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Progress on 19.01 release notes...
This commit is contained in:
John Chilton
+145
-246
@@ -11,74 +11,73 @@ Enhancements
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||||
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.. major_feature
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||||
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* Initial work on updating styles
|
||||
`Pull Request 6422`_
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* Unified webpack4
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||||
`Pull Request 6917`_
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||||
|
||||
.. feature
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||||
|
||||
* Feature/isa data type
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||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__).
|
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`Pull Request 5787`_
|
||||
* Cloud Authorization
|
||||
`Pull Request 5903`_
|
||||
* Adds Aequatus visualisation plugin
|
||||
(thanks to `@anilthanki <https://github.com/anilthanki>`__).
|
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`Pull Request 6484`_
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* Send data to cloud
|
||||
`Pull Request 6583`_
|
||||
* Add utility function to create history entries
|
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`Pull Request 6693`_
|
||||
* Give all model objects with an id a __repr__ that includes the id
|
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`Pull Request 6757`_
|
||||
* Allow API import/export of format 2 workflows.
|
||||
`Pull Request 6776`_
|
||||
* adding itp and mdp datatypes (for gromacs)
|
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(thanks to `@simonbray <https://github.com/simonbray>`__).
|
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`Pull Request 6812`_
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* Datatype pqr
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(thanks to `@jj-umn <https://github.com/jj-umn>`__).
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`Pull Request 6816`_
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* nmrML data type.
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(thanks to `@phnmnl <https://github.com/phnmnl>`__).
|
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`Pull Request 6903`_
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* Quick 'make all datasets private' implementation.
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||||
`Pull Request 6952`_
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||||
* add RMA6 data type (MEGAN6 read-match archive)
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(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
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`Pull Request 6962`_
|
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* datatype_fastg
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
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`Pull Request 6987`_
|
||||
* Added support for chaining dynamic destinations
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
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`Pull Request 7006`_
|
||||
* Add styled loader vue component
|
||||
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
|
||||
`Pull Request 7052`_
|
||||
* Add datatype for Mash Sketch files.
|
||||
(thanks to `@dfornika <https://github.com/dfornika>`__).
|
||||
`Pull Request 7087`_
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||||
* Configurable job/workflow handler assignment methods
|
||||
`Pull Request 7091`_
|
||||
* Use singularity build / exec with biocontainers
|
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7125`_
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* Perform job assignment using DB serialization techniques
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`Pull Request 7129`_
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|
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.. enhancement
|
||||
|
||||
* Adds Aequatus visualisation plugin
|
||||
(thanks to `@anilthanki <https://github.com/anilthanki>`__).
|
||||
`Pull Request 6484`_
|
||||
* Integrate framework code for interfacing with cloud authorization providers.
|
||||
`Pull Request 5903`_
|
||||
* Added support for chaining dynamic destinations
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 7006`_
|
||||
* Upgrade web client building to use `webpack <https://webpack.js.org/>`__ 4
|
||||
`Pull Request 6917`_
|
||||
* Implement 'make all datasets private' functionality.
|
||||
`Pull Request 6952`_
|
||||
* Add datatype sniff button to edit dataset attributes page
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 7018`_
|
||||
* Overhaul handler assignment methods.
|
||||
`Pull Request 7129`_, `Pull Request 7091`_
|
||||
* Add tool for sending dataset to the cloud.
|
||||
`Pull Request 6583`_
|
||||
* Infrastructure/API Support for composite uploads/downloads.
|
||||
`Pull Request 6844`_
|
||||
* Improvements to tool testing including aloowing tests without admin API keys.
