[galaxyproject/galaxy] 959e6f: Add a wrapper for the download-to-cloud tool.

6 Nov 2018


      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:
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    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 client/galaxy/scripts/mvc/collection/list-collection-creator.js
    M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
    M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
    M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
    M client/galaxy/scripts/mvc/dataset/dataset-error.js
    M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
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    M client/galaxy/scripts/mvc/form/form-repeat.js
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    M client/galaxy/scripts/mvc/form/form-view.js
    M client/galaxy/scripts/mvc/form/form-wrapper.js
    M client/galaxy/scripts/mvc/history/history-contents.js
    M client/galaxy/scripts/mvc/lazy/lazy-limited.js
    M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
    M client/galaxy/scripts/mvc/rules/rule-definitions.js
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M client/galaxy/scripts/mvc/tool/tools.js
    M client/galaxy/scripts/mvc/toolshed/categories-view.js
    R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
    M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
    M client/galaxy/scripts/mvc/toolshed/repositories-view.js
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    M client/galaxy/scripts/mvc/toolshed/repository-view.js
    M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
    M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
    M client/galaxy/scripts/mvc/toolshed/util.js
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    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/scripts/mvc/ui/ui-select-default.js
    M client/galaxy/scripts/mvc/ui/ui-select-genomespace.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/ui/ui-table.js
    M client/galaxy/scripts/mvc/ui/ui-tabs.js
    R client/galaxy/scripts/mvc/ui/ui-thumbnails.js
    M client/galaxy/scripts/mvc/upload/collection/collection-row.js
    M client/galaxy/scripts/mvc/upload/collection/collection-view.js
    M client/galaxy/scripts/mvc/upload/composite/composite-row.js
    M client/galaxy/scripts/mvc/upload/composite/composite-view.js
    M client/galaxy/scripts/mvc/upload/default/default-row.js
    M client/galaxy/scripts/mvc/upload/default/default-view.js
    M client/galaxy/scripts/mvc/upload/upload-extension.js
    M client/galaxy/scripts/mvc/upload/upload-ftp.js
    M client/galaxy/scripts/mvc/upload/upload-settings.js
    M client/galaxy/scripts/mvc/upload/upload-view.js
    M client/galaxy/scripts/mvc/user/user-custom-builds.js
    M client/galaxy/scripts/mvc/user/user-preferences.js
    M client/galaxy/scripts/mvc/visualization/chart/views/description.js
    M client/galaxy/scripts/mvc/visualization/chart/views/editor.js
    M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
    M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
    M client/galaxy/scripts/mvc/visualization/chart/views/settings.js
    M client/galaxy/scripts/mvc/workflow/workflow-connector.js
    M client/galaxy/scripts/mvc/workflow/workflow-forms.js
    M client/galaxy/scripts/mvc/workflow/workflow-manager.js
    M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
    M client/galaxy/scripts/mvc/workflow/workflow-view.js
    M client/galaxy/scripts/qunit/test.js
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    R client/galaxy/scripts/qunit/tests/popover_tests.js
    M client/galaxy/scripts/qunit/tests/ui_tests.js
    M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
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    M client/galaxy/style/scss/charts.scss
    M client/galaxy/style/scss/frame.scss
    R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
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    M client/galaxy/style/scss/history.scss
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    R client/galaxy/style/scss/theme/plain.scss
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    A client/galaxy/style/source_material/warn_icon.svg
    M client/package.json
    M config/datatypes_conf.xml.sample
    M config/error_report.yml.sample
    M config/galaxy.yml.sample
    M config/job_conf.xml.sample_advanced
    M config/oidc_backends_config.xml.sample
    M config/plugins/tours/core.galaxy_ui.yaml
    M config/reports.yml.sample
    M config/tool_conf.xml.sample
    M config/tool_shed.yml.sample
    M contrib/nagios/check_galaxy.py
    M cron/build_chrom_db.py
    M cron/parse_builds_3_sites.py
    M doc/parse_gx_xsd.py
    M doc/schema_template.md
    M doc/source/admin/cluster.md
    M doc/source/admin/conda_faq.rst
    M doc/source/admin/config.rst
