From 4dcba21d838bd2bad806687d7c212d7da0b8e85e Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 9 Oct 2017 13:49:37 -0400 Subject: [PATCH 01/15] initial release notes for 17.09 --- doc/source/releases/17.09.rst | 1152 ++++++++++++++++++++++++ doc/source/releases/17.09_announce.rst | 39 +- doc/source/releases/18.01_announce.rst | 10 + 3 files changed, 1198 insertions(+), 3 deletions(-) create mode 100644 doc/source/releases/17.09.rst create mode 100644 doc/source/releases/18.01_announce.rst diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst new file mode 100644 index 000000000000..2c859f2c3fe1 --- /dev/null +++ b/doc/source/releases/17.09.rst @@ -0,0 +1,1152 @@ + +.. to_doc + +17.09 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + + +.. feature + +* Galaxy Workflow support for GenomeSpace + (thanks to `@gvlproject `__). + `Pull Request 1814`_ +* HiCBrowser as Galaxy IE + (thanks to `@bgruening `__). + `Pull Request 3330`_ +* Synnefo/Pithos+ object store backend + (thanks to `@saxtouri `__). + `Pull Request 3611`_ +* Add job runner for Chronos + (thanks to `@theosotr `__). + `Pull Request 3946`_ +* Add entry for empty_extra_files_path validator + (thanks to `@gregvonkuster `__). + `Pull Request 3994`_ +* Add possibility for downloading entire collections + (thanks to `@mvdbeek `__). + `Pull Request 4098`_ +* Implement Singularity Support + `Pull Request 4175`_ +* Async update: support to collections + (thanks to `@fabio-cumbo `__). + `Pull Request 4198`_ +* Add API repository uninstall endpoint + (thanks to `@mvdbeek `__). + `Pull Request 4248`_ +* Vcf gz datatype + (thanks to `@ffinfo `__). + `Pull Request 4254`_ +* Add ptkscmp datatype + (thanks to `@gregvonkuster `__). + `Pull Request 4259`_ +* Library tags + (thanks to `@bwlang `__). + `Pull Request 4262`_ +* Display preview feature for Bam datatype + (thanks to `@ashvark `__). + `Pull Request 4279`_ +* Add Unipept taxonomy viewer plugin + (thanks to `@caleb-easterly `__). + `Pull Request 4310`_ +* Created alphabetic and numerical sort tool for collection operations + (thanks to `@glormph `__). + `Pull Request 4329`_ +* Paramiko based shell runner + (thanks to `@mvdbeek `__). + `Pull Request 4358`_ +* Add imzML datatype + (thanks to `@bgruening `__). + `Pull Request 4370`_ +* Allow switching tool versions in workflow editor + (thanks to `@mvdbeek `__). + `Pull Request 4373`_ +* Stop loading tools that require a newer galaxy + (thanks to `@mvdbeek `__). + `Pull Request 4382`_ +* Add deepTools datatypes to Galaxy + (thanks to `@bgruening `__). + `Pull Request 4392`_ +* Add support for the MEME psp format + (thanks to `@gregvonkuster `__). + `Pull Request 4430`_ +* Nicer tool click targets for base + "plain" theme + (thanks to `@erasche `__). + `Pull Request 4470`_ +* A round of data libraries improvements. + `Pull Request 4512`_ +* add biom2 datatype + (thanks to `@shiltemann `__). + `Pull Request 4519`_ +* respect expose_user_email configuration in datalibraries permissions list + `Pull Request 4611`_ +* Explicitly include PyPI as an --extra-index-url to pip + `Pull Request 4674`_ + +.. enhancement + +* Install tools and workflow + (thanks to `@manabuishii `__). + `Pull Request 3064`_ +* GFF3 support in filter by attribute + (thanks to `@peterjc `__). + `Pull Request 3076`_ +* Configuration & Server Overhaul - Tool Shed and Reports + `Pull Request 3179`_ +* Add extension point for user preferences + (thanks to `@bgruening `__). + `Pull Request 3383`_ +* Kubernetes runner: Non-privileged filesystem access, updated k8s Job version + (thanks to `@phnmnl `__). + `Pull Request 3972`_ +* Setup framework for retrying failed Selenium tests. + `Pull Request 3993`_ +* add dev requirement + `Pull Request 4008`_ +* Tool-Describing-Tours + (thanks to `@anatskiy `__). + `Pull Request 4019`_ +* Prevent graphite from dying loudly + (thanks to `@erasche `__). + `Pull Request 4036`_ +* Updated parameters check for OpenID + (thanks to `@VJalili `__). + `Pull Request 4039`_ +* Tooltip translation . Add Deutsch,Spanish + (thanks to `@ValentinChCloud `__). + `Pull Request 4045`_ +* New Workflow Management Screen UI using JavaScript + (thanks to `@bgruening `__). + `Pull Request 4047`_ +* Improve release checklist + `Pull Request 4077`_ +* Fix French translation errors + (thanks to `@yvanlebras `__). + `Pull Request 4080`_ +* remove the content alert from TS response + `Pull Request 4082`_ +* Touchup .gitignore to not ignore new bundles. + `Pull Request 4091`_ +* New Configure Workflow Menu UI + (thanks to `@bgruening `__). + `Pull Request 4092`_ +* get real user name from username and email (for submission as real user with + drmaa) + (thanks to `@bernt-matthias `__). + `Pull Request 4096`_ +* Security policy + (thanks to `@erasche `__). + `Pull Request 4113`_ +* Improved styling of workflow list. + `Pull Request 4138`_ +* Swap over all URLs to new wiki location + (thanks to `@erasche `__). + `Pull Request 4141`_ +* Documentation fixes and improvements + (thanks to `@nsoranzo `__). + `Pull Request 4146`_ +* Slider enhancement, shared event listeners + `Pull Request 4149`_ +* Add the ability to control job conf plugin loading from environment + variables. + `Pull Request 4154`_ +* Remove saved pages grid mako + `Pull Request 4157`_ +* Set content type to application/json for JSON text types. + `Pull Request 4160`_ +* Remove histories grid mako + `Pull Request 4167`_ +* Mako to JavaScript views for Workflow's Run and Import actions + (thanks to `@bgruening `__). + `Pull Request 4169`_ +* 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... + `Pull Request 4185`_ +* Make updateucsc.sh.sample usable without any change + (thanks to `@nsoranzo `__). + `Pull Request 4192`_ +* deals with .xls older file extension + (thanks to `@FredericBGA `__). + `Pull Request 4200`_ +* Remove makos for published list grids + `Pull Request 4201`_ +* Improve search plugin + (thanks to `@bgruening `__). + `Pull Request 4213`_ +* Upgrading Neo4j IE to 3.1 + (thanks to `@thobalose `__). + `Pull Request 4216`_ +* Running a word count on a compressed fastq file now runs wc on the un… + (thanks to `@dpryan79 `__). + `Pull Request 4226`_ +* "Join two Datasets" (join1) preserve column headers + (thanks to `@lecorguille `__). + `Pull Request 4229`_ +* add public-only filter for data libraries + (thanks to `@pvanheus `__). + `Pull Request 4232`_ +* Fix import order and Python3 compatibility for 51 files + (thanks to `@nsoranzo `__). + `Pull Request 4236`_ +* Sniff fastqsanger and prefer it over fastq if the quality scores match + (thanks to `@dpryan79 `__). + `Pull Request 4237`_ +* Enable skipping comment lines while sniffing files + (thanks to `@dpryan79 `__). + `Pull Request 4239`_ +* Expose 4 more rows from the galaxy_user table to help out sys admins + (thanks to `@XDtim `__). + `Pull Request 4255`_ +* Change 'register or login' to just 'login' if 'allow_user_creation=False' + (thanks to `@scholtalbers `__). + `Pull Request 4258`_ +* Keep tool parameters when rerunning a job + (thanks to `@mvdbeek `__). + `Pull Request 4271`_ +* Uniform titles + (thanks to `@erasche `__). + `Pull Request 4272`_ +* Fix blockquote>p sizing + (thanks to `@erasche `__). + `Pull Request 4273`_ +* Expose more user properties to admins via the API. + `Pull Request 4274`_ +* Ensure tags are copied and presented when moving Collections + (thanks to `@pvanheus `__). + `Pull Request 4277`_ +* Add test_errors to .gitignore. + `Pull Request 4278`_ +* Package locking for node modules. + `Pull Request 4283`_ +* Enhancement for Phylocanvas plugin + (thanks to `@bgruening `__). + `Pull Request 4284`_ +* Local network access restrictions + (thanks to `@erasche `__). + `Pull Request 4289`_ +* Grid published histories + `Pull Request 4291`_ +* Enhancement for Phyloviz viz plugin + (thanks to `@bgruening `__). + `Pull Request 4292`_ +* Use dictionary endpoints for item selection grids in page editor + `Pull Request 4293`_ +* Submitting the galaxy jobs as a predefined system user: using + 'real_system_username' + (thanks to `@ashvark `__). + `Pull Request 4294`_ +* Trackster selection grids and feature fixes + `Pull Request 4302`_ +* Update Japanese translation + (thanks to `@manabuishii `__). + `Pull Request 4304`_ +* Refactor bug reporting into plugins / Remove bug report mako + (thanks to `@erasche `__). + `Pull Request 4305`_ +* Localization support for Tool Help + (thanks to `@manabuishii `__). + `Pull Request 4306`_ +* Support Localization Scratchbook + (thanks to `@manabuishii `__). + `Pull Request 4307`_ +* Removes saved visualizations grid mako + `Pull Request 4311`_ +* Allow import of history archives via simple file upload + (thanks to `@mvdbeek `__). + `Pull Request 4326`_ +* Fix some French errors + (thanks to `@loraine-gueguen `__). + `Pull Request 4337`_ +* Updated the version requirements + (thanks to `@VJalili `__). + `Pull Request 4342`_ +* CSRF protection for login, logout, and user registration. + `Pull Request 4365`_ +* Implement default_identifier_source for outputs and sort input keys by + default + (thanks to `@mvdbeek `__). + `Pull Request 4368`_ +* Allow removal of dataset tags in workflows + (thanks to `@mvdbeek `__). + `Pull Request 4369`_ +* Galactic Radio Telescope Update + (thanks to `@erasche `__). + `Pull Request 4376`_ +* Remove makos of admin user grid forms + `Pull Request 4377`_ +* Admin grid roles revision + `Pull Request 4385`_ +* Show minimum required galaxy version in tool shed and galaxy installation + process + (thanks to `@mvdbeek `__). + `Pull Request 4386`_ +* Cleanup of Unit Test Code for Loading Tools + `Pull Request 4387`_ +* Refactor ToolOutputCollectionStructure... + `Pull Request 4389`_ +* Slightly improve workflow warnings/errors logging. + `Pull Request 4396`_ +* Better Error Summaries for API Tests + `Pull Request 4397`_ +* Fix import order and Python3 compatibility for lib/galaxy/web/base/ + (thanks to `@nsoranzo `__). + `Pull Request 4403`_ +* Generalize allow_library_path_paste to allow_path_paste. + `Pull Request 4404`_ +* Admin grid groups revision + `Pull Request 4405`_ +* Small GRT bugfixes + (thanks to `@erasche `__). + `Pull Request 4408`_ +* Update conda channel order to sync with Bioconda + (thanks to `@nsoranzo `__). + `Pull Request 4409`_ +* Add Excel97 Datatype + `Pull Request 4410`_ +* replace mako templates for tool lineage and quotas grids + `Pull Request 4411`_ +* Fixes and enhancements for the upload API + `Pull Request 4417`_ +* Avoid adding `(imported from API)` to workflows + (thanks to `@chambm `__). + `Pull Request 4434`_ +* Enhanced tool options for dataset discovery + `Pull Request 4437`_ +* Augment form module separation + `Pull Request 4438`_ +* Fix E201 and E202 style errors + (thanks to `@nsoranzo `__). + `Pull Request 4440`_ +* Add autopep8 script to help rebasing branches after `#4440 + `__. + `Pull Request 4447`_ +* Interactive Environment: possibility to don't uppercase env variables + (thanks to `@xgaia `__). + `Pull Request 4454`_ +* Uniform indentation of multiline if conditionals + (thanks to `@nsoranzo `__). + `Pull Request 4455`_ +* Logging fixes + (thanks to `@nsoranzo `__). + `Pull Request 4456`_ +* More detailed sentry reports + (thanks to `@erasche `__). + `Pull Request 4457`_ +* don't uppercase envoverride + (thanks to `@xgaia `__). + `Pull Request 4458`_ +* Fix checking WorkflowInvocation for published workflows + (thanks to `@mvdbeek `__). + `Pull Request 4465`_ +* add mz5 datatype + (thanks to `@bgruening `__). + `Pull Request 4466`_ +* More items per page in saved history and directly show tags + (thanks to `@mvdbeek `__). + `Pull Request 4467`_ +* needed for sentry functionality in reports webapp + (thanks to `@erasche `__). + `Pull Request 4471`_ +* Show tags, import by drag-and-drop and avoid refreshed in workflow page + (thanks to `@mvdbeek `__). + `Pull Request 4476`_ +* Use pysam instead of samtools binary + (thanks to `@nsoranzo `__). + `Pull Request 4479`_ +* replace exclamation with a clock icon + `Pull Request 4485`_ +* Minor copy datasets dialog improvement. + `Pull Request 4486`_ +* New Dependency resolver for the LMOD environment modules system + (thanks to `@arbernard `__). + `Pull Request 4489`_ +* 41% reduction in freiburg galaxy startup time + (thanks to `@erasche `__). + `Pull Request 4495`_ +* Allow paramiko cli to recover from ssh timeout + (thanks to `@mvdbeek `__). + `Pull Request 4503`_ +* Tests and clarifications for composite uploads. + `Pull Request 4505`_ +* Load tools with collection type source attributes into the workflow editor + `Pull Request 4514`_ +* Display d3 hierarchy datatype in upload interface + `Pull Request 4522`_ +* Selenium test fixes and improvements. + `Pull Request 4523`_ +* Fix workflow run Selenium test and make it more robust. + `Pull Request 4524`_ +* Implement influxdb error reporter + (thanks to `@erasche `__). + `Pull Request 4533`_ +* Sync non-CWL galaxy-lib changes. + `Pull Request 4535`_ +* Add a small howto on profiling galaxy code + (thanks to `@mvdbeek `__). + `Pull Request 4542`_ +* allow linking, posix and spaces conversions in datalib imports + `Pull Request 4547`_ +* Assorted Selenium test fixes + `Pull Request 4549`_ +* Allow exporting workflows when tool is uninstalled + (thanks to `@mvdbeek `__). + `Pull Request 4553`_ +* Lower threshold for auto-matching dataset pairs in the collection builder + `Pull Request 4555`_ +* Allow working with pbzip2 compressed files + (thanks to `@mvdbeek `__). + `Pull Request 4559`_ +* add logging to ts index building + `Pull Request 4567`_ +* Add show/hide deleted/hidden links when history is filtered... + (thanks to `@chambm `__). + `Pull Request 4581`_ +* Make history sharing Selenium tests more robust and informative. + `Pull Request 4588`_ +* Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails. + `Pull Request 4589`_ +* Python 3 fixes for set_metadata.py + `Pull Request 4607`_ +* Allow adding new data tables without restart + (thanks to `@mvdbeek `__). + `Pull Request 4617`_ +* remove .git and .hg from recursive file search + (thanks to `@bgruening `__). + `Pull Request 4636`_ +* Improved state handling for @anatskiy-style Selenium tests. + `Pull Request 4647`_ +* Better handling of long id secrets when generating per-kind encryption keys. + `Pull Request 4713`_ + +.. small_enhancement + +* API installation of toolshed repositories. + `Pull Request 3626`_ +* Add test case clarifying datasets do get "renamed" by rename PJA in + collections. + `Pull Request 3983`_ +* Fixes for Selenium workflow run test case. + `Pull Request 3992`_ +* Fix handling main_panel switching in various Selenium tests. + `Pull Request 4003`_ +* One more fix for main_panel fix in `#3992 + `__. + `Pull Request 4042`_ +* Add some test tools for collection job failures. + `Pull Request 4044`_ +* Reset Selenium test connection between test retries. + `Pull Request 4053`_ +* Add admin app + `Pull Request 4067`_ +* Preparation for grids mako removal + `Pull Request 4101`_ +* Merge ShedToolLineage and StockLineage to ToolLineage + (thanks to `@mvdbeek `__). + `Pull Request 4119`_ +* Move PlantTribes datatypes to a separate file with enhancements and fixes + (thanks to `@gregvonkuster `__). + `Pull Request 4137`_ +* Move galaxy.tools.toolbox.cache to galaxy.tools.cache. + `Pull Request 4155`_ +* Removes mako for datasets grid + `Pull Request 4163`_ +* Spacing convention, -> util.asbool, atribute -> attribute + (thanks to `@bwlang `__). + `Pull Request 4250`_ +* refactors tag manager to use only what it needs… + (thanks to `@bwlang `__). + `Pull Request 4253`_ +* Use contextmanager when using compression_util.get_fileobj() + (thanks to `@mvdbeek `__). + `Pull Request 4270`_ +* Swap the deprecated unescape() for decodeURIComponent + `Pull Request 4321`_ +* Separate admin controllers + `Pull Request 4327`_ +* Some formatting + (thanks to `@VJalili `__). + `Pull Request 4333`_ +* Replacing Edit Attributes Mako by JavaScript + (thanks to `@bgruening `__). + `Pull Request 4334`_ +* Admin user grid conversion + `Pull Request 4341`_ +* Merging configure menu with main workflow view + (thanks to `@bgruening `__). + `Pull Request 4353`_ +* Delete conda_exec_home instead of env['HOME'] + (thanks to `@mvdbeek `__). + `Pull Request 4360`_ +* Add test