New upstream version 2.3.1

*.iws

out

web-app/jbrowse

jbrowse-github

jbrowse-download

jbrowse

log4j2.json

log4j2-test.json

tmp

package-lock.json

jb_run.js

jb_setup.js

.DS_Store

yarn.lock

bin

    "browser": true,

    "dojo": true,

    "evil": true,     // allow eval

    "esversion": 6,

    "laxbreak": true,

    "laxcomma": true,

    "loopfunc": true,

    "funcscope": true,

    "maxlen": 10000,

    "indent": 4,

    "shadow": true,

    "maxerr": 250,

    "sub": true,

    "predef": [ "require", "define", "SockJS", "Stomp", "bbop", "amigo" ],

    "maxcomplexity": 40,

    "indent": 2,

    "undef": true,

    "trailing": true,

    "devel": true

sudo: required

dist: trusty

group: deprecated

language: groovy

language: java

node_js:

  - "iojs"

    - mysql-server-5.6

    - mysql-client-core-5.6

    - mysql-client-5.6

    - oracle-java8-installer

services:

- postgresql

before_script:

  - node -v

  - npm -v

  - npm install -g yarn

  - "echo $JAVA_OPTS"

  - "export JAVA_OPTS='-Xmx2048m'"

  - "echo $JAVA_OPTS"

    - $HOME/.gradle/caches/

    - $HOME/.gradle/wrapper/

script:

  - travis_wait ./gradlew handleJBrowse copy-resources gwtc && ./grailsw refresh-dependencies --stacktrace && ./grailsw test-app -coverage -xml --stacktrace

  - node web-app/jbrowse/src/dojo/dojo.js load=build --require "web-app/jbrowse/src/JBrowse/init.js" --profile "web-app/jbrowse/plugins/WebApollo/js/WebApollo"

  - travis_wait ./gradlew installJBrowseWebOnly gwtc installJBrowseTools && ./grailsw refresh-dependencies --stacktrace && ./grailsw test-app -coverage -xml --stacktrace

  #- node web-app/jbrowse/src/dojo/dojo.js load=build --require "web-app/jbrowse/src/JBrowse/init.js" --profile "web-app/jbrowse/plugins/WebApollo/js/WebApollo"

  - jshint client/apollo/js

after_success:

  - ./grailsw coveralls

## 2.3.1

Bug Fixes

- Fixed issue when dragging features to resize was not providing an indicator box [1988](https://github.com/GMOD/Apollo/pull/1988)

- Fixed issue when sequence alterations were not rendering the full height of the sequence track [2049](https://github.com/GMOD/Apollo/pull/2049)

- Making organisms obsolete should remove associated permissions [2043](https://github.com/GMOD/Apollo/pull/2043)

- User-created features taken from split reads should create features with introns [2036](https://github.com/GMOD/Apollo/pull/2036)

- Should indicate split reads properly in evidence [2034](https://github.com/GMOD/Apollo/pull/2034)[2054](https://github.com/GMOD/Apollo/pull/2054)

- Temporary files not removed during export of GFF3 or other file types [1966](https://github.com/GMOD/Apollo/pull/1966)

- Fixed issue where you could not alter an isoform after deleting a gene name [1961](https://github.com/GMOD/Apollo/pull/1961)

- Fixed some minor issues associated with sequence alterations [1497](https://github.com/GMOD/Apollo/pull/1497)

- Multiple owners tagged on GFF3 export [29](https://github.com/GMOD/Apollo/pull/29)

- Setting gene description puts UcA into a bad state [2056](https://github.com/GMOD/Apollo/issues/2056)

- Fixes plugin inclusion error by reverting prior fix [2055](https://github.com/GMOD/Apollo/issues/2055)

Minor Features

- Allowed duplication of organism from the Organism Panel [1968](https://github.com/GMOD/Apollo/pull/1968)

- Allows making an organism obsolete [1967](https://github.com/GMOD/Apollo/pull/1967)

