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Merge branch '17.09_release_notes' of github.com:martenson/galaxy into 17.09_release_notes

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Martin Cech
2017-10-24 10:36:56 -04:00
parent d1190bb067 00bc7a51f9
commit fe440d2736
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@@ -29,10 +29,11 @@ Enhancements
`Pull Request 3611`_
* Add job runner for `Chronos <https://mesos.github.io/chronos/>`__
(thanks to `@theosotr <https://github.com/theosotr>`__).
`Pull Request 3946`_
* Paramiko based shell job runner
`Pull Request 3946`_, `Pull Request 4120`_
* Many improvements to the shell job runner (including a new Paramiko based
runner with retry support)
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4358`_
`Pull Request 4358`_, `Pull Request 4599`_, `Pull Request 4343`_
* Add entry for ``empty_extra_files_path`` validator
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 3994`_
@@ -94,10 +95,13 @@ Enhancements
`Pull Request 3179`_
* Speed up and optimize the process of identifying public libraries.
`Pull Request 4640`_
* Various data libraries improvements.
`Pull Request 4512`_
* Enhance workflow import API endpoint to allow admins to install repositories corresponding to a supplied
workflow (thanks to `@manabuishii <https://github.com/manabuishii>`__).
* Numerous data library fixes and improvements - both to the frontend and backend.
`Pull Request 4568`_, `Pull Request 4595`_,
`Pull Request 4594`_, `Pull Request 4579`_, `Pull Request 4560`_
`Pull Request 4512`_, `Pull Request 4621`_, `Pull Request 4752`_
* Enhance workflow import API endpoint to allow admins to install repositories corresponding
to a supplied workflow
(thanks to `@manabuishii <https://github.com/manabuishii>`__).
`Pull Request 3064`_
* GFF3 support in filter by attribute
(thanks to `@peterjc <https://github.com/peterjc>`__).
@@ -188,11 +192,9 @@ Enhancements
`Pull Request 4163`_, `Pull Request 4101`_
* Set content type to application/json for JSON text types.
`Pull Request 4160`_
* Improved Mulled Containers
`Pull Request 4173`_
* Allow Galaxy to use cached mulled containers for Singularity.
`Pull Request 4179`_
* Build mulled images for Singularity on demand...
* Assorted enhancements for container support (both for mulled container generation
and fetching as well as to new Singularity support).
`Pull Request 4173`_, `Pull Request 4179`_, `Pull Request 4180`_,
`Pull Request 4185`_
* Make updateucsc.sh.sample usable without any change
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -214,7 +216,7 @@ Enhancements
* "Join two Datasets" (join1) preserve column headers
(thanks to `@lecorguille <https://github.com/lecorguille>`__).
`Pull Request 4229`_
* add public-only filter for data libraries
* Add public-only filter for data libraries
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
`Pull Request 4232`_
* Fix import order and Python3 compatibility for 51 files
@@ -467,16 +469,9 @@ Enhancements
* Check user roles only once if user has no roles
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4546`_
* Fix data library collection import.
`Pull Request 4568`_
* Various fixes for data libraries.
`Pull Request 4595`_
* Remove unused bam to bai converter
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4598`_
* Retry job submissions in ShellJobRunner
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4599`_
* Remove various unreachable statements
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4603`_
@@ -492,186 +487,152 @@ Fixes
.. major_bug
.. bug
* Various hashtag (or name tag) fixes (also backported to 17.05).
`Pull Request 4139`_, `Pull Request 4188`_
* Simplify RC creation in Makefile.
`Pull Request 4011`_
* Do not recurse in ensure_installed()
* Do not recurse in ``ensure_installed()``
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 4049`_
* Minor fixes for new locales, rebuild of client.
`Pull Request 4050`_
* French error
* French translation error
(thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
`Pull Request 4051`_
* Very minor history tour tweaks
* Minor history tour tweaks.
`Pull Request 4061`_
* conditional postclick execution onNext
* Improve tour button logic
(thanks to `@bagnacan <https://github.com/bagnacan>`__).
