| 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 | -- |
| 538 | Text for copyright statement associated with PLoS feeds in the publishing applicaiton. | new | rich | task | critical | |
| 653 | trackback spam filter is too conservative | new | | enhancement | critical | |
| 675 | Admin application needs to handle journals better. | assigned | jsuttor | enhancement | critical | |
| 724 | automate volume/issue collections on ingest | new | jsuttor | task | critical | |
| 744 | Advanced Search - Lucene / Mulgara | new | | task | critical | |
| 780 | Support for Java 'generics'. | new | pradeep | enhancement | critical | 0.9.1 |
| 854 | Ambra Webapp Integration Tests | new | | defect | critical | |
| 910 | Fix and rework user handling | new | | defect | critical | |
| 919 | support external template sets | new | amit | enhancement | critical | |
| 926 | global default journal - get rid of requirement to configure overlay journal | new | pradeep | enhancement | critical | |
| 972 | standardize parameter names for actions | new | | task | critical | |
| 995 | article-state cache key is not cleared when article is published | new | russ | clarification | critical | 0.9.1 |
| 1004 | related articles not displaying in plosgenetics | new | rich | defect | critical | 0.9.1 |
| 57 | Create a group profile service. get/set/list profile info for user groups. | new | pradeep | task | high | -- |
| 66 | Wiki page to articles for various interesting applications (RDF Abstract, language translation, etc.) | new | rich | enhancement | high | -- |
| 69 | Provide more info to policy in article access-control | new | ronald | enhancement | high | -- |
| 175 | ensure uniqueness of display-names | new | pradeep | defect | high | -- |
| 345 | Move Plos Registration database to Mulgara | new | amit | 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 | | defect | high | |
| 418 | Update Annotation data model (After #357 is done) | new | rich | defect | high | 0.9.1 |
| 440 | Rating content model need fixing. | new | ronald | defect | high | 0.9.1 |
| 441 | Replies content model needs fixing. | new | pradeep | defect | high | 0.9.1 |
| 467 | Remove Publishing application RDF dependency on Topaz URI RDF namespace. | new | amit | defect | high | -- |
| 605 | return user to origination journal after createNewUser or editProfile | assigned | jsuttor | enhancement | high | -- |
| 614 | Email address(es) specified for correspondence with article's creators is not being migrated or ingested | new | rich | task | high | |
| 630 | Masthead questions | new | rich | enhancement | high | |
| 640 | annotations in the paragraphs following equations are placed incorrectly | new | | defect | high | |
| 690 | pull image attribution info from the cover image article and display on TOC page | new | rich | enhancement | high | |
| 717 | add plos article type, related articles to feed, add group by article type sorting option | new | jsuttor | enhancement | high | |
| 725 | configurable rating categories by article type | new | jsuttor | enhancement | high | |
| 729 | article is missing from feed, but shows up in browse list | new | jkirton | clarification | high | 0.9.1 |
| 765 | Change name and usage from 'model' to graph name and similar attribute for blob. | new | pradeep | clarification | high | 0.9.1 |
| 783 | Correction annotations outside of <body> element. | new | jkirton | task | high | |
| 818 | Change the Embedded class concept: instead of treating them as values ala Hibernate, treat them as Entities too. | new | pradeep | enhancement | high | 0.9.1 |
| 819 | Criteria should allow childCriteria() creation for embedded classes in addition to using '.' as a separator. | new | pradeep | enhancement | high | 0.9.1 |
| 820 | Use ontologies to store content model info and have references to them from ClassMetadata etc. | new | pradeep | enhancement | high | |
| 842 | Download Citation page citation need better formatting | assigned | jkirton | defect | high | |
| 869 | Browse by Date: use most recent pub date as the endDate for "past week", "past month", and "past 3 months" | new | | task | high | |
| 870 | annotation in numbered list messes up formatting | assigned | jkirton | defect | high | |
| 916 | Define a naming convention for Model classes and rename all Model classes | new | | task | high | |
| 931 | extend cascading file lookup filter to freemarker templates | new | | enhancement | high | |
| 945 | support article packages >4GB in size | new | amit | enhancement | high | |
