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[galaxyproject/galaxy] a8eb94: test/selenium_tests/test_library_contents.py
by GitHub 07 Nov '18

07 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8eb9463a6778772b7c00cf3e80364cdb5956edd https://github.com/galaxyproject/galaxy/commit/a8eb9463a6778772b7c00cf3e803… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- test/selenium_tests/test_library_contents.py Commit: 10723c789f83f2a3ec9e4ba73ec3d08321d02ed3 https://github.com/galaxyproject/galaxy/commit/10723c789f83f2a3ec9e4ba73ec3… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- Added white space to pass linter Commit: 1b18e9ea2dcc403d44a972433c0f75c823107a8c https://github.com/galaxyproject/galaxy/commit/1b18e9ea2dcc403d44a972433c0f… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- More linting fun Commit: 09186c991ae88f9f4edf67f4ba98cc73286831b3 https://github.com/galaxyproject/galaxy/commit/09186c991ae88f9f4edf67f4ba98… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-07 (Wed, 07 Nov 2018) Changed paths: M test/selenium_tests/test_library_contents.py Log Message: ----------- Merge pull request #6982 from Nerdinacan/selenium_test_library_contents Update test/selenium_tests/test_library_contents.py Compare: https://github.com/galaxyproject/galaxy/compare/2f2153292b39...09186c991ae8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 959e6f: Add a wrapper for the download-to-cloud tool.
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 959e6f0d55a7647ae096d996d91e18f8755ce2f2 https://github.com/galaxyproject/galaxy/commit/959e6f0d55a7647ae096d996d91e… Author: vjalili <jalili.vahid(a)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/21602ba426ce2363f54529c0f306… Author: vjalili <jalili.vahid(a)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/90e879c5d773f79c2e0544ba9bb5… Author: vjalili <jalili.vahid(a)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/1d1b72999a0022644a22b99c5db1… Author: vjalili <jalili.vahid(a)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/5567d5121f640c3b314a4be3a37c… Author: vjalili <jalili.vahid(a)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/335c79cc972e6265bb764f69b5e0… Author: vjalili <jalili.vahid(a)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/ad6a4334f42ca36b677adc0e93aa… Author: vjalili <jalili.vahid(a)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/06371f3e84408124469e80f8b7a6… Author: vjalili <jalili.vahid(a)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/114b9bde8baccc6512ab7bfc5a9e… Author: vjalili <jalili.vahid(a)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/d6a9c202b103c65f77f8105ca9e4… Author: vjalili <jalili.vahid(a)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/f21e1b18eed88bbe5dd70d2831cd… Author: vjalili <jalili.vahid(a)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/2ce272484a2fce1ab3bac3f16739… Author: vjalili <jalili.vahid(a)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/aa4f8d7cf9dcf9a65f8d90cdedaa… Author: vjalili <jalili.vahid(a)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/82d6a80d9e7f4f93ab65a3994d42… Author: vjalili <jalili.vahid(a)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/2419c7107739a1894d8ce6be45d4… Author: vjalili <jalili.vahid(a)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/880d0bcd69669b8f31f81b4c6e53… Author: vjalili <jalili.vahid(a)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/244638690c9b587c660f0ec65506… Author: vjalili <jalili.vahid(a)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/264796eddf7ee689c9a2746f3891… Author: vjalili <jalili.vahid(a)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/ac40ad52035fa3ef4856fa31c728… Author: vjalili <jalili.vahid(a)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/72cd57d0114c4d90f7eb146247f0… Author: vjalili <jalili.vahid(a)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/ce5b05853aa86f054d5ed9e910c0… Author: vjalili <jalili.vahid(a)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/999f3b07aff9c65f46576314e5e2… Author: vjalili <jalili.vahid(a)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/0a2f838352634aba28fbd62f9370… Author: vjalili <jalili.vahid(a)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/ffc8d42daf36451ebf1aebd95b4d… Author: vjalili <jalili.vahid(a)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/35459b23c9c107e1c9f5820103ea… Author: vjalili <jalili.vahid(a)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/94d14567847141ea18763870fd11… Author: vjalili <jalili.vahid(a)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/2d6ed38e6fb7e580a5a3d15f4f73… Author: vjalili <jalili.vahid(a)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/cbca243eb70c1bcc2d4d523450b0… Author: vjalili <jalili.vahid(a)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/275953be06073e83a9711f06d8fa… Author: vjalili <jalili.vahid(a)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/73b32652c3e02d9d8635cde9c114… Author: vjalili <jalili.vahid(a)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/df283962bb829b78da5fe4758e28… Author: vjalili <jalili.vahid(a)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/4b7615e98d18c2657c25ab8254ba… Author: vjalili <jalili.vahid(a)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/b6196323d878c84bc9b4c7446590… Author: vjalili <jalili.vahid(a)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/fc8ae7eeefffc88124aeeb7b7076… Author: vjalili <jalili.vahid(a)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/a9dc89e5aa0e5e54c34748966859… Author: vjalili <jalili.vahid(a)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/b60246c8e12fd469a2e248c1770e… Author: vjalili <jalili.vahid(a)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/f8ee1c161434d9cdc77422f4360f… Author: vjalili <jalili.vahid(a)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/ef0dbb293165c829083359292733… Author: vjalili <jalili.vahid(a)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/6c62cc57eb5ea337b0889a3f6bad… Author: vjalili <jalili.vahid(a)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/f2d1db9c23c10c8299ea2786e942… Author: vjalili <jalili.vahid(a)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/4d83b83c22014580e373e36abb8b… Author: vjalili <jalili.vahid(a)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/ab7741548475319006ef65d232b7… Author: vjalili <jalili.vahid(a)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/9d15ce4b21396b13e2a9a4237328… Author: vjalili <jalili.vahid(a)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/13aa6be72090dcd056f96b93db6c… Author: vjalili <jalili.vahid(a)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/b4950a9678251ceb065add2f0cc3… Author: vjalili <jalili.vahid(a)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/6c710ed85f444e3672c8aaf12e26… Author: vjalili <jalili.vahid(a)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/35eabd5543379702b92c439d7239… Author: vjalili <jalili.vahid(a)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/8502dc5b6138133319301ae926a4… Author: vjalili <jalili.vahid(a)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/0aae0505951b7a0a33bebd263c10… Author: vjalili <jalili.vahid(a)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/1dd62afa7f16cee7b20c4b87ba70… Author: vjalili <jalili.vahid(a)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/b5cbaaecbc3bc30e34c0700345ea… Author: vjalili <jalili.vahid(a)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/9de5927b5bbe9c3baddef22ea89d… Author: vjalili <jalili.vahid(a)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/2528c83bf2bc3483779fd509f5a8… Author: vjalili <jalili.vahid(a)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/909c7a72d6fb9fce30844cee3090… Author: vjalili <jalili.vahid(a)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/4d73ea6a6e61563d6f02787f7a85… Author: vjalili <jalili.vahid(a)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/897d024ef7301403ec1ead144524… Author: vjalili <jalili.vahid(a)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/8413f778294cc2e45ec15f8d03d0… Author: vahid <jalili.vahid(a)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 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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/5c35813e302eab21db4f9c8e1e7c… Author: vahid <jalili.vahid(a)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/8198b336bdbcf71264962b1eda7b… Author: vahid <jalili.vahid(a)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/08703ec87750e11bf41ceb1e6864… Author: vahid <jalili.vahid(a)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/0e4045755f90f3d997e9200f036a… Author: vahid <jalili.vahid(a)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/f3ebdae0ce05b1543839a15dd600… Author: vahid <jalili.vahid(a)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/5f8c0dfa342e12f10e06273a90c9… Author: vahid <jalili.vahid(a)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. 