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7160`_,
|
||||
`Pull Request 7199`_, `Pull Request 7167 <https://github.com/galaxyproject/galaxy/pulls/7167>`__
|
||||
* Add ISA-TAB datatype
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__).
|
||||
`Pull Request 5787`_
|
||||
* Adding itp and mdp datatypes (for gromacs)
|
||||
(thanks to `@simonbray <https://github.com/simonbray>`__).
|
||||
`Pull Request 6812`_
|
||||
* Add pqr datatype
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 6816`_
|
||||
* Add nmrML datatype
|
||||
(thanks to `@phnmnl <https://github.com/phnmnl>`__).
|
||||
`Pull Request 6903`_
|
||||
* Add RMA6 datatype (MEGAN6 read-match archive)
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6962`_
|
||||
* Add fastg datatype
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 6987`_
|
||||
* Add datatype for Mash Sketch files.
|
||||
(thanks to `@dfornika <https://github.com/dfornika>`__).
|
||||
`Pull Request 7087`_
|
||||
* Add JavaScript client library utility function to create history entries.
|
||||
`Pull Request 6693`_
|
||||
* Give all model objects with an id a __repr__ that includes the id
|
||||
`Pull Request 6757`_
|
||||
* Add styled loader vue component
|
||||
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
|
||||
`Pull Request 7052`_
|
||||
* Restore the ability to track jobs for a WF invocation step.
|
||||
`Pull Request 6559`_
|
||||
* improved grouping tool
|
||||
* Improvements to the grouping tool
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6577`_
|
||||
* Trim whitespace from data manager conf paths
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 6682`_
|
||||
* Deprecate `size` attribute of `<param/>` and remove it from tools
|
||||
* Track workflow step input definitions in our model.
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||||
`Pull Request 6850`_, `Pull Request 7103`_
|
||||
* Deprecate `size` attribute of `<param/>` and remove it from tools
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6684`_
|
||||
* Create container_resolvers_conf.xml.sample
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||||
@@ -86,48 +85,32 @@ Enhancements
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||||
`Pull Request 6700`_
|
||||
* Update to latest galaxy-lib.
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||||
`Pull Request 6709`_
|
||||
* Updates to OIDC backends default config
|
||||
* Updates to OIDC backends default config.
|
||||
`Pull Request 6727`_
|
||||
* Vue rewrite of admin data manager (local data) in steps
|
||||
(thanks to `@scrathat <https://github.com/scrathat>`__).
|
||||
`Pull Request 6729`_
|
||||
* Look up collection_type if collection_type_source is set
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6732`_
|
||||
* pgcleanup.py enhancements
|
||||
`Pull Request 6736`_
|
||||
* Small local testing improvements
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6738`_
|
||||
* Fill in needed state defaults when importing manually crafted workflows.
|
||||
`Pull Request 6746`_
|
||||
* Add backrefs to mapped objects pointing at Dataset
|
||||
* Add backrefs to mapped objects pointing at `Dataset`.
|
||||
`Pull Request 6754`_
|
||||
* Fixes for the upload row template
|
||||
* Fixes for the upload row template.
|
||||
`Pull Request 6758`_
|
||||
* Disable file name text field after upload
|
||||
* Disable file name text field after upload.
|
||||
`Pull Request 6762`_
|
||||
* Remove empty log messages
|
||||
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
|
||||
* Remove empty log messages.
|
||||
`Pull Request 6763`_
|
||||
* Display input and output tool labels in the workflow editor
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6770`_
|
||||
* Release issue scaffold tweaks
|
||||
* Release issue scaffold tweaks.
|
||||
`Pull Request 6778`_
|
||||
* Warn job runner plugin writers not to emulate condor.py.
|
||||
* Warn job runner plugin writers not to emulate `condor.py`.
|
||||
`Pull Request 6783`_
|
||||
* Add PB and EB to util.size_to_bytes
|
||||
* Add `PB` and `EB` to `util.size_to_bytes`
|
||||
`Pull Request 6786`_
|
||||
* CLI plugin for LSF
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 6788`_
|
||||
* Add a pgcleanup action to purge HDAs of purged histories
|
||||
* Add a `pgcleanup.py` action to purge HDAs of purged histories.
|
||||
`Pull Request 6801`_
|
||||
* Support for Enhancements to gxformat2.
|
||||
`Pull Request 6807`_
|
||||
* Support for Enhancements to gxformat2 (part II)
|
||||
`Pull Request 6811`_
|
||||
* Various `pgcleanup.py` enhancements.