`Pull Request 4062`_
* Don't try to get the file name of purged files
* Bug fix to prevent fetching the file path of purged files
(thanks to `@dpryan79 <https://github.com/dpryan79>`__).
`Pull Request 4066`_
* Rebuild to provide new localization.
`Pull Request 4081`_
* ToolShed tool dependency install fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4105`_
* Fix failed merge for populate model
`Pull Request 4112`_
* Fix legacy Python path for genome diversity tools from miller lab.
`Pull Request 4117`_
* Fix chronos client initialization
(thanks to `@theosotr <https://github.com/theosotr>`__).
`Pull Request 4120`_
* Avoid locale specific string.letters for job_name
(thanks to `@peterjc <https://github.com/peterjc>`__).
`Pull Request 4121`_
* New workflow menu message fix
`Pull Request 4124`_
* Fix typo
* Fix typo in job_conf.xml.sample
(thanks to `@manabuishii <https://github.com/manabuishii>`__).
`Pull Request 4126`_
* Tag fixes
`Pull Request 4139`_
* Hide error highlighting if user interacts with highlighted field
`Pull Request 4147`_
* fix webhooks loading url
* Fix webhooks loading URL.
`Pull Request 4158`_
* Fix older GIE config sample description.
`Pull Request 4164`_
* Improve default handling of Singularity volumes.
`Pull Request 4180`_
* Fix `#3990 <https://github.com/galaxyproject/galaxy/issues/3990>`__, don't
chown non-galaxy files
(thanks to `@dpryan79 <https://github.com/dpryan79>`__).
`Pull Request 4186`_
* Hashtags w/ workflow-defined tags fix
`Pull Request 4188`_
* Debug of script library_upload_dir.py
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 4199`_
* Correct name of neo4j datatype class
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
`Pull Request 4223`_
* Fix Registry.get_datatype_by_extension() to return None if ext is unknown
* Fix ``Registry.get_datatype_by_extension()`` to return ``None`` if ``ext`` is unknown
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4224`_
* avoids broken version of mercurial in conda
* Avoid broken version of Mercurial in conda
(thanks to `@bwlang <https://github.com/bwlang>`__).
`Pull Request 4227`_
* Fix empty tabular output error when using discover_datasets.
(thanks to `@pkrog <https://github.com/pkrog>`__).
`Pull Request 4240`_
* Importing old exported histories failing
* Fix importing old exported histories.
(thanks to `@cche <https://github.com/cche>`__).
`Pull Request 4268`_
* Update tool_conf.xml.main to reflect main's current state.
* Update ``tool_conf.xml.main`` to reflect usegalaxy.org's current state.
`Pull Request 4295`_
* Fix TypeError when uploading large files from ftp to s3
* Fix ``TypeError`` when uploading large files from FTP to S3.
(thanks to `@jlhg <https://github.com/jlhg>`__).
`Pull Request 4315`_
* Fix for loading tools when tool.lineage is None.
* Fix for loading tools when ``tool.lineage is None``.
`Pull Request 4317`_
* Fix for the caching of location filenames when they are broken symlinks.
`Pull Request 4318`_
* Remove print debug option from toolshed.
`Pull Request 4332`_
* Prevent early dataset state changes in the ShellJobRunner
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4343`_
* Fix default output labels for subworkflows
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4346`_
* Search Overlay plugin bug fix
* Search overlay plugin bug fix
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 4348`_
* Patch bug preventing creation of dataset library folders
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 4357`_
* Tool version and lineage fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4375`_
* Bugfix: Ensure task splitting handles before job resolution.
* Fix bug in ``scripts/extract_dataset_part.py`` during task splitting.
`Pull Request 4383`_
* Fix get_tool returning list when it shouldn't.
* Fix ``get_tool`` returning list when it shouldn't.
`Pull Request 4390`_
* Bugfix for loading subworkflows from workflow descriptions.
* Bug fix for loading subworkflows from workflow descriptions.