    M doc/source/admin/dependency_resolvers.rst
    M doc/source/admin/framework_dependencies.rst
    M doc/source/admin/galaxy_options.rst
    M doc/source/admin/jobs.md
    M doc/source/admin/production.md
    M doc/source/admin/scaling.md
    M doc/source/admin/special_topics/interactive_environments.rst
    M doc/source/admin/special_topics/performance_tracking.rst
    M doc/source/api_doc.rst
    M doc/source/conf.py
    M doc/source/lib/galaxy.actions.rst
    M doc/source/lib/galaxy.auth.rst
    A doc/source/lib/galaxy.authnz.rst
    M doc/source/lib/galaxy.containers.rst
    M doc/source/lib/galaxy.datatypes.converters.rst
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    R doc/source/lib/galaxy.external_services.result_handlers.rst
    R doc/source/lib/galaxy.external_services.rst
    R doc/source/lib/galaxy.jobs.deferred.rst
    M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
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    R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst
    M doc/source/lib/galaxy.jobs.runners.util.rst
    M doc/source/lib/galaxy.managers.rst
    M doc/source/lib/galaxy.objectstore.rst
    M doc/source/lib/galaxy.rst
    R doc/source/lib/galaxy.sample_tracking.rst
    M doc/source/lib/galaxy.tools.cwl.rst
    M doc/source/lib/galaxy.tools.deps.resolvers.rst
    M doc/source/lib/galaxy.tools.deps.rst
    A doc/source/lib/galaxy.tools.error_reports.plugins.rst
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    M doc/source/lib/galaxy.tools.parser.rst
    M doc/source/lib/galaxy.tools.rst
    M doc/source/lib/galaxy.tools.toolbox.lineages.rst
    M doc/source/lib/galaxy.tools.toolbox.rst
    M doc/source/lib/galaxy.tools.verify.rst
    R doc/source/lib/galaxy.util.backports.rst
    R doc/source/lib/galaxy.util.log.rst
    A doc/source/lib/galaxy.util.logging.rst
    A doc/source/lib/galaxy.util.path.rst
    M doc/source/lib/galaxy.util.rst
    M doc/source/lib/galaxy.visualization.plugins.rst
    R doc/source/lib/galaxy.web.base.controllers.rst
    M doc/source/lib/galaxy.web.base.rst
    M doc/source/lib/galaxy.web.framework.helpers.rst
    M doc/source/lib/galaxy.web.framework.middleware.rst
    M doc/source/lib/galaxy.web.framework.rst
    M doc/source/lib/galaxy.web.stack.rst
    M doc/source/lib/galaxy.webapps.galaxy.api.rst
    M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
    M doc/source/lib/galaxy.webapps.reports.controllers.rst
    A doc/source/lib/galaxy.webapps.reports.framework.rst
    M doc/source/lib/galaxy.webapps.reports.rst
    M doc/source/lib/galaxy.webapps.rst
    A doc/source/lib/galaxy.workflow.resources.rst
    M doc/source/lib/galaxy.workflow.rst
    M doc/source/lib/tool_shed.util.rst
    M doc/source/releases/16.04_announce.rst
    M doc/source/releases/16.10.rst
    M lib/galaxy/authnz/managers.py
    M lib/galaxy/authnz/psa_authnz.py
    M lib/galaxy/config.py
    M lib/galaxy/dataset_collections/matching.py
    M lib/galaxy/datatypes/binary.py
    M lib/galaxy/datatypes/data.py
    M lib/galaxy/datatypes/molecules.py
    M lib/galaxy/datatypes/neo4j.py
    M lib/galaxy/datatypes/sequence.py
    M lib/galaxy/datatypes/tabular.py
    A lib/galaxy/datatypes/test/md.cpt
    A lib/galaxy/datatypes/test/md.trr
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    A lib/galaxy/datatypes/test/test.loom
    A lib/galaxy/datatypes/test/test_charmm.vel
    A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd
    M lib/galaxy/datatypes/text.py
    M lib/galaxy/datatypes/util/gff_util.py
    M lib/galaxy/dependencies/conditional-requirements.txt
    M lib/galaxy/dependencies/dev-requirements.txt
    M lib/galaxy/dependencies/pipfiles/default/Pipfile
    A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
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    R lib/galaxy/dependencies/pipfiles/develop/Pipfile
    R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
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    M lib/galaxy/dependencies/pipfiles/update.sh
    R lib/galaxy/dependencies/requirements.txt
    M lib/galaxy/exceptions/error_codes.py
    M lib/galaxy/jobs/__init__.py
    M lib/galaxy/jobs/handler.py
    M lib/galaxy/jobs/output_checker.py
    M lib/galaxy/jobs/runners/__init__.py
    M lib/galaxy/jobs/runners/chronos.py
    M lib/galaxy/jobs/runners/local.py
    M lib/galaxy/jobs/runners/pulsar.py
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    M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
    M lib/galaxy/jobs/runners/util/job_script/__init__.py
    M lib/galaxy/jobs/runners/util/kill.py
    M lib/galaxy/jobs/splitters/multi.py
    M lib/galaxy/managers/cloud.py
    A lib/galaxy/managers/cloudauthzs.py
    M lib/galaxy/managers/collections.py
    M lib/galaxy/managers/collections_util.py
    M lib/galaxy/managers/datasets.py