|
||||
`Pull Request 6736`_, `Pull Request 6877`_
|
||||
* Fix typos on "reserve_memory" / "reserve_cpu"
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 6817`_
|
||||
@@ -137,50 +120,39 @@ Enhancements
|
||||
* Add docs about running jobs in containers
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 6820`_
|
||||
* Remove `trans` from OIDC-related types
|
||||
* Remove `trans` from OIDC-related types.
|
||||
`Pull Request 6826`_
|
||||
* Clarify code used in output <filter> tags
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 6827`_
|
||||
* Convert user_is_admin and user_can_do_run_as to properties
|
||||
* Convert `user_is_admin` and `user_can_do_run_as` to properties.
|
||||
`Pull Request 6835`_
|
||||
* Don't create jobs for inactive users
|
||||
* Don't create jobs for inactive users.
|
||||
`Pull Request 6837`_
|
||||
* Replace deprecated assertEquals() method
|
||||
* Replace deprecated `assertEquals()` method
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6841`_
|
||||
* Infrastructure/API Support for Composite Uploads/Downloads
|
||||
`Pull Request 6844`_
|
||||
* Updated GIE docs
|
||||
* Improvements to GIE docs
|
||||
(thanks to `@thobalose <https://github.com/thobalose>`__).
|
||||
`Pull Request 6846`_
|
||||
* Indicate language in client docs to enable syntax highlighting.
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
* Indicate language in client docs to enable syntax highlighting..
|
||||
`Pull Request 6848`_
|
||||
* Track workflow step input definitions in our model.
|
||||
`Pull Request 6850`_
|
||||
* Fix panel header margins in history and tool panel
|
||||
`Pull Request 6854`_
|
||||
* Small fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6861`_
|
||||
* Use card-styles for display applications, job manager and other admin views
|
||||
`Pull Request 6868`_
|
||||
* Datatype upload integration test and fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6869`_
|
||||
* Refactor pgcleanup.py and add new routines
|
||||
`Pull Request 6877`_
|
||||
* Use small button for editable text fields in history annotation
|
||||
`Pull Request 6878`_
|
||||
* Improve k8s job error handling
|
||||
(thanks to `@ilveroluca <https://github.com/ilveroluca>`__).
|
||||
`Pull Request 6886`_
|
||||
* Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9
|
||||
* Fixes and updates to the Neo4j GIE
|
||||
(thanks to `@thobalose <https://github.com/thobalose>`__).
|
||||
`Pull Request 6897`_
|
||||
* Fix style for legacy toolshed selection page
|
||||
`Pull Request 6910`_
|
||||
* Allow ``remove_value`` filter on data tables
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6914`_
|
||||
@@ -188,28 +160,25 @@ Enhancements
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6921`_
|
||||
* Be more precise with the job runner worker thread join timeout and improve
|
||||
documentation
|
||||
documentation.
|
||||
`Pull Request 6924`_
|
||||
* Add workflow step parameters to workflow editor (try 3)
|
||||
`Pull Request 6925`_
|
||||
* Allocate more memory for selenium Python 3 client.
|
||||
`Pull Request 6927`_
|
||||
* Selenium test enhancements and fixes.
|
||||
`Pull Request 6927`_, `Pull Request 6982`_
|
||||
* Small testing tweaks from the CWL branch.
|
||||
`Pull Request 6929`_
|
||||
* tests need to count data sets and collections
|
||||
* Tests need to count data sets and collections
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6931`_
|
||||
* Eliminate some mutable defaults in populators.py.
|
||||
* Eliminate some mutable defaults in `populators.py`.
|
||||
`Pull Request 6933`_
|
||||
* Default shed tool installation to database/shed_tools
|
||||
* Default shed tool installation to `database/shed_tools`.
|
||||
`Pull Request 6937`_
|
||||
* Collection builder: add option to strip url prefix from pair names
|
||||
* Add option to strip url prefix from pair names to collection builder
|
||||
(thanks to `@shiltemann <https://github.com/shiltemann>`__).
