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

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

Style Rules

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

Diagrams

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
Full SNOMED