2.7.0

Features

Add info icon with tooltip describing meaning of fmin and fmax in "Partial". @garrettjstevens. 2649.

Infrastructure Changes

Upgrade Log4j to 2.19.0. Thanks @cmdcolin. 2654.
- Due to this change, export of instructor reports is no longer available

2.6.6

Features

Update Docker container to use Ubuntu 20.04 as the base image (was 18.04). Thanks @christabone. 2645

Bug Fixes

Fix typo in Docker docs. Thanks @christabone. 2638
Use fmin and fmax instead of 3' and 5' in the UI when marking feature ends as partial. This more accurately reflects how Apollo stores the data about partials. 2646

2.6.5

Features

Added method to upload bulk functional annotations from JSON in the interface. 2617,2618
Added a "topLevel" option to the "getFeatures" web services endpoint that causes the endpoint to return top-level (e.g. gene) features. 2616

Bug Fixes

Removed deprecation from SequenceController.sequenceByName. 2619
Fix contextual menu for blastview tracks. Thanks @abretaud. 2621
Make Python libraries installed globally in Docker image. 2622
Update mavenRepo to fix error grails server error during build, see grails/grails-core#11825. 2624

Infrastructure Changes

2.6.4

Features

Added getAttributions method 2591 via @mbc32.
Make getting track features by location optional to pull unique code 2600.
Added additional websocket authentication support 2598.
Added 'set optimal ORF' function 2129.

Bug Fix

Provide better detection and fallback for detecting proper Grails version 2020.
Bad WithOrFrom functional annotation evidence can hide display 2595.
Fixed bad API doc 2605.
Fix safari annotation panel layout 2603.

Infrastructure Changes

Upgrade to JBrowse 1.16.11
Removed server phone home 2614.

2.6.3

Features

Added ability to use posts to sequence methods 2555.
Added system info web service 2557.
Add "merged from" comment to merged in transcript and gene 2567.
Added support for "obsolete", and partials in the interface for GFF3s 2573.
Allow overlap filter to be configurable 2582.

Bug Fixes:

Fix empty attribute list in annotation panel 2552.
Bad coordinate value in genomic element details screen in annotator panel 2559.
Web services indicated user had no organism permissions when checking the login 2554.
Vcf reads as ISO-8859-1 instead of UTF-8 from reader mangling some symbols. 2498.
Added security fixes for web services. 2564, 2587.
In some cases web services tries to create a preference which results in incorrect results 2580.
For the track service, the overlap filter is too restrictive when converting NCList to JSON 2586.
History track names for Gene Produce and Provenance were being cast as GO 2590.

Infrastructure Changes

Removed travis in favor of GitHub Actions 2546.

2.6.2

Features

Add option to suppress calculation of non-canonical splice site 2509.
Added the ability to sync the gene and transcript name with the click of a button 2519.
Added organism and species to menus 2537.
Added UUID lookup and link 2539.
Added status filter for recent annotations 2543.
Add feature name loc to loadLink 2544.
loc loadLink now supports UUID and ID popup provides link 2549.

Bug Fixes

BLAT search should send annotation creation results to the proper reference sequence 2514.
Properly handle Shine_Dalgarno sequences when added as part of gene model 2515.
Now able to resize terminators by dragging 2521.
Added missing GO annotations 2535.
findAllOrganism webserver failed when user is not an admin and no session is present 2540.
Provide minor UI and bug fixes 2548.

Infrastructure Changes

Upgrade to JBrowse 1.16.10

2.6.1

Infrastructure Changes

Upgrade to JBrowse 1.16.9 / 2489.
Fixed Python dependency for Travis for BioPython (3.7) and upgraded to Xenial 2493.
Updated internal Docker Python script to add to use the Apollo 4.2.3 library.
Shows and hide annotation detail panels on demand so list is not obscured 2538

Bug Fixes

Tabix upload of tracks was not including the index file 2487.
Fasta file was displaying the wrong file formats 2486.
Removed unused database migration script causing issues with mysql d50f061887.
Allow addition of a controller vocabulary for Gene Product Description 2488.
Fixed ECO evidence code links 2491.
Fixed load-link urls 2500.

2.6.0

Features

Remove popups for annotations in favor of annotator panel 2334
Added 2 more pseudogenic SO terms and several more non-coding RNA terms and updated interfaces to reflect these 2475
Implemented gene product and field provenance annotations with evidence and GFF3 export 2371, 2234, 2312, 2424
Added name and type to top of annotation details 2423
Added GO Annotations to GFF3 export and extended to transcript 2400
loadLink can take name of gene in evidence (if JBrowse names have been processed) 2444
Add alias to user interface and GFF3 export 2277
Add help menu feedback 2344
Allows for better performance when a large number of annotations are present 2477
Show genome features in current view 2346
Remove sequence lookup at the top 2407
Provide better security and feedback when trying to export with insufficient permissions 2431
Split out default GO Evidence Codes from ECO codes 2429
Added more info (e.g, JBrowse and general settings) to the about window and is visible on login 47f469f7

Infrastructure Changes

Upgrade to JBrowse 1.16.8
Upgrade to Node 13 compatibility.
Add python library to the docker image 2409