tool for API tests + (thanks to `@mvdbeek `__). + `Pull Request 4380`_ +* Replace list with generator when iterating headers + (thanks to `@mvdbeek `__). + `Pull Request 4388`_ +* Get tools with tool_version in more places + (thanks to `@mvdbeek `__). + `Pull Request 4391`_ +* Fix lgtm alerts + (thanks to `@xiemaisi `__). + `Pull Request 4421`_ +* Remove /mobile and associated templates + `Pull Request 4494`_ +* Workflow loading speedup + (thanks to `@mvdbeek `__). + `Pull Request 4500`_ +* Published History Grid tests + (thanks to `@anatskiy `__). + `Pull Request 4502`_ +* Prevent transient job state test failures from failing the build. + `Pull Request 4510`_ +* More robust workflow invocation testing. + `Pull Request 4530`_ +* Another fix for Selenium worklow tests. + `Pull Request 4531`_ +* Refactor history import/export tests to allow collection testing. + `Pull Request 4534`_ +* Refactor test modules toward cleaner dependencies + `Pull Request 4536`_ +* Prevent in-place editing of uploaded files if files are imported from the + FTP folder + (thanks to `@mvdbeek `__). + `Pull Request 4539`_ +* Speedup toolform building + (thanks to `@mvdbeek `__). + `Pull Request 4541`_ +* Check user roles only once if user has no roles + (thanks to `@mvdbeek `__). + `Pull Request 4546`_ +* Revert "Remove Selenium test that is broken because Galaxy is broken." + (thanks to `@mvdbeek `__). + `Pull Request 4561`_ +* Increase the robustness of Selenium workflow management tests. + `Pull Request 4564`_ +* Fix datalib collection import + `Pull Request 4568`_ +* Make submitting logins for Selenium tests a bit more robust. + `Pull Request 4576`_ +* Delegate displaying of page titles to Layout.display() + `Pull Request 4578`_ +* Retry failed clicks more aggressively for Selenium tests. + `Pull Request 4582`_ +* Fix another issue with sorting by owner for published histories Selenium + test. + `Pull Request 4586`_ +* Add Selenium tests for the Saved Histories + (thanks to `@anatskiy `__). + `Pull Request 4587`_ +* Small improvements to workflow editor Selenium tests. + `Pull Request 4592`_ +* Datalibs various fixes + `Pull Request 4595`_ +* Remove bam to bai converter + (thanks to `@mvdbeek `__). + `Pull Request 4598`_ +* Retry job submissions in ShellJobRunner + (thanks to `@mvdbeek `__). + `Pull Request 4599`_ +* Write datatypes registry xml to working directory + (thanks to `@mvdbeek `__). + `Pull Request 4600`_ +* Remove unreachable statements + (thanks to `@erasche `__). + `Pull Request 4603`_ +* Refactored a dataset variable to hda + (thanks to `@VJalili `__). + `Pull Request 4630`_ +* disable MacOS CI on travis + `Pull Request 4631`_ +* optimize the process of identifying public libraries + `Pull Request 4640`_ +* Custom Builds tests + (thanks to `@anatskiy `__). + `Pull Request 4641`_ + + +Fixes +------------------------------- + +.. major_bug + + +.. bug + +* Simplify RC creation in Makefile. + `Pull Request 4011`_ +* Do not recurse in ensure_installed() + (thanks to `@bernt-matthias `__). + `Pull Request 4049`_ +* Minor fixes for new locales, rebuild of client. + `Pull Request 4050`_ +* French error + (thanks to `@yvanlebras `__). + `Pull Request 4051`_ +* Very minor history tour tweaks + `Pull Request 4061`_ +* conditional postclick execution onNext + (thanks to `@bagnacan `__). + `Pull Request 4062`_ +* Don't try to get the file name of purged files + (thanks to `@dpryan79 `__). + `Pull Request 4066`_ +* Rebuild to provide new localization. + `Pull Request 4081`_ +* ToolShed tool dependency install fixes + (thanks to `@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 `__). + `Pull Request 4120`_ +* Avoid locale specific string.letters for job_name + (thanks to `@peterjc `__). + `Pull Request 4121`_ +* New workflow menu message fix + `Pull Request 4124`_ +* Fix typo + (thanks to `@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 + `Pull Request 4158`_ +* Fix older GIE config sample description. + `Pull Request 4164`_ +* Improve default handling of Singularity volumes. + `Pull Request 4180`_ +* Fix `#3990 `__, don't + chown non-galaxy files + (thanks to `@dpryan79 `__). + `Pull Request 4186`_ +* Hashtags w/ workflow-defined tags fix + `Pull Request 4188`_ +* Debug of script library_upload_dir.py + (thanks to `@FredericBGA `__). + `Pull Request 4199`_ +* Correct name of neo4j datatype class + (thanks to `@pvanheus `__). + `Pull Request 4223`_ +* Fix Registry.get_datatype_by_extension() to return None if ext is unknown + (thanks to `@nsoranzo `__). + `Pull Request 4224`_ +* avoids broken version of mercurial in conda + (thanks to `@bwlang `__). + `Pull Request 4227`_ +* Fix empty tabular output error when using discover_datasets. + (thanks to `@pkrog `__). + `Pull Request 4240`_ +* Fix shared history grid + `Pull Request 4263`_ +* Importing old exported histories failing + (thanks to `@cche `__). + `Pull Request 4268`_ +* Update tool_conf.xml.main to reflect main's current state. + `Pull Request 4295`_ +* Fix TypeError when uploading large files from ftp to s3 + (thanks to `@jlhg `__). + `Pull Request 4315`_ +* 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 `__). + `Pull Request 4343`_ +* Fix default output labels for subworkflows + (thanks to `@mvdbeek `__). + `Pull Request 4346`_ +* Search Overlay plugin bug fix + (thanks to `@bgruening `__). + `Pull Request 4348`_ +* Patch bug preventing creation of dataset library folders + (thanks to `@galaxyproject `__). + `Pull Request 4357`_ +* Tool version and lineage fixes + (thanks to `@mvdbeek `__). + `Pull Request 4375`_ +* Bugfix: Ensure task splitting handles before job resolution. + `Pull Request 4383`_ +* Fix get_tool returning list when it shouldn't. + `Pull Request 4390`_ +* Bugfix for loading subworkflows from workflow descriptions. + `Pull Request 4394`_ +* Bugfix: __str__ method on tool parsers would throw an Exception. + `Pull Request 4395`_ +* Add missing chemical formats to datatypes_conf.xml.sample + (thanks to `@nsoranzo `__). + `Pull Request 4413`_ +* Don't cast tool_version to string if tool_version is None-type + (thanks to `@mvdbeek `__). + `Pull Request 4420`_ +* some unicoding for local runner + (thanks to `@erasche `__). + `Pull Request 4426`_ +* Break connection in workflow editor if necessary + (thanks to `@mvdbeek `__). + `Pull Request 4431`_ +* Fix private role validation + `Pull Request 4432`_ +* Remove print of non-existent attribute 'content' + (thanks to `@chambm `__). + `Pull Request 4439`_ +* Fix API tests broken in `#4434 + `__ + (thanks to `@nsoranzo `__). + `Pull Request 4445`_ +* Fix E201 errors (spaces in parens) in new memepsp datatype + `Pull Request 4446`_ +* Fixes for advanced grid search + `Pull Request 4449`_ +* Fix quota function name + `Pull Request 4469`_ +* Fixes for VCF/BCF datatypes + (thanks to `@nsoranzo `__). + `Pull Request 4477`_ +* 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 `__). + `Pull Request 4501`_ +* import of history works even if we use symlink in database directory + (thanks to `@FredericBGA `__). + `Pull Request 4511`_ +* Fix missing tools wf editor alternative + (thanks to `@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 + `__. + `Pull Request 4565`_ +* Bug: Fix startup of galaxy when webhooks dir is empty + (thanks to `@mvdbeek `__). + `Pull Request 4570`_ +* 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 `__). + `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. + `Pull Request 4626`_ +* Typo fix + (thanks to `@VJalili `__). + `Pull Request 4628`_ +* Updated function description and fix some typos + (thanks to `@VJalili `__). + `Pull Request 4629`_ +* Fix data order in Custom Builds + (thanks to `@anatskiy `__). + `Pull Request 4634`_ +* do not wrap lines in the upload url fetch + `Pull Request 4639`_ +* BUG: Explicitly write registry.xml when creating a job for the upload tool + (thanks to `@mvdbeek `__). + `Pull Request 4644`_ +* Fix links on workflow, history items. + `Pull Request 4656`_ +* Fix modules resolver + `Pull Request 4663`_ +* Remove chatty debug statement + `Pull Request 4671`_ +* Client side fixes for GIEs + `Pull Request 4680`_ +* Update versions of conda and conda-build + (thanks to `@nsoranzo `__). + `Pull Request 4701`_ +* Correct base route for workflows, allowing proxy-prefix to work. + `Pull Request 4705`_ +* Append fewer characters to id_secret by default for encrypting csrf tokens. + `Pull Request 4710`_ +* Cachebust IE require'd files (jupyter.js, etc). + `Pull Request 4714`_ +* 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 + `Pull Request 4726`_ +* 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 `__). + `Pull Request 4742`_ +* Fix joiner tool to inherit datatype from the input format + `Pull Request 4745`_ +* Fix auth with ldaps:// + (thanks to `@abretaud `__). + `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`_ + +.. github_links +.. _Pull Request 1814: https://github.com/galaxyproject/galaxy/pull/1814 +.. _Pull Request 3064: https://github.com/galaxyproject/galaxy/pull/3064 +.. _Pull Request 3076: https://github.com/galaxyproject/galaxy/pull/3076 +.. _Pull Request 3179: https://github.com/galaxyproject/galaxy/pull/3179 +.. _Pull Request 3330: https://github.com/galaxyproject/galaxy/pull/3330 +.. _Pull Request 3383: https://github.com/galaxyproject/galaxy/pull/3383 +.. _Pull Request 3611: https://github.com/galaxyproject/galaxy/pull/3611 +.. _Pull Request 3626: https://github.com/galaxyproject/galaxy/pull/3626 +.. _Pull Request 3946: https://github.com/galaxyproject/galaxy/pull/3946 +.. _Pull Request 3972: https://github.com/galaxyproject/galaxy/pull/3972 +.. _Pull Request 3983: https://github.com/galaxyproject/galaxy/pull/3983 +.. _Pull Request 3992: https://github.com/galaxyproject/galaxy/pull/3992 +.. _Pull Request 3993: https://github.com/galaxyproject/galaxy/pull/3993 +.. _Pull Request 3994: https://github.com/galaxyproject/galaxy/pull/3994 +.. _Pull Request 3995: https://github.com/galaxyproject/galaxy/pull/3995 +.. _Pull Request 4003: https://github.com/galaxyproject/galaxy/pull/4003 +.. _Pull Request 4008: https://github.com/galaxyproject/galaxy/pull/4008 +.. _Pull Request 4010: https://github.com/galaxyproject/galaxy/pull/4010 +.. _Pull Request 4011: https://github.com/galaxyproject/galaxy/pull/4011 +.. _Pull Request 4019: https://github.com/galaxyproject/galaxy/pull/4019 +.. _Pull Request 4036: https://github.com/galaxyproject/galaxy/pull/4036 +.. _Pull Request 4039: https://github.com/galaxyproject/galaxy/pull/4039 +.. _Pull Request 4042: https://github.com/galaxyproject/galaxy/pull/4042 +.. _Pull Request 4044: https://github.com/galaxyproject/galaxy/pull/4044 +.. _Pull Request 4045: https://github.com/galaxyproject/galaxy/pull/4045 +.. _Pull Request 4047: https://github.com/galaxyproject/galaxy/pull/4047 +.. _Pull Request 4049: https://github.com/galaxyproject/galaxy/pull/4049 +.. _Pull Request 4050: https://github.com/galaxyproject/galaxy/pull/4050 +.. _Pull Request 4051: https://github.com/galaxyproject/galaxy/pull/4051 +.. _Pull Request 4053: https://github.com/galaxyproject/galaxy/pull/4053 +.. _Pull Request 4061: https://github.com/galaxyproject/galaxy/pull/4061 +.. _Pull Request 4062: https://github.com/galaxyproject/galaxy/pull/4062 +.. _Pull Request 4066: https://github.com/galaxyproject/galaxy/pull/4066 +.. _Pull Request 4067: https://github.com/galaxyproject/galaxy/pull/4067 +.. _Pull Request 4077: https://github.com/galaxyproject/galaxy/pull/4077 +.. _Pull Request 4080: https://github.com/galaxyproject/galaxy/pull/4080 +.. _Pull Request 4081: https://github.com/galaxyproject/galaxy/pull/4081 +.. _Pull Request 4082: https://github.com/galaxyproject/galaxy/pull/4082 +.. _Pull Request 4087: https://github.com/galaxyproject/galaxy/pull/4087 +.. _Pull Request 4088: https://github.com/galaxyproject/galaxy/pull/4088 +.. _Pull Request 4091: https://github.com/galaxyproject/galaxy/pull/4091 +.. _Pull Request 4092: https://github.com/galaxyproject/galaxy/pull/4092 +.. _Pull Request 4093: https://github.com/galaxyproject/galaxy/pull/4093 +.. _Pull Request 4096: https://github.com/galaxyproject/galaxy/pull/4096 +.. _Pull Request 4098: https://github.com/galaxyproject/galaxy/pull/4098 +.. _Pull Request 4101: https://github.com/galaxyproject/galaxy/pull/4101 +.. _Pull Request 4105: https://github.com/galaxyproject/galaxy/pull/4105 +.. _Pull Request 4112: https://github.com/galaxyproject/galaxy/pull/4112 +.. _Pull Request 4113: https://github.com/galaxyproject/galaxy/pull/4113 +.. _Pull Request 4117: https://github.com/galaxyproject/galaxy/pull/4117 +.. _Pull Request 4119: https://github.com/galaxyproject/galaxy/pull/4119 +.. _Pull Request 4120: https://github.com/galaxyproject/galaxy/pull/4120 +.. _Pull Request 4121: https://github.com/galaxyproject/galaxy/pull/4121 +.. _Pull Request 4124: https://github.com/galaxyproject/galaxy/pull/4124 +.. _Pull Request 4126: https://github.com/galaxyproject/galaxy/pull/4126 +.. _Pull Request 4137: https://github.com/galaxyproject/galaxy/pull/4137 +.. _Pull Request 4138: https://github.com/galaxyproject/galaxy/pull/4138 +.. _Pull Request 4139: https://github.com/galaxyproject/galaxy/pull/4139 +.. _Pull Request 4141: https://github.com/galaxyproject/galaxy/pull/4141 +.. _Pull Request 4146: https://github.com/galaxyproject/galaxy/pull/4146 +.. _Pull Request 4147: https://github.com/galaxyproject/galaxy/pull/4147 +.. _Pull Request 4149: https://github.com/galaxyproject/galaxy/pull/4149 +.. _Pull Request 4154: https://github.com/galaxyproject/galaxy/pull/4154 +.. _Pull Request 4155: https://github.com/galaxyproject/galaxy/pull/4155 +.. _Pull Request 4156: https://github.com/galaxyproject/galaxy/pull/4156 +.. _Pull Request 4157: https://github.com/galaxyproject/galaxy/pull/4157 +.. _Pull Request 4158: https://github.com/galaxyproject/galaxy/pull/4158 +.. _Pull Request 4160: https://github.com/galaxyproject/galaxy/pull/4160 +.. _Pull Request 4163: https://github.com/galaxyproject/galaxy/pull/4163 +.. _Pull Request 4164: https://github.com/galaxyproject/galaxy/pull/4164 +.. _Pull Request 4167: https://github.com/galaxyproject/galaxy/pull/4167 +.. _Pull Request 4169: https://github.com/galaxyproject/galaxy/pull/4169 +.. _Pull Request 4173: https://github.com/galaxyproject/galaxy/pull/4173 +.. _Pull Request 4175: https://github.com/galaxyproject/galaxy/pull/4175 +.. _Pull Request 4179: https://github.com/galaxyproject/galaxy/pull/4179 +.. _Pull Request 4180: https://github.com/galaxyproject/galaxy/pull/4180 +.. _Pull Request 4185: https://github.com/galaxyproject/galaxy/pull/4185 +.. _Pull Request 4186: https://github.com/galaxyproject/galaxy/pull/4186 +.. _Pull Request 4188: https://github.com/galaxyproject/galaxy/pull/4188 +.. _Pull Request 4192: https://github.com/galaxyproject/galaxy/pull/4192 +.. _Pull Request 4198: https://github.com/galaxyproject/galaxy/pull/4198 +.. _Pull Request 4199: https://github.com/galaxyproject/galaxy/pull/4199 +.. _Pull Request 4200: https://github.com/galaxyproject/galaxy/pull/4200 +.. _Pull Request 4201: https://github.com/galaxyproject/galaxy/pull/4201 +.. _Pull Request 4207: https://github.com/galaxyproject/galaxy/pull/4207 +.. _Pull Request 4208: https://github.com/galaxyproject/galaxy/pull/4208 +.. _Pull Request 4210: https://github.com/galaxyproject/galaxy/pull/4210 +.. _Pull Request 4213: https://github.com/galaxyproject/galaxy/pull/4213 +.. _Pull Request 4216: https://github.com/galaxyproject/galaxy/pull/4216 +.. _Pull Request 4223: https://github.com/galaxyproject/galaxy/pull/4223 +.. _Pull Request 4224: https://github.com/galaxyproject/galaxy/pull/4224 +.. _Pull Request 4226: https://github.com/galaxyproject/galaxy/pull/4226 +.. _Pull Request 4227: https://github.com/galaxyproject/galaxy/pull/4227 +.. _Pull Request 4229: https://github.com/galaxyproject/galaxy/pull/4229 +.. _Pull Request 4232: https://github.com/galaxyproject/galaxy/pull/4232 +.. _Pull Request 4236: https://github.com/galaxyproject/galaxy/pull/4236 +.. _Pull Request 4237: https://github.com/galaxyproject/galaxy/pull/4237 +.. _Pull Request 4239: https://github.com/galaxyproject/galaxy/pull/4239 +.. _Pull Request 4240: https://github.com/galaxyproject/galaxy/pull/4240 +.. _Pull Request 4248: https://github.com/galaxyproject/galaxy/pull/4248 +.. _Pull Request 