| 981 | 'see all ratings' needs paging | assigned | stoomey | enhancement | high | |
| 989 | Add an @Reference or @Predicate(ref=...) annotation to denote references for "usage-models" | new | pradeep | enhancement | high | |
| 996 | disallow text selection based article annotations for text adjacent to figures and tables | new | jkirton | defect | high | |
| 104 | Handling different forms of copyright | new | rich | defect | medium | -- |
| 150 | Need to track licenses. | new | | task | medium | -- |
| 171 | Future of standalone libraries within Topaz | new | amit | task | medium | -- |
| 420 | logging: bad article ID should give 404, not site error | new | jsuttor | enhancement | medium | -- |
| 421 | Upgrade CAS to 3.1 | new | pradeep | task | medium | -- |
| 462 | Create a filter framework to allow for 'smart' collection of objects. | new | ronald | enhancement | medium | |
| 502 | Add references (cited articles etc.) to the article feed data | assigned | jsuttor | 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 | jsuttor | defect | medium | -- |
| 520 | Line wrap for lengthy gene sequences | new | alex | enhancement | medium | -- |
| 539 | Journal definition via a XML file. | new | rich | task | medium | -- |
| 565 | browse pages should have a feedicon and link to the feed as well as a feed link in <head> | assigned | russ | enhancement | medium | |
| 593 | group authors do not show up in feed | new | alex | defect | medium | |
| 600 | handle multiple abstracts correctly on ingest | new | rich | task | medium | |
| 641 | bad behavior when user tries to annotate in acknowledgement section illegal area | new | jsuttor | defect | medium | |
| 715 | group author name missing from citation download | reopened | jkirton | defect | medium | |
| 718 | PLoS webapp should register a TemplateExceptionHandler to avoid Exception traces as Results in Templates | new | jsuttor | defect | medium | |
| 745 | caching improvements for feeds | new | rich | clarification | medium | 0.9.1 |
| 771 | Add new built-in function for 'type' in OQL and Criteria queries. | new | ronald | unassigned | medium | |
| 778 | Developer friendly mechanism for discovering annotated classes. | new | pradeep | enhancement | medium | |
| 785 | Migrate Formal Correction Header HTML markup assembly from javascript to viewnlm-v2.xsl | new | jkirton | task | medium | |
| 787 | retraction annotation | new | jkirton | task | medium | |
| 821 | Restrictions as sub-classes | new | pradeep | enhancement | medium | |
| 823 | Support tx recovery in OTM for local transactions | new | ronald | enhancement | medium | |
| 858 | cache search | assigned | jsuttor | enhancement | medium | |
| 859 | placing a note directly on a reference link breaks the link | new | jkirton | defect | medium | |
| 875 | RH nav bar too long for page if article contains many sections | new | amit | defect | medium | |
| 913 | odd behavior in admin on deleting/readding issues | new | russ | task | medium | 0.9.1 |
| 930 | handle site-wide overrides | new | | enhancement | medium | |
| 932 | Roll back r5648 after move to JDK 1.6 | new | | task | medium | 0.9.1 |
| 934 | admin/findUser.action "Find User by Id" form needs updating | new | alex | task | medium | 0.9.1 |
| 939 | New tests in OTM needed for Interceptor | new | pradeep | task | medium | 0.9.1 |
| 940 | Verify that ambra-theme is up to date and also only maintain copies of what we changed, | new | alex | task | medium | |
| 946 | support very large assets (supporting info, etc.) | new | amit | enhancement | medium | |
| 971 | there are "note" annotations in production with state 0 | new | pradeep | defect | medium | 0.9.1 |
| 976 | IE6: Login page is too wide - missing fixed width | new | jkirton | defect | medium | |
| 979 | display total number of search results | new | | task | medium | |
| 982 | Add HTTP exires header to served static resources | new | russ | enhancement | medium | |
| 990 | Invalid annotation URI supplied to listReplyAction | assigned | jkirton | defect | medium | |
| 1007 | article "linkback" URL on listThread.action uses deprecated fetchArticle.action format | new | rich | defect | medium | |
| 402 | XSL transform of RA abstracts with subsections | assigned | stoomey | enhancement | low | |
| 512 | Publishing Application does not create deceased footnote when <contrib> element has deceased="yes" attribute | new | alex | enhancement | low | -- |