Bug Fixes

Open by uniquename to get only the results of the name we are interested in 2338
Fixed ability to add multiple BAMs at once 2352
Fixed export of non-coding RNA if exon not present 2353
Removed sequence panel lookup 2388
Annotator/updateFeature should store history properly 2390
Makes sure that parent directory exists when unpacking 2437
Fixed bug when decompressing gff3.gz data when adding a new track 2434
Fixed boolean environment options being interpreted correctly be31b81f7

2.5.0

Features

Moved blat / blast search to its own tab 2259
Allow creation of annotations from blat features 2225
On upload of fasta file execute faToTwoBit if present to create searchable blat file 2262
Allows history tracking for non-structural edits 2246
Search pop-up links directly to sequence search 2253
Organism and Group tab should searchable 2081
Allow upload of blat data from web-services 2209
Added citation and documentation link to help menu 2243
Allow update of organism via rest API 2227
Allow inhibition of reloading sequences when uploading sequences to the data directory2293
Adds GO annotation to right-click menu 2213
Adds support for GPI export 2238

Bug Fixes

Fixed color by type error 2203
Find all organisms creates exception when organism does not exist 2275
Fixed bug where in the track web-service that hides genomic element that is overlapped by a larger genomic element 2255
Fixed errors with remote services organism info update 2248
Numerous GO annotation fixes 2229, 2233, 2171
Allow deletion of exon with properties on it(2228
Fixed bug where automated name generation generates unusable names 2134
Errors in the track panel create a popup-error 2204
Numerous web-service fixes 2298 2290 2275

Infrastructure Changes

Fixed Docker build to pull directly from current source instead of GitHub 2300
Upgrade to JBrowse 1.16.6, which fixes drag error on Chrome mac GMOD/jbrowse#1397
Allowed for Node 12 2274
Reorder of documentation into multiple layers, moving user's guide into local documentation / read the doc.
Added web-services tests using arrow's python-apollo from the galaxy-genome-annoation group 2285.

2.4.0

Features

Added GO Annotations. 2172, 2162 1134
Allow upload of genomic data to create new organisms. 2023
Allow upload of track data to create new removable tracks. 2024 2084
Allow indication of variant effects 1971
Added ability to provide suggestable names 1991
Provide community level private evidence tracks 17
Automatically kill or disable server if a common directory is not defined 2079
Added support for Shine Dalgarno sequence 2149 1955
Allow for the export of a gene with uncertain internal structure - allow no CDS for an gene 1989
Added shortcut for sequence and GFF3 popups 2116
Added the ability to do group add /delete in bulk and group update in bulk 2105

Infrastructure Changes

Integrated Docker into the Apollo repository directly so that latest is always the current snapshot and stable is always the latest release. 2184
Upgrade to JBrowse 1.16.5
Added script to delete features by name and unique name 2138

Bug Fixes

Fix issue with rendering neat features 2063
Fix issue with creating annotations for reads with indels in them 2085
Fixes error when changing annotation type when status is set 2167
Fixes for variant search in annotator panel 2147
Fixed bug where txtz is not supported when adding a gnome feature 2136
Fixed bug where sequence panel is VERY narrow 2118
Fixed bug where setting the 5' and 3' based on reads does not work 2110
Numerous UI issue fixes 2109 2113
Fixed rendering of certain exons 2063
Fixed bug where indels in long RNAseq reads interpreted as introns when used to make annotations 2085
Fixed bug where unable to drag features when the new inferHTMLSubfeatures is fals 2099
Unable to create variants in some cases 2103

2.3.1

Features

Allowed duplication of organism from the Organism Panel 1968
Allows making an organism obsolete 1967
Create a filter and flag for inactive users 1937
Allowed deletion of feature from the Sequence and Annotator Panels 2040
Allow export of orig_id as an optional attribute 2002

Bug Fixes

Fixed issue when dragging features to resize was not providing an indicator box 1988
Fixed issue when sequence alterations were not rendering the full height of the sequence track 2049
Making organisms obsolete should remove associated permissions 2043
User-created features taken from split reads should create features with introns 2036
Should indicate split reads properly in evidence 2034 2054
Temporary files not removed during export of GFF3 or other file types 1966
Fixed issue where you could not alter an isoform after deleting a gene name 1961
Fixed some minor issues associated with sequence alterations 1497
Multiple owners tagged on GFF3 export 29
Setting gene description puts UcA into a bad state 2056
Fixes plugin inclusion error by reverting prior fix 2055

2.3.0

Features

Moved to JBrowse 1.16.2 by default 1988, which also fixed track styling issues #1942
Moved to Neat Features as the default 2021
Improved terminator annotation 1997

Bug Fixes

JBrowse bin directory not properly being installed 2017
Workaround for declaring plugins in trackList.json via a JBrowse bug 2014
Fixed problems with creating variant annotations with soft masking 2009
Fixed bugs in reporting code 2008
Fixed several build bugs #1996, #1994, #1993
Fixed bug where deletions, insertions, and substitutions were not editable in the side-bpanel #1923

2.2.0

Features

Move to JBrowse 1.15 and webpack (smaller file size) 1928,1986
Add ability to annotate terminators 1954
Added a script for removing all features from a sequence 1935
Allowed removal of ALL user permissions (instead of deleting) to inactivate 777
Clarified edge-detection 9