`Pull Request 4394`_
* Bugfix: __str__ method on tool parsers would throw an Exception.
* Bug fix ``__str__`` method on tool parsers that previously would throw an ``Exception``.
`Pull Request 4395`_
* Add missing chemical formats to datatypes_conf.xml.sample
* Add missing chemical formats to ``datatypes_conf.xml.sample``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4413`_
* Don't cast tool_version to string if tool_version is None-type
* Don't cast ``tool_version`` to string if ``tool_version`` is None-type
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4420`_
* some unicoding for local runner
* Some unicoding for local runner
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4426`_
* Break connection in workflow editor if necessary
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4431`_
* Fix private role validation
* Fix private role validation.
`Pull Request 4432`_
* Remove print of non-existent attribute 'content'
(thanks to `@chambm <https://github.com/chambm>`__).
`Pull Request 4439`_
* Fix API tests broken in `#4434
<https://github.com/galaxyproject/galaxy/issues/4434>`__
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4445`_
* Fix E201 errors (spaces in parens) in new memepsp datatype
`Pull Request 4446`_
* Fix quota function name
`Pull Request 4469`_
* Fixes for VCF/BCF datatypes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4477`_
* Validate workflow step after step argument injection
* Validate workflow step after step argument injection.
`Pull Request 4483`_
* Fix drag and drop from history for Firefox
`Pull Request 4496`_
* 2017-08 Security Patch
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 4501`_
* import of history works even if we use symlink in database directory
* Fix history import if using symlink in database directory
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 4511`_
* Fix missing tools wf editor alternative
* Fix missing tools in the workflow editor
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4552`_
* Prevent unbound variable error history controller.
`Pull Request 4557`_
* improve docs and access checks in datalibs manager/api
`Pull Request 4560`_
* Backport uwsgi fix from `#2836
<https://github.com/galaxyproject/galaxy/issues/2836>`__.
`Pull Request 4565`_
* Bug: Fix startup of galaxy when webhooks dir is empty
* Bug fix startup of galaxy when webhooks dir is empty
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4570`_
* Fix delete option in history menu
* Fix delete option in history menu.
`Pull Request 4574`_
* datalibs: fix two bugs, refactor
`Pull Request 4579`_
* Cancel workflow invocations when histories are deleted.
`Pull Request 4580`_
* Fix datalib search pagination
`Pull Request 4594`_
* Multiview missing histories fix
`Pull Request 4610`_
* Fix virtualenv activation for some scripts
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4616`_
* replace separators in library sharing role names
`Pull Request 4621`_
* Pulsar remote metadata fixes
`Pull Request 4622`_
* Swap sanitize whitelist form to use a post.
`Pull Request 4625`_
* Misc. spelling/grammatical error fixes.
* Fix various spelling and grammatical error fixes.
`Pull Request 4626`_
* Typo fix
(thanks to `@VJalili <https://github.com/VJalili>`__).
@@ -687,7 +648,6 @@ Fixes
* Explicitly write registry.xml when creating a job for the upload tool
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4644`_, `Pull Request 4600`_
* Fix links on workflow, history items.
`Pull Request 4656`_
* Fix for modules resolver.
@@ -706,9 +666,9 @@ Fixes
* Add message (error and info) display to workflows display list.
`Pull Request 4716`_
* If the newest version of a tool is hidden, load the newest older version, if
any, into the tool panel
any, into the tool panel.
`Pull Request 4726`_
* Fix missing support for command_inject when using containers lib in GIEs
* Fix missing support for command_inject when using containers lib in GIEs.
`Pull Request 4740`_
* Fix t, a, g, s returned in to_dict() method
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -720,8 +680,6 @@ Fixes
`Pull Request 4748`_
* Force onload webhooks to wait for Galaxy object (and root) resolution.
`Pull Request 4750`_
* replace selector for selecting selected rows
`Pull Request 4752`_
* GIEs: Grandfather automatic uppercasing of some env_override variables
`Pull Request 4760`_