- Create a filter and flag for inactive users [1937](https://github.com/GMOD/Apollo/pull/1937)

- Allowed deletion of feature from the Sequence and Annotator Panels [2040](https://github.com/GMOD/Apollo/pull/2040)

- Allow export of orig_id as an optional attribute [2002](https://github.com/GMOD/Apollo/pull/2002)

## 2.3.0

Features

- Moved to JBrowse 1.16.2 by default [1988](https://github.com/GMOD/Apollo/pull/1988), which also fixed track styling issues [#1942](https://github.com/GMOD/Apollo/pull/1942)

- Moved to Neat Features as the default  [2021](https://github.com/GMOD/Apollo/pull/2021)

- Improved terminator annoation [1997](https://github.com/GMOD/Apollo/pull/1997)

Bug Fixes

- JBrowse bin directory not properly being installed [2017](https://github.com/GMOD/Apollo/pull/2017)

- Workaround for declaring plugins in trackList.json via a JBrowse bug [2014](https://github.com/GMOD/Apollo/pull/2014)

- Fixed problems with creating variant annotations with soft masking [2009](https://github.com/GMOD/Apollo/pull/2009)

- Fixed bugs in reporting code [2008](https://github.com/GMOD/Apollo/pull/2008)

- Fixed several build bugs #1996, #1994, #1993

- Fixed bug where deletions, insertions, and substitutions were not editable in the side-bpanel [#1923](https://github.com/GMOD/Apollo/pull/2008)

## 2.2.0

Features

- Move to JBrowse 1.15 and webpack (smaller file size) [1928](https://github.com/GMOD/Apollo/pull/1928),[1986](https://github.com/GMOD/Apollo/pull/1986)

- Add ability to annotate terminators [1954](https://github.com/GMOD/Apollo/issues/1954)

- Added a script for removing all features from a sequence [1935](https://github.com/GMOD/Apollo/pull/1935)

- Allowed removal of ALL user permissions (instead of deleting) to inactivate [777](https://github.com/GMOD/Apollo/issues/777)

- Clarified edge-detection [9](https://github.com/GMOD/Apollo/issues/9)

Bug Fixes

- Fixed bug where showing annotations by users was lost [1952](https://github.com/GMOD/Apollo/issues/1952)

- Fixed by where lowercase reference sequence does not translate correctly in 'Get Sequence' output  [1944](https://github.com/GMOD/Apollo/issues/1944)

- Fixed problem where removing an available status type caused an error [1909](https://github.com/GMOD/Apollo/issues/1909)

- Fixed bug where a logged-in link location was ignored when passed in by copying the logged in URL [1982](https://github.com/GMOD/Apollo/issues/1982)

- Fixed bug where insertion and deletion details did not come up in the Annotator Panel when clicked [1984](https://github.com/GMOD/Apollo/issues/1984)

## 2.1.0

Features

- Added ability to annotate a variant from VCF evidence tracks [1892](https://github.com/GMOD/Apollo/pull/1892)

- Allow forced assignment of transcript to a gene [#1851](https://github.com/GMOD/Apollo/pull/1851)

- Added proper Instructor and Organism Admin permission level [#1178](https://github.com/GMOD/Apollo/issues/1178)

- Indicate start / stop codons with color [#1852](https://github.com/GMOD/Apollo/pull/1852)

- Set the default biotype on track [#1861](https://github.com/GMOD/Apollo/issues/1861)

- Focus annotator panel on the current transcript [#1846](https://github.com/GMOD/Apollo/issues/1846)

- Allow fetching variant data from evidence tracks via web service [#1867](https://github.com/GMOD/Apollo/pull/1867)

- Recognized dot notation from JBrowse / Apollo [#1839](https://github.com/GMOD/Apollo/issues/1839)

- Allow setting default native track to true [#1848](https://github.com/GMOD/Apollo/pull/1848)