Bug Fixes

Fixed bug where showing annotations by users was lost 1952
Fixed by where lowercase reference sequence does not translate correctly in 'Get Sequence' output 1944
Fixed problem where removing an available status type caused an error 1909
Fixed bug where a logged-in link location was ignored when passed in by copying the logged in URL 1982
Fixed bug where insertion and deletion details did not come up in the Annotator Panel when clicked 1984

2.1.0

Features

Added ability to annotate a variant from VCF evidence tracks 1892
Allow forced assignment of transcript to a gene #1851
Added proper Instructor and Organism Admin permission level #1178
Indicate start / stop codons with color #1852
Set the default biotype on track #1861
Focus annotator panel on the current transcript #1846
Allow fetching variant data from evidence tracks via web service #1867
Recognized dot notation from JBrowse / Apollo #1839
Allow setting default native track to true #1848
Provide sample data (and links in doc)#1817

Bug Fixes

Fixed descriptor leak when loading bulk loading GFF3 #1187
Fixed adding ability to create sequence alterations of uneven length #1883
Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case #1879
Prevents setting bad translation starts and ends #1838
Improved performance of cache deletion code #1824
Allow more special characters in the password #1859
Fixed bug with 'Update Membership' and 'Update Group Admin' call in web services #1891
Fixed bug with 'Update Organism Permission' call in web services #1885
In some cases when the name store is not properly configured, the location is not remembered #1895

2.0.8

Features

Added the ability to annotate from high performance Alignments2 BAM reads #1789
Added support for indexed FASTA to be used as reference sequence. #1791
Added sequence API #1799
Added ability to remove gridlines from the view menu in both light and dark themes #1547

Bug Fixes

Fixed bug when flipping strand fails to flip the strand of the owning gene #1769
Fixes to track services to allow remote jbrowse tracks and jsonz #1767
Fixes to track services to return 404 when bad URL is given #1768
Fixed CORS issues #1760
Fixed bug where gene positions are sometimes wrong when a longer isoform is deleted from a gene #1770
Fixed permissions for REMOTE_USER when using web services #1759
Fixes build issues #1756 #1752 #1773
Fixes error in SQL query for listing alterations #1754
Minimum node version is version 6
Fix UserPanel for a large number of users #1800
Fixes recalculated gene positions for some delete exon operations #1808
Fix big when updating organism via web-service #1804

2.0.7

Features

Add the ability to upload organism sequence data and track data to a remote Apollo instance via Apollo Web Services #1670.
Allow setting of alternate translation table per organism using the Details panel under the Organism tab in the Annotator panel. #95
Draggable BAM tracks now support coloring by strand. Reads aligned to forward strand are colored blue, while those in the reverse strand are red. #412
The list of Tracks in the Annotator panel now allows for the separation of data types into categories. #536
Tracks in a category can be added or removed all at once. #1733
When applicable, warnings now alert users of insufficient permissions to perform certain functions. #553
Restrictions are now in place to prevent users from modifying or deleting annotations that they did not create. #1260
Updated settings for the ability to filter by organism when applying metadata. For instance, admin may now apply canned comments, keys and values, only to a subset of organisms in their server. As well, statuses can be retrieved per type of genomic element, per organism, etc. #1676
Admins can now build public URLs to hyperlink directly to a specific genomic element. #1482
It is now possible to set Statuses as well as adding or editing Canned elements using our Web Service (REST) API. #1538
In the absence of Name attribute in GFF3 file, Apollo uses ID attribute to name the annotation in JSON. #1639
A number of other improvements to performance have been made, such as fetching preferences from session. #1604 #1725
Added date created field to changes report. #1728
Removal of bower in favor of npm to install JBrowse. #1691
Added documentation for a Web Service wrapper for Python, PHP, etc. See Web Services API documentation.

Bug Fixes

Fixed bug in which add_transcripts_from_gff3_to_annotations.pl replaced valid mRNA name with gene name. #1475
Fixed bug in which REMOTE_USER was not cached everywhere and was being ignored on ping request. #1492
Added warning to Production pre-requisites: if using gradle and gradlew, admins should define JAVA_HOME to avoid build fails. See documentation here.
Fixed sorting bug on the dropdown list of organisms. #1497
Fixed a bug in which the absence of an organism created downstream issues such as errors listing groups of users in Annotator panel. (Feature for admins). #1504
Fixed a bug in which creating a user via Web Service API generated an error message. #1510
Fixed import script add_transcripts_from_gff3_to_annotations.pl to introduce correct handling of sequence alterations and read-through stop codons. #1524
Fixed bug that now allows leading start non-M codons in organisms with non-standard code to be translated as Methionine (M). #1544
Updated GWT code to fix a bug that prevented Apollo from generating URLs appropriately - pipes were not being encoded. #1606
Fixed bug in the calculation of open reading frames for the negative strand for the purpose of coloring each exon according to the CDS. Exported sequences had been - and remain - correctly generated. #1629
Fixed bug that delayed propagation of updates when boundaries for an annotation's parent element were changed. #1631
Restored 'Pin to top' and 'Delete track' functionality for tracks with HTMLFeatures. #1632
Fixed cascade bug when changing annotation type for an annotation that has a read-through stop codon. #1717
Apollo client being initialized twice in some instances. #1742