4250: https://github.com/galaxyproject/galaxy/pull/4250 +.. _Pull Request 4253: https://github.com/galaxyproject/galaxy/pull/4253 +.. _Pull Request 4254: https://github.com/galaxyproject/galaxy/pull/4254 +.. _Pull Request 4255: https://github.com/galaxyproject/galaxy/pull/4255 +.. _Pull Request 4258: https://github.com/galaxyproject/galaxy/pull/4258 +.. _Pull Request 4259: https://github.com/galaxyproject/galaxy/pull/4259 +.. _Pull Request 4262: https://github.com/galaxyproject/galaxy/pull/4262 +.. _Pull Request 4263: https://github.com/galaxyproject/galaxy/pull/4263 +.. _Pull Request 4268: https://github.com/galaxyproject/galaxy/pull/4268 +.. _Pull Request 4270: https://github.com/galaxyproject/galaxy/pull/4270 +.. _Pull Request 4271: https://github.com/galaxyproject/galaxy/pull/4271 +.. _Pull Request 4272: https://github.com/galaxyproject/galaxy/pull/4272 +.. _Pull Request 4273: https://github.com/galaxyproject/galaxy/pull/4273 +.. _Pull Request 4274: https://github.com/galaxyproject/galaxy/pull/4274 +.. _Pull Request 4277: https://github.com/galaxyproject/galaxy/pull/4277 +.. _Pull Request 4278: https://github.com/galaxyproject/galaxy/pull/4278 +.. _Pull Request 4279: https://github.com/galaxyproject/galaxy/pull/4279 +.. _Pull Request 4281: https://github.com/galaxyproject/galaxy/pull/4281 +.. _Pull Request 4283: https://github.com/galaxyproject/galaxy/pull/4283 +.. _Pull Request 4284: https://github.com/galaxyproject/galaxy/pull/4284 +.. _Pull Request 4285: https://github.com/galaxyproject/galaxy/pull/4285 +.. _Pull Request 4289: https://github.com/galaxyproject/galaxy/pull/4289 +.. _Pull Request 4291: https://github.com/galaxyproject/galaxy/pull/4291 +.. _Pull Request 4292: https://github.com/galaxyproject/galaxy/pull/4292 +.. _Pull Request 4293: https://github.com/galaxyproject/galaxy/pull/4293 +.. _Pull Request 4294: https://github.com/galaxyproject/galaxy/pull/4294 +.. _Pull Request 4295: https://github.com/galaxyproject/galaxy/pull/4295 +.. _Pull Request 4302: https://github.com/galaxyproject/galaxy/pull/4302 +.. _Pull Request 4304: https://github.com/galaxyproject/galaxy/pull/4304 +.. _Pull Request 4305: https://github.com/galaxyproject/galaxy/pull/4305 +.. _Pull Request 4306: https://github.com/galaxyproject/galaxy/pull/4306 +.. _Pull Request 4307: https://github.com/galaxyproject/galaxy/pull/4307 +.. _Pull Request 4309: https://github.com/galaxyproject/galaxy/pull/4309 +.. _Pull Request 4310: https://github.com/galaxyproject/galaxy/pull/4310 +.. _Pull Request 4311: https://github.com/galaxyproject/galaxy/pull/4311 +.. _Pull Request 4315: https://github.com/galaxyproject/galaxy/pull/4315 +.. _Pull Request 4317: https://github.com/galaxyproject/galaxy/pull/4317 +.. _Pull Request 4318: https://github.com/galaxyproject/galaxy/pull/4318 +.. _Pull Request 4321: https://github.com/galaxyproject/galaxy/pull/4321 +.. _Pull Request 4326: https://github.com/galaxyproject/galaxy/pull/4326 +.. _Pull Request 4327: https://github.com/galaxyproject/galaxy/pull/4327 +.. _Pull Request 4329: https://github.com/galaxyproject/galaxy/pull/4329 +.. _Pull Request 4332: https://github.com/galaxyproject/galaxy/pull/4332 +.. _Pull Request 4333: https://github.com/galaxyproject/galaxy/pull/4333 +.. _Pull Request 4334: https://github.com/galaxyproject/galaxy/pull/4334 +.. _Pull Request 4337: https://github.com/galaxyproject/galaxy/pull/4337 +.. _Pull Request 4341: https://github.com/galaxyproject/galaxy/pull/4341 +.. _Pull Request 4342: https://github.com/galaxyproject/galaxy/pull/4342 +.. _Pull Request 4343: https://github.com/galaxyproject/galaxy/pull/4343 +.. _Pull Request 4346: https://github.com/galaxyproject/galaxy/pull/4346 +.. _Pull Request 4348: https://github.com/galaxyproject/galaxy/pull/4348 +.. _Pull Request 4353: https://github.com/galaxyproject/galaxy/pull/4353 +.. _Pull Request 4357: https://github.com/galaxyproject/galaxy/pull/4357 +.. _Pull Request 4358: https://github.com/galaxyproject/galaxy/pull/4358 +.. _Pull Request 4360: https://github.com/galaxyproject/galaxy/pull/4360 +.. _Pull Request 4365: https://github.com/galaxyproject/galaxy/pull/4365 +.. _Pull Request 4368: https://github.com/galaxyproject/galaxy/pull/4368 +.. _Pull Request 4369: https://github.com/galaxyproject/galaxy/pull/4369 +.. _Pull Request 4370: https://github.com/galaxyproject/galaxy/pull/4370 +.. _Pull Request 4371: https://github.com/galaxyproject/galaxy/pull/4371 +.. _Pull Request 4373: https://github.com/galaxyproject/galaxy/pull/4373 +.. _Pull Request 4375: https://github.com/galaxyproject/galaxy/pull/4375 +.. _Pull Request 4376: https://github.com/galaxyproject/galaxy/pull/4376 +.. _Pull Request 4377: https://github.com/galaxyproject/galaxy/pull/4377 +.. _Pull Request 4380: https://github.com/galaxyproject/galaxy/pull/4380 +.. _Pull Request 4382: https://github.com/galaxyproject/galaxy/pull/4382 +.. _Pull Request 4383: https://github.com/galaxyproject/galaxy/pull/4383 +.. _Pull Request 4385: https://github.com/galaxyproject/galaxy/pull/4385 +.. _Pull Request 4386: https://github.com/galaxyproject/galaxy/pull/4386 +.. _Pull Request 4387: https://github.com/galaxyproject/galaxy/pull/4387 +.. _Pull Request 4388: https://github.com/galaxyproject/galaxy/pull/4388 +.. _Pull Request 4389: https://github.com/galaxyproject/galaxy/pull/4389 +.. _Pull Request 4390: https://github.com/galaxyproject/galaxy/pull/4390 +.. _Pull Request 4391: https://github.com/galaxyproject/galaxy/pull/4391 +.. _Pull Request 4392: https://github.com/galaxyproject/galaxy/pull/4392 +.. _Pull Request 4394: https://github.com/galaxyproject/galaxy/pull/4394 +.. _Pull Request 4395: https://github.com/galaxyproject/galaxy/pull/4395 +.. _Pull Request 4396: https://github.com/galaxyproject/galaxy/pull/4396 +.. _Pull Request 4397: https://github.com/galaxyproject/galaxy/pull/4397 +.. _Pull Request 4403: https://github.com/galaxyproject/galaxy/pull/4403 +.. _Pull Request 4404: https://github.com/galaxyproject/galaxy/pull/4404 +.. _Pull Request 4405: https://github.com/galaxyproject/galaxy/pull/4405 +.. _Pull Request 4408: https://github.com/galaxyproject/galaxy/pull/4408 +.. _Pull Request 4409: https://github.com/galaxyproject/galaxy/pull/4409 +.. _Pull Request 4410: https://github.com/galaxyproject/galaxy/pull/4410 +.. _Pull Request 4411: https://github.com/galaxyproject/galaxy/pull/4411 +.. _Pull Request 4413: https://github.com/galaxyproject/galaxy/pull/4413 +.. _Pull Request 4417: https://github.com/galaxyproject/galaxy/pull/4417 +.. _Pull Request 4420: https://github.com/galaxyproject/galaxy/pull/4420 +.. _Pull Request 4421: https://github.com/galaxyproject/galaxy/pull/4421 +.. _Pull Request 4426: https://github.com/galaxyproject/galaxy/pull/4426 +.. _Pull Request 4427: https://github.com/galaxyproject/galaxy/pull/4427 +.. _Pull Request 4430: https://github.com/galaxyproject/galaxy/pull/4430 +.. _Pull Request 4431: https://github.com/galaxyproject/galaxy/pull/4431 +.. _Pull Request 4432: https://github.com/galaxyproject/galaxy/pull/4432 +.. _Pull Request 4434: https://github.com/galaxyproject/galaxy/pull/4434 +.. _Pull Request 4437: https://github.com/galaxyproject/galaxy/pull/4437 +.. _Pull Request 4438: https://github.com/galaxyproject/galaxy/pull/4438 +.. _Pull Request 4439: https://github.com/galaxyproject/galaxy/pull/4439 +.. _Pull Request 4440: https://github.com/galaxyproject/galaxy/pull/4440 +.. _Pull Request 4445: https://github.com/galaxyproject/galaxy/pull/4445 +.. _Pull Request 4446: https://github.com/galaxyproject/galaxy/pull/4446 +.. _Pull Request 4447: https://github.com/galaxyproject/galaxy/pull/4447 +.. _Pull Request 4449: https://github.com/galaxyproject/galaxy/pull/4449 +.. _Pull Request 4454: https://github.com/galaxyproject/galaxy/pull/4454 +.. _Pull Request 4455: https://github.com/galaxyproject/galaxy/pull/4455 +.. _Pull Request 4456: https://github.com/galaxyproject/galaxy/pull/4456 +.. _Pull Request 4457: https://github.com/galaxyproject/galaxy/pull/4457 +.. _Pull Request 4458: https://github.com/galaxyproject/galaxy/pull/4458 +.. _Pull Request 4465: https://github.com/galaxyproject/galaxy/pull/4465 +.. _Pull Request 4466: https://github.com/galaxyproject/galaxy/pull/4466 +.. _Pull Request 4467: https://github.com/galaxyproject/galaxy/pull/4467 +.. _Pull Request 4469: https://github.com/galaxyproject/galaxy/pull/4469 +.. _Pull Request 4470: https://github.com/galaxyproject/galaxy/pull/4470 +.. _Pull Request 4471: https://github.com/galaxyproject/galaxy/pull/4471 +.. _Pull Request 4476: https://github.com/galaxyproject/galaxy/pull/4476 +.. _Pull Request 4477: https://github.com/galaxyproject/galaxy/pull/4477 +.. _Pull Request 4479: https://github.com/galaxyproject/galaxy/pull/4479 +.. _Pull Request 4483: https://github.com/galaxyproject/galaxy/pull/4483 +.. _Pull Request 4485: https://github.com/galaxyproject/galaxy/pull/4485 +.. _Pull Request 4486: https://github.com/galaxyproject/galaxy/pull/4486 +.. _Pull Request 4489: https://github.com/galaxyproject/galaxy/pull/4489 +.. _Pull Request 4492: https://github.com/galaxyproject/galaxy/pull/4492 +.. _Pull Request 4494: https://github.com/galaxyproject/galaxy/pull/4494 +.. _Pull Request 4495: https://github.com/galaxyproject/galaxy/pull/4495 +.. _Pull Request 4496: https://github.com/galaxyproject/galaxy/pull/4496 +.. _Pull Request 4500: https://github.com/galaxyproject/galaxy/pull/4500 +.. _Pull Request 4501: https://github.com/galaxyproject/galaxy/pull/4501 +.. _Pull Request 4502: https://github.com/galaxyproject/galaxy/pull/4502 +.. _Pull Request 4503: https://github.com/galaxyproject/galaxy/pull/4503 +.. _Pull Request 4505: https://github.com/galaxyproject/galaxy/pull/4505 +.. _Pull Request 4508: https://github.com/galaxyproject/galaxy/pull/4508 +.. _Pull Request 4510: https://github.com/galaxyproject/galaxy/pull/4510 +.. _Pull Request 4511: https://github.com/galaxyproject/galaxy/pull/4511 +.. _Pull Request 4512: https://github.com/galaxyproject/galaxy/pull/4512 +.. _Pull Request 4514: https://github.com/galaxyproject/galaxy/pull/4514 +.. _Pull Request 4515: https://github.com/galaxyproject/galaxy/pull/4515 +.. _Pull Request 4519: https://github.com/galaxyproject/galaxy/pull/4519 +.. _Pull Request 4522: https://github.com/galaxyproject/galaxy/pull/4522 +.. _Pull Request 4523: https://github.com/galaxyproject/galaxy/pull/4523 +.. _Pull Request 4524: https://github.com/galaxyproject/galaxy/pull/4524 +.. _Pull Request 4530: https://github.com/galaxyproject/galaxy/pull/4530 +.. _Pull Request 4531: https://github.com/galaxyproject/galaxy/pull/4531 +.. _Pull Request 4533: https://github.com/galaxyproject/galaxy/pull/4533 +.. _Pull Request 4534: https://github.com/galaxyproject/galaxy/pull/4534 +.. _Pull Request 4535: https://github.com/galaxyproject/galaxy/pull/4535 +.. _Pull Request 4536: https://github.com/galaxyproject/galaxy/pull/4536 +.. _Pull Request 4539: https://github.com/galaxyproject/galaxy/pull/4539 +.. _Pull Request 4541: https://github.com/galaxyproject/galaxy/pull/4541 +.. _Pull Request 4542: https://github.com/galaxyproject/galaxy/pull/4542 +.. _Pull Request 4546: https://github.com/galaxyproject/galaxy/pull/4546 +.. _Pull Request 4547: https://github.com/galaxyproject/galaxy/pull/4547 +.. _Pull Request 4549: https://github.com/galaxyproject/galaxy/pull/4549 +.. _Pull Request 4552: https://github.com/galaxyproject/galaxy/pull/4552 +.. _Pull Request 4553: https://github.com/galaxyproject/galaxy/pull/4553 +.. _Pull Request 4555: https://github.com/galaxyproject/galaxy/pull/4555 +.. _Pull Request 4556: https://github.com/galaxyproject/galaxy/pull/4556 +.. _Pull Request 4557: https://github.com/galaxyproject/galaxy/pull/4557 +.. _Pull Request 4559: https://github.com/galaxyproject/galaxy/pull/4559 +.. _Pull Request 4560: https://github.com/galaxyproject/galaxy/pull/4560 +.. _Pull Request 4561: https://github.com/galaxyproject/galaxy/pull/4561 +.. _Pull Request 4562: https://github.com/galaxyproject/galaxy/pull/4562 +.. _Pull Request 4564: https://github.com/galaxyproject/galaxy/pull/4564 +.. _Pull Request 4565: https://github.com/galaxyproject/galaxy/pull/4565 +.. _Pull Request 4567: https://github.com/galaxyproject/galaxy/pull/4567 +.. _Pull Request 4568: https://github.com/galaxyproject/galaxy/pull/4568 +.. _Pull Request 4570: https://github.com/galaxyproject/galaxy/pull/4570 +.. _Pull Request 4574: https://github.com/galaxyproject/galaxy/pull/4574 +.. _Pull Request 4576: https://github.com/galaxyproject/galaxy/pull/4576 +.. _Pull Request 4577: https://github.com/galaxyproject/galaxy/pull/4577 +.. _Pull Request 4578: https://github.com/galaxyproject/galaxy/pull/4578 +.. _Pull Request 4579: https://github.com/galaxyproject/galaxy/pull/4579 +.. _Pull Request 4580: https://github.com/galaxyproject/galaxy/pull/4580 +.. _Pull Request 4581: https://github.com/galaxyproject/galaxy/pull/4581 +.. _Pull Request 4582: https://github.com/galaxyproject/galaxy/pull/4582 +.. _Pull Request 4586: https://github.com/galaxyproject/galaxy/pull/4586 +.. _Pull Request 4587: https://github.com/galaxyproject/galaxy/pull/4587 +.. _Pull Request 4588: https://github.com/galaxyproject/galaxy/pull/4588 +.. _Pull Request 4589: https://github.com/galaxyproject/galaxy/pull/4589 +.. _Pull Request 4592: https://github.com/galaxyproject/galaxy/pull/4592 +.. _Pull Request 4594: https://github.com/galaxyproject/galaxy/pull/4594 +.. _Pull Request 4595: https://github.com/galaxyproject/galaxy/pull/4595 +.. _Pull Request 4598: https://github.com/galaxyproject/galaxy/pull/4598 +.. _Pull Request 4599: https://github.com/galaxyproject/galaxy/pull/4599 +.. _Pull Request 4600: https://github.com/galaxyproject/galaxy/pull/4600 +.. _Pull Request 4603: https://github.com/galaxyproject/galaxy/pull/4603 +.. _Pull Request 4607: https://github.com/galaxyproject/galaxy/pull/4607 +.. _Pull Request 4610: https://github.com/galaxyproject/galaxy/pull/4610 +.. _Pull Request 4611: https://github.com/galaxyproject/galaxy/pull/4611 +.. _Pull Request 4616: https://github.com/galaxyproject/galaxy/pull/4616 +.. _Pull Request 4617: https://github.com/galaxyproject/galaxy/pull/4617 +.. _Pull Request 4619: https://github.com/galaxyproject/galaxy/pull/4619 +.. _Pull Request 4621: https://github.com/galaxyproject/galaxy/pull/4621 +.. _Pull Request 4622: https://github.com/galaxyproject/galaxy/pull/4622 +.. _Pull Request 4625: https://github.com/galaxyproject/galaxy/pull/4625 +.. _Pull Request 4626: https://github.com/galaxyproject/galaxy/pull/4626 +.. _Pull Request 4628: https://github.com/galaxyproject/galaxy/pull/4628 +.. _Pull Request 4629: https://github.com/galaxyproject/galaxy/pull/4629 +.. _Pull Request 4630: https://github.com/galaxyproject/galaxy/pull/4630 +.. _Pull Request 4631: https://github.com/galaxyproject/galaxy/pull/4631 +.. _Pull Request 4632: https://github.com/galaxyproject/galaxy/pull/4632 +.. _Pull Request 4634: https://github.com/galaxyproject/galaxy/pull/4634 +.. _Pull Request 4636: https://github.com/galaxyproject/galaxy/pull/4636 +.. _Pull Request 4639: https://github.com/galaxyproject/galaxy/pull/4639 +.. _Pull Request 4640: https://github.com/galaxyproject/galaxy/pull/4640 +.. _Pull Request 4641: https://github.com/galaxyproject/galaxy/pull/4641 +.. _Pull Request 4644: https://github.com/galaxyproject/galaxy/pull/4644 +.. _Pull Request 4647: https://github.com/galaxyproject/galaxy/pull/4647 +.. _Pull Request 4648: https://github.com/galaxyproject/galaxy/pull/4648 +.. _Pull Request 4650: https://github.com/galaxyproject/galaxy/pull/4650 +.. _Pull Request 4652: https://github.com/galaxyproject/galaxy/pull/4652 +.. _Pull Request 4656: https://github.com/galaxyproject/galaxy/pull/4656 +.. _Pull Request 4663: https://github.com/galaxyproject/galaxy/pull/4663 +.. _Pull Request 4671: https://github.com/galaxyproject/galaxy/pull/4671 +.. _Pull Request 4674: https://github.com/galaxyproject/galaxy/pull/4674 +.. _Pull Request 4680: https://github.com/galaxyproject/galaxy/pull/4680 +.. _Pull Request 4701: https://github.com/galaxyproject/galaxy/pull/4701 +.. _Pull Request 4705: https://github.com/galaxyproject/galaxy/pull/4705 +.. _Pull Request 4710: https://github.com/galaxyproject/galaxy/pull/4710 +.. _Pull Request 4713: https://github.com/galaxyproject/galaxy/pull/4713 +.. _Pull Request 4714: https://github.com/galaxyproject/galaxy/pull/4714 +.. _Pull Request 4715: https://github.com/galaxyproject/galaxy/pull/4715 +.. _Pull Request 4716: https://github.com/galaxyproject/galaxy/pull/4716 +.. _Pull Request 4726: https://github.com/galaxyproject/galaxy/pull/4726 +.. _Pull Request 4740: https://github.com/galaxyproject/galaxy/pull/4740 +.. _Pull Request 4742: https://github.com/galaxyproject/galaxy/pull/4742 +.. _Pull Request 4743: https://github.com/galaxyproject/galaxy/pull/4743 +.. _Pull Request 4745: https://github.com/galaxyproject/galaxy/pull/4745 +.. _Pull Request 4748: https://github.com/galaxyproject/galaxy/pull/4748 +.. _Pull Request 4750: https://github.com/galaxyproject/galaxy/pull/4750 +.. _Pull Request 4752: https://github.com/galaxyproject/galaxy/pull/4752 +.. _Pull Request 4760: https://github.com/galaxyproject/galaxy/pull/4760 + diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index e32481ef2401..a533c03f235e 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -3,8 +3,41 @@ September 2017 Galaxy Release (v 17.09) =========================================================== +.. include:: _header.rst -Schedule +Highlights =========================================================== - * Planned Freeze Date: 2017-09-04 - * Planned Release Date: 2017-09-25 + +**Feature1** + Feature description. + +**Feature2** + Feature description. + +**Feature3** + Feature description. + +Get Galaxy +========== + +The code lives at `Github `__ and you should have `Git `__ to obtain it. + +To get a new Galaxy repository run: + .. code-block:: shell + + $ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git + +To update an existing Galaxy repository run: + .. code-block:: shell + + $ git checkout release_17.09 && git pull --ff-only origin release_17.09 + +See `our wiki `__ for additional details regarding the source code locations. + +Release Notes +=========================================================== + +.. include:: 17.09.