|
||||
`Pull Request 6943`_
|
||||
* Small API Workflow Test Improvements.
|
||||
* Small API workflow test improvements.
|
||||
`Pull Request 6954`_
|
||||
* Switch from PhantomJS to Chrome Headless for unit tests
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Switch from PhantomJS to Chrome Headless for unit tests.
|
||||
`Pull Request 6959`_
|
||||
* Added a metadata element to the biom1 datatype
|
||||
(thanks to `@Slugger70 <https://github.com/Slugger70>`__).
|
||||
@@ -217,81 +186,67 @@ Enhancements
|
||||
* Update locale.js
|
||||
(thanks to `@istevenshen <https://github.com/istevenshen>`__).
|
||||
`Pull Request 6974`_
|
||||
* Use virtualenv when conda is on PATH
|
||||
* Use `virtualenv` when `conda` is on `PATH`
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6975`_
|
||||
* changed exit code and regex parsing
|
||||
* Improvements to exit code and regex parsing
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6977`_
|
||||
* optimize images with optipng
|
||||
* Optimize images with optipng
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 6980`_
|
||||
* List tags as attribute of TestCollection
|
||||
* Fix tool XSD to list tags as attribute of `TestCollection`
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6983`_
|
||||
* Apply new styling theme to workflow editor
|
||||
`Pull Request 6985`_
|
||||
* Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6989`_
|
||||
* Don't mount external /tmp for tests.
|
||||
* Don't mount external `/tmp` for tests.
|
||||
`Pull Request 6990`_
|
||||
* Upgrade nodeenv's nodejs to 10.13.0 LTS
|
||||
* Upgrade nodeenv's nodejs to 10.13.0 LTS.
|
||||
`Pull Request 6991`_
|
||||
* Fix broken links on Job Configuration page (documentation)
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
* Fix broken links on Job Configuration page.
|
||||
`Pull Request 6992`_
|
||||
* Allow rules module override and refactor submodule imports
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 6993`_
|
||||
* external_runner: load json template first
|
||||
* Fix external_runner to load json template first
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6995`_
|
||||
* drmaa: soft catch of external runner fails
|
||||
* CLI plugin for `LSF <https://en.wikipedia.org/wiki/Platform_LSF>`__
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__), `Pull Request 7007`_
|
||||
`Pull Request 6788`_
|
||||
* A new UNIVA extension to the DRMAA job runner
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7004`_, `Pull Request 7161`_
|
||||
* DRMAA fix to soft catch of external runner fails
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 6997`_
|
||||
* A new runner for DRMAA (currently UNIVA)
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7004`_
|
||||
* Replace global Galaxy references with galaxy singleton accessor/setter
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Replace global Galaxy references with galaxy singleton accessor/setter.
|
||||
`Pull Request 7005`_
|
||||
* Workflow test case - test marking inputs as outputs.
|
||||
`Pull Request 7016`_
|
||||
* Fix login and registration form appearance
|
||||
`Pull Request 7017`_
|
||||
* Add datatype sniff button to edit dataset attributes page
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 7018`_
|
||||
* File-based Workflow Editor
|
||||
`Pull Request 7019`_
|
||||
* Expose published workflows through API
|
||||
(thanks to `@frederikcoppens <https://github.com/frederikcoppens>`__).
|
||||
`Pull Request 7020`_
|
||||
* Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7023`_
|
||||
* Provide element_identifier attribute in DatsetCollectionWrapper
|
||||
* Fix `element_identifier` access
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7031`_
|
||||
* Avoid replacing data-referenced input values with default values
|
||||
`Pull Request 7043`_
|
||||
* doc: updated error parsing docs
|
||||
* Udate error parsing docs
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7049`_
|
||||
* Added resubmit handlers on Pulsar connection failures
|
||||
* Add resubmit handlers on Pulsar connection failures
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 7053`_
|
||||
* add new item to the help menu
|
||||
* Add new "Help" item to the help menu.
|
||||
`Pull Request 7054`_
|
||||
* Eliminate dependency on make for automatic client build
|
||||
* Eliminate dependency on make for automatic client build.