2.0.6

Features

Moved the native track panel button to the main window #1398
Add new 'default_group' param for remote_user auth #1445
Added icon to toggle view of native JBrowse tracks that is always visible #1452

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
When logged in, clicking on JBrowse would not load the Annotator Panel #1395
server_data may lock some times in dev mode #1419
Intron persists in tracks if a single exon if neat features enabled #1417
Authentication error with galaxy tools + remote_user #1423
When logged in as non-admin user, the show track panel button does not look or work properly #1429
When deleting an organism from the interface, should instantly update the organism list similar to add organism #1431
404 errors on CSV metadata in some cases #1448
Problems loading list of Tracks when switching organisms on slower connection #1434
Setting exon details in details panel fails to set transcript boundaries properly #1428
Error opening on double-click for annotations listed in the second page of the annotation panel #1459
Transcripts of pseudogenes should NOT have the word 'transcript' or other type in the name #1451
Issue with gene names when performing undo and redo right after changing annotation type #1464
Interface freezes if right-clicking an unselected annotation #1465
Fixed issue where double-click on transcript navigates and then closes the transcript / gene #1467
Remote_user not authorized properly everywhere #1468
Fixes the small problem with the sticky tracks from loadLinks #1474
Bumped default JBrowse version

2.0.5

Features

Increase UI and performance by calling setCurrentSequenceLocation less aggressively #1007
Various performance improvements #1272,#1276
Added ability for Apollo to call home to track server usage #1339
Allow multiple calls to google analytics to support users internally #1340
Numerous annotator tab user interface improvements #1343,#333
Updated 'changes' report page for more detail and better filtering #806
Added URL option to open and close the track panels #1332
Adds a findChanges web-services method #1316
Importing features should be able to optionally include metadata #52
Make organism, groups, users tabs more consistent #622
Convert javascript "alert" to something more appealing visually #630
Using Bootstrap in all panels #847
Improved report login window look and feel #1103
Upgraded to Java 8 #1327
Upgraded to Gwt 2.8.0 and Gwt-Bootstrap 0.9.4 #1075
Delete expired preferences #1368
Location URLs are now encapsulated in links #1361
Bumped default JBrowse version

Bug Fixes

Web-service method 'getUserPermissionsForUser' #1230
UI glitch with more than ten groups #1242
Error going between full-screen and annotator panel when stored are loaded in the URL #1156,#1214,#1271,#1330,#1331, #1008, #1371
'use_cds_for_new_transcripts' was not being picked up properly #1297
Client interprets 5'UTR and 3'UTR features as exons #1308
Flag when 3' end or 5' end are missing, still calculate longest ORF #1302
Limit Chado export to admins #1322
Improved security of non-public genomes #861
Adding transcripts via the load transcripts script added preferences #1277
Was not validating scaffold against organism on import #1173
Sequence display with annotation did not update automatically when moved to opposed strand #645
Needed to update the coding detail panel when changing transcript details #379
Warn user when making an intron is not possible #1331
Load script was returning the wrong error when the wrong password was given #1275
use_cds_for_new_transcripts is not being picked up properly #1297
Improve merging of functional annotations data during merge operation #646
Annotator panel calls the official set exon boundaries method #653
Pinstripes disappear in small scaffolds. #709
Spring to splice site functionality works once only #735
Genomic insertion coordinates: start is greater than end in gff3 output from Reference Sequence tab #747
Remove errant bootstrap calls #746
Remove Environment.TEST from code #655
No glyphs for sequence alterations #908
getUserPermissionsForUser is non-standard #1230
Fixed case in Webservices docs #1244
UI glitch on Groups tab when more than ten groups #1242
Fixed error with setting upstream donor failing #1379
NCBI Pubmed upgraded to use https form discontinued http #1377
Updating exon details in annotator panel fails #1375

2.0.4

Features

Upgraded to Grails 2.5.5
Allow REMOTE_USER authentication (apache / nginx) and added pluggable user authentication (#1042)
Ability to enter pre-specified (canned) values for Attributes in the 'Information Editor', similar to canned Comments. (#86)
Users may download the genomic sequence from highlighted regions using the export menu in the User-created Annotations area export (#1163)
Information from parent features can be retained when loading transcripts onto the 'User-created Annotations' area using the add_transcript_from_gff3_to_annotations.pl loading script (#1171)
Added documentation for using Apollo with Docker (#1016)

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)
Fixed bugs in certain web service scripts (#1155)
Fixed bug where garbage client token is created (#1172)
Fixed several deployment and installation issues (#1135, #1137, #1138, #1150)
Fixed adding comments to a sequence alteration fails to create the sequence alteration (#1179)
Parameters passed into loadLink are no longer dropped (#1140)
Fixed bug not allowing addition of FeatureType in admin menu (#1144)
Improved performance of loading the information editor for large genes (#1152)
Fixes error when deleting a DBXref or GO ID error (#1163)

2.0.3

Warnings

Before doing the build with Apollo v2.0.3, make sure to install node.js (which includes npm) and install bower. This process will be automatic in v2.0.4 and fixes are detailed in #1138.
Download node.js from https://nodejs.org/en/download/
To install bower:
- npm install -g bower
Then:
- ./apollo clean-all
- ./apollo deploy

Features

Added Ability to export Apollo annotations to a Chado database (#145).
Added ability to update an existing Chado database for Chado export (#967).
Updated application to use Grails 2.5.4 (#444).
Allow apollo-config.groovy configuration to create admin user on startup (#1040).
Added ability to change feature type in User created annotations track (#220).
Added ability to use multiple organisms at the same time (#441).
Added ability to search selected sequences (for export) and clear selection in Sequence Panel (#730).
Added ability to allow username to be a non-email based name (#939).
Sync with JBrowse 1.12.2-apollo for stability (#971).