| 531 | redirect to login page at https://cas-FQDN/ | assigned | russ | defect | low | -- |
| 564 | browse by subject pages should include the main feed as well as the subject feed in the <head> section | new | jsuttor | enhancement | low | |
| 567 | add 'delete' button to editAnnotation page | new | jsuttor | enhancement | low | |
| 719 | dynamic title for browseIssue | new | alex | task | low | |
| 741 | Struts 2 URLHelper bug | new | jkirton | defect | low | |
| 746 | fix lazy loading browse cache without losing related performance gains | new | amit | enhancement | low | |
| 775 | mulgara connects to pub-app on random high port for ehcache, should use specified port 8111 | new | ronald | task | low | 0.9.1 |
| 929 | move freemarker templates out of WEB-INF/pages | new | russ | task | low | 0.9.1 |
| 997 | Update javascript [dojo] in the ambra/registration/webapp project | new | jkirton | defect | low | |
| 89 | Prevent as far as possible automated registration of users. | new | rich | task | unassigned | -- |
| 111 | Define user roles to simplify access control management | new | | enhancement | unassigned | -- |
| 124 | Write a new alert service | new | jsuttor | defect | unassigned | -- |
| 145 | Implement profile access-control tests | new | alex | 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 | -- |
| 186 | Topaz should handle users authenticated from multiple signon registries | new | | defect | unassigned | -- |
| 191 | Fix handling of fedora exceptions | new | | defect | unassigned | -- |
| 225 | Support different languages in search | new | rich | defect | unassigned | -- |
| 492 | should configure struts2 http (and https) port properties | new | alex | enhancement | unassigned | -- |
| 494 | Need to get author affiliations into mulgara | new | amit | defect | unassigned | -- |
| 516 | update XSL file to 2.0 | new | rich | enhancement | unassigned | -- |
| 698 | Need a way to return the language tag associated with an RDF string literal. | new | pradeep | enhancement | unassigned | |
| 781 | findArticle.action constructs invalid pubmed search URLs in some cases | new | jsuttor | defect | unassigned | |
| 824 | Support tx recovery in OTM for global transactions | new | ronald | unassigned | unassigned | 0.9.1 |
| 832 | Make ItqlStore.createModel/dropModel session aware | new | ronald | unassigned | unassigned | 0.9.1 |
| 840 | Mapper selection needs to be revisited | new | | enhancement | unassigned | 0.9.1 |
| 867 | provide a link to annotated article in admin list of flagged comments | new | jsuttor | unassigned | unassigned | |
| 871 | Admin interface to change a user's password | new | jsuttor | enhancement | unassigned | |
| 872 | discussion thread: too many RE:'s | new | jsuttor | enhancement | unassigned | |
| 883 | View Projection var serialization is POJO specific. | new | ronald | enhancement | unassigned | |
| 884 | @PredicateMap improvements | new | ronald | enhancement | unassigned | |
| 885 | Definition updates as an undoable set | new | ronald | enhancement | unassigned | |
| 886 | @Predicate must be present to mark a persisted field. The rest are considered transient. | new | ronald | enhancement | unassigned | 0.9.1 |
| 889 | allow admin to set volume and issue of formal correction note | new | rich | enhancement | unassigned | |
| 899 | extend DOI resolver to handle supplementary-material | new | jsuttor | enhancement | unassigned | |
| 911 | "First" concept for representations is bogus. Replace with something else. | new | | defect | unassigned | 0.9.1 |
| 921 | Remove CitationInfo and use Citation instead | new | ronald | unassigned | unassigned | 0.9.1 |
| 927 | use overlay journal name as title of admin pages | new | russ | task | unassigned | |
| 949 | Create and publish rdfs/owl description of our content model | new | amit | unassigned | 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 | jkirton | defect | unassigned | |
| 1001 | AllegroGraph connector? | new | ronald | enhancement | unassigned | |
| 1006 | it's bad to have ambra.virtualJournals.JournalName.url defined in template | new | russ | defect | unassigned | |
| 1009 | add PMC article-type to extended feed | new | rich | task | unassigned | |
| 1010 | add article type restriction to home page recent article block | new | rich | task | unassigned | |
| 1013 | cas login page is wide in IE6 | new | stoomey | defect | unassigned | |
| 1014 | correction citation format should match article citation format | new | rich | defect | unassigned | 0.9.1 |