|
||||
`Pull Request 7060`_
|
||||
* Make tags more colourful
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7072`_
|
||||
* Follow-up on `#7070 <https://github.com/galaxyproject/galaxy/issues/7070>`__
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7079`_
|
||||
* Remove legacy job handling hacks.
|
||||
`Pull Request 7082`_
|
||||
* De-couple objectstore abstraction from XML.
|
||||
@@ -303,18 +258,17 @@ Enhancements
|
||||
* Run singularity in silent mode
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7104`_
|
||||
* Eliminate unused code block in output_collect.
|
||||
* Eliminate unused code block in `output_collect`.
|
||||
`Pull Request 7109`_
|
||||
* Add to_dict() to ObjectStores.
|
||||
* Add `to_dict()` to ObjectStores.
|
||||
`Pull Request 7110`_
|
||||
* Enable tagging+annotation of jobs regardless of state
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
* Enable tagginga and annotation of jobs regardless of state.
|
||||
`Pull Request 7115`_
|
||||
* Remove unused __collected_datasets__ from tool hook dict.
|
||||
* Remove unused `__collected_datasets__` from tool hook dict.
|
||||
`Pull Request 7123`_
|
||||
* Adds a vue component to display tool errors in the admin panel
|
||||
* Add a vue component to display tool errors in the admin panel.
|
||||
`Pull Request 7124`_
|
||||
* Update help text as per suggestion from CWunder
|
||||
* Update help text in `filter_from_file` tool.
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 7127`_
|
||||
* Remove unneeded session flushes and adds when discovering outputs.
|
||||
@@ -322,61 +276,32 @@ Enhancements
|
||||
* Drop tools without installable dependencies
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7136`_
|
||||
* Small de-duplication cleanups to galaxy.jobs
|
||||
* Small de-duplication cleanups to `galaxy.jobs`
|
||||
`Pull Request 7155`_
|
||||
* Unprivileged remote tool tests
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7160`_
|
||||
* doc: added missing docs for new UNIVA runner
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7161`_
|
||||
* Add error listener for input elements
|
||||
`Pull Request 7183`_
|
||||
* Backport `#7167 <https://github.com/galaxyproject/galaxy/issues/7167>`__ -
|
||||
interactor improvements
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7199`_
|
||||
* Properly deal with missing tools in workflows
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7227`_
|
||||
* Backport `#7183 <https://github.com/galaxyproject/galaxy/issues/7183>`__
|
||||
input element listener
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7229`_
|
||||
* Stop tool migrations checking by default...
|
||||
* Improve tool form client to add error listener for input elements.
|
||||
`Pull Request 7183`_, `Pull Request 7229`_
|
||||
* Stop tool migrations checking by default (was broken in some cases).
|
||||
`Pull Request 7275`_
|
||||
|
||||
.. small_enhancement
|
||||
|
||||
* Remove legacy tool form styles from structure history view and admin tables
|
||||
`Pull Request 6790`_
|
||||
* Replace trans with session and request in psa Storage
|
||||
* Replace `trans` with `session` and `request` in PSA Storage.
|
||||
`Pull Request 6838`_
|
||||
* Share ssh key generation across tests
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6865`_
|
||||
* Specify POST and GET actions for cloudauthz API actions
|
||||
* Specify `POST` and `GET` actions for cloudauthz API actions.
|
||||
`Pull Request 6876`_
|
||||
* prevent sanitized history names being saved in database
|
||||
* Prevent sanitized history names being saved in database.
|
||||
`Pull Request 6898`_
|
||||
* Refactor cloud "Upload" > "Get"
|
||||
* Rework language in cloud data fetch tool from "Upload" to "Get"
|
||||
`Pull Request 6899`_
|
||||
* Refactor collection mapping workflows toward independence from tools.
|
||||
`Pull Request 6911`_
|
||||
* Refactor workflow editor styles and move from mako to css
|
||||
`Pull Request 6967`_
|
||||
* Normalized jquery bundle
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Normalized jquery bundle.