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).
Fixed clientToken not found error for operation get_gff3 and get_sequence (#1027).
Fixed a bug where PubMed and Gene Ontology lookup, in Information Editor, fails (#1028).
Fixed issues with export sequence API (#1045).
Fixed a bug where changing the number of transcripts of a gene did not update the drop-down in Information Editor (#587).
Fixed a bug where the bookmark icon did not show up for the current feature in History window upon revert (#769).
Fixed a bug where CDS FASTA export was attempting to export sequences of ncRNAs. (#833).
Fixed a bug where using ?organism=organismName does not work if logged in (#845).
Fixed a bug where if a mRNA, without a strand, is added to the annotations track then it cannot be assigned a strand (#873).
Fixed a bug where import generates unique 'gene' name based on the existing gene (#879).
Fixed a bug where Comments field was restricted to 256 characters (#963).
Fixed a bug where an undo operation on a pseudogene causes an error (#1001).
Fixed inconsistencies when converting a feature to a JSONObject and vice-versa (#1003).
Fixed clientToken error originating from getCurrentOrganismForCurrentUser (#1054).
Fixed UI problems with 'Full-screen view' mode (#1055).
Fixed a bug where targetURL was not preserved properly through login in loadLink and Reports page (#1058).
Fixed a bug where user/group selection drop-down goes the wrong direction (#1066).
Fixed a bug where creating a pseudogene, repeat region or transposable element from a Canvas feature track led to an error (#1077).
Fixed a bug when creating a non-coding Transcript owner was not set and the username was not being displayed when hovering (#1085).

2.0.2

Features

Added ability to filter summary of annotations by user (#79).
Re-added translation table support (#757).
Improved speed of GFF3 export via optimization (#274).
Enhanced GFF3 export of sequence alterations by including the altered residues (#754).
Added warning for Tomcat memory settings when doing apollo deploy (#767).
Replaced the Split Panel interface of Annotator with Dock Panel (#768).
Added label to the 'Revert' button in History window (#769).
Added ability to sort annotations by 'Last Updated' on the Annotator Panel (#770).
Added ability to add a comment to sequence alterations (#781).
Added annotation count to the Sequences Panel (#803).
Optimized pagination in Annotator Panel when dealing with large number of annotations (#820).
Enhanced the web service API to enable the ability to edit name of features (#776).
Enhanced the web service API to enable the ability to add GO, Dbxref, attributes and publications to features (#829).
Improved the speed of FASTA export via optimization (#854).
Updated history window to indicate current position (#797).

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).
Fixed a bug that causes a persistent screen over 'Links to this Location' popup (#778).
Fixed a bug that made it unable to retrieve GFF3 of pseudogenes (#784).
Fixed a bug where merging or splitting transcripts and then doing an undo causes error (#842).
Fixed a bug which causes links to transcript on the second page of the Annotator Panel to fail (#801).
Fixed a bug which causes filter and sort to be mutually exclusive in Changes report page (#824).
Fixed a bug where repeat regions, transposable elements and sequence alterations were not part of GFF3 export (#836).
Fixed a bug where merging of transcripts fail in certain cases (#850).
Fixed a bug that was as a result of using native javascript confirm boxes (#851).
Fixed a bug where removing a dbxref visually removes the feature from track (#764).
Fixed a bug which causes all genomic elements to disappear when 'Show minus strand' option was selected (#782).
Fixed a bug where modification of a gene model was taking a long time when the backend was MySQL (#743).

2.0.1

Features

Added more intuitive paging to sidebar panels (#700).
Added support for flatfile-to-json tracks loaded with the --compress option in the data loading pipeline (#517).
Added right-click option to CanvasFeatures tracks to "Create new annotation" (alternative to drag and drop) (#576).
Added an option for enabling/disabling the public JBrowse mode (#433).
Added an -ignoressl option to bypass certificate authority for groovy command line scripts (#557).
Made the administration of group membership more clear from the User/Group panels (#598).
Added scripts and web services for managing user and group permissions (#595).
Added additional Web Services API documentation generated from source code annotations (#582).
Added ability to toggle the JBrowse tracklist from the annotator panel (#597).
Added ability to collapse HTMLFeatures evidence tracks from track menu (#571).
Added case insensitive search to annotator panel search boxes (#575).
Added some bootstrap styling to annotator panel features (#489).
Added a feature to remember the width of the annotator panel (#591).
Added scripts and web services for deleting all features from a given organism (#539).
Added proxy support to support https servers and general user-configurable proxy support (#148).
Improved user experience for login, user, and group pages (#603, #601, #592).
Improved, expanded, and automated web services documentation (#546).
Added feature to let users change their own password (#620).
Updated the /featureEvent/changes page to show list of recently changed features (#642).
Enhanced the loadGroups and loadUsers API to retrieve the info of specific groups or users (#643).
Enhanced the findAllOrganisms API to retrieve the info of specific organisms (#666).
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.