- Provide [sample data](https://github.com/GMOD/Apollo/blob/master/docs/Apollo2Build.md#adding-sample-data) (and links in doc)[#1817](https://github.com/GMOD/Apollo/pull/1817) 

Bug Fixes

- Fixed descriptor leak when loading bulk loading GFF3 [#1187](https://github.com/GMOD/Apollo/pull/1887)

- Fixed adding ability to create sequence alterations of uneven length [#1883](https://github.com/GMOD/Apollo/issues/1883)

- Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case [#1879](https://github.com/GMOD/Apollo/issues/1879)

- Prevents setting bad translation starts and ends [#1838](https://github.com/GMOD/Apollo/issues/1838)

- Improved performance of cache deletion code [#1824](https://github.com/GMOD/Apollo/pull/1824)

- Allow more special characters in the password [#1859](https://github.com/GMOD/Apollo/issues/1859)

- Fixed bug with 'Update Membership' and 'Update Group Admin' call in web services [#1891](https://github.com/GMOD/Apollo/issues/1891)

- Fixed bug with 'Update Organism Permission' call in web services [#1885](https://github.com/GMOD/Apollo/issues/1885)

- In some cases when the name store is not properly configured, the location is not remembered [#1895](https://github.com/GMOD/Apollo/issues/1895)

## 2.0.8

- Added the ability to annotate from high performance [Alignments2](http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignments2) BAM reads [#1789](https://github.com/GMOD/Apollo/pull/1789)

- Added support for indexed FASTA to be used as reference sequence. [#1791](https://github.com/GMOD/Apollo/pull/1791)

- Added sequence API [#1799](https://github.com/GMOD/Apollo/pull/1799)

- Added ability to remove gridlines from the view menu in both light and dark themes [#1547](https://github.com/GMOD/Apollo/pull/1547)

Bugfixes 

Bug Fixes 

- Fixed bug when flipping strand fails to flip the strand of the owning gene [#1769](https://github.com/GMOD/Apollo/issues/1769)

- Fixes to track services to allow remote jbrowse tracks and jsonz [#1767](https://github.com/GMOD/Apollo/issues/1767)

- Removal of bower in favor of npm to install JBrowse. [#1691](https://github.com/GMOD/Apollo/pull/1691)

- Added documentation for a Web Service wrapper for Python, PHP, etc. See [Web Services API documentation](http://genomearchitect.readthedocs.io/en/latest/Web_services.html).

Bugfixes

Bug Fixes

- Fixed bug in which ```add_transcripts_from_gff3_to_annotations.pl``` replaced valid mRNA name with gene name. [#1475](https://github.com/GMOD/Apollo/issues/1475)

- Fixed bug in which ```REMOTE_USER``` was not cached everywhere and was being ignored on ping request. [#1492](https://github.com/GMOD/Apollo/pull/1492)

+ Add new 'default_group' param for remote_user auth #1445

+ Added icon to toggle view of native JBrowse tracks that is always visible #1452

Bugfixes

Bug Fixes

+ Failure to load tracks when switching organisms with identical Sequence IDs #1391

+ Unable to add organism from script without a pre-existing organism #1388

+ Bumped default JBrowse version 

Bugfixes

Bug Fixes

+ Web-service method 'getUserPermissionsForUser' #1230

+ UI glitch with more than ten groups #1242

+ Added [documentation for using Apollo with Docker](https://github.com/GMOD/Apollo/blob/master/docs/Setup.md#configure-for-docker) (#1016)

Bugfixes

Bug Fixes

+ Fixed multiple errors in the add_transcript_from_gff3_to_annotations.pl loading script (#1146)

+ Expired sessions or server disconnection triggers reconnection instead of a silent failure (#493)

+ Added ability to allow username to be a non-email based name (#939).

+ Sync with JBrowse 1.12.2-apollo for stability (#971).