|
||||
`Pull Request 6970`_
|
||||
* Replaced jStorage with store
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Replaced jStorage with store.
|
||||
`Pull Request 6994`_
|
||||
* Fix handling of forgotten LSF jobs in cli
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 7007`_
|
||||
* Remove ``sudo: false`` from .travis.yml, it will stop being supported soon
|
||||
`Pull Request 7035`_
|
||||
* Fixes state-change animations causing 'block' display
|
||||
* Fixes state-change animations causing 'block' display.
|
||||
`Pull Request 7122`_
|
||||
|
||||
|
||||
@@ -388,10 +313,10 @@ Fixes
|
||||
|
||||
.. bug
|
||||
|
||||
* Allow schema to validate
|
||||
* Fixes to allow config schema to validate
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 5919`_
|
||||
* Patch update.sh to address dependency update issues on a macOS.
|
||||
* Patch `update.sh` to address dependency update issues on a macOS.
|
||||
`Pull Request 6694`_
|
||||
* Fix wrong version being returned if requested version doesn't exist
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
@@ -414,27 +339,20 @@ Fixes
|
||||
`Pull Request 6843`_
|
||||
* Revert selective metadata flushing - breaks multiple uploads/outputs.
|
||||
`Pull Request 6858`_
|
||||
* Use fluid container for slider to get full width
|
||||
`Pull Request 6870`_
|
||||
* prevent double sanitizing history name when renaming
|
||||
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
|
||||
`Pull Request 6871`_
|
||||
* Fix rule editor element alignment
|
||||
* Fix rule editor element alignment.
|
||||
`Pull Request 6874`_
|
||||
* Fix styleguide; change permissions on jstree.scss.
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
`Pull Request 6879`_
|
||||
* Fix selenium test selectors for alert messages
|
||||
`Pull Request 6881`_
|
||||
* Username filtering for published workflows
|
||||
* Fix username filtering for published workflows
|
||||
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
|
||||
`Pull Request 6882`_
|
||||
* Align toolshed makos used in the admin panel, fix slider height
|
||||
* Align toolshed makos used in the admin panel, fix slider height.
|
||||
`Pull Request 6883`_
|
||||
* Improve resilience on handling sharing attributes
|
||||
* Improve resilience on handling sharing attributes.
|
||||
`Pull Request 6884`_
|
||||
* Fixes for built-in Scatterplot plugin
|
||||
`Pull Request 6905`_
|
||||
* Update Bug Reports docs to use YAML syntax
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6909`_
|
||||
@@ -469,9 +387,6 @@ Fixes
|
||||
* Fix traceback when starting under Python3 with ``galaxy.ini``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 6978`_
|
||||
* Update test/selenium_tests/test_library_contents.py
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
`Pull Request 6982`_
|
||||
* Fix charts entrypoint for compatibility with newer chunk changes.
|
||||
`Pull Request 6984`_
|
||||
* reclaim ownership for failed jobs
|
||||
@@ -513,14 +428,13 @@ Fixes
|
||||
* Update ``galaxy.yml.sample`` and ``galaxy_options.rst``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7064`_
|
||||
* Fix link to requirements.txt
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
* Fix link to requirements.txt.
|
||||
`Pull Request 7065`_
|
||||
* Improved parsing of sizes (bytes)
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7067`_
|
||||
* downgrade bdbag, 1.5.0 requires python:>=2.7.9
|
||||
`Pull Request 7070`_
|
||||
* Downgrade bdbag - 1.5.0 requires python:>=2.7.9
|
||||
`Pull Request 7070`_, `Pull Request 7079`_
|
||||
* Fix process key
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7071`_
|
||||
@@ -532,9 +446,6 @@ Fixes
|
||||
* Fix toolshed repository error display
|
||||
(thanks to `@jvanbraekel <https://github.com/jvanbraekel>`__).
|
||||
`Pull Request 7080`_
|
||||
* Fix hashing, AND was not the right operation
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7081`_
|
||||
* Fix via refactor set_metadata so more output metadata pruned properly.