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.
Fixed the calculation of isoform overlap (#558).
Fixed a bug that made certain annotation operations slow down over time (#555).
Fixed a bug that made changing the location of the organisms's data directory cause problems (#567).
Fixed a bug that occured when splitting and merging a transcript back together again (#588).
Fixed a bug that prevented multiple values for an attribute in the Information Editor (#579).
Fixed a bug preventing features with long names (#580).
Fixed a bug where a closed track in the genome browser was not showing up as un-checked in the side-panel (#554).
Fixed a bug where the group permissions where not being displayed correctly on the Group panel (#664).

2.0.0

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

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).
JBrowse only mode not listening to websockets (#537).

2.0.0-RC5

Features

Optimized transcript merging (#529,#515).

Bug Fixes

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

2.0.0-RC4

Features

Optimized transcript merging (#529).
Added "add_comment", "add_attribute", "set_status" to the web services API (#492).
Add an interim export panel (#78).
Added google analytics integration (#146).

Bug Fixes

User's last location isn't preserved on page on page refresh (#522).
Added security to report pages (#513).
Unble to add / view more than 4 organism permissions (#512).
Set current sequence dropdown not selecting sequence (#511).
Peptide sequence not exporting properly (#453).
Peptide sequence not exporting properly (#453).

2.0.0-RC3

Features

Added CSV downloads of reports, and created more extensible framework for creating customizable reports.
Updated application to use Grails 2.4.5.
Updated bulk loader to support loading for a specific organism with the --organism parameter (See #505).
Updated bulk loader to support looking up the name of a feature from a specific GFF3 tag with the --name_attributes. Thanks to @anaome for the idea and implementation (See #396).
Raise limit on number of tracks allowed in track panel (#502).
Added some database optimizations for retrieving sequence features (#504, #452).
Optimized annotation panel (#389).
UI improvements (#385).
Add compression to gzip / fasta (#252).
Add stress testing frameworks (#137).

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).
Secure GFF3 / FASTA export (#464, #467).
Unable to add organisms from some users (#463).
Fixed bug when not stopping (#448).
Readthrough stop codons are not being highlighted after undo/redo (#400).

2.0.0-RC2

Features

Added a PDF version of documentation to readthedocs.
Added a button to generate a public link to the genome browser for a particular organism.
Added ability to manage statuses, custom comments, and feature types using the "Admin panel".
Added a feature to logout all instances of webapollo from different windows if one window is logged out (#409).
Added stress testing scripts using JMeter and tested application reliability.
Added new report pages for getting overview of annotations, organisms, sequences, users, and system performance statistics.
Added asynchronous data provider to the "Annotator panel" for faster "on-demand" download of data.
Added customizable data adapter configurations in the configuration guide.
Added gzip functionality to data downloads (#252).
Added command line exporter for GFF3.

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).
Fixed bug with stop codon readthrough features not being restored after "Undo/Redo" (#400).
Fixed a bug with downloading data files (#464).
Fixed a bug that prevented running multiple instances of Apollo at the same time (#462).
Fixed a bug where tracks without a key would cause track panel to produce error (#461).

2.0.0-RC1

Features

Created a major rewrite of the backend using Grails, which is a scalable, high-concurrency framework based on Spring and Hibernate
Added ability to support multiple organisms in a single application instance.
Added organism-level permissions for users and groups and created new admin panel for setting these permissions.
Added webservices and command-line scripts for creating new organisms (#360).
Added webservices and command line scripts for adding users and support for migrating annotations from WA1 to WA2 (#255).
Created a new "Annotator panel", a side-bar for viewing annotations, reference sequences, export options, and admin features.
Added ability to load Apollo client-side plugin automatically, so there is no need to run add-webapollo-plugin.pl (#435).
Implemented new data models for Hibernate with support for MySQL, PostgreSQL, Oracle, and H2.
Implemented simplified configuration via apollo-config.groovy.
Added websocket implementation for annotation updates, with long-polling fallback (#14).
Optimized non-canonical splice site search (#454).
Updated undo/redo operations to work in WA2.0 and fixed several issues with undoing merged transcript operations (#356).

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).
Fixed bug with exon identified as having non-canonical splice site with non-existent boundaries (#16).
Fix merge of unlike annotation types, causes mixed subfeatures (#23).
Fixed bug with where CDS calculation was triggered on non-coding features (#30).
Extension of mRNA causes 500 error (#27).

1.0.4 release

Features

Update to JBrowse 1.11.6 (http://jbrowse.org/jbrowse-1-11-6/)
Added new Help page with Web Apollo specific content (#153).
Added Drupal authentication module to share authentication with an existing Drupal DB (#117).
Made "Show track labels" and "Color by CDS" more persistent (#120).
Added a "Collapse" option to the "User-created Annotations" track. The track labels are automatically removed when selecting to "Collapse" the track, but can be shown again. (#155).
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).

