| 345 | Move Plos Registration database to Mulgara | new | dragisak | enhancement | critical | |
| 410 | REST based interface for Annotations, Users, Journals, Issues. | new | | enhancement | critical | -- |
| 515 | develop a proper way to include freemarker templates on a per virtual journal basis | new | | defect | critical | -- |
| 653 | trackback spam filter is too conservative | new | | enhancement | critical | |
| 675 | Admin application needs to handle journals better. | new | dragisak | enhancement | critical | |
| 724 | automate volume/issue collections on ingest | new | dragisak | task | critical | |
| 854 | Ambra Webapp Integration Tests | new | dragisak | task | critical | |
| 910 | Fix and rework user handling | new | dragisak | defect | critical | |
| 919 | support external template sets | new | dragisak | enhancement | critical | 0.9.3_rc2 |
| 972 | standardize parameter names for actions | new | dragisak | task | critical | |
| 1034 | Remove all TQL queries in Ambra | new | ronald | defect | critical | |
| 1108 | promoted a note to a formal correction and the body was eaten | new | russ | clarification | critical | 0.9.3_rc2 |
| 1197 | unable to order volumes withing a journal | new | npeterson | clarification | critical | |
| 1269 | publishing articles is slow | new | wtoconnor | defect | critical | 0.9.3_rc2 |
| 66 | Wiki page to articles for various interesting applications (RDF Abstract, language translation, etc.) | new | rich | enhancement | high | -- |
| 407 | push email change through to mulgara in emailConfirmationSuccess.action - do not require user to logout and then log back in to propagate change to mulgara | new | dragisak | defect | high | |
| 467 | Remove Publishing application RDF dependency on Topaz URI RDF namespace. | new | dragisak | defect | high | -- |
| 605 | return user to origination journal after createNewUser or editProfile | new | wtoconnor | enhancement | high | -- |
| 614 | Email address(es) specified for correspondence with article's creators is not being migrated or ingested | new | rich | task | high | |
| 690 | pull image attribution info from the cover image article and display on TOC page | new | wtoconnor | enhancement | high | |
| 783 | Correction annotations outside of <body> element. | new | josowski | task | high | |
| 870 | annotation in numbered list messes up formatting | new | josowski | defect | high | 0.9.3_rc2 |
| 891 | genericize article delete - expect the article zip filename to match the doi suffix, rather than removing the string "journal" | new | rich | enhancement | high | -- |
| 996 | disallow text selection based article annotations for text adjacent to figures and tables | new | rich | clarification | high | 0.9.3_rc2 |
| 1039 | Use Composite View Pattern / Tiles in Ambra | new | dragisak | task | high | |
| 1061 | Move generation of xref xml blob outside of Ambra. | new | dragisak | defect | high | |
| 1184 | Updated the anchor codes for Article Blurbs | new | rich | enhancement | high | |
| 1216 | ONE homepage timeout | new | rich | clarification | high | |
| 1274 | serialization errors in 0.9.3 | assigned | wtoconnor | defect | high | 0.9.3_rc2 |
| 1286 | Notes Across Different Sections of Text Should Not Be Allowed | new | josowski | defect | high | 0.9.3_rc2 |
| 1303 | deleting a volume in admin panel orphans the issues | new | npeterson | defect | high | |
| 1304 | UnhandledException(PLoSMedicine)> max(1, startPage - 9) is undefined | new | josowski | defect | high | 0.9.3_rc2 |
| 1305 | Blog links missing | new | rich | clarification | high | 0.9.3_rc2 |
| 1311 | Provide a way to override configuration file for embedded Mulgara | new | dragisak | enhancement | high | |
| 420 | logging: bad article ID should give 404, not site error | new | ssterling | enhancement | medium | -- |
| 421 | Upgrade CAS to 3.3.1 | new | | task | medium | |
| 440 | Rating content model need fixing. | new | dragisak | defect | medium | |
| 502 | Add references (cited articles etc.) to the article feed data | new | wtoconnor | enhancement | medium | |