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/18.01_announce.rst b/doc/source/releases/18.01_announce.rst new file mode 100644 index 000000000000..b62092b1e063 --- /dev/null +++ b/doc/source/releases/18.01_announce.rst @@ -0,0 +1,10 @@ + +=========================================================== +January 2018 Galaxy Release (v 18.01) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2018-01-08 + * Planned Release Date: 2018-01-29 From 272ed6217d4662f7bdc6b385206a7f301295a033 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 16 Oct 2017 11:50:32 -0400 Subject: [PATCH 02/15] add deprecations --- doc/source/releases/17.09_announce.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index a533c03f235e..9d1819dc430b 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -34,6 +34,16 @@ To update an existing Galaxy repository run: See `our wiki `__ for additional details regarding the source code locations. + +Deprecation Notices +=================== + +* The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related + user interface and introduce configuration option to keep relevant controllers active if desired. `Related PR `__. +* The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release. +* + + Release Notes =========================================================== From 06d3f4051543e7c319e775884ea3aab8abef9a2c Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 16 Oct 2017 11:51:26 -0400 Subject: [PATCH 03/15] amend add missing line --- doc/source/releases/17.09_announce.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 9d1819dc430b..8c98d04799a8 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -41,7 +41,7 @@ Deprecation Notices * The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related user interface and introduce configuration option to keep relevant controllers active if desired. `Related PR `__. * The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release. -* +* Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available. Release Notes From eab76b9ae014c4fa2dd3a1ba09199f3351536924 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 16 Oct 2017 12:46:46 -0400 Subject: [PATCH 04/15] add listing of 17.09 release to index --- doc/source/releases/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst index c57cbc5e46d1..448ab9bfbd00 100644 --- a/doc/source/releases/index.rst +++ b/doc/source/releases/index.rst @@ -4,6 +4,7 @@ Releases .. toctree:: :maxdepth: 1 + 17.09_announce 17.05_announce 17.01_announce 16.10_announce From 812b04d14eb1c3d3ec016efb6aa8f1024811c560 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 16 Oct 2017 13:21:48 -0400 Subject: [PATCH 05/15] more work on RN --- doc/source/releases/17.09.rst | 70 ++++++++++++-------------- doc/source/releases/17.09_announce.rst | 14 +++--- 2 files changed, 39 insertions(+), 45 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 2c859f2c3fe1..5cdd4b96ab06 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -29,24 +29,13 @@ Enhancements * Add entry for empty_extra_files_path validator (thanks to `@gregvonkuster `__). `Pull Request 3994`_ -* Add possibility for downloading entire collections - (thanks to `@mvdbeek `__). - `Pull Request 4098`_ -* Implement Singularity Support - `Pull Request 4175`_ * Async update: support to collections (thanks to `@fabio-cumbo `__). `Pull Request 4198`_ * Add API repository uninstall endpoint (thanks to `@mvdbeek `__). `Pull Request 4248`_ -* Vcf gz datatype - (thanks to `@ffinfo `__). - `Pull Request 4254`_ -* Add ptkscmp datatype - (thanks to `@gregvonkuster `__). - `Pull Request 4259`_ -* Library tags +* Data Library tags support (thanks to `@bwlang `__). `Pull Request 4262`_ * Display preview feature for Bam datatype @@ -61,54 +50,62 @@ Enhancements * Paramiko based shell runner (thanks to `@mvdbeek `__). `Pull Request 4358`_ -* Add imzML datatype - (thanks to `@bgruening `__). - `Pull Request 4370`_ -* Allow switching tool versions in workflow editor - (thanks to `@mvdbeek `__). - `Pull Request 4373`_ * Stop loading tools that require a newer galaxy (thanks to `@mvdbeek `__). `Pull Request 4382`_ +* Vcf gz datatype + (thanks to `@ffinfo `__). + `Pull Request 4254`_ +* Add ptkscmp datatype + (thanks to `@gregvonkuster `__). + `Pull Request 4259`_ +* Add imzML datatype + (thanks to `@bgruening `__). + `Pull Request 4370`_ * Add deepTools datatypes to Galaxy (thanks to `@bgruening `__). `Pull Request 4392`_ * Add support for the MEME psp format (thanks to `@gregvonkuster `__). `Pull Request 4430`_ -* Nicer tool click targets for base + "plain" theme - (thanks to `@erasche `__). - `Pull Request 4470`_ -* A round of data libraries improvements. - `Pull Request 4512`_ * add biom2 datatype (thanks to `@shiltemann `__). `Pull Request 4519`_ -* respect expose_user_email configuration in datalibraries permissions list - `Pull Request 4611`_ -* Explicitly include PyPI as an --extra-index-url to pip - `Pull Request 4674`_ +* Add Excel97 Datatype + `Pull Request 4410`_ +* add mz5 datatype + (thanks to `@bgruening `__). + `Pull Request 4466`_ .. enhancement +* Configuration & Server Overhaul - Tool Shed and Reports + `Pull Request 3179`_ +* Speed up and optimize the process of identifying public libraries. + `Pull Request 4640`_ +* A round of data libraries improvements. + `Pull Request 4512`_ * Install tools and workflow (thanks to `@manabuishii `__). `Pull Request 3064`_ * GFF3 support in filter by attribute (thanks to `@peterjc `__). `Pull Request 3076`_ -* Configuration & Server Overhaul - Tool Shed and Reports - `Pull Request 3179`_ * Add extension point for user preferences (thanks to `@bgruening `__). `Pull Request 3383`_ +* respect expose_user_email configuration in datalibraries permissions list + `Pull Request 4611`_ +* Explicitly include PyPI as an --extra-index-url to pip + `Pull Request 4674`_ * Kubernetes runner: Non-privileged filesystem access, updated k8s Job version (thanks to `@phnmnl `__). `Pull Request 3972`_ +* Nicer tool click targets for base + "plain" theme + (thanks to `@erasche `__). + `Pull Request 4470`_ * Setup framework for retrying failed Selenium tests. `Pull Request 3993`_ -* add dev requirement - `Pull Request 4008`_ * Tool-Describing-Tours (thanks to `@anatskiy `__). `Pull Request 4019`_ @@ -179,6 +176,8 @@ Enhancements `Pull Request 4200`_ * Remove makos for published list grids `Pull Request 4201`_ +* add dev requirement + `Pull Request 4008`_ * Improve search plugin (thanks to `@bgruening `__). `Pull Request 4213`_ @@ -310,8 +309,6 @@ Enhancements * Update conda channel order to sync with Bioconda (thanks to `@nsoranzo `__). `Pull Request 4409`_ -* Add Excel97 Datatype - `Pull Request 4410`_ * replace mako templates for tool lineage and quotas grids `Pull Request 4411`_ * Fixes and enhancements for the upload API @@ -347,9 +344,6 @@ Enhancements * Fix checking WorkflowInvocation for published workflows (thanks to `@mvdbeek `__). `Pull Request 4465`_ -* add mz5 datatype - (thanks to `@bgruening `__). - `Pull Request 4466`_ * More items per page in saved history and directly show tags (thanks to `@mvdbeek `__). `Pull Request 4467`_ @@ -566,8 +560,6 @@ Enhancements `Pull Request 4630`_ * disable MacOS CI on travis `Pull Request 4631`_ -* optimize the process of identifying public libraries - `Pull Request 4640`_ * Custom Builds tests (thanks to `@anatskiy `__). `Pull Request 4641`_ @@ -806,7 +798,7 @@ Fixes `Pull Request 4742`_ * Fix joiner tool to inherit datatype from the input format `Pull Request 4745`_ -* Fix auth with ldaps:// +* Fix auth with ``ldaps://`` (thanks to `@abretaud `__). `Pull Request 4748`_ * Force onload webhooks to wait for Galaxy object (and root) resolution. diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 8c98d04799a8..36b8ea58df2c 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -8,14 +8,16 @@ September 2017 Galaxy Release (v 17.09) Highlights =========================================================== -**Feature1** - Feature description. +**Singularity** + `Pull Request 4175`_ -**Feature2** - Feature description. +**Download entire collection** + Downloading whole colections is now possible from the history interface. `Pull Request 4098`_ + Thanks to `@mvdbeek `__. -**Feature3** - Feature description. +**Switch tool versions in workflows** + You can now select exactly what version of tool you want to use when building workflows. `Pull Request 4373`_ + Thanks to `@mvdbeek `__. Get Galaxy ========== From 5bde1d1c3a0239ef37369f59e90ceca863d6821f Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 16 Oct 2017 14:04:39 -0400 Subject: [PATCH 06/15] Small progress on 17.09 release notes. --- doc/source/releases/17.09.rst | 102 +++++++++---------------- doc/source/releases/17.09_announce.rst | 7 +- 2 files changed, 43 insertions(+), 66 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 5cdd4b96ab06..8e617ba64596 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -15,29 +15,33 @@ Enhancements .. feature * Galaxy Workflow support for GenomeSpace - (thanks to `@gvlproject `__). + (thanks to `@nuwang `__ and + `@gvlproject `__). `Pull Request 1814`_ +* Support tags (including new "name" tags) in data libraries. + (thanks to `@bwlang `__). + `Pull Request 4262`_ * HiCBrowser as Galaxy IE (thanks to `@bgruening `__). `Pull Request 3330`_ * Synnefo/Pithos+ object store backend (thanks to `@saxtouri `__). `Pull Request 3611`_ -* Add job runner for Chronos +* Add job runner for `Chronos `__ (thanks to `@theosotr `__). `Pull Request 3946`_ -* Add entry for empty_extra_files_path validator +* Paramiko based shell job runner + (thanks to `@mvdbeek `__). + `Pull Request 4358`_ +* Add entry for ``empty_extra_files_path`` validator (thanks to `@gregvonkuster `__). `Pull Request 3994`_ -* Async update: support to collections +* Extend async data sources to support dataset collections (thanks to `@fabio-cumbo `__). `Pull Request 4198`_ -* Add API repository uninstall endpoint +* Add a repository uninstall endpoint to the tool dependency API (thanks to `@mvdbeek `__). `Pull Request 4248`_ -* Data Library tags support - (thanks to `@bwlang `__). - `Pull Request 4262`_ * Display preview feature for Bam datatype (thanks to `@ashvark `__). `Pull Request 4279`_ @@ -47,13 +51,10 @@ Enhancements * Created alphabetic and numerical sort tool for collection operations (thanks to `@glormph `__). `Pull Request 4329`_ -* Paramiko based shell runner - (thanks to `@mvdbeek `__). - `Pull Request 4358`_ -* Stop loading tools that require a newer galaxy +* Prevent loading tools that require a newer galaxy (thanks to `@mvdbeek `__). `Pull Request 4382`_ -* Vcf gz datatype +* Add explicit support for gzipped VCF files (thanks to `@ffinfo `__). `Pull Request 4254`_ * Add ptkscmp datatype @@ -68,25 +69,26 @@ Enhancements * Add support for the MEME psp format (thanks to `@gregvonkuster `__). `Pull Request 4430`_ -* add biom2 datatype +* Add biom2 datatype (thanks to `@shiltemann `__). `Pull Request 4519`_ * Add Excel97 Datatype `Pull Request 4410`_ -* add mz5 datatype +* Add mz5 datatype (thanks to `@bgruening `__). `Pull Request 4466`_ .. enhancement -* Configuration & Server Overhaul - Tool Shed and Reports +* Revamp configuration and default server for tool shed and Galaxy reports application + (these now use a uwsgi server by default configured with a YAML configuration file). `Pull Request 3179`_ * Speed up and optimize the process of identifying public libraries. `Pull Request 4640`_ -* A round of data libraries improvements. +* Various data libraries improvements. `Pull Request 4512`_ -* Install tools and workflow - (thanks to `@manabuishii `__). +* Enhance workflow import API endpoint to allow admins to install repositories corresponding to a supplied + workflow (thanks to `@manabuishii `__). `Pull Request 3064`_ * GFF3 support in filter by attribute (thanks to `@peterjc `__). @@ -94,18 +96,28 @@ Enhancements * Add extension point for user preferences (thanks to `@bgruening `__). `Pull Request 3383`_ -* respect expose_user_email configuration in datalibraries permissions list +* Respect ``expose_user_email`` configuration in data libraries permissions list. `Pull Request 4611`_ -* Explicitly include PyPI as an --extra-index-url to pip +* Explicitly include PyPI as an ``--extra-index-url`` to pip. `Pull Request 4674`_ -* Kubernetes runner: Non-privileged filesystem access, updated k8s Job version +* Improved Kubernetes support (non-privileged filesystem access, updated k8s Job API target) (thanks to `@phnmnl `__). `Pull Request 3972`_ -* Nicer tool click targets for base + "plain" theme +* Nicer tool click targets for toolbox + (thanks to `@erasche `__). + `Pull Request 4470`_ +* Implement a "plain" bootstrap theme for the UX (thanks to `@erasche `__). `Pull Request 4470`_ -* Setup framework for retrying failed Selenium tests. - `Pull Request 3993`_ +* Add Selenium tests for the "saved histories" and "published histories" + (thanks to `@anatskiy `__). + `Pull Request 4587`_, `Pull Request 4502`_ +* Dozens of Selenium functional test enhancements and fixes + `Pull Request 3993`_, `Pull Request 4523`_, `Pull Request 4524`_, `Pull Request 4549`_, + `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_, + `Pull Request 3992`_, `Pull Request 4003`_, `Pull Request 4053`_, + `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_, + `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_ * Tool-Describing-Tours (thanks to `@anatskiy `__). `Pull Request 4019`_ @@ -375,10 +387,6 @@ Enhancements `Pull Request 4514`_ * Display d3 hierarchy datatype in upload interface `Pull Request 4522`_ -* Selenium test fixes and improvements. - `Pull Request 4523`_ -* Fix workflow run Selenium test and make it more robust. - `Pull Request 4524`_ * Implement influxdb error reporter (thanks to `@erasche `__). `Pull Request 4533`_ @@ -389,8 +397,6 @@ Enhancements `Pull Request 4542`_ * allow linking, posix and spaces conversions in datalib imports `Pull Request 4547`_ -* Assorted Selenium test fixes - `Pull Request 4549`_ * Allow exporting workflows when tool is uninstalled (thanks to `@mvdbeek `__). `Pull Request 4553`_ @@ -404,10 +410,6 @@ Enhancements * Add show/hide deleted/hidden links when history is filtered... (thanks to `@chambm `__). `Pull Request 4581`_ -* Make history sharing Selenium tests more robust and informative. - `Pull