|
||||
`Pull Request 7084`_
|
||||
* Replace `credentials` with `authz_id`
|
||||
@@ -546,13 +457,11 @@ Fixes
|
||||
`Pull Request 7096`_
|
||||
* Client readme updates.
|
||||
`Pull Request 7102`_
|
||||
* Fix migration 0146 column selection on downgrade
|
||||
`Pull Request 7103`_
|
||||
* Don't write outputs to object store twice.
|
||||
`Pull Request 7111`_
|
||||
* Fix `make client-watch` extra error message.
|
||||
`Pull Request 7113`_
|
||||
* Properly escape history names in scratchbook titles
|
||||
* Properly escape history names in scratchbook titles.
|
||||
`Pull Request 7114`_
|
||||
* Fix activation of ``_galaxy_`` conda env
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
@@ -561,27 +470,20 @@ Fixes
|
||||
`Pull Request 7120`_
|
||||
* Fixes and tests for collecting extra files for discovered datasets.
|
||||
`Pull Request 7131`_
|
||||
* Address CORS issue in toolshed iframe handlers
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Address CORS issue in toolshed iframe handlers.
|
||||
`Pull Request 7135`_
|
||||
* Use regular js-event handling instead of jquery for uploader
|
||||
`Pull Request 7145`_
|
||||
* Fixes toolshed and reports styling that was previously applied at the…
|
||||
`Pull Request 7146`_
|
||||
* Correct code error in 'build job runner' tutorial
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
* Correct code error in 'build job runner' tutorial.
|
||||
`Pull Request 7148`_
|
||||
* added store library to exported libs in bundleEntries
|
||||
(thanks to `@Nerdinacan <https://github.com/Nerdinacan>`__).
|
||||
* Added store library to exported libs in bundleEntries.
|
||||
`Pull Request 7149`_
|
||||
* Follow-up on handling connectable and collapsible parameters in workflows
|
||||
`Pull Request 7150`_
|
||||
* Fix dataset discovery for YAML/dictified tools.
|
||||
`Pull Request 7152`_
|
||||
* Fix for parsing collection outputs for YAML/dictified tools.
|
||||
`Pull Request 7153`_
|
||||
* Do not use default values for runtime values in workflow execution form
|
||||
`Pull Request 7157`_
|
||||
* Lower provider name
|
||||
(thanks to `@machristie <https://github.com/machristie>`__).
|
||||
`Pull Request 7166`_
|
||||
@@ -599,16 +501,16 @@ Fixes
|
||||
`Pull Request 7174`_
|
||||
* Prevent XSS on toolshed when browsing repo changeset
|
||||
`Pull Request 7180`_
|
||||
* Fix hda accessibility check in Page's renderForSave name fetching
|
||||
* Fix HDA accessibility check in Page's renderForSave name fetching
|
||||
`Pull Request 7181`_
|
||||
* Fix workflow parameter test case?
|
||||
* Fix for workflow parameter test case.
|
||||
`Pull Request 7188`_
|
||||
* fix library dataset permission API
|
||||
* Fixes for library dataset permission API.
|
||||
`Pull Request 7190`_
|
||||
* Properly document handler assignment method configuration and fix logging
|
||||
configuration docs
|
||||
configuration docs.
|
||||
`Pull Request 7191`_
|
||||
* Re-enable script staging
|
||||
* Re-enable script staging.
|
||||
`Pull Request 7196`_
|
||||
* Fix error in view_tool_metadata
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
@@ -616,7 +518,7 @@ Fixes
|
||||
* Data library: fix tag_using_filenames not properly converted to bool
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 7204`_
|
||||
* Swap to normal event bindings for multipanel drag/drop.
|
||||
* Fix GUI wap to normal event bindings for multipanel drag/drop.