Bugfixes

Bug Fixes

+ Fixed a bug were set translation start, in an intron, produces an uncaught out of bounds exception (#532).

+ Remove alternate hover CSS on tables in Annotator Panel for better visibility of entries (#632).

+ Improved the speed of FASTA export via optimization (#854).

+ Updated history window to indicate current position (#797).

Bugfixes

Bug Fixes

+ Fixed a bug where sequence modifications weren't being included in the GFF3 export (#748).

+ Provide alternate translation table support on the client (#759).

+ Added ability to reference the organism by name in the jbrowse URL for easier to remember URL formats (#653).

+ Added a get_fasta.groovy script to fetch FASTA for annotations via web services.

Bugfixes

Bug Fixes

+ Fixed the permissions to only allow the global admin role to create and delete organisms (#542).

+ Fixed an issue with JBrowse compatibility for certain refSeqs.json files not containing length.

## 2.0.0

Bugfixes

Bug Fixes

+ Organism panel not showing all organisms (#540).

+ Admins for specific organisms have issues with giving other users permissions (#542).

## 2.0.0-RC6

Bugfixes

Bug Fixes

+ Fixed multiple bugs having to do with sequence alterations (#534, #531, #458, #456).

+ Fixed logout for multiple windows on the same browser (#480).

+ Optimized transcript merging (#529,#515).

Bugfixes

Bug Fixes

+ History operations fail when setting acceptor / donor (#530). 

+ Add an interim export panel (#78).

+ Added google analytics integration (#146).

Bugfixes

Bug Fixes

+ User's last location isn't preserved on page on page refresh (#522).

+ Added security to report pages (#513).

+ Add compression to gzip / fasta (#252).

+ Add stress testing frameworks (#137).

Bugfixes

Bug Fixes

+ Fixed bug that prevented deleting of certain isoforms after database optimizations were applied in RC2 (#497).

+ Moving to opposite strand was not recalculating the ORF (#468).

+ Added gzip functionality to data downloads (#252).

+ Added command line exporter for GFF3.

Bugfixes

Bug Fixes

+ Fixed small bug with permission checking on creating new organism permissions (#463).

+ Fixed bug with stop codons being retained in peptide sequence exports (#448).

+ Updated undo/redo operations to work in WA2.0 and fixed several issues with undoing merged transcript operations (#356).

Bugfixes

Bug Fixes

+ Fixed several bugs with sequence alternations (#442, #447, 428, #420).

+ Fixed bug with in-frame stop codons not being identified after manually setting translation start (#55).

+ Changed maxHeight on "User-created Annotations" track to prevent overflow (#124).

+ Allow single-level features to be dragged to the "User-created Annotations" track for editing (#193).

Bugfixes

Bug Fixes

+ Updated URL to new server to access Gene Ontology terms (GOLR) (#190).

+ Fixed an issue where the API could be used to create random berkeley DBs (#152).

+ Added ability to view GFF3 for individual annotations

Bugfixes

Bug Fixes

+ Speed up set\_track\_permissions.pl (#118)

+ Fix some cases where error reporting was broken on login pages (#111)

+ Added command line exporters for GFF3 files.

+ Added light / dark color schemes.

Bugfixes:

Bug Fixes:

+ Fixed phase in GFF3 output

+ Disabled scrollToPreviousEdge/scrollToNextEdge if the feature is fully visible at the current zoom level

+ Can now directly set an annotation to a specific state from the history display

+ Added / updated filters for changes and sequences to be more memory efficient and added added filters.

Bugfixes:

Bug Fixes:

+ Fixed bug of not applying timestamp to temporary BLAT searches (also now requires unique token to guarantee uniqueness)

+ Fixed building of feature_relationship pointers in hybrid data store

-------

Copyright (c) 2015, Regents of the University of California. 

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Note: This license has also been called the "New BSD License" or "Modified BSD License". See also the 2-clause BSD License.

Copyright 2018, Regents of the University of California. 

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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