    M lib/galaxy/managers/hdas.py
    M lib/galaxy/managers/jobs.py
    M lib/galaxy/managers/lddas.py
    M lib/galaxy/managers/rbac_secured.py
    M lib/galaxy/managers/sharable.py
    M lib/galaxy/managers/tags.py
    M lib/galaxy/managers/users.py
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/model/__init__.py
    M lib/galaxy/model/custom_types.py
    M lib/galaxy/model/mapping.py
    M lib/galaxy/model/metadata.py
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    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/cloud.py
    M lib/galaxy/security/__init__.py
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    M lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/actions/model_operations.py
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    M lib/galaxy/tools/data/__init__.py
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    M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
    M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
    M lib/galaxy/tools/parameters/__init__.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/meta.py
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    M lib/galaxy/tools/search/__init__.py
    M lib/galaxy/tools/test.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/util/maf_utilities.py
    M lib/galaxy/tools/verify/__init__.py
    M lib/galaxy/tools/verify/interactor.py
    M lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/tools/wrappers.py
    M lib/galaxy/tools/xsd/galaxy.xsd
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/bunch.py
    M lib/galaxy/util/checkers.py
    M lib/galaxy/util/expressions.py
    M lib/galaxy/util/hash_util.py
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    M lib/galaxy/util/object_wrapper.py
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    M lib/galaxy/util/rules_dsl.py
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    M lib/galaxy/util/ucsc.py
    M lib/galaxy/util/xml_macros.py
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    M lib/galaxy/web/base/controller.py
    M lib/galaxy/web/form_builder.py
    M lib/galaxy/web/framework/base.py
    M lib/galaxy/web/framework/decorators.py
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    M lib/galaxy/web/stack/__init__.py
    M lib/galaxy/web/stack/transport.py
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    M scripts/apply_tags.py
    M scripts/check_galaxy.py
    M scripts/cleanup_datasets/pgcleanup.py
    M scripts/functional_tests.py
    M scripts/galaxy-main
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    A test/functional/tools/collection_cat_group_tag_multiple.xml
    M test/functional/tools/metadata_biom1.xml
    M test/functional/tools/parallelism.xml
    M test/functional/tools/parallelism_optional.xml
    M test/functional/tools/samples_tool_conf.xml
    M test/functional/tools/unicode_stream.xml
    R test/functional/twilltestcase.py
    M test/galaxy_selenium/has_driver.py
    M test/galaxy_selenium/navigates_galaxy.py
    M test/galaxy_selenium/navigation.yml
    M test/galaxy_selenium/smart_components.py
    A test/integration/delay_job_conf.xml
    A test/integration/delay_rules/__init__.py
    A test/integration/delay_rules/rules.py
    A test/integration/objectstore_selection_job_conf.xml
    A test/integration/objectstore_selection_job_resource_parameters_conf.xml
    A test/integration/objectstore_selection_rules/__init__.py
    A test/integration/objectstore_selection_rules/rules.py
    M test/integration/test_data_manager_table_reload.py
    M test/integration/test_job_environments.py
    A test/integration/test_job_recovery.py
    M test/integration/test_job_resubmission.py
    M test/integration/test_mules_as_job_handlers.py
    A test/integration/test_objectstore_selection.py
    M test/integration/test_scripts.py
    M test/integration/test_upload_configuration_options.py
    M test/integration/tool_sheds_conf.xml
    M test/integration/uses_shed.py
    M test/selenium_tests/framework.py
    M test/selenium_tests/test_collection_builders.py
    M test/selenium_tests/test_history_sharing.py
    M test/selenium_tests/test_published_histories_grid.py
    M test/selenium_tests/test_saved_histories.py
    M test/selenium_tests/test_stock_tours.py
    M 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 client/galaxy/scripts/mvc/workflow/workflow-view-data.js
    M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
    M client/galaxy/scripts/ui/fa-icon-button.js
    M client/galaxy/style/scss/base.scss
    M client/galaxy/style/scss/theme/blue.scss
    M client/galaxy/style/scss/ui.scss
    M client/galaxy/style/scss/upload.scss
    M client/gulpfile.js
    M client/package.json
    M client/yarn.lock
    M config/containers_conf.yml.sample
    M config/datatypes_conf.xml.sample