|
||||
`Pull Request 7218`_
|
||||
* Fix displaying tool help images on python 3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
@@ -627,24 +529,21 @@ Fixes
|
||||
* Interval datatype fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7237`_
|
||||
* strip() text when parsing xml
|
||||
* `strip()` text when parsing xml
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7252`_
|
||||
* Fix install operation in installed_repository_grid
|
||||
* Fix install operation in `installed_repository_grid`
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7253`_
|
||||
* Not all workflow outputs have a UUID
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7258`_
|
||||
* Update sqlalchemy-migrate requirement to 0.12.0
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7265`_
|
||||
* Fix _.escape typo in toolshed group detail view
|
||||
* Fix `_.escape` typo in toolshed group detail view.
|
||||
`Pull Request 7267`_
|
||||
* Fix installing tools via tool_id
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7277`_
|
||||
* Remove errant space in intermine_simple_display.loc.sample
|
||||
* Remove errant space in `intermine_simple_display.loc.sample`.
|
||||
`Pull Request 7298`_
|
||||
|
||||
.. github_links
|
||||
|
||||
@@ -8,14 +8,44 @@ January 2019 Galaxy Release (v 19.01)
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
**Feature1**
|
||||
Feature description.
|
||||
**Revised UI Style**
|
||||
The Galaxy stylesheet has been substantially reworked resulting in the largest visual
|
||||
refresh to Galaxy in years.
|
||||
|
||||
**Feature2**
|
||||
Feature description.
|
||||
`Pull Request 6422`_, `Pull Request 6910`_, `Pull Request 6881`_,
|
||||
`Pull Request 6967`_, `Pull Request 6790`_, `Pull Request 6868`_,
|
||||
`Pull Request 7017`_, `Pull Request 6985`_, `Pull Request 6870`_,
|
||||
`Pull Request 6905`_
|
||||
|
||||
**More Colorful Tags**
|
||||
Use consistently hashed randomized colors for history dataset name tags to allow increase visual
|
||||
distinction between tags making it easier to track data flow in complex histories.
|
||||
Thanks to `@erasche <https://github.com/erasche>`__.
|
||||
`Pull Request 7072`_, `Pull Request 7081`_
|
||||
|
||||
**Extensive Workflow Enhancements (continued)**
|
||||
18.09 featured a bunch of important and diverse fixes and enhancements to workflows on
|
||||
both the frontend and backend. That progress continues in 19.01.
|
||||
|
||||
The workflow editor now features explicit step parameter nodes for non-file data (integers,
|
||||
strings, booleans, etc) and the ability to connect these to all tool inputs - not just files
|
||||
(`Pull Request 6925`_, `Pull Request 7150`_).
|
||||
The YAML-based Galaxy Format 2 workflow language is now included in Galaxy as a beta option
|
||||
and allows import and export of human readable workflows (`Pull Request 6776`_, `Pull Request 6811`_,
|
||||
`Pull Request 6807`_, `Pull Request 6746`_) as well as extensions to allow Galaxy
|
||||
to serve as a file editor for such workflows (`Pull Request 7019`_). The workflow editor features
|
||||
more helpful labels on inputs and outputs (`Pull Request 6770`_) and important fixes including
|
||||
logic for connecting collections (`Pull Request 6732`_) and dealing with missing tools
|
||||
(`Pull Request 7227`_, `Pull Request 7258`_). The workflow run form now deals with default
|
||||
values more correctly (`Pull Request 7157`_).
|
||||
|
||||
**Support for Singularity Biocontainers**
|
||||
Galaxy can now be configured to fetch `Biocontainers <https://biocontainers.pro/>`__ automatically
|
||||
for `Singularity <https://singularity.lbl.gov/>`__ enabled job destinations. Previously this
|
||||
would happen automatically for Docker containers but not Singularity containers. Thanks to
|
||||
`@mvdbeek <https://github.com/mvdbeek>`__.
|
||||
`Pull Request 7125`_
|
||||
|
||||
**Feature3**
|
||||
Feature description.
|
||||
|
||||
Get Galaxy
|
||||
==========
|
||||
|
||||
@@ -4,6 +4,7 @@ Releases
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
19.01_announce
|
||||
18.09_announce
|
||||
18.05_announce
|
||||
18.01_announce
|
||||
|
||||
Reference in New Issue
Block a user