| 509 | footnote links for figures with footnotes don't work (also, footnote links are showing the rid instead of the footnote) | new | rich | defect | medium | -- |
| 517 | group author name missing from "email this article" template | new | wtoconnor | defect | medium | -- |
| 539 | Journal definition via a XML file. | new | rich | task | medium | -- |
| 593 | group authors do not show up in feed | new | wtoconnor | defect | medium | |
| 600 | handle multiple abstracts correctly on ingest | new | dragisak | task | medium | |
| 641 | bad behavior when user tries to annotate in acknowledgement section illegal area | new | josowski | defect | medium | |
| 718 | Ambra should register a TemplateExceptionHandler to avoid Exception traces as Results in Templates | new | dragisak | defect | medium | |
| 858 | cache search | new | wtoconnor | enhancement | medium | |
| 859 | placing a note directly on a reference link breaks the link | new | josowski | defect | medium | |
| 930 | handle site-wide overrides for css, javascript, and image files | new | | enhancement | medium | 0.9.3_rc2 |
| 940 | Verify that ambra-theme is up to date and also only maintain copies of what we changed, | new | dragisak | task | medium | 0.9.3_rc2 |
| 990 | Invalid annotation URI supplied to listReplyAction | new | josowski | defect | medium | |
| 1007 | article "linkback" URL on listThread.action uses deprecated fetchArticle.action format | new | rich | defect | medium | |
| 1019 | note range select bug in firefox 3.0 | new | josowski | defect | medium | |
| 1021 | 'between' criterion or a generic 'alias' criterion that allows alternate $s and $varPrefix | new | pag | enhancement | medium | |
| 1051 | improve feedCache invalidation | new | rich | task | medium | |
| 1056 | Must always create definitions for superseded properties (even when not annotated) | new | pag | defect | medium | |
| 1060 | Filter out rows from OQL result if all columns are null | new | pag | defect | medium | |
| 1088 | get rid of PLoSJournals override directory, use default journal instead | new | dragisak | enhancement | medium | 0.9.3_rc2 |
| 1116 | Change author e-mail to comply with NLM DTD 2.3 | new | rich | enhancement | medium | |
| 1128 | users with + in email address are given invalid verification URLs | new | rich | defect | medium | |
| 1140 | Mulgara query returns UnhandledException Error | new | dragisak | defect | medium | |
| 1142 | prepare-sip sax error | new | rich | defect | medium | |
| 1143 | prepare-sip creates a bad MANIFEST.xml | new | npeterson | defect | medium | |
| 1158 | IE6 - Advanced search form date range calendar position is wrong | new | josowski | clarification | medium | |
| 1226 | r7512 adds links that don't point to a valid destination | new | rich | defect | medium | |
| 1227 | r7512 adds absolute pathed URLs that don't work in a build | new | rich | defect | medium | |
| 1230 | Adding note to URI in figure legend causes incorrect placement | new | josowski | clarification | medium | 0.9.3_rc2 |
| 1249 | Search on article abstract does not find expected results | new | ronald | defect | medium | |
| 402 | Redesign of RA abstract and summary sections | new | stoomey | enhancement | low | |
| 492 | should configure struts2 http (and https) port properties | new | dragisak | enhancement | low | -- |
| 512 | Publishing Application does not create deceased footnote when <contrib> element has deceased="yes" attribute | new | dragisak | enhancement | low | -- |
| 567 | add 'delete' button to editAnnotation page | new | wtoconnor | enhancement | low | |
| 618 | make article URL human friendly - no escaped characters and as short as possible | new | rich | enhancement | low | |
| 698 | Need a way to return the language tag associated with an RDF string literal. | new | pag | enhancement | low | |
| 719 | dynamic title for browseIssue | assigned | wtoconnor | task | low | |
| 741 | Struts 2 URLHelper bug | new | dragisak | defect | low | |
| 746 | fix lazy loading browse cache without losing related performance gains | new | dragisak | enhancement | low | |
