SPRINT 6 - Finish 11/30/2015

Overview

Sprint to extend some of the "read only" APIs, to finalize unit/integration testing for existing functionality, to extend the interface, to develop additional loaders, and to begin developing editing capabilities.

Priority things

• Video tutorial - 5 min walk through (e.g. "vet" - one for each - make a consistent script - put all on youtube and link back)
• User Preferences - borrow from refset - don't need anything specific yet, just infrastructure.
• Move "authorize" methods over from refset
• Borrow error handling from refset
  • expand to use refset dailog directives for "errors" and warnings -requires a container
• For "semantic type" mechanism - if there are tree numbers, order by that and indent"
• BAC: OWL - NCIt
• BAC: remove "void addXXX" and "void removeXXX" methods from model objects. Use getObjects().add/remove(...) only
• Model
  • Remove the "name" attributes on @XmlElement annotations and fix the javascript to properly handle the return values of services. TEST
  • Mapping, MapRecord, MapEntry (each with attributes) - similar to Subset, SubsetMember except with one more layer.
    • Then implement this for RRF loader
    • Then implement this for RF2 loader (snapshot)
    • Then implement this for RF2 loader (delta)
• User Interface
  • Enable glass pane while switching tabs - need to say increment in tab controller and decrement at the end of the controller.
• Integration Tests - Jpa/REST - get them tested again
• For @IndexedEmbedded, make sure to use targetElement, also make sure that addXXX and setYYY are called ,and the service.addXXX and service.updateYYY calls are always made.  Important for indexing to work properly.

Marketing/SEO

• Create a video demo of the site (camtasia) and post as a link on the header (video glyphicon if there is one)
• Verify all entry pages for applications are officially mobile friendly
• Consider advertising SNOMED/UMLS/ICD browsers on google adwords.
• Training Video for UMLS browser (need 10 min)
• Training Video for SNOMED browser (simple 5 min)

User Interface Enhancements

• Implement Diagramming
• Add features for "deep" relationships when browsing UMLS.    
  
  • Need a generalized way to know when to use this
  • it is definitely only for "concept"
  • It may be that if any "atoms" of the concept don't match the terminology, then we show it.
• Reimplement the component report as a directive (with service callbacks for  history and other features)
• Implement routing for terminologyId/terminology/version/type so we can preserve URLs.  can even include ?query=... for the query
  • Also clean up the way routes work first so we have
    • https://umls.terminology.tools/content
  • instead of
    • https://umls.terminology.tools/#/content
  • This is likely related to the starting URL redirected to https://umls.terminology.tools/#/
  • See http://stackoverflow.com/questions/14319967/angularjs-routing-without-the-hash
  • e.g. https://umls.terminology.tools/content/CUI/SNOMEDCT/2015_01_31/12738006
• Support opening a concept in a new window (e.g. there's a pointing off arrow icon that opens a new window with a routing URL that  shows exactly that concept - then drag/drop between windows can be editing mechanism).
  • https://umls.terminology.tools/report/SNOMEDCT/2015_01_31/12738006
• Do something useful with websocket
• Expression-based searching (get harold's parser?)
• Consider adding "LABELFOR" all subsets and making the star pop up a picklist of the things to highlight (ordered by type with extensions first, subsets later)
• RECURRING: Mobile-friendly and other style issues

Additional/Enhanced  Loaders

• Owl loader - have a snorocket (2) reasoner for role relationships.

Services

• Action Service
  • Implement classification.
  • Need to go to/from Owl so do Owl loader FIRST.

Testing 

• Rename unit tests!
• Implement additional unit tests for model objects (PrecedenceListJpa, LabelSet, etc)
• RRF loader -> create label set for SNOMED (both "single" and "umls")
• Handler002Test for normal use
• Implement Handler003/008Test - for ID assignment algorithms.  Borrow code from other project (though there may be differences).  The uuidHash algorithm is implemented properly for UMLS and may be different than for SNOMED.

Editing Features

• Basic metathesaurus editing
• Project
  • Figure out how to capture "project scope" for SNOMED and for UMLS in a generalized way.  Update project objects to be able to properly capture (and compute) project scope.  NOTE: the scope definition may involve concepts/terminologies/semantic types.  IN that event, the scope computer gets a little bit more complicated.
• Test loading a DB with envers auditing disabled and then making changes in a DB while it is enabled. Does it properly create audit entries?
  • for the old edition of the component?
  • for the new edition?
• Metathesaurus editing actions
  • MetathesaurusContentEditingRest
    • methods for each "edit action"
    • Create a RestImpl
    • Create a client
    • Create integration tests to run against a "stock" dev  database
  • Add a semantic type component, Remove a semantic type component
    • Have a pencil icon by  the STYs section
    • clicking gives you a list of available STYs assigned, in tree order with a filter box for typing characters of the STY you want.
      • See the metadata "semantic type" option
    • User may want to choose multiple ones (so have a "finished" button)
    • Dont allow user to choose STYs already assigned to the concept.
    • Final action is to call "contentService.addSemanticTypeComponent"
    • Consider what happens to workflow status
    • Consider how to show "NEEDS_REVIEW" content in the browser
    • Consider how to support "Undo". - perhaps an action log (atomic/molecular) is a good idea still for that
  • Implement this completely including testing before moving on to other actions (each which requires a UI enhancement)
    • Approve a concept (e.g. set workflow status values).
    • Add an atom (e.g. MTH/PN - that needs to be generalized somehow)
    • Merge two concepts (consider the "workflow status "when this happens).
    • Move an atom (or atoms) from one concept to another
    • Split an atom (or atoms) out of a concept and specify a relationship type between the two concept
• Terminology Editing (first use case)
  • Add a concept (as a child of an existing concept) with one or more atoms and a PAR/CHD relationship.
  • Run the classifier
  • Show classifier results (e.g. new inferred relationships, etc)
  • NOTE: this only works with a description logic based source that tracks inferred relationships.
  • PREREQ: SNOMEDCT RF2 loader.

Admin Tools

• Test QA queries and flesh them out for 100% coverage.

Optimizations

• TBD

Future Stuff

• Test conditional envers auditing: http://stackoverflow.com/questions/14250612/conditional-envers-auditing
• escg (expression grammar - research)
• Use Lucene SynonymFilter with synonym table
• Component-Component relationships (between any two components).
• Value set definitions (and marking of subset.isValueSet()) and linking to definition? via attribute?
• Owl loader, Owl export of DL terminologies (e.g. RF2-loaded SNOMED)

  • http://owlapi.sourceforge.net/owled2011_tutorial.pdf

• Rdf export (flat)
• Classifier (owl interface)
• Expression language (based on SNOMED expression constraint grammar)
• Sub-branching
  • branchResolutionHandler - figures out how to copy and mark branched objects  and update indexes  - for different branching strategies.
• Handle mappings - may be not worth it
• Implement an RF2 loader (use DL features)
• Implement a ClaML loader
• Support semantic network (e.g. sty rels, etc).  - probably want to wait for a real ontology - and maybe even load it as such.