Remove _ and capitalize each work in "overwrite_existing". Commit: ef70f20a58828b892e6af9b6b7515dbfd8f24e15 https://github.com/galaxyproject/galaxy/commit/ef70f20a58828b892e6af9b6b7515... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Swap authz_id and bucket; bucket is the first parameter now. Commit: 6f56ff10b9bc341fdaae879dec281e99fce6b1fc https://github.com/galaxyproject/galaxy/commit/6f56ff10b9bc341fdaae879dec281... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Remove `@` & msec from send tool timestamp. Commit: 39bdb67273700b0766250241801112a27dbc4b87 https://github.com/galaxyproject/galaxy/commit/39bdb67273700b076625024180111... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- Make duplicate object timestamp shorter and use `_` instead of `-`. Commit: 7433e2640bc87fc76381eb7fcdcf07a1fde4671a https://github.com/galaxyproject/galaxy/commit/7433e2640bc87fc76381eb7fcdcf0... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-28 (Sun, 28 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Extend the help section and refactor `Authz` to `Cloud Authorization`. Commit: a71db8384cc512efd95c4ac89695d1584899874f https://github.com/galaxyproject/galaxy/commit/a71db8384cc512efd95c4ac89695d... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Raise an exception in cloud get/send managers if OIDC is not enabled. Commit: 43e5a1828d2ba1ed11b7a5c7321fe075f06b9c0b https://github.com/galaxyproject/galaxy/commit/43e5a1828d2ba1ed11b7a5c7321fe... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-29 (Mon, 29 Oct 2018) Changed paths: M tools/cloud/send.py Log Message: ----------- In Cloud send tool: surround error raising blocks of code in try-catch. Commit: 341f7d6372aa62bc6e84527925e0fb96622d1b84 https://github.com/galaxyproject/galaxy/commit/341f7d6372aa62bc6e84527925e0f... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update output label & tool name to compose a more intuitive log label. Commit: 6c07a0370dadfdf0b9352c63b2d6f3357c33853d https://github.com/galaxyproject/galaxy/commit/6c07a0370dadfdf0b9352c63b2d6f... Author: vahid <jalili.vahid@gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update description on send tool wrapper. Commit: 566ffaf9d549e3d1096db4996fc9133f133dee19 https://github.com/galaxyproject/galaxy/commit/566ffaf9d549e3d1096db4996fc91... Author: Enis Afgan <afgane@gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M tools/cloud/send.xml Log Message: ----------- Update send tool help text Commit: 2f2153292b39d3a2718c0950303f2b48b18838c9 https://github.com/galaxyproject/galaxy/commit/2f2153292b39d3a2718c0950303f2... Author: Enis Afgan <afgane@gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py A tools/cloud/send.py A tools/cloud/send.xml Log Message: ----------- Merge pull request #6583 from VJalili/cloud_download_tool Send data to cloud Compare: https://github.com/galaxyproject/galaxy/compare/eb57469eef96...2f2153292b39 **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.