Developer Space

Overview

This page is a developer space for this project.

Developer Accounts Needed

• Amazon EC2 Server (e.g. 10.230.174.166, terminology.tools, term-server.com) - (user/key)
  • Tomcat runs as ec2-tomcat.  Admins should have sudo access to root or ec2-tomcat.
• UTS Account (each user has their own account)
• Github (obtain on your own)
• WCI Wiki (only needed for editing, email bcarlsen@westcoastinformatics.com)
• MAILING LIST: TBD

Software Setup

• Prerequisites and Software Dependencies
• Building and Deploying in Eclipse
• Git Setup
• Eclipse Setup

Project Resources

• Github Project - https://github.com/WestCoastInformatics/UMLS-Terminology-Server.git
• Portal Site - http://wiki.terminology.tools/confluence 
• JIRA Site: https://wcinformatics.atlassian.net/secure/RapidBoard.jspa?rapidView=1&projectKey=NE&view=planning.nodetail&selectedIssue=NE-8&epics=visible
  
• NCI Deltek charge code : 4019-003 

Sprints and Milestones and Meeting Notes

• MEME Development
  • Master Plan
  • NLM-NCI Demo

• Meetings
• TODO Items Removed From Code
• UMLS Notes
• SPRINT 9 - Finish 20160531
• SPRINT 8 - Finish 20160430
• SPRINT 7 - Finish 20160131
• SPRINT 6 - Finish 11/30/2015
• SPRINT 5 - Finish 9/30/2015
• SPRINT 4 - Finish 7/31/2015
• SPRINT 3 - Finish 6/12/2015
• SPRINT 2 - Finish 5/15/2015
• SPRINT 1 - Finish 4/24/2015
• Future Features to consider
  • a switch to disable changes at rest layer (so that server doesn't have to be taken down for admin tasks).

UI Testing Scripts

• Test Case Criteria and Examples
• Login and Metadata Test Script
• Tree and List Search Test Script
• Concept Report Test Script
• History and Component Type Test Script
• Mobile Friendly Test Script

Style Rules

• Use "uib-tooltip" for more info (no action)
• When using ng-click, use "title" for buttons and for icons. 

Diagrams

• /wiki/spaces/IO/pages/2495622
• Term Server System Architecture
• Refset Tool Architecture
• Meta Editing Worfklow Diagram
• EMS and WMS Screenshots
• Jekyll Editing Screenshots

Coding Standards

Only commit projects when the following things are the case:

• General
  • Declare variables as final by default.
• Non-parent maven projects should not directly reference versions
  • where absolutely necessary, they should use variables for version info
• All java errors and warnings should be removed.
• Javadoc should be added and fleshed out
• Imports should be properly organized and code is formatted
• No "TODO" sections should remain in the code - create additional tickets if necessary
• Service (JPA) calls should take parameters in general (except "add" and "update" calls).
• Swagger annotations should be up to date and reflect current state of REST APIs
• Exception handling "catch" clauses should always properly handle errors
  • Low-level code (e.g. services) should NEVER handle exceptions, they should show them
  • The right level at which to handle an error is any code that is capable of showing the user an error message.
• System.out and System.err calls should be replaced by Logger.getLogger... calls
• Remove any explicit package names, class names, file paths, database names, or other hard coded environment information that makes assumptions about what exists and where it exists.  All of this should be data-driven (either from config files or from the database.

Git Best Practice

• WCI project is configured with branches "master" and "develop" and "release-prep" 
• Use Maven jGitFlow to manage feature/hotfix/releases.
• For any work, start a feature.  When finished, finish the feature.
• When fixing but
• Git Branching Strategy: http://nvie.com/posts/a-successful-git-branching-model/

References/Links

• Identfying terminologies that require loading rather than computation of hierarchies

  /bin/rm -f x
  # find counts of ptr+aui
  perl -ne '@_=split/\|/; print "|$_[3]|$_[4]|$_[5]|$_[6]\@$_[1]\n";' MRHIER.RRF | cut -d\@ -f 1 | sort | uniq -c | sort -n > x
  # find cases where counts of ptr+aui are different (e.g. different numbers of children for same tree position)?
  cut -d\| -f 1,2,3,4 x | sort -u | cut -d\| -f 2,3,4 |  sort | uniq -d | cut -d\| -f 2 | sort -u
   

• MEME requirements: 
  • https://wiki.nci.nih.gov/display/EVS/Metathesaurus+Editing%3A+NCI-NLM+Editing+Systems+Workgroup#MetathesaurusEditing:NCI-NLMEditingSystemsWorkgroup-7.OverviewofEditingCycleandHigh-LevelRequirementsforMEME
• Deploy Site - http://snomed.terminology.tools/term-server-rest/index.html
  • Deploy Instructions (for Amazon EC2 - AMI instance)
• /wiki/spaces/UTS/pages/2436504
• Good SNOMED examples:
  

  • 17231009 Fetal valproate syndrome (see stated vs. inferred)

• Full UMLS
  • Building and Deploying UMLS
  • DB: https://s3.amazonaws.com/wci1/TermServer/umls-sql.zip
  • Indexes: https://s3.amazonaws.com/wci1/TermServer/umls-indexes.zip 
• Full SNOMED 
  • Building and Deploying SNOMEDCT
    
  • DB: https://s3.amazonaws.com/wci1/TermServer/snomed.zip
  • Indexes: https://s3.amazonaws.com/wci1/TermServer/snomedct.zip