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).
Fixed the sample log4j2 implementation and added extra notes on it to the documentation (#151).
Fixed an issue where the config files were readable by the outside world in previous 1.x versions.
Changed default user database to be encrypted. Unencrypted options are still available via command line scripts for people with older configurations (#147).
Fixed bug where Tomcat could report "Too many open files error" (#162).
Fixed bug where the dark theme made the reference sequence too dark (#119).
Added some basic help text for search parameters in the sequences view (#160).
Added MIME types for bigwig files (#166).
Added labels to the boxes in the Sequence Search page to inform user of acceptable query options (#158).
Fixed GFF3 export to update fileds with non-specified phase, score, and strand (#177).
Fixed "Previous" button on sequence page to update datagrid appropriately (#176).
Fixed "Show track labels" feature that was causing feature labels to go offscreen (#179).
Renamed "Edit Annotation" menu item to "Edit Information" and camel-case file-menu options. (#172)
Fixed mislabeled column in "Changes" page (#169).
Fixed "Add sequence search track" function not matching amino acid queries (#168).
Fixed bad layout on "Changes" page (#180).
Fixed plus/minus strand filters making bigwig score go to zero (#181).
Fixed problem encountered with using iframe embedded mode options (#183).
Fixed problem with "Add user" popup using outdated server configuration (#182).
Fixed minor issue raised when attempting to retrieve (non-existent) peptides from untranslated regions (#157).

1.0.3 release

Features

Added ability to view GFF3 for individual annotations

Bug Fixes

Speed up set_track_permissions.pl (#118)
Fix some cases where error reporting was broken on login pages (#111)
Fix Chado export case where DBXref or DB were not pre-existing (#103)
Fixed issue where HTTP header size could become large when exporting all tracks (#101)
Fixed issue when jbrowse "bin" directory not created properly during deployment (#97)
Added apollo "release" target to build a precompiled target (#96)
Provided support to visualize GFF3 files on a per-feature basis (#89)
Fixed URL encoding of multiple attributes with the same key in GFF3 export (#82)
Fixed GFF3 and FASTA export where no annotations existed (#62)
Fixed where genome insertion trigers recalculate CDS on non-coding features (#30)

1.0.2 release

Features:

Using JBrowse 1.11.5
Make subfeature unresizable after it becomes unselected
Added functionality for extending to downstream/upstream acceptor/donor splice sites
Added EncryptedLocalDbUserAuthentication option which allows use of encrypted database but does not require it
Added support for EncryptedLocalDbUserAuthentication in add_user.pl,change_user_password.pl
Added ability to encrypt an unencrypted database via encrypt_passwords.pl
Added "revert" buttons on rows in history to allow one click change of state
Added "{" and "}" for navigating between top level features
Added feature coordinates for get_sequence output
Added "disableJBrowseMode" option to disable JBrowse mode
Added a forceRedirect option for logins that can be used for custom login classes
Added tool to split all isoforms into individual genes (RemoveIsoforms.java)
Added tool for fixing gene boundaries based on children transcripts (FixGeneBoundaries.java)
Using javascript minimization for JBrowse+Apollo to allow faster initial load time
Using Maven build system for deployment ([See new installation guide] (https://github.com/GMOD/Apollo/blob/master/docs/index.md))
Integrate with TravisCI: https://travis-ci.org/GMOD/Apollo
Added menus for changes / sequences to annotation screen, fixing memory issues from selectTrack.jsp and recentChanges.jsp pages.
Added ability to hide track labels under "view".
alt/Option click brings up Information Editor on annotated track.
Added webservices doc links to interface.
Added command line exporters for GFF3 files.
Added light / dark color schemes.

Bug Fixes:

Fixed phase in GFF3 output
Disabled scrollToPreviousEdge/scrollToNextEdge if the feature is fully visible at the current zoom level
Included Chado libraries that were missing in 2014-04-03 release
Removed 'null' tracks from changes.
Menus use proper CSS pointer.

2014-04-03 release

Features:

Using JBrowse 1.11.3

Removed "Information" from context menu

Renamed "Annotation Info Editor" to "Information Editor" and added date created and date last modified fields
Added tooltips when hovering over annotations in annotation track (displays type, owner, date of most recent modification)
Changed the behavior when dragging discontiguous features into annotation track from creating separate features to creating a single feature
Added functionality for setting end of translation
Added the ability to switch between isoforms when editing meta data in the annotation info editor
Enabled floating arrow heads appear to show orientation of feature when zoomed in too much to see the whole feature
Added <export_source_genomic_sequence> option for whether to export the underlying source genomic sequence data for GFF3 adapter
Search results from reference sequence selection screen how opens up JBrowse with the region highlighted (the same behavior as when searching from within JBrowse itself)
Search result window within JBrowse now doesn't automatically close when selecting a result (requires explicit closing from the user)
Deleting all subfeatures now pops up a warning about deleting the whole feature not being undoable, like when selecting the parent feature and deleting that
History page (recentChanges.jsp)
Added the ability to export metadata in in deflines for FASTA exporting
Can now continue dragging an exon boundary after initial drag (used to require reclicking on the exon)
FASTA output in GFF3 now contains at most 60 residues per line
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.