| 785 | Migrate Formal Correction Header HTML markup assembly from javascript to viewnlm-v2.xsl | new | josowski | task | low | 0.9.3_rc2 |
| 818 | Change the Embedded class concept: instead of treating them as values ala Hibernate, treat them as Entities too. | new | pag | enhancement | low | |
| 819 | Criteria should allow childCriteria() creation for embedded classes in addition to using '.' as a separator. | new | pag | enhancement | low | |
| 820 | Use ontologies to store content model info and have references to them from ClassMetadata etc. | new | pag | enhancement | low | |
| 821 | Restrictions as sub-classes | new | pag | enhancement | low | |
| 823 | Support tx recovery in OTM for local transactions | new | pag | enhancement | low | |
| 824 | Support tx recovery in OTM for global transactions | new | pag | unassigned | low | |
| 840 | Mapper selection needs to be revisited | new | pag | enhancement | low | |
| 883 | View Projection var serialization is POJO specific. | new | pag | enhancement | low | |
| 884 | @PredicateMap improvements | new | pag | enhancement | low | |
| 885 | Definition updates as an undoable set | new | pag | enhancement | low | |
| 932 | Roll back r5648 after move to JDK 1.6 | new | | defect | low | |
| 939 | New tests in OTM needed for Interceptor | new | dragisak | task | low | |
| 981 | 'see all ratings' needs paging | assigned | stoomey | enhancement | low | |
| 1001 | AllegroGraph connector? | new | pag | enhancement | low | |
| 1020 | when editing a user through the admin pages, user cache is not cleared for logged in user | new | rich | defect | low | |
| 1035 | Delete Criterias completely as an option in Topaz | new | pag | enhancement | low | |
| 1036 | Register all store resources at begin of transaction | new | pag | defect | low | |
| 1044 | StringCompareResolver should use new "DefaultGraphs" feature in mulgara | new | pag | enhancement | low | |
| 1045 | Use default graphs for xsd and prefix graphs | new | pag | enhancement | low | |
| 1049 | runitql swallows data types of literals | new | pag | enhancement | low | |
| 1054 | Register a default 'Top' level object in Topaz by default. Similar to owl:Thing and Object in Java. | new | pag | enhancement | low | |
| 1055 | Move preload() and preloadFromSearch() out of SessionFactory | new | pag | enhancement | low | |
| 1057 | Clean up metadata definitions and mapping | new | pag | task | low | |
| 1059 | Stores must do queries for Session.get() in sub-class graphs also. | new | pag | enhancement | low | |
| 1067 | Add Akubra as blob store to Ambra. | new | pag | enhancement | low | |
| 1078 | Formal correction text overlaps with list number | new | josowski | defect | low | |
| 1127 | freemarker.journal.page.title configuration does not propagate from default journal to other journals | new | rich | defect | low | 0.9.3_rc2 |
| 1132 | add ttl and set eternal false for some caches | new | russ | clarification | low | 0.9.3_rc2 |
| 1135 | ambra hangs when multiple ambras are in use on the same stack | new | npeterson | clarification | low | 0.9.3_rc2 |
| 1200 | article display messed up in topazproject plos templates | new | dragisak | clarification | low | 0.9.3_rc2 |
| 1203 | Deletion of an Article does not update Issues list of articles. | new | wtoconnor | enhancement | low | |
| 1213 | delete volume without deleting issues | new | wtoconnor | defect | low | |
| 1221 | adminTop annotation links don't respect journal context | new | rich | defect | low | |
| 1222 | editAnnotation action doesn't work in edge case | new | rich | defect | low | |
| 1241 | Competing Interest Statement Radio button text | new | josowski | enhancement | low | |
| 1243 | Relative URI's not properly handled | new | pag | defect | low | |
| 1272 | Embedded mulgara shutdown problem | new | pag | defect | low | |
| 1291 | Wrong selection error in Authors list and References list | new | josowski | defect | low | 0.9.3_rc2 |
| 89 | Prevent as far as possible automated registration of users. | new | rich | task | unassigned | -- |
| 124 | Write a new alert service | new | dragisak | defect | unassigned | -- |