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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/9cf7cf6b1ea45478424bad81ffa2… Author: vahid <jalili.vahid(a)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/cf919d7befb7ef1c76e6afc71093… Author: vahid <jalili.vahid(a)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/81eabec6e6517d9ef40b9880925b… Author: vahid <jalili.vahid(a)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/b3a12919cab11f9a174b723cc2d6… Author: vahid <jalili.vahid(a)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/68251722e346fc8fa4d9cec18608… Author: vahid <jalili.vahid(a)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/171b1dd26ea58f666e37672d7308… Author: vahid <jalili.vahid(a)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/90f0a8615d927f1343bc1bc12519… Author: vahid <jalili.vahid(a)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/1b3855cc88cee647f70676f54c82… Author: vahid <jalili.vahid(a)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/8d0b4e0c04cc003b02d9b9d5e089… Author: vahid <jalili.vahid(a)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/4bcd3366ef5eabea4f89571c845b… Author: vahid <jalili.vahid(a)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/e31c7768fb49966961fc8630672f… Author: vahid <jalili.vahid(a)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/d9baf394d528586b44308f41cfa7… Author: vahid <jalili.vahid(a)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/5821fc1f1e932962f92bbabd9c7c… Author: vahid <jalili.vahid(a)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/9a8daa5e746203cd5fd537015aea… Author: vahid <jalili.vahid(a)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/93a5a22b61f4cbea9a5def0928be… Author: vahid <jalili.vahid(a)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/8cd1b0e118062555cdb7bc41c29b… Author: vahid <jalili.vahid(a)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/1efa29419840425072d42db783af… Author: vahid <jalili.vahid(a)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/9eabf5c6c61f18c0a91407c748e9… Author: vahid <jalili.vahid(a)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/8d68e8e5d33ca1c91c1f5b424d60… Author: vahid <jalili.vahid(a)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/0061562bd8c112827c7cd0fd3a6a… Author: vahid <jalili.vahid(a)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/7c599f8a8d762d5783e2534f9158… Author: vahid <jalili.vahid(a)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/081e4eb96de77200322d4fb2998b… Author: vahid <jalili.vahid(a)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/d316b9d7656c60a2888423790c9c… Author: vahid <jalili.vahid(a)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/6504fe6ef1a15d379e8fad68dfe4… Author: vahid <jalili.vahid(a)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/010c512855ea83a94a27d9ce754b… Author: vahid <jalili.vahid(a)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/be34b7501829bdbadf13f502651c… Author: vahid <jalili.vahid(a)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/bd4023f521ed33cdaf9975e517b9… Author: vahid <jalili.vahid(a)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/4305e2c56cc92a8cc67a29640897… Author: vahid <jalili.vahid(a)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/847f66340d1346fe7cd405b614c2… Author: vahid <jalili.vahid(a)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/3ce2a3564799595fef08e5692a95… Author: vahid <jalili.vahid(a)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/e943ec2bb48c6cbd693e0981d613… Author: vahid <jalili.vahid(a)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/01a124314db553c2b9f646addc18… Author: vahid <jalili.vahid(a)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/b62e0476be4e27064efffd56a951… Author: vahid <jalili.vahid(a)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/8f11f78aa2b9e1e342b03a7b3a8e… Author: vahid <jalili.vahid(a)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/d304068161dce41eba53a5ec2c47… Author: vahid <jalili.vahid(a)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/24ed804ab40c931716c5f2f15b76… Author: vahid <jalili.vahid(a)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/a35b686dfda36439dd7bdfe632ce… Author: vahid <jalili.vahid(a)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/4e0b09499ec58cb90449ef15fb3f… Author: vahid <jalili.vahid(a)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/47b41d1bb058244bcb06b88a5c61… Author: vahid <jalili.vahid(a)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/b01ff7c2289bbfe7e6e9e543f0a9… Author: vahid <jalili.vahid(a)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/b9771b7ccc417b9e4326151058f0… Author: vahid <jalili.vahid(a)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/8543231b401bf3eec4d44d63f41c… Author: vahid <jalili.vahid(a)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/8c95f174ba0d61c9632a03e9bec2… Author: vahid <jalili.vahid(a)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/d4d659a85191bbf8e7683c8840c7… Author: vahid <jalili.vahid(a)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. 