Request 4588`_ -* Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails. - `Pull Request 4589`_ * Python 3 fixes for set_metadata.py `Pull Request 4607`_ * Allow adding new data tables without restart @@ -416,8 +418,6 @@ Enhancements * remove .git and .hg from recursive file search (thanks to `@bgruening `__). `Pull Request 4636`_ -* Improved state handling for @anatskiy-style Selenium tests. - `Pull Request 4647`_ * Better handling of long id secrets when generating per-kind encryption keys. `Pull Request 4713`_ @@ -428,17 +428,11 @@ Enhancements * Add test case clarifying datasets do get "renamed" by rename PJA in collections. `Pull Request 3983`_ -* Fixes for Selenium workflow run test case. - `Pull Request 3992`_ -* Fix handling main_panel switching in various Selenium tests. - `Pull Request 4003`_ * One more fix for main_panel fix in `#3992 `__. `Pull Request 4042`_ * Add some test tools for collection job failures. `Pull Request 4044`_ -* Reset Selenium test connection between test retries. - `Pull Request 4053`_ * Add admin app `Pull Request 4067`_ * Preparation for grids mako removal @@ -497,15 +491,10 @@ Enhancements * Workflow loading speedup (thanks to `@mvdbeek `__). `Pull Request 4500`_ -* Published History Grid tests - (thanks to `@anatskiy `__). - `Pull Request 4502`_ * Prevent transient job state test failures from failing the build. `Pull Request 4510`_ * More robust workflow invocation testing. `Pull Request 4530`_ -* Another fix for Selenium worklow tests. - `Pull Request 4531`_ * Refactor history import/export tests to allow collection testing. `Pull Request 4534`_ * Refactor test modules toward cleaner dependencies @@ -520,27 +509,10 @@ Enhancements * Check user roles only once if user has no roles (thanks to `@mvdbeek `__). `Pull Request 4546`_ -* Revert "Remove Selenium test that is broken because Galaxy is broken." - (thanks to `@mvdbeek `__). - `Pull Request 4561`_ -* Increase the robustness of Selenium workflow management tests. - `Pull Request 4564`_ * Fix datalib collection import `Pull Request 4568`_ -* Make submitting logins for Selenium tests a bit more robust. - `Pull Request 4576`_ * Delegate displaying of page titles to Layout.display() `Pull Request 4578`_ -* Retry failed clicks more aggressively for Selenium tests. - `Pull Request 4582`_ -* Fix another issue with sorting by owner for published histories Selenium - test. - `Pull Request 4586`_ -* Add Selenium tests for the Saved Histories - (thanks to `@anatskiy `__). - `Pull Request 4587`_ -* Small improvements to workflow editor Selenium tests. - `Pull Request 4592`_ * Datalibs various fixes `Pull Request 4595`_ * Remove bam to bai converter diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 36b8ea58df2c..62c63764ecf0 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -9,7 +9,12 @@ Highlights =========================================================== **Singularity** - `Pull Request 4175`_ + Tool execution using the HPC-friendly container technology `Singularity `__ + is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis + or standardized containers can be built or downloaded corresponding to Conda requirements automatically + using the mulled toolkit built into Galaxy (just like is possible for Docker). For more information + checkout `this presentation `__ from the 2017 Galaxy Community Conference. + `Pull Request 4175`_ **Download entire collection** Downloading whole colections is now possible from the history interface. `Pull Request 4098`_ From ee27188b59d174f4db16d2ce4b7cd2181ea93517 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 23 Oct 2017 17:15:52 -0400 Subject: [PATCH 07/15] add security release notes --- .../scripts/libs/jquery/jquery.complexify.js | 192 ++++++++++ doc/source/api/api.rst | 348 ++++++++++++++++++ doc/source/api/ts_api.rst | 68 ++++ doc/source/releases/17.09_announce.rst | 69 +++- 4 files changed, 676 insertions(+), 1 deletion(-) create mode 100644 client/galaxy/scripts/libs/jquery/jquery.complexify.js create mode 100644 doc/source/api/api.rst create mode 100644 doc/source/api/ts_api.rst diff --git a/client/galaxy/scripts/libs/jquery/jquery.complexify.js b/client/galaxy/scripts/libs/jquery/jquery.complexify.js new file mode 100644 index 000000000000..9d09a8d61dec --- /dev/null +++ b/client/galaxy/scripts/libs/jquery/jquery.complexify.js @@ -0,0 +1,192 @@ +/* + http://github.com/danpalmer/jquery.complexify.js + + This code is distributed under the WTFPL v2: +*/ +(function ($) { + + $.fn.extend({ + complexify: function(options, callback) { + + var MIN_COMPLEXITY = 49; // 12 chars with Upper, Lower and Number + var MAX_COMPLEXITY = 120; // 25 chars, all charsets + var CHARSETS = [ + // Commonly Used + //////////////////// + [0x0020, 0x0020], // Space + [0x0030, 0x0039], // Numbers + [0x0041, 0x005A], // Uppercase + [0x0061, 0x007A], // Lowercase + [0x0021, 0x002F], // Punctuation + [0x003A, 0x0040], // Punctuation + [0x005B, 0x0060], // Punctuation + [0x007B, 0x007E], // Punctuation + // Everything Else + //////////////////// + [0x0080, 0x00FF], // Latin-1 Supplement + [0x0100, 0x017F], // Latin Extended-A + [0x0180, 0x024F], // Latin Extended-B + [0x0250, 0x02AF], // IPA Extensions + [0x02B0, 0x02FF], // Spacing Modifier Letters + [0x0300, 0x036F], // Combining Diacritical Marks + [0x0370, 0x03FF], // Greek + [0x0400, 0x04FF], // Cyrillic + [0x0530, 0x058F], // Armenian + [0x0590, 0x05FF], // Hebrew + [0x0600, 0x06FF], // Arabic + [0x0700, 0x074F], // Syriac + [0x0780, 0x07BF], // Thaana + [0x0900, 0x097F], // Devanagari + [0x0980, 0x09FF], // Bengali + [0x0A00, 0x0A7F], // Gurmukhi + [0x0A80, 0x0AFF], // Gujarati + [0x0B00, 0x0B7F], // Oriya + [0x0B80, 0x0BFF], // Tamil + [0x0C00, 0x0C7F], // Telugu + [0x0C80, 0x0CFF], // Kannada + [0x0D00, 0x0D7F], // Malayalam + [0x0D80, 0x0DFF], // Sinhala + [0x0E00, 0x0E7F], // Thai + [0x0E80, 0x0EFF], // Lao + [0x0F00, 0x0FFF], // Tibetan + [0x1000, 0x109F], // Myanmar + [0x10A0, 0x10FF], // Georgian + [0x1100, 0x11FF], // Hangul Jamo + [0x1200, 0x137F], // Ethiopic + [0x13A0, 0x13FF], // Cherokee + [0x1400, 0x167F], // Unified Canadian Aboriginal Syllabics + [0x1680, 0x169F], // Ogham + [0x16A0, 0x16FF], // Runic + [0x1780, 0x17FF], // Khmer + [0x1800, 0x18AF], // Mongolian + [0x1E00, 0x1EFF], // Latin Extended Additional + [0x1F00, 0x1FFF], // Greek Extended + [0x2000, 0x206F], // General Punctuation + [0x2070, 0x209F], // Superscripts and Subscripts + [0x20A0, 0x20CF], // Currency Symbols + [0x20D0, 0x20FF], // Combining Marks for Symbols + [0x2100, 0x214F], // Letterlike Symbols + [0x2150, 0x218F], // Number Forms + [0x2190, 0x21FF], // Arrows + [0x2200, 0x22FF], // Mathematical Operators + [0x2300, 0x23FF], // Miscellaneous Technical + [0x2400, 0x243F], // Control Pictures + [0x2440, 0x245F], // Optical Character Recognition + [0x2460, 0x24FF], // Enclosed Alphanumerics + [0x2500, 0x257F], // Box Drawing + [0x2580, 0x259F], // Block Elements + [0x25A0, 0x25FF], // Geometric Shapes + [0x2600, 0x26FF], // Miscellaneous Symbols + [0x2700, 0x27BF], // Dingbats + [0x2800, 0x28FF], // Braille Patterns + [0x2E80, 0x2EFF], // CJK Radicals Supplement + [0x2F00, 0x2FDF], // Kangxi Radicals + [0x2FF0, 0x2FFF], // Ideographic Description Characters + [0x3000, 0x303F], // CJK Symbols and Punctuation + [0x3040, 0x309F], // Hiragana + [0x30A0, 0x30FF], // Katakana + [0x3100, 0x312F], // Bopomofo + [0x3130, 0x318F], // Hangul Compatibility Jamo + [0x3190, 0x319F], // Kanbun + [0x31A0, 0x31BF], // Bopomofo Extended + [0x3200, 0x32FF], // Enclosed CJK Letters and Months + [0x3300, 0x33FF], // CJK Compatibility + [0x3400, 0x4DB5], // CJK Unified Ideographs Extension A + [0x4E00, 0x9FFF], // CJK Unified Ideographs + [0xA000, 0xA48F], // Yi Syllables + [0xA490, 0xA4CF], // Yi Radicals + [0xAC00, 0xD7A3], // Hangul Syllables + [0xD800, 0xDB7F], // High Surrogates + [0xDB80, 0xDBFF], // High Private Use Surrogates + [0xDC00, 0xDFFF], // Low Surrogates + [0xE000, 0xF8FF], // Private Use + [0xF900, 0xFAFF], // CJK Compatibility Ideographs + [0xFB00, 0xFB4F], // Alphabetic Presentation Forms + [0xFB50, 0xFDFF], // Arabic Presentation Forms-A + [0xFE20, 0xFE2F], // Combining Half Marks + [0xFE30, 0xFE4F], // CJK Compatibility Forms + [0xFE50, 0xFE6F], // Small Form Variants + [0xFE70, 0xFEFE], // Arabic Presentation Forms-B + [0xFEFF, 0xFEFF], // Specials + [0xFF00, 0xFFEF], // Halfwidth and Fullwidth Forms + [0xFFF0, 0xFFFD] // Specials + ]; + + var defaults = { + minimumChars: 8, + strengthScaleFactor: 1, + bannedPasswords: window.COMPLEXIFY_BANLIST || [], + banMode: 'strict' // (strict|loose) + }; + + if($.isFunction(options) && !callback) { + callback = options; + options = {}; + } + + options = $.extend(defaults, options); + + function additionalComplexityForCharset(str, charset) { + for (var i = str.length - 1; i >= 0; i--) { + if (charset[0] <= str.charCodeAt(i) && str.charCodeAt(i) <= charset[1]) { + return charset[1] - charset[0] + 1; + } + } + return 0; + } + + function inBanlist(str) { + if (options.banMode === 'strict') { + for (var i = 0; i < options.bannedPasswords.length; i++) { + if (str.toLowerCase().indexOf(options.bannedPasswords[i].toLowerCase()) !== -1) { + return true; + } + } + return false; + } else { + return $.inArray(str, options.bannedPasswords) > -1 ? true : false; + } + } + + function evaluateSecurity() { + var password = $(this).val(); + var complexity = 0, valid = false; + + // Reset complexity to 0 when banned password is found + if (!inBanlist(password)) { + + // Add character complexity + for (var i = CHARSETS.length - 1; i >= 0; i--) { + complexity += additionalComplexityForCharset(password, CHARSETS[i]); + } + + } else { + complexity = 1; + } + + // Use natural log to produce linear scale + complexity = Math.log(Math.pow(complexity, password.length)) * (1/options.strengthScaleFactor); + + valid = (complexity > MIN_COMPLEXITY && password.length >= options.minimumChars); + + // Scale to percentage, so it can be used for a progress bar + complexity = (complexity / MAX_COMPLEXITY) * 100; + complexity = (complexity > 100) ? 100 : complexity; + + callback.call(this, valid, complexity); + } + + this.each(function () { + if($(this).val()) { + evaluateSecurity.apply(this); + } + }); + + return this.each(function () { + $(this).bind('keyup focus input propertychange mouseup', evaluateSecurity); + }); + + } + }); + +})(jQuery); diff --git a/doc/source/api/api.rst b/doc/source/api/api.rst new file mode 100644 index 000000000000..d7ae13cc5643 --- /dev/null +++ b/doc/source/api/api.rst @@ -0,0 +1,348 @@ +Galaxy API +========== + +annotations module +------------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.annotations + :members: + :undoc-members: + :show-inheritance: + +authenticate module +------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.authenticate + :members: + :undoc-members: + :show-inheritance: + +configuration module +-------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.configuration + :members: + :undoc-members: + :show-inheritance: + +dataset\_collections module +--------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.dataset_collections + :members: + :undoc-members: + :show-inheritance: + +datasets module +--------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +datatypes module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datatypes + :members: + :undoc-members: + :show-inheritance: + +extended\_metadata module +------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.extended_metadata + :members: + :undoc-members: + :show-inheritance: + +folder\_contents module +----------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +folders module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +forms module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +genomes module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +group\_roles module +------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +group\_users module +------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +groups module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +histories module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +history\_contents module +------------------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +item\_tags module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.item_tags + :members: + :undoc-members: + :show-inheritance: + +job\_files module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.job_files + :members: + :undoc-members: + :show-inheritance: + +jobs module +----------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.jobs + :members: + :undoc-members: + :show-inheritance: + +lda\_datasets module +-------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + :members: + :undoc-members: + :show-inheritance: + +libraries module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +library\_contents module +------------------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +metrics module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.metrics + :members: + :undoc-members: + :show-inheritance: + +page\_revisions module +---------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.page_revisions + :members: + :undoc-members: + :show-inheritance: + +pages module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.pages + :members: + :undoc-members: + :show-inheritance: + +provenance module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.provenance + :members: + :undoc-members: + :show-inheritance: + +quotas module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +remote\_files module +-------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.remote_files + :members: + :undoc-members: + :show-inheritance: + +request\_types module +--------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +requests module +--------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +roles module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +samples module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +search module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.search + :members: + :undoc-members: + :show-inheritance: + +tool\_data module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_data + :members: + :undoc-members: + :show-inheritance: + +tool\_dependencies module +------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_dependencies + :members: + :undoc-members: + :show-inheritance: + +tool\_shed\_repositories module +------------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories + :members: + :undoc-members: + :show-inheritance: + +tools module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +toolshed module +--------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.toolshed + :members: + :undoc-members: + :show-inheritance: + +tours module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.tours + :members: + :undoc-members: + :show-inheritance: + +users module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +visualizations module +--------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +webhooks module +--------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.webhooks + :members: + :undoc-members: + :show-inheritance: + +workflows module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/api/ts_api.rst b/doc/source/api/ts_api.rst new file mode 100644 index 000000000000..c8257587a17b --- /dev/null +++ b/doc/source/api/ts_api.rst @@ -0,0 +1,68 @@ +Tool Shed API +============= + +authenticate module +----------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.authenticate + :members: + :undoc-members: + :show-inheritance: + +categories module +--------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.categories + :members: + :undoc-members: + :show-inheritance: + +configuration module +------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.api.configuration + :members: + :undoc-members: + :show-inheritance: + +groups module +----------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.groups + :members: + :undoc-members: + :show-inheritance: + +repositories module +----------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repositories + :members: + :undoc-members: + :show-inheritance: + +repository\_revisions module +-------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions + :members: + :undoc-members: + :show-inheritance: + +tools module +---------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.tools + :members: + :undoc-members: + :show-inheritance: + +users module +---------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.users + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 62c63764ecf0..bd42499a539f 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -42,11 +42,78 @@ To update an existing Galaxy repository run: See `our wiki `__ for additional details regarding the source code locations. +Security +======== + +Together with the 17.09 Galaxy version we release the following three security patches. Per our `Security Policy `__ these has been already applied to all Galaxy releases in the last 12 months. + +If you maintain a publicly accessible Galaxy please consider signing up for this [mailing list](https://lists.galaxyproject.org/listinfo/galaxy-public-servers) to receive the future security patches in advance of the public disclosure. + +Limited Galaxy Data Library unauthorized filesystem access +---------------------------------------------------------- + +Tracked as `GX-2017-0001 `__ + +A medium severity security vulnerability in Galaxy Data Libraries was +recently discovered by Jelle Scholtalbers. This vulnerability allows the following unauthorized actions: + +1. Any user that has been granted the permission to add datasets to a +library, library folder, or to modify an existing library dataset (an +"authorized user"), is able to import any file on the system that is +readable by the user running the Galaxy server. + +2. Anyone can create libraries and library folders (but not add datasets to them) + +The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit `__ + +Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled +---------------------------------------------------------------------------------------- + +Tracked as `GX-2017-0002 `__ + +A high severity security vulnerability was recently discovered in Galaxy +Interactive Environments (GIEs) by the Galaxy Committers Team. Anyone with +a Galaxy account can exploit this vulnerability to execute arbitrary code +on the Galaxy server as the user running the Galaxy server process. + +The vulnerability only affects Galaxy servers on which Galaxy Interactive +Environments are enabled (by setting the +`interactive_environment_plugins_directory` +option in galaxy.ini). Because the vulnerability can be exploited to +execute arbitrary code, the impact for affected servers is severe. + +Administrators of Galaxy servers where GIEs *are* enabled should update +immediately. + +The fix for this issue has been applied to Galaxy releases back to 17.05 and can be found in this `commit `__ + +Unauthorized filesystem access via data source tools +---------------------------------------------------- + +Tracked as `GX-2017-0003 `__ + +A medium severity security vulnerability in tools utilizing the Galaxy data +source protocol was recently discovered by the Galaxy Committers Team. This +vulnerability allows anyone able to run an external data source tool to add +to their history any file that is readable by the user running Galaxy jobs +on the host where the job runs. + +Many such "external data source" tools are provided with the Galaxy +distribution and are enabled by default (most tools under the "Get Data" +section of the tool panel), meaning that its exploitability is fairly high, +as only one such tool needs to be enabled to be vulnerable, including any +custom data source tools (any tool that uses +`tools/data_source/data_source.py`). +What files will be readable depends entirely upon what the job's user has +access to read on the host(s) where jobs run. + +The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit `__ + Deprecation Notices =================== * The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related - user interface and introduce configuration option to keep relevant controllers active if desired. `Related PR `__. + user interface and introduce configuration option to keep relevant API controllers active if desired. `Related PR `__. * The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release. * Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available. From 180472a3d8ceb40f6d015c0bfe5ef1dd08da5513 Mon Sep 17 00:00:00 2001 From: Dave Clements Date: Mon, 23 Oct 2017 23:49:07 -0600 Subject: [PATCH 08/15] Small edits to 17.09 release notes. --- doc/source/releases/17.09_announce.rst | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index bd42499a539f..0d0622faf8ce 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -11,7 +11,7 @@ Highlights **Singularity** Tool execution using the HPC-friendly container technology `Singularity `__ is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis - or standardized containers can be built or downloaded corresponding to Conda requirements automatically + or standardized containers corresponding to Conda requirements can be built or downloaded automatically using the mulled toolkit built into Galaxy (just like is possible for Docker). For more information checkout `this presentation `__ from the 2017 Galaxy Community Conference. `Pull Request 4175`_ @@ -39,7 +39,7 @@ To update an existing Galaxy repository run: $ git checkout release_17.09 && git pull --ff-only origin release_17.09 -See `our wiki `__ for additional details regarding the source code locations. +See `the community hub `__ for additional details regarding the source code locations. Security @@ -55,7 +55,8 @@ Limited Galaxy Data Library unauthorized filesystem access Tracked as `GX-2017-0001 `__ A medium severity security vulnerability in Galaxy Data Libraries was -recently discovered by Jelle Scholtalbers. This vulnerability allows the following unauthorized actions: +recently discovered by `Jelle Scholtalbers `__. +This vulnerability allows the following unauthorized actions: 1. Any user that has been granted the permission to add datasets to a library, library folder, or to modify an existing library dataset (an @@ -79,7 +80,7 @@ on the Galaxy server as the user running the Galaxy server process. The vulnerability only affects Galaxy servers on which Galaxy Interactive Environments are enabled (by setting the `interactive_environment_plugins_directory` -option in galaxy.ini). Because the vulnerability can be exploited to +option in `galaxy.ini`). Because the vulnerability can be exploited to execute arbitrary code, the impact for affected servers is severe. Administrators of Galaxy servers where GIEs *are* enabled should update @@ -93,9 +94,9 @@ Unauthorized filesystem access via data source tools Tracked as `GX-2017-0003 `__ A medium severity security vulnerability in tools utilizing the Galaxy data -source protocol was recently discovered by the Galaxy Committers Team. This -vulnerability allows anyone able to run an external data source tool to add -to their history any file that is readable by the user running Galaxy jobs +source protocol was recently discovered by the Galaxy Committers Team. +Anyone who is able to run an external data source tool can access +any file that is readable by the user running Galaxy jobs on the host where the job runs. Many such "external data source" tools are provided with the Galaxy @@ -104,7 +105,7 @@ section of the tool panel), meaning that its exploitability is fairly high, as only one such tool needs to be enabled to be vulnerable, including any custom data source tools (any tool that uses `tools/data_source/data_source.py`). -What files will be readable depends entirely upon what the job's user has +What files are readable depends entirely upon what the job's user has access to read on the host(s) where jobs run. The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit `__ From c8efbb3327cb4e2805c0099975c5a2be70b95a21 Mon Sep 17 00:00:00 2001 From: Dave Clements Date: Mon, 23 Oct 2017 23:50:27 -0600 Subject: [PATCH 09/15] Fixed indenting in release notes. --- doc/source/releases/17.09_announce.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 0d0622faf8ce..8ed3e92ad214 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -59,9 +59,9 @@ recently discovered by `Jelle Scholtalbers `__. This vulnerability allows the following unauthorized actions: 1. Any user that has been granted the permission to add datasets to a -library, library folder, or to modify an existing library dataset (an -"authorized user"), is able to import any file on the system that is -readable by the user running the Galaxy server. + library, library folder, or to modify an existing library dataset (an + "authorized user"), is able to import any file on the system that is + readable by the user running the Galaxy server. 2. Anyone can create libraries and library folders (but not add datasets to them) From 4252f4f813c3d5a390ead3d86c4eec78273163cb Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 24 Oct 2017 09:08:33 -0400 Subject: [PATCH 10/15] Small 17.09 release note improvements. --- doc/source/releases/17.09.rst | 29 ++++++++++++++--------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 8e617ba64596..96740bc45763 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -103,6 +103,9 @@ Enhancements * Improved Kubernetes support (non-privileged filesystem access, updated k8s Job API target) (thanks to `@phnmnl `__). `Pull Request 3972`_ +* New Dependency resolver for the LMOD environment modules system + (thanks to `@arbernard `__). + `Pull Request 4489`_ * Nicer tool click targets for toolbox (thanks to `@erasche `__). `Pull Request 4470`_ @@ -344,37 +347,33 @@ Enhancements * Uniform indentation of multiline if conditionals (thanks to `@nsoranzo `__). `Pull Request 4455`_ -* Logging fixes +* Small logging improvements (thanks to `@nsoranzo `__). `Pull Request 4456`_ -* More detailed sentry reports +* Improvements to `Sentry `__ integration (thanks to `@erasche `__). - `Pull Request 4457`_ -* don't uppercase envoverride + `Pull Request 4457`_, `Pull Request 4471`_ +* Fix for GIEs to not automatically uppercase environment variables (thanks to `@xgaia `__). `Pull Request 4458`_ -* Fix checking WorkflowInvocation for published workflows +* Fix security checking of WorkflowInvocation for published workflows (thanks to `@mvdbeek `__). `Pull Request 4465`_ -* More items per page in saved history and directly show tags +* Show more items per page in saved history view and directly show tags (thanks to `@mvdbeek `__). `Pull Request 4467`_ -* needed for sentry functionality in reports webapp - (thanks to `@erasche `__). - `Pull Request 4471`_ -* Show tags, import by drag-and-drop and avoid refreshed in workflow page +* A variety of usability improvements to the workflow index page (show tags, + allow import by drag-and-drop, and avoid unneeded page refreshs) (thanks to `@mvdbeek `__). `Pull Request 4476`_ -* Use pysam instead of samtools binary +* Use pysam instead of samtools binary when discovering BAM metadata in one + place (samtools is still required by Galaxy) (thanks to `@nsoranzo `__). `Pull Request 4479`_ -* replace exclamation with a clock icon +* Replace exclamation with a clock icon for "new" datasets in the history panel. `Pull Request 4485`_ * Minor copy datasets dialog improvement. `Pull Request 4486`_ -* New Dependency resolver for the LMOD environment modules system - (thanks to `@arbernard `__). - `Pull Request 4489`_ * 41% reduction in freiburg galaxy startup time (thanks to `@erasche `__). `Pull Request 4495`_ From 199ec6dd4c70c733edd200e61d6470dedcf0da85 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 24 Oct 2017 09:26:44 -0400 Subject: [PATCH 11/15] Condense several 17.09 release notes items. --- doc/source/releases/17.09.rst | 83 ++++++++++------------------------- 1 file changed, 24 insertions(+), 59 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 96740bc45763..41b4e08d3d4d 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -112,9 +112,10 @@ Enhancements * Implement a "plain" bootstrap theme for the UX (thanks to `@erasche `__). `Pull Request 4470`_ -* Add Selenium tests for the "saved histories" and "published histories" +* Add Selenium tests for the "saved histories", "published histories", and + "custom builds" (thanks to `@anatskiy `__). - `Pull Request 4587`_, `Pull Request 4502`_ + `Pull Request 4587`_, `Pull Request 4502`_, `Pull Request 4641`_, * Dozens of Selenium functional test enhancements and fixes `Pull Request 3993`_, `Pull Request 4523`_, `Pull Request 4524`_, `Pull Request 4549`_, `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_, @@ -168,15 +169,18 @@ Enhancements * Add the ability to control job conf plugin loading from environment variables. `Pull Request 4154`_ -* Remove saved pages grid mako - `Pull Request 4157`_ +* Replace various mako templates with client side JavaScript rendering. + `Pull Request 4157`_, `Pull Request 4167`_, `Pull Request 4169`_, + `Pull Request 4201`_, `Pull Request 4311`_, `Pull Request 4377`_, + `Pull Request 4411`_, `Pull Request 4334`_ +* Related to the above mako transition, rework various "grid" rendering code + to do more on the client side as well. + `Pull Request 4302`_, `Pull Request 4291`_, `Pull Request 4293`_, + `Pull Request 4385`_, `Pull Request 4405`_, + `Pull Request 4449`_, `Pull Request 4263`_, `Pull Request 4341`_, + `Pull Request 4163`_, `Pull Request 4101`_ * Set content type to application/json for JSON text types. `Pull Request 4160`_ -* Remove histories grid mako - `Pull Request 4167`_ -* Mako to JavaScript views for Workflow's Run and Import actions - (thanks to `@bgruening `__). - `Pull Request 4169`_ * Improved Mulled Containers `Pull Request 4173`_ * Allow Galaxy to use cached mulled containers for Singularity. @@ -189,8 +193,6 @@ Enhancements * deals with .xls older file extension (thanks to `@FredericBGA `__). `Pull Request 4200`_ -* Remove makos for published list grids - `Pull Request 4201`_ * add dev requirement `Pull Request 4008`_ * Improve search plugin @@ -247,19 +249,13 @@ Enhancements * Local network access restrictions (thanks to `@erasche `__). `Pull Request 4289`_ -* Grid published histories - `Pull Request 4291`_ * Enhancement for Phyloviz viz plugin (thanks to `@bgruening `__). `Pull Request 4292`_ -* Use dictionary endpoints for item selection grids in page editor - `Pull Request 4293`_ * Submitting the galaxy jobs as a predefined system user: using 'real_system_username' (thanks to `@ashvark `__). `Pull Request 4294`_ -* Trackster selection grids and feature fixes - `Pull Request 4302`_ * Update Japanese translation (thanks to `@manabuishii `__). `Pull Request 4304`_ @@ -272,8 +268,6 @@ Enhancements * Support Localization Scratchbook (thanks to `@manabuishii `__). `Pull Request 4307`_ -* Removes saved visualizations grid mako - `Pull Request 4311`_ * Allow import of history archives via simple file upload (thanks to `@mvdbeek `__). `Pull Request 4326`_ @@ -284,21 +278,14 @@ Enhancements (thanks to `@VJalili `__). `Pull Request 4342`_ * CSRF protection for login, logout, and user registration. - `Pull Request 4365`_ -* Implement default_identifier_source for outputs and sort input keys by - default + `Pull Request 4365`_, `Pull Request 4710`_ +* Implement ``default_identifier_source`` for tool collection outputs and sort + input keys by default (thanks to `@mvdbeek `__). `Pull Request 4368`_ -* Allow removal of dataset tags in workflows - (thanks to `@mvdbeek `__). - `Pull Request 4369`_ * Galactic Radio Telescope Update (thanks to `@erasche `__). `Pull Request 4376`_ -* Remove makos of admin user grid forms - `Pull Request 4377`_ -* Admin grid roles revision - `Pull Request 4385`_ * Show minimum required galaxy version in tool shed and galaxy installation process (thanks to `@mvdbeek `__). @@ -316,16 +303,12 @@ Enhancements `Pull Request 4403`_ * Generalize allow_library_path_paste to allow_path_paste. `Pull Request 4404`_ -* Admin grid groups revision - `Pull Request 4405`_ * Small GRT bugfixes (thanks to `@erasche `__). `Pull Request 4408`_ * Update conda channel order to sync with Bioconda (thanks to `@nsoranzo `__). `Pull Request 4409`_ -* replace mako templates for tool lineage and quotas grids - `Pull Request 4411`_ * Fixes and enhancements for the upload API `Pull Request 4417`_ * Avoid adding `(imported from API)` to workflows @@ -365,7 +348,7 @@ Enhancements * A variety of usability improvements to the workflow index page (show tags, allow import by drag-and-drop, and avoid unneeded page refreshs) (thanks to `@mvdbeek `__). - `Pull Request 4476`_ + `Pull Request 4476`_, `Pull Request 4369`_ * Use pysam instead of samtools binary when discovering BAM metadata in one place (samtools is still required by Galaxy) (thanks to `@nsoranzo `__). @@ -434,8 +417,6 @@ Enhancements `Pull Request 4044`_ * Add admin app `Pull Request 4067`_ -* Preparation for grids mako removal - `Pull Request 4101`_ * Merge ShedToolLineage and StockLineage to ToolLineage (thanks to `@mvdbeek `__). `Pull Request 4119`_ @@ -444,8 +425,6 @@ Enhancements `Pull Request 4137`_ * Move galaxy.tools.toolbox.cache to galaxy.tools.cache. `Pull Request 4155`_ -* Removes mako for datasets grid - `Pull Request 4163`_ * Spacing convention, -> util.asbool, atribute -> attribute (thanks to `@bwlang `__). `Pull Request 4250`_ @@ -462,11 +441,6 @@ Enhancements * Some formatting (thanks to `@VJalili `__). `Pull Request 4333`_ -* Replacing Edit Attributes Mako by JavaScript - (thanks to `@bgruening `__). - `Pull Request 4334`_ -* Admin user grid conversion - `Pull Request 4341`_ * Merging configure menu with main workflow view (thanks to `@bgruening `__). `Pull Request 4353`_ @@ -531,9 +505,6 @@ Enhancements `Pull Request 4630`_ * disable MacOS CI on travis `Pull Request 4631`_ -* Custom Builds tests - (thanks to `@anatskiy `__). - `Pull Request 4641`_ Fixes @@ -613,8 +584,6 @@ Fixes * Fix empty tabular output error when using discover_datasets. (thanks to `@pkrog `__). `Pull Request 4240`_ -* Fix shared history grid - `Pull Request 4263`_ * Importing old exported histories failing (thanks to `@cche `__). `Pull Request 4268`_ @@ -675,8 +644,6 @@ Fixes `Pull Request 4445`_ * Fix E201 errors (spaces in parens) in new memepsp datatype `Pull Request 4446`_ -* Fixes for advanced grid search - `Pull Request 4449`_ * Fix quota function name `Pull Request 4469`_ * Fixes for VCF/BCF datatypes @@ -732,29 +699,27 @@ Fixes * Updated function description and fix some typos (thanks to `@VJalili `__). `Pull Request 4629`_ -* Fix data order in Custom Builds +* Fix display of data in "custom builds" page (thanks to `@anatskiy `__). `Pull Request 4634`_ -* do not wrap lines in the upload url fetch +* Do not wrap lines in the upload URL fetch. `Pull Request 4639`_ -* BUG: Explicitly write registry.xml when creating a job for the upload tool +* Explicitly write registry.xml when creating a job for the upload tool (thanks to `@mvdbeek `__). `Pull Request 4644`_ * Fix links on workflow, history items. `Pull Request 4656`_ -* Fix modules resolver +* Fix for modules resolver. `Pull Request 4663`_ -* Remove chatty debug statement +* Remove overly chatty debug statement. `Pull Request 4671`_ -* Client side fixes for GIEs +* Client side fixes for GIEs. `Pull Request 4680`_ -* Update versions of conda and conda-build +* Update target versions of conda and conda-build (thanks to `@nsoranzo `__). `Pull Request 4701`_ * Correct base route for workflows, allowing proxy-prefix to work. `Pull Request 4705`_ -* Append fewer characters to id_secret by default for encrypting csrf tokens. - `Pull Request 4710`_ * Cachebust IE require'd files (jupyter.js, etc). `Pull Request 4714`_ * Add message (error and info) display to workflows display list. From 3e8bf27fca44f5b70ac9e7e1f66acbdb11c98162 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 24 Oct 2017 09:48:51 -0400 Subject: [PATCH 12/15] More release notes improvements. Move a couple things higher, merge a couple more things, improved language (toward sentences). --- doc/source/releases/17.09.rst | 115 ++++++++++++++-------------------- 1 file changed, 48 insertions(+), 67 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 41b4e08d3d4d..87fcb327abce 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -77,6 +77,15 @@ Enhancements * Add mz5 datatype (thanks to `@bgruening `__). `Pull Request 4466`_ +* Refactor tool error reporting into plugins and implement a new + plugin for `influxdb `__ + (thanks to `@erasche `__). + `Pull Request 4305`_, `Pull Request 4533`_ +* Implement second toolshed installation UX targetting the API. + `Pull Request 3626`_ +* Tool-Describing-Tours + (thanks to `@anatskiy `__). + `Pull Request 4019`_ .. enhancement @@ -121,10 +130,7 @@ Enhancements `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_, `Pull Request 3992`_, `Pull Request 4003`_, `Pull Request 4053`_, `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_, - `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_ -* Tool-Describing-Tours - (thanks to `@anatskiy `__). - `Pull Request 4019`_ + `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_ * Prevent graphite from dying loudly (thanks to `@erasche `__). `Pull Request 4036`_ @@ -172,7 +178,8 @@ Enhancements * Replace various mako templates with client side JavaScript rendering. `Pull Request 4157`_, `Pull Request 4167`_, `Pull Request 4169`_, `Pull Request 4201`_, `Pull Request 4311`_, `Pull Request 4377`_, - `Pull Request 4411`_, `Pull Request 4334`_ + `Pull Request 4411`_, `Pull Request 4334`_, `Pull Request 4305`_, + `Pull Request 4067`_, `Pull Request 4327`_ * Related to the above mako transition, rework various "grid" rendering code to do more on the client side as well. `Pull Request 4302`_, `Pull Request 4291`_, `Pull Request 4293`_, @@ -228,46 +235,40 @@ Enhancements * Keep tool parameters when rerunning a job (thanks to `@mvdbeek `__). `Pull Request 4271`_ -* Uniform titles +* More uniform backend code for generating page titles (thanks to `@erasche `__). - `Pull Request 4272`_ + `Pull Request 4272`_, `Pull Request 4578`_ * Fix blockquote>p sizing (thanks to `@erasche `__). `Pull Request 4273`_ * Expose more user properties to admins via the API. `Pull Request 4274`_ -* Ensure tags are copied and presented when moving Collections +* Ensure tags are copied and presented when moving collections (thanks to `@pvanheus `__). `Pull Request 4277`_ -* Add test_errors to .gitignore. +* Add ``test_errors`` to .gitignore. `Pull Request 4278`_ -* Package locking for node modules. +* Implement package locking for node modules. `Pull Request 4283`_ * Enhancement for Phylocanvas plugin (thanks to `@bgruening `__). `Pull Request 4284`_ -* Local network access restrictions +* Improve security via local network access restrictions (thanks to `@erasche `__). `Pull Request 4289`_ * Enhancement for Phyloviz viz plugin (thanks to `@bgruening `__). `Pull Request 4292`_ -* Submitting the galaxy jobs as a predefined system user: using - 'real_system_username' +* Allow submitting the galaxy jobs as a predefined system user using + ``real_system_username`` (thanks to `@ashvark `__). `Pull Request 4294`_ * Update Japanese translation (thanks to `@manabuishii `__). `Pull Request 4304`_ -* Refactor bug reporting into plugins / Remove bug report mako - (thanks to `@erasche `__). - `Pull Request 4305`_ -* Localization support for Tool Help - (thanks to `@manabuishii `__). - `Pull Request 4306`_ -* Support Localization Scratchbook +* Allow localization of more UI strings (thanks to `@manabuishii `__). - `Pull Request 4307`_ + `Pull Request 4306`_, `Pull Request 4307`_ * Allow import of history archives via simple file upload (thanks to `@mvdbeek `__). `Pull Request 4326`_ @@ -277,12 +278,13 @@ Enhancements * Updated the version requirements (thanks to `@VJalili `__). `Pull Request 4342`_ -* CSRF protection for login, logout, and user registration. +* CSRF protection for login, logout, and user registration (most parts of the + Galaxy UI still don't have explicit CSRF protection). `Pull Request 4365`_, `Pull Request 4710`_ * Implement ``default_identifier_source`` for tool collection outputs and sort input keys by default (thanks to `@mvdbeek `__). - `Pull Request 4368`_ + `Pull Request 4368`_, `Pull Request 4380`_ * Galactic Radio Telescope Update (thanks to `@erasche `__). `Pull Request 4376`_ @@ -324,9 +326,6 @@ Enhancements * Add autopep8 script to help rebasing branches after `#4440 `__. `Pull Request 4447`_ -* Interactive Environment: possibility to don't uppercase env variables - (thanks to `@xgaia `__). - `Pull Request 4454`_ * Uniform indentation of multiline if conditionals (thanks to `@nsoranzo `__). `Pull Request 4455`_ @@ -338,7 +337,7 @@ Enhancements `Pull Request 4457`_, `Pull Request 4471`_ * Fix for GIEs to not automatically uppercase environment variables (thanks to `@xgaia `__). - `Pull Request 4458`_ + `Pull Request 4458`_, `Pull Request 4454`_ * Fix security checking of WorkflowInvocation for published workflows (thanks to `@mvdbeek `__). `Pull Request 4465`_ @@ -369,9 +368,6 @@ Enhancements `Pull Request 4514`_ * Display d3 hierarchy datatype in upload interface `Pull Request 4522`_ -* Implement influxdb error reporter - (thanks to `@erasche `__). - `Pull Request 4533`_ * Sync non-CWL galaxy-lib changes. `Pull Request 4535`_ * Add a small howto on profiling galaxy code @@ -405,66 +401,55 @@ Enhancements .. small_enhancement -* API installation of toolshed repositories. - `Pull Request 3626`_ * Add test case clarifying datasets do get "renamed" by rename PJA in collections. `Pull Request 3983`_ -* One more fix for main_panel fix in `#3992 - `__. - `Pull Request 4042`_ * Add some test tools for collection job failures. `Pull Request 4044`_ -* Add admin app - `Pull Request 4067`_ * Merge ShedToolLineage and StockLineage to ToolLineage (thanks to `@mvdbeek `__). `Pull Request 4119`_ * Move PlantTribes datatypes to a separate file with enhancements and fixes (thanks to `@gregvonkuster `__). `Pull Request 4137`_ -* Move galaxy.tools.toolbox.cache to galaxy.tools.cache. +* Move ``galaxy.tools.toolbox.cache`` to ``galaxy.tools.cache``. `Pull Request 4155`_ -* Spacing convention, -> util.asbool, atribute -> attribute +* Small code style and error message fixes for data library code (thanks to `@bwlang `__). `Pull Request 4250`_ -* refactors tag manager to use only what it needs… +* Refactors tag manager to not consume the unneeded ``app`` argument (thanks to `@bwlang `__). `Pull Request 4253`_ -* Use contextmanager when using compression_util.get_fileobj() +* Use contextmanager when using ``compression_util.get_fileobj()`` (thanks to `@mvdbeek `__). `Pull Request 4270`_ -* Swap the deprecated unescape() for decodeURIComponent +* Swap the deprecated ``unescape()`` for ``decodeURIComponent``. `Pull Request 4321`_ -* Separate admin controllers - `Pull Request 4327`_ -* Some formatting +* More consistent formatting for model mapping code (thanks to `@VJalili `__). `Pull Request 4333`_ -* Merging configure menu with main workflow view +* Merge configure menu with main workflow view (thanks to `@bgruening `__). `Pull Request 4353`_ -* Delete conda_exec_home instead of env['HOME'] +* Delete ``conda_exec_home`` instead of ``env['HOME']`` (thanks to `@mvdbeek `__). `Pull Request 4360`_ -* Add test tool for API tests - (thanks to `@mvdbeek `__). - `Pull Request 4380`_ -* Replace list with generator when iterating headers +* Replace list with generator when iterating headers in datatypes code (thanks to `@mvdbeek `__). `Pull Request 4388`_ -* Get tools with tool_version in more places +* Get tools with ``tool_version`` in more places (thanks to `@mvdbeek `__). `Pull Request 4391`_ -* Fix lgtm alerts +* Fix issues identified by the JavaScript linting application + `lgtm `__. (thanks to `@xiemaisi `__). `Pull Request 4421`_ -* Remove /mobile and associated templates +* Remove /mobile and associated templates (the code was unused and broken). `Pull Request 4494`_ * Workflow loading speedup (thanks to `@mvdbeek `__). `Pull Request 4500`_ -* Prevent transient job state test failures from failing the build. +* Prevent transient job state API test failures from failing the build. `Pull Request 4510`_ * More robust workflow invocation testing. `Pull Request 4530`_ @@ -482,28 +467,23 @@ Enhancements * Check user roles only once if user has no roles (thanks to `@mvdbeek `__). `Pull Request 4546`_ -* Fix datalib collection import +* Fix data library collection import. `Pull Request 4568`_ -* Delegate displaying of page titles to Layout.display() - `Pull Request 4578`_ -* Datalibs various fixes +* Various fixes for data libraries. `Pull Request 4595`_ -* Remove bam to bai converter +* Remove unused bam to bai converter (thanks to `@mvdbeek `__). `Pull Request 4598`_ * Retry job submissions in ShellJobRunner (thanks to `@mvdbeek `__). `Pull Request 4599`_ -* Write datatypes registry xml to working directory - (thanks to `@mvdbeek `__). - `Pull Request 4600`_ -* Remove unreachable statements +* Remove various unreachable statements (thanks to `@erasche `__). `Pull Request 4603`_ -* Refactored a dataset variable to hda +* Refactored a dataset variable to HDA (thanks to `@VJalili `__). `Pull Request 4630`_ -* disable MacOS CI on travis +* Disable MacOS tests on TravisCI. `Pull Request 4631`_ @@ -706,7 +686,8 @@ Fixes `Pull Request 4639`_ * Explicitly write registry.xml when creating a job for the upload tool (thanks to `@mvdbeek `__). - `Pull Request 4644`_ + `Pull Request 4644`_, `Pull Request 4600`_ + * Fix links on workflow, history items. `Pull Request 4656`_ * Fix for modules resolver. From 00bc7a51f9c780e15041b465e0245848f7b26244 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 24 Oct 2017 10:34:18 -0400 Subject: [PATCH 13/15] More 17.09 release note fixes. Merge more items, fix more sentences, etc... --- doc/source/releases/17.09.rst | 136 ++++++++++++---------------------- 1 file changed, 47 insertions(+), 89 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 87fcb327abce..da30a7417c6e 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -29,10 +29,11 @@ Enhancements `Pull Request 3611`_ * Add job runner for `Chronos `__ (thanks to `@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 `__). - `Pull Request 4358`_ + `Pull Request 4358`_, `Pull Request 4599`_, `Pull Request 4343`_ * Add entry for ``empty_extra_files_path`` validator (thanks to `@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 `__). +* 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 `__). `Pull Request 3064`_ * GFF3 support in filter by attribute (thanks to `@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 `__). @@ -214,7 +216,7 @@ Enhancements * "Join two Datasets" (join1) preserve column headers (thanks to `@lecorguille `__). `Pull Request 4229`_ -* add public-only filter for data libraries +* Add public-only filter for data libraries (thanks to `@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 `__). `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 `__). `Pull Request 4598`_ -* Retry job submissions in ShellJobRunner - (thanks to `@mvdbeek `__). - `Pull Request 4599`_ * Remove various unreachable statements (thanks to `@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 `__). `Pull Request 4049`_ * Minor fixes for new locales, rebuild of client. `Pull Request 4050`_ -* French error +* French translation error (thanks to `@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 `__). `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 `__). `Pull Request 4066`_ -* Rebuild to provide new localization. - `Pull Request 4081`_ * ToolShed tool dependency install fixes (thanks to `@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 `__). - `Pull Request 4120`_ * Avoid locale specific string.letters for job_name (thanks to `@peterjc `__). `Pull Request 4121`_ -* New workflow menu message fix - `Pull Request 4124`_ -* Fix typo +* Fix typo in job_conf.xml.sample (thanks to `@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 `__, don't chown non-galaxy files (thanks to `@dpryan79 `__). `Pull Request 4186`_ -* Hashtags w/ workflow-defined tags fix - `Pull Request 4188`_ * Debug of script library_upload_dir.py (thanks to `@FredericBGA `__). `Pull Request 4199`_ * Correct name of neo4j datatype class (thanks to `@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 `__). `Pull Request 4224`_ -* avoids broken version of mercurial in conda +* Avoid broken version of Mercurial in conda (thanks to `@bwlang `__). `Pull Request 4227`_ * Fix empty tabular output error when using discover_datasets. (thanks to `@pkrog `__). `Pull Request 4240`_ -* Importing old exported histories failing +* Fix importing old exported histories. (thanks to `@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 `__). `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 `__). - `Pull Request 4343`_ * Fix default output labels for subworkflows (thanks to `@mvdbeek `__). `Pull Request 4346`_ -* Search Overlay plugin bug fix +* Search overlay plugin bug fix (thanks to `@bgruening `__). `Pull Request 4348`_ -* Patch bug preventing creation of dataset library folders - (thanks to `@galaxyproject `__). - `Pull Request 4357`_ * Tool version and lineage fixes (thanks to `@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 `__). `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 `__). `Pull Request 4420`_ -* some unicoding for local runner +* Some unicoding for local runner (thanks to `@erasche `__). `Pull Request 4426`_ * Break connection in workflow editor if necessary (thanks to `@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 `__). `Pull Request 4439`_ -* Fix API tests broken in `#4434 - `__ - (thanks to `@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 `__). `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 `__). `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 `__). `Pull Request 4511`_ -* Fix missing tools wf editor alternative +* Fix missing tools in the workflow editor (thanks to `@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 `__. `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 `__). `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 `__). `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 `__). @@ -687,7 +648,6 @@ Fixes * Explicitly write registry.xml when creating a job for the upload tool (thanks to `@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 `__). @@ -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`_ From d1190bb067146d76bc16ec403562d4ba2d905710 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 24 Oct 2017 10:36:10 -0400 Subject: [PATCH 14/15] deprecate undocumented refresh_on_change functionality --- doc/source/releases/17.09_announce.