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
Long polling now tries to reconnect when connection returns a status of 0 (up to five times, at increasing timeouts)
Fixed coloring by CDS bug
Fixed showing DNA residues on annotation when zoomed in enough
Create DB entry on Chado if it doesn't already exist when writing data to Chado
Fixed issue with null time last modified meta data
Fixed issue with null owner meta data
Chado writer will now throw an exception if an expected entity isn't found
Fixed 1-off error in BLAT searches for the end of the match
Added fixes for properly setting name for non mRNA features
Fixed issue where single level features sometimes disappeared while scrolling
Fix error adding transposable_element annotation with only a match and no match_part
Fix off-by-one error in blat highlight
Fixed empty block that hides tracks on top when zooming in to base level then zooming out while not logged in
In sequences, data adapters will now not appear in the Export submenu if the current user does not have sufficient privileges to use the adapter (assumes same privileges through all genomic regions for the user)

2013-11-22 release

Features:

using JBrowse 1.10.9 release
new hybrid store (memory/disk) should use much less memory than the pure memory store (with a small degrade in performance) - useful for genomes with many annotations (you can configure which one to use as best fits your needs)
viewing of annotation info editor for users without write privilege (cannot modify the data)
FASTA data adapter
different annotation info editor configurations for different annotation types
database/history merger tool (command line)
data adapters now use iterators when exporting data (improves memory footprint)
add a configurable option for dumping owner and other meta-data to the GFF3 adapter
undoing an "add_feature/add_transcript" operation will now warn the user that proceed will delete the feature
data adapter grouping (see FASTA adapter)
adding/updating PubMed ID will now show the publication title for confirmation
improved add_transcripts_from_gff3_to_annotations.pl
adding of different annotation types (gene, pseudogene, tRNA, snRNA, snoRNA, ncRNA, rRNA, miRNA, repeat_region, transposable_element)
adding GO terms now supports searching/autocompletion
annotation info editor now requests data from the server in batch mode (should improve speed)

Fixes:

Chado featureprop writeback for generic attributes
add_transcripts_from_gff3_to_annotations.pl now properly loads status attributes
attributes being lost after undo/redo
redo of a merge_transcript operation after deleting one of the transcripts should work now
properly handle dragged transcripts that contain UTR elements
compressed data sent to the client no longer causes the client to hang when there are too many annotations
rewrote much of the split_transcript operation to better handle gene splitting

2013-09-02 release

Features:

Updated core client base code to JBrowse 1.10.2
'Share' tab has been removed from the toolbar on top. The complete URL can be obtained from the browser line, it keeps track of all displayed tracks, and highlighted regions, if any.
in the aligned sequence BAM reads display, green, yellow and red colors flag insertions, substitutions and deletions (respectively). When the user hovers over them, details about the substituting nucleotide, or the size of the insertion or deletion are displayed.
Pinning a track to the top is now possible. The "User-Created Annotations" track is always pinned to the top, and may not be removed.
Alternate codon translation tables are now available and configurable.
Alternate splice sites are now configurable.
Filtering the list of available tracks is now possible.
It is also possible to combine the information from different quantitative tracks into a 'Combination Track', under the 'File' menu. Data from tracks containing graphs may be compared and combined in an additive, subtractive, or divisive manner. The resulting track highlights the differences between the data. This feature is useful for visualization of differential expression analyses, to observe changes in expression depending on he conditions.
The 'View' tab in the toolbar at the top now contains the menus from the 'Options' tab in the last version. Also, it is possible to 'Highlight' a region by selecting the option, then rubber-band marking the region. The highlight option will automatically be turned 'On' when inspecting the results from a BLAT search.
From the 'right/apple-click' menu, there are a number of new options.
- It is now possible to set the 5', 3', or both boundaries from a track of evidence or alignment, as the boundaries of an exon in the 'User-Created Annotations' area.
- It is also possible to annotate 'Readthrough Stop' signals using the apple/right-click menu. The current 'Stop' exon will be highlighted in purple, and the next 'Stop' signal in frame will be used as the end of translation.
- It is also possible to use the 'Set longest ORF' option.
New metadata configuration in the 'Annotation Information Editor' now includes:
- Name, Symbol, and Description Lines
- Fields to input crossed references to other Data Bases (DBXRefs) such as WormBase, FlyBase, NCBI, etc.
- PubMed IDs
- GO Terms/IDs
- The field 'Attributes' captures all additional metadata not already included in Comments, PubMed IDs, GO, and DBXRefs in a 'Tag/Value' format.
- When ready to export, all metadata in the AIE goes to the 9th column of the GFF3.
GFF3 adapter now allows configuring the value to be put in the source column (column 2)
Rewrote 'add_transcripts_to_annotations_from_gff3.pl' script to write data to server in chunks (helps with efficiency and timeouts), no longer using BioPerl so it can properly handle CDS features
Numerous bug fixes

2013-05-17 release:

Features:

Fully revamped genomic sequence selection screen
sorting by name and length
uses customizable JavaScript function
filtering of genomic sequence names
Annotation info editor
allows editing of symbols
editing of comments
- editing of dbxrefs
- Script for bulk loading gene/transcript/exons to annotation track
Improved login system
- allows logging in from either genomic region selection screen or editor
Configuration for using computed CDS (if available) when first creating a transcript (rather that using the longest ORF)
Improved memory management
Improved handling of concurrent edits
HTTPS support
Deletion of transcripts now warn users
Accessing editor without logging in hides annotation track
Using "[" and "]" to navigate through subfeatures when a feature in the annotation track is selected
Improved interface for adding insertions and deletions
Option to hide plus and/or minus strand
Various bugfixes

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ChangeLog.md

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