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config/container_resolvers_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/visualizations/scatterplot/package.json M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.css M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M doc/source/admin/galaxy_options.rst M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/interactive_environments.rst M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M lib/galaxy/authnz/managers.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/managers/cloud.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M 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lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M 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/a236c64ea79ac45ed8bcde67c586… Author: vahid <jalili.vahid(a)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/e30460049ff2ab7ec64b703fca59… Author: vahid <jalili.vahid(a)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/ef70f20a58828b892e6af9b6b751… Author: vahid <jalili.vahid(a)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/6f56ff10b9bc341fdaae879dec28… Author: vahid <jalili.vahid(a)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/39bdb67273700b07662502418011… Author: vahid <jalili.vahid(a)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/7433e2640bc87fc76381eb7fcdcf… Author: vahid <jalili.vahid(a)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/a71db8384cc512efd95c4ac89695… Author: vahid <jalili.vahid(a)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/43e5a1828d2ba1ed11b7a5c7321f… Author: vahid <jalili.vahid(a)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/341f7d6372aa62bc6e84527925e0… Author: vahid <jalili.vahid(a)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/6c07a0370dadfdf0b9352c63b2d6… Author: vahid <jalili.vahid(a)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/566ffaf9d549e3d1096db4996fc9… Author: Enis Afgan <afgane(a)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/2f2153292b39d3a2718c0950303f… Author: Enis Afgan <afgane(a)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.

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[galaxyproject/usegalaxy-playbook] 37602f: Have Test load UCSC dbkeys from CVMFS
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37602f74bf7b35e4dc4819db4bff287cd77ed916 https://github.com/galaxyproject/usegalaxy-playbook/commit/37602f74bf7b35e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/test/files/galaxy/config/tool_data_table_conf.xml Log Message: ----------- Have Test load UCSC dbkeys from CVMFS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c42ea4: Fixed monitor Proxy set function
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c42ea4d9c5e38bc365b54d97f51c96def0f3def7 https://github.com/galaxyproject/galaxy/commit/c42ea4d9c5e38bc365b54d97f51c… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Fixed monitor Proxy set function Commit: 9b7b6ab04d4f0eaa6500cabacf632ef45acf5bcf https://github.com/galaxyproject/galaxy/commit/9b7b6ab04d4f0eaa6500cabacf63… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js Log Message: ----------- Added jquery.custom.js to lib folder Commit: eb57469eef96f7225192128bd846237443e9b437 https://github.com/galaxyproject/galaxy/commit/eb57469eef96f7225192128bd846… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Merge pull request #6970 from Nerdinacan/jquery_bundle Normalized jquery bundle Compare: https://github.com/galaxyproject/galaxy/compare/a4f21fca773c...eb57469eef96 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 443170: optimize images with optipng
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 443170e9128cd785dcfc24f73bddc5bcc1035fa3 https://github.com/galaxyproject/galaxy/commit/443170e9128cd785dcfc24f73bdd… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- optimize images with optipng Commit: a4f21fca773c91032e11804e4a4c71646c213da0 https://github.com/galaxyproject/galaxy/commit/a4f21fca773c91032e11804e4a4c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- Merge pull request #6980 from bgruening/optipng optimize images with optipng Compare: https://github.com/galaxyproject/galaxy/compare/b7c8bd47c907...a4f21fca773c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] a2fcc8: Update Main