| 145 | Implement profile access-control tests | new | dragisak | defect | unassigned | |
| 159 | xmlns(x=foo) is broken in xpointer lib | new | rich | defect | unassigned | -- |
| 182 | CAS email lookup service needs to be secured | new | rich | defect | unassigned | -- |
| 225 | Support different languages in search | new | rich | defect | unassigned | -- |
| 516 | update XSL file to 2.0 | new | rich | enhancement | unassigned | -- |
| 781 | findArticle.action constructs invalid pubmed search URLs in some cases | new | ssterling | defect | unassigned | |
| 871 | Admin interface to change a user's password | new | ssterling | enhancement | unassigned | |
| 872 | discussion thread: too many RE:'s | new | ssterling | enhancement | unassigned | |
| 889 | allow admin to set volume and issue of formal correction note | new | dragisak | enhancement | unassigned | 0.9.3_rc2 |
| 899 | extend DOI resolver to handle supplementary-material | new | rich | enhancement | unassigned | |
| 974 | dummy/login page has incorrect help text | new | pradeep | task | unassigned | |
| 985 | it is impossible to remove all issues from a volume | new | rich | defect | unassigned | |
| 987 | Annotation display messed up | new | josowski | defect | unassigned | 0.9.3_rc2 |
| 1009 | add PMC article-type to extended feed | new | wtoconnor | task | unassigned | |
| 1013 | cas login page is wide in IE6 | new | rich | clarification | unassigned | |
| 1015 | include issn in extended feed | new | wtoconnor | task | unassigned | |
| 1018 | return a helpful error if user tries to verify their email address twice | new | pradeep | defect | unassigned | |
| 1025 | remove need for freemarker config in defaults.xml | new | dragisak | task | unassigned | 0.9.3_rc2 |
| 1042 | Tombstone Annotations, Replies and Ratings | new | dragisak | task | unassigned | |
| 1043 | Modification of annotations should result in creation of superseded versions. | new | dragisak | task | unassigned | |
| 1064 | prepare-sip: better handling of tar.gz packages | new | pradeep | enhancement | unassigned | |
| 1077 | CrossRef XSL: if no object-id, don't include component | new | dragisak | defect | unassigned | |
| 1079 | article_content.ftl DOI Resolver Link | new | | task | unassigned | |
| 1080 | article_content.ftl docURL Setting | new | | task | unassigned | |
| 1081 | Sending abstract to Digg.com in artle_content.ftl | new | | task | unassigned | |
| 1091 | feed cache keys are not invalidated correctly on article publish | new | rich | defect | unassigned | |
| 1093 | transient error viewing annotations | new | rich | defect | unassigned | |
| 1123 | genericize prepare-sip | new | rich | task | unassigned | |
| 1238 | favicon URL in feed is bad | new | rich | defect | unassigned | |
| 1239 | get rid of config.ambra.platform.cisStartDate | new | rich | task | unassigned | |
| 1242 | Annotation window positioning after error | new | josowski | defect | unassigned | |
| 1252 | track outgoing links with google analytics | new | rich | enhancement | unassigned | |
| 1253 | improve validation in prepare-sip | new | rich | enhancement | unassigned | |
| 1259 | Google Scholar link returning incorrect result set | new | josowski | defect | unassigned | 0.9.3_rc2 |
| 1260 | Multiple Scopus Citations in Cited By Links | assigned | josowski | defect | unassigned | 0.9.3_rc2 |
| 1278 | change author list format in extended feed | new | npeterson | task | unassigned | 0.9.3_rc2 |
| 1298 | Cannot access install scripts for ambra | new | npeterson | defect | unassigned | 0.9.3_rc2 |
| 1301 | removing crosspubbed article doesn't clean up after itself | new | npeterson | defect | unassigned | |
| 1302 | Filter has not been registered with the session-factory | new | dragisak | defect | unassigned | 0.9.3_rc2 |
| 1306 | test | new | dragisak | defect | unassigned | |
| 1307 | Test | new | dragisak | defect | unassigned | |
| 1310 | Change search OQL to make queries faster | new | dragisak | defect | unassigned | |
| 1312 | type=PropType.DATA should be implicitly guessed for user-defined serializable literals | new | pradeep | defect | unassigned | |