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 8ed3e92ad214..2a536dad649c 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -55,7 +55,7 @@ Limited Galaxy Data Library unauthorized filesystem access Tracked as `GX-2017-0001 `__ A medium severity security vulnerability in Galaxy Data Libraries was -recently discovered by `Jelle Scholtalbers `__. +recently discovered by `Jelle Scholtalbers `__. This vulnerability allows the following unauthorized actions: 1. Any user that has been granted the permission to add datasets to a @@ -95,7 +95,7 @@ Tracked as `GX-2017-0003 `__. * The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release. * Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available. +* The ``refresh_on_change`` attribute of a ```` tag in the tool syntax can no longer be set to a value of another parameter. Use boolean instead (e.g.``refresh_on_change="True"``). `Details `__ Release Notes From 6bbf345c282782efac6a026d36f60296571deabe Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 24 Oct 2017 10:44:12 -0400 Subject: [PATCH 15/15] remove wrongly added files --- .../scripts/libs/jquery/jquery.complexify.js | 192 ---------- doc/source/api/api.rst | 348 ------------------ doc/source/api/ts_api.rst | 68 ---- 3 files changed, 608 deletions(-) delete mode 100644 client/galaxy/scripts/libs/jquery/jquery.complexify.js delete mode 100644 doc/source/api/api.rst delete mode 100644 doc/source/api/ts_api.rst diff --git a/client/galaxy/scripts/libs/jquery/jquery.complexify.js b/client/galaxy/scripts/libs/jquery/jquery.complexify.js deleted file mode 100644 index 9d09a8d61dec..000000000000 --- a/client/galaxy/scripts/libs/jquery/jquery.complexify.js +++ /dev/null @@ -1,192 +0,0 @@ -/* - http://github.com/danpalmer/jquery.complexify.js - - This code is distributed under the WTFPL v2: -*/ -(function ($) { - - $.fn.extend({ - complexify: function(options, callback) { - - var MIN_COMPLEXITY = 49; // 12 chars with Upper, Lower and Number - var MAX_COMPLEXITY = 120; // 25 chars, all charsets - var CHARSETS = [ - // Commonly Used - //////////////////// - [0x0020, 0x0020], // Space - [0x0030, 0x0039], // Numbers - [0x0041, 0x005A], // Uppercase - [0x0061, 0x007A], // Lowercase - [0x0021, 0x002F], // Punctuation - [0x003A, 0x0040], // Punctuation - [0x005B, 0x0060], // Punctuation - [0x007B, 0x007E], // Punctuation - // Everything Else - //////////////////// - [0x0080, 0x00FF], // Latin-1 Supplement - [0x0100, 0x017F], // Latin Extended-A - [0x0180, 0x024F], // Latin Extended-B - [0x0250, 0x02AF], // IPA Extensions - [0x02B0, 0x02FF], // Spacing Modifier Letters - [0x0300, 0x036F], // Combining Diacritical Marks - [0x0370, 0x03FF], // Greek - [0x0400, 0x04FF], // Cyrillic - [0x0530, 0x058F], // Armenian - [0x0590, 0x05FF], // Hebrew - [0x0600, 0x06FF], // Arabic - [0x0700, 0x074F], // Syriac - [0x0780, 0x07BF], // Thaana - [0x0900, 0x097F], // Devanagari - [0x0980, 0x09FF], // Bengali - [0x0A00, 0x0A7F], // Gurmukhi - [0x0A80, 0x0AFF], // Gujarati - [0x0B00, 0x0B7F], // Oriya - [0x0B80, 0x0BFF], // Tamil - [0x0C00, 0x0C7F], // Telugu - [0x0C80, 0x0CFF], // Kannada - [0x0D00, 0x0D7F], // Malayalam - [0x0D80, 0x0DFF], // Sinhala - [0x0E00, 0x0E7F], // Thai - [0x0E80, 0x0EFF], // Lao - [0x0F00, 0x0FFF], // Tibetan - [0x1000, 0x109F], // Myanmar - [0x10A0, 0x10FF], // Georgian - [0x1100, 0x11FF], // Hangul Jamo - [0x1200, 0x137F], // Ethiopic - [0x13A0, 0x13FF], // Cherokee - [0x1400, 0x167F], // Unified Canadian Aboriginal Syllabics - [0x1680, 0x169F], // Ogham - [0x16A0, 0x16FF], // Runic - [0x1780, 0x17FF], // Khmer - [0x1800, 0x18AF], // Mongolian - [0x1E00, 0x1EFF], // Latin Extended Additional - [0x1F00, 0x1FFF], // Greek Extended - [0x2000, 0x206F], // General Punctuation - [0x2070, 0x209F], // Superscripts and Subscripts - [0x20A0, 0x20CF], // Currency Symbols - [0x20D0, 0x20FF], // Combining Marks for Symbols - [0x2100, 0x214F], // Letterlike Symbols - [0x2150, 0x218F], // Number Forms - [0x2190, 0x21FF], // Arrows - [0x2200, 0x22FF], // Mathematical Operators - [0x2300, 0x23FF], // Miscellaneous Technical - [0x2400, 0x243F], // Control Pictures - [0x2440, 0x245F], // Optical Character Recognition - [0x2460, 0x24FF], // Enclosed Alphanumerics - [0x2500, 0x257F], // Box Drawing - [0x2580, 0x259F], // Block Elements - [0x25A0, 0x25FF], // Geometric Shapes - [0x2600, 0x26FF], // Miscellaneous Symbols - [0x2700, 0x27BF], // Dingbats - [0x2800, 0x28FF], // Braille Patterns - [0x2E80, 0x2EFF], // CJK Radicals Supplement - [0x2F00, 0x2FDF], // Kangxi Radicals - [0x2FF0, 0x2FFF], // Ideographic Description Characters - [0x3000, 0x303F], // CJK Symbols and Punctuation - [0x3040, 0x309F], // Hiragana - [0x30A0, 0x30FF], // Katakana - [0x3100, 0x312F], // Bopomofo - [0x3130, 0x318F], // Hangul Compatibility Jamo - [0x3190, 0x319F], // Kanbun - [0x31A0, 0x31BF], // Bopomofo Extended - [0x3200, 0x32FF], // Enclosed CJK Letters and Months - [0x3300, 0x33FF], // CJK Compatibility - [0x3400, 0x4DB5], // CJK Unified Ideographs Extension A - [0x4E00, 0x9FFF], // CJK Unified Ideographs - [0xA000, 0xA48F], // Yi Syllables - [0xA490, 0xA4CF], // Yi Radicals - [0xAC00, 0xD7A3], // Hangul Syllables - [0xD800, 0xDB7F], // High Surrogates - [0xDB80, 0xDBFF], // High Private Use Surrogates - [0xDC00, 0xDFFF], // Low Surrogates - [0xE000, 0xF8FF], // Private Use - [0xF900, 0xFAFF], // CJK Compatibility Ideographs - [0xFB00, 0xFB4F], // Alphabetic Presentation Forms - [0xFB50, 0xFDFF], // Arabic Presentation Forms-A - [0xFE20, 0xFE2F], // Combining Half Marks - [0xFE30, 0xFE4F], // CJK Compatibility Forms - [0xFE50, 0xFE6F], // Small Form Variants - [0xFE70, 0xFEFE], // Arabic Presentation Forms-B - [0xFEFF, 0xFEFF], // Specials - [0xFF00, 0xFFEF], // Halfwidth and Fullwidth Forms - [0xFFF0, 0xFFFD] // Specials - ]; - - var defaults = { - minimumChars: 8, - strengthScaleFactor: 1, - bannedPasswords: window.COMPLEXIFY_BANLIST || [], - banMode: 'strict' // (strict|loose) - }; - - if($.isFunction(options) && !callback) { - callback = options; - options = {}; - } - - options = $.extend(defaults, options); - - function additionalComplexityForCharset(str, charset) { - for (var i = str.length - 1; i >= 0; i--) { - if (charset[0] <= str.charCodeAt(i) && str.charCodeAt(i) <= charset[1]) { - return charset[1] - charset[0] + 1; - } - } - return 0; - } - - function inBanlist(str) { - if (options.banMode === 'strict') { - for (var i = 0; i < options.bannedPasswords.length; i++) { - if (str.toLowerCase().indexOf(options.bannedPasswords[i].toLowerCase()) !== -1) { - return true; - } - } - return false; - } else { - return $.inArray(str, options.bannedPasswords) > -1 ? true : false; - } - } - - function evaluateSecurity() { - var password = $(this).val(); - var complexity = 0, valid = false; - - // Reset complexity to 0 when banned password is found - if (!inBanlist(password)) { - - // Add character complexity - for (var i = CHARSETS.length - 1; i >= 0; i--) { - complexity += additionalComplexityForCharset(password, CHARSETS[i]); - } - - } else { - complexity = 1; - } - - // Use natural log to produce linear scale - complexity = Math.log(Math.pow(complexity, password.length)) * (1/options.strengthScaleFactor); - - valid = (complexity > MIN_COMPLEXITY && password.length >= options.minimumChars); - - // Scale to percentage, so it can be used for a progress bar - complexity = (complexity / MAX_COMPLEXITY) * 100; - complexity = (complexity > 100) ? 100 : complexity; - - callback.call(this, valid, complexity); - } - - this.each(function () { - if($(this).val()) { - evaluateSecurity.apply(this); - } - }); - - return this.each(function () { - $(this).bind('keyup focus input propertychange mouseup', evaluateSecurity); - }); - - } - }); - -})(jQuery); diff --git a/doc/source/api/api.rst b/doc/source/api/api.rst deleted file mode 100644 index d7ae13cc5643..000000000000 --- a/doc/source/api/api.rst +++ /dev/null @@ -1,348 +0,0 @@ -Galaxy API -========== - -annotations module ------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.annotations - :members: - :undoc-members: - :show-inheritance: - -authenticate module -------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.authenticate - :members: - :undoc-members: - :show-inheritance: - -configuration module --------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.configuration - :members: - :undoc-members: - :show-inheritance: - -dataset\_collections module ---------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.dataset_collections - :members: - :undoc-members: - :show-inheritance: - -datasets module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -datatypes module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datatypes - :members: - :undoc-members: - :show-inheritance: - -extended\_metadata module -------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.extended_metadata - :members: - :undoc-members: - :show-inheritance: - -folder\_contents module ------------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -folders module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -forms module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -genomes module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -group\_roles module -------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -group\_users module -------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -groups module -------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -histories module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -history\_contents module ------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -item\_tags module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.item_tags - :members: - :undoc-members: - :show-inheritance: - -job\_files module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.job_files - :members: - :undoc-members: - :show-inheritance: - -jobs module ------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.jobs - :members: - :undoc-members: - :show-inheritance: - -lda\_datasets module --------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.lda_datasets - :members: - :undoc-members: - :show-inheritance: - -libraries module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -library\_contents module ------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -metrics module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.metrics - :members: - :undoc-members: - :show-inheritance: - -page\_revisions module ----------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.page_revisions - :members: - :undoc-members: - :show-inheritance: - -pages module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.pages - :members: - :undoc-members: - :show-inheritance: - -provenance module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.provenance - :members: - :undoc-members: - :show-inheritance: - -quotas module -------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -remote\_files module --------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.remote_files - :members: - :undoc-members: - :show-inheritance: - -request\_types module ---------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -requests module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -roles module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -samples module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -search module -------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.search - :members: - :undoc-members: - :show-inheritance: - -tool\_data module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.tool_data - :members: - :undoc-members: - :show-inheritance: - -tool\_dependencies module -------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tool_dependencies - :members: - :undoc-members: - :show-inheritance: - -tool\_shed\_repositories module -------------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories - :members: - :undoc-members: - :show-inheritance: - -tools module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -toolshed module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.toolshed - :members: - :undoc-members: - :show-inheritance: - -tours module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tours - :members: - :undoc-members: - :show-inheritance: - -users module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -visualizations module ---------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -webhooks module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.webhooks - :members: - :undoc-members: - :show-inheritance: - -workflows module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/api/ts_api.rst b/doc/source/api/ts_api.rst deleted file mode 100644 index c8257587a17b..000000000000 --- a/doc/source/api/ts_api.rst +++ /dev/null @@ -1,68 +0,0 @@ -Tool Shed API -============= - -authenticate module ------------------------------------------------------ - -.. automodule:: galaxy.webapps.tool_shed.api.authenticate - :members: - :undoc-members: - :show-inheritance: - -categories module ---------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.categories - :members: - :undoc-members: - :show-inheritance: - -configuration module ------------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.configuration - :members: - :undoc-members: - :show-inheritance: - -groups module ------------------------------------------------ - -.. automodule:: galaxy.webapps.tool_shed.api.groups - :members: - :undoc-members: - :show-inheritance: - -repositories module ------------------------------------------------------ - -.. automodule:: galaxy.webapps.tool_shed.api.repositories - :members: - :undoc-members: - :show-inheritance: - -repository\_revisions module --------------------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions - :members: - :undoc-members: - :show-inheritance: - -tools module ----------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.tools - :members: - :undoc-members: - :show-inheritance: - -users module ----------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.users - :members: - :undoc-members: - :show-inheritance: - -