    M config/galaxy.yml.sample
    M config/job_conf.xml.sample_advanced
    M config/plugins/visualizations/graphviz/config/graphviz.xml
    M config/plugins/webhooks/demo/tour_generator/__init__.py
    M doc/source/admin/conda_faq.rst
    M doc/source/admin/dependency_resolvers.rst
    M doc/source/admin/framework_dependencies.rst
    M doc/source/admin/galaxy_options.rst
    M doc/source/admin/jobs.md
    M lib/galaxy/actions/library.py
    M lib/galaxy/authnz/managers.py
    M lib/galaxy/authnz/psa_authnz.py
    M lib/galaxy/dependencies/conda-file.sh
    M 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 lib/galaxy/tools/cwl/parser.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/cwl/util.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/docker_util.py
    M lib/galaxy/tools/deps/mulled/mulled_build.py
    M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/evaluation.py
    M lib/galaxy/tools/execute.py
    M lib/galaxy/tools/lint.py
    M lib/galaxy/tools/linters/stdio.py
    M lib/galaxy/tools/linters/tests.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/tools/parameters/wrapped.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/tag_collection_from_file.xml
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/examples.py.sample
    M lib/galaxy/tools/verify/interactor.py
    M lib/galaxy/tools/xsd/galaxy.xsd
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/compression_utils.py
    M lib/galaxy/util/create_history_template.py
    M lib/galaxy/util/rules_dsl.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/web/framework/decorators.py
    M lib/galaxy/web/framework/helpers/__init__.py
    M lib/galaxy/webapps/galaxy/api/configuration.py
    M lib/galaxy/webapps/galaxy/api/folder_contents.py
    M lib/galaxy/webapps/galaxy/api/folders.py
    M lib/galaxy/webapps/galaxy/api/forms.py
    M lib/galaxy/webapps/galaxy/api/groups.py
    M lib/galaxy/webapps/galaxy/api/history_contents.py
    M lib/galaxy/webapps/galaxy/api/jobs.py
    M lib/galaxy/webapps/galaxy/api/libraries.py
    M lib/galaxy/webapps/galaxy/api/library_contents.py
    M lib/galaxy/webapps/galaxy/api/library_datasets.py
    M lib/galaxy/webapps/galaxy/api/pages.py
    M lib/galaxy/webapps/galaxy/api/roles.py
    M lib/galaxy/webapps/galaxy/api/search.py
    M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
    M lib/galaxy/webapps/galaxy/api/tools.py
    M lib/galaxy/webapps/galaxy/api/users.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/config_schema.yml
    M lib/galaxy/webapps/galaxy/controllers/admin.py
    M 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...
  Author: vahid <jalili.vahid@gmail.com>
  Date:   2018-10-25 (Thu, 25 Oct 2018)

  Changed paths:
    M client/README.md
    A client/galaxy/docs/README.md
    M client/galaxy/docs/bootstrap.md
    M client/galaxy/docs/galaxy-buttons.md
    M client/galaxy/docs/galaxy-forms.md
    M client/galaxy/docs/galaxy-masthead.md
    M client/galaxy/docs/galaxy-menus.md
    M client/galaxy/docs/galaxy-messages.md
    M client/galaxy/docs/galaxy-panels.md
    M client/galaxy/docs/galaxy-tables.md
    M client/galaxy/docs/galaxy-tabs.md
    M client/galaxy/scripts/apps/analysis.js
    M client/galaxy/scripts/mvc/ui/ui-rules-edit.js
    M client/galaxy/scripts/mvc/ui/ui-slider.js
    M client/galaxy/scripts/ui/editable-text.js
    M client/galaxy/style/scss/base.scss
    M client/galaxy/style/scss/history.scss
    M client/galaxy/style/scss/jstree.scss
    M client/galaxy/style/scss/list-item.scss
    M client/galaxy/style/scss/ui.scss
    A 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 lib/galaxy/tools/actions/__init__.py
    M lib/galaxy/tools/actions/history_imp_exp.py
    M lib/galaxy/tools/actions/metadata.py
    M lib/galaxy/tools/actions/model_operations.py
    M lib/galaxy/tools/actions/upload.py
    M lib/galaxy/tools/data/__init__.py
    M lib/galaxy/tools/error_reports/plugins/biostars.py
    M lib/galaxy/tools/error_reports/plugins/email.py
    M lib/galaxy/tools/error_reports/plugins/github.py
    M lib/galaxy/tools/error_reports/plugins/influxdb.py
    M lib/galaxy/tools/error_reports/plugins/json.py
    M lib/galaxy/tools/error_reports/plugins/sentry.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/dynamic_options.py
    M lib/galaxy/tools/xsd/galaxy.xsd
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/monitors.py
    M lib/galaxy/util/pastescript/serve.py
    M lib/galaxy/web/base/controller.py
    M lib/galaxy/webapps/galaxy/api/cloudauthz.py
    M lib/galaxy/webapps/galaxy/buildapp.py
    M lib/galaxy/webapps/galaxy/config_schema.yml
    M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
    M 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/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
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