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a2fcc8d915037f895985c1553eee651b51eb0198 https://github.com/galaxyproject/usegalaxy-playbook/commit/a2fcc8d915037f89… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dc9128: Fix traceback when starting under Python3 with ``g...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Compare: https://github.com/galaxyproject/galaxy/compare/9029b95e6979...6487d52d513b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 558335: Disable legacy late eager object store assignment ...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5583358d1318a5cf9418cdb2a05962e3e3bb7e49 https://github.com/galaxyproject/usegalaxy-playbook/commit/5583358d1318a5cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable legacy late eager object store assignment on Main since bugs should be fixed **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ccb1e0: In enqueue, always set an object_store_id if one i...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Compare: https://github.com/galaxyproject/galaxy/compare/dbf5ef33604a...9029b95e6979 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Commit: 717605af96bcb5fb9a5193295c9941d0d4632a93 https://github.com/galaxyproject/galaxy/commit/717605af96bcb5fb9a5193295c99… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: 20cecd2a68527015d8b98a430367b8fcdf9a364d https://github.com/galaxyproject/galaxy/commit/20cecd2a68527015d8b98a430367… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. Commit: 4e098c5d5291209f4760010ff8bebd919ba19479 https://github.com/galaxyproject/galaxy/commit/4e098c5d5291209f4760010ff8be… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- tests: add parameter to output_filter Commit: 03eac8315d64e05df74f1f6fb286cff29e75f6b2 https://github.com/galaxyproject/galaxy/commit/03eac8315d64e05df74f1f6fb286… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix for workflow parameter collection in workflows view. Commit: 18644f91cf59265c1473d806845baffbf7a8132f https://github.com/galaxyproject/galaxy/commit/18644f91cf59265c1473d806845b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Avoid using var; let. Commit: 69b447169fb96048ea492a1d99d653585571c15b https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/data.py Log Message: ----------- Allow deferring 'to_ext' extension to the server, implement for collections. Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Commit: 357e2f39c77026c81c56ed30ffae9f1905d2d82a https://github.com/galaxyproject/galaxy/commit/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 3d91738a697ff57047bc3cd505d5afc75de38f45 https://github.com/galaxyproject/galaxy/commit/3d91738a697ff57047bc3cd505d5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6955 from dannon/wf_param_fix [18.09] Fix for workflow parameter collection in workflows view. Commit: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a3773… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Remove unncecessary implementations of display_data These were not updated to use `_download_filename`, and so this fixes the download name for collection elements to include the element identifier. Note that the Data class should handle composite data just fine. Commit: f8b160535c5f9363e85c6c1d041b69ce5c3e9cc2 https://github.com/galaxyproject/galaxy/commit/f8b160535c5f9363e85c6c1d041b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Some minor fixes for the blast datatype The signature for Data.display_data wasn't quite correct, and the description of display_data was also a little misleading. Commit: 9b42032098edaae076f5f88c48f135d8035a9ad6 https://github.com/galaxyproject/galaxy/commit/9b42032098edaae076f5f88c48f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fill in default state for test_optional_workflow_output Commit: 2deb302ae7be93924a8bdcaff17a43caa0b5e3b4 https://github.com/galaxyproject/galaxy/commit/2deb302ae7be93924a8bdcaff17a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6951 from bernt-matthias/topic/test-colouts-backport [18.09] Backport: tests need to count data sets and collections Commit: 61bda3d11a1d608ac8e1a731faf144ff989affc9 https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Merge pull request #6960 from dannon/collection_ext_dl [18.09] Allow deferring 'to_ext' extension to the server Commit: dbf5ef33604aae1a7294abf7bd5303504e8a4d2a https://github.com/galaxyproject/galaxy/commit/dbf5ef33604aae1a7294abf7bd53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #6974 from istevenshen/patch-2 Update locale.js Commit: fefa132cd741779a9c6a4bd03c44f473036a462a https://github.com/galaxyproject/galaxy/commit/fefa132cd741779a9c6a4bd03c44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py A lib/galaxy/datatypes/test/1.qname_sorted.bam M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/315ca74305f1...fefa132cd741 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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