Merge branch 'kwende-master'

.gitignore

@@ -11,3 +11,292 @@ java/nbproject/*
 # IntelliJ
 java/.idea/*
 java/*.iml
+
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+##
+## Get latest from https://github.com/github/gitignore/blob/master/VisualStudio.gitignore
+
+# User-specific files
+*.suo
+*.user
+*.userosscache
+*.sln.docstates
+
+# User-specific files (MonoDevelop/Xamarin Studio)
+*.userprefs
+
+# Build results
+[Dd]ebug/
+[Dd]ebugPublic/
+[Rr]elease/
+[Rr]eleases/
+x64/
+x86/
+bld/
+[Bb]in/
+[Oo]bj/
+[Ll]og/
+
+# Visual Studio 2015 cache/options directory
+.vs/
+# Uncomment if you have tasks that create the project's static files in wwwroot
+#wwwroot/
+
+# MSTest test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+# NUNIT
+*.VisualState.xml
+TestResult.xml
+
+# Build Results of an ATL Project
+[Dd]ebugPS/
+[Rr]eleasePS/
+dlldata.c
+
+# .NET Core
+project.lock.json
+project.fragment.lock.json
+artifacts/
+**/Properties/launchSettings.json
+
+*_i.c
+*_p.c
+*_i.h
+*.ilk
+*.meta
+*.obj
+*.pch
+*.pdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*.log
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.svclog
+*.scc
+
+# Chutzpah Test files
+_Chutzpah*
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opendb
+*.opensdf
+*.sdf
+*.cachefile
+*.VC.db
+*.VC.VC.opendb
+
+# Visual Studio profiler
+*.psess
+*.vsp
+*.vspx
+*.sap
+
+# TFS 2012 Local Workspace
+$tf/
+
+# Guidance Automation Toolkit
+*.gpState
+
+# ReSharper is a .NET coding add-in
+_ReSharper*/
+*.[Rr]e[Ss]harper
+*.DotSettings.user
+
+# JustCode is a .NET coding add-in
+.JustCode
+
+# TeamCity is a build add-in
+_TeamCity*
+
+# DotCover is a Code Coverage Tool
+*.dotCover
+
+# Visual Studio code coverage results
+*.coverage
+*.coveragexml
+
+# NCrunch
+_NCrunch_*
+.*crunch*.local.xml
+nCrunchTemp_*
+
+# MightyMoose
+*.mm.*
+AutoTest.Net/
+
+# Web workbench (sass)
+.sass-cache/
+
+# Installshield output folder
+[Ee]xpress/
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish/
+
+# Publish Web Output
+*.[Pp]ublish.xml
+*.azurePubxml
+# TODO: Comment the next line if you want to checkin your web deploy settings
+# but database connection strings (with potential passwords) will be unencrypted
+*.pubxml
+*.publishproj
+
+# Microsoft Azure Web App publish settings. Comment the next line if you want to
+# checkin your Azure Web App publish settings, but sensitive information contained
+# in these scripts will be unencrypted
+PublishScripts/
+
+# NuGet Packages
+*.nupkg
+# The packages folder can be ignored because of Package Restore
+**/packages/*
+# except build/, which is used as an MSBuild target.
+!**/packages/build/
+# Uncomment if necessary however generally it will be regenerated when needed
+#!**/packages/repositories.config
+# NuGet v3's project.json files produces more ignorable files
+*.nuget.props
+*.nuget.targets
+
+# Microsoft Azure Build Output
+csx/
+*.build.csdef
+
+# Microsoft Azure Emulator
+ecf/
+rcf/
+
+# Windows Store app package directories and files
+AppPackages/
+BundleArtifacts/
+Package.StoreAssociation.xml
+_pkginfo.txt
+
+# Visual Studio cache files
+# files ending in .cache can be ignored
+*.[Cc]ache
+# but keep track of directories ending in .cache
+!*.[Cc]ache/
+
+# Others
+ClientBin/
+~$*
+*~
+*.dbmdl
+*.dbproj.schemaview
+*.jfm
+*.pfx
+*.publishsettings
+orleans.codegen.cs
+
+# Since there are multiple workflows, uncomment next line to ignore bower_components
+# (https://github.com/github/gitignore/pull/1529#issuecomment-104372622)
+#bower_components/
+
+# RIA/Silverlight projects
+Generated_Code/
+
+# Backup & report files from converting an old project file
+# to a newer Visual Studio version. Backup files are not needed,
+# because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+UpgradeLog*.htm
+
+# SQL Server files
+*.mdf
+*.ldf
+*.ndf
+
+# Business Intelligence projects
+*.rdl.data
+*.bim.layout
+*.bim_*.settings
+
+# Microsoft Fakes
+FakesAssemblies/
+
+# GhostDoc plugin setting file
+*.GhostDoc.xml
+
+# Node.js Tools for Visual Studio
+.ntvs_analysis.dat
+node_modules/
+
+# Typescript v1 declaration files
+typings/
+
+# Visual Studio 6 build log
+*.plg
+
+# Visual Studio 6 workspace options file
+*.opt
+
+# Visual Studio 6 auto-generated workspace file (contains which files were open etc.)
+*.vbw
+
+# Visual Studio LightSwitch build output
+**/*.HTMLClient/GeneratedArtifacts
+**/*.DesktopClient/GeneratedArtifacts
+**/*.DesktopClient/ModelManifest.xml
+**/*.Server/GeneratedArtifacts
+**/*.Server/ModelManifest.xml
+_Pvt_Extensions
+
+# Paket dependency manager
+.paket/paket.exe
+paket-files/
+
+# FAKE - F# Make
+.fake/
+
+# JetBrains Rider
+.idea/
+*.sln.iml
+
+# CodeRush
+.cr/
+
+# Python Tools for Visual Studio (PTVS)
+__pycache__/
+*.pyc
+
+# Cake - Uncomment if you are using it
+# tools/**
+# !tools/packages.config
+
+# Telerik's JustMock configuration file
+*.jmconfig
+
+# BizTalk build output
+*.btp.cs
+*.btm.cs
+*.odx.cs
+*.xsd.cs

csharp/ncbo.sln

@@ -0,0 +1,22 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 15
+VisualStudioVersion = 15.0.26403.3
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "ncbo", "ncbo\ncbo.csproj", "{AC37CC07-66F9-4F08-A5A4-B65316598005}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{AC37CC07-66F9-4F08-A5A4-B65316598005}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{AC37CC07-66F9-4F08-A5A4-B65316598005}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{AC37CC07-66F9-4F08-A5A4-B65316598005}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{AC37CC07-66F9-4F08-A5A4-B65316598005}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

csharp/ncbo/AnnotateText.cs

@@ -0,0 +1,64 @@
+using ncbo.Common;
+using System;
+using System.Collections.Generic;
+using System.Text;
+using ncbo.DataTypes; 
+
+namespace ncbo
+{
+    public static class AnnotateText
+    {
+        private static void PrintAnnotations(AnnotationResult[] annotationResults)
+        {
+            foreach(AnnotationResult annotationResult in annotationResults)
+            {
+                AnnotationPage annotationPage = 
+                    Network.GetResponseAs<AnnotationPage>(annotationResult.AnnotatedClass.Link.Self);
+
+                Console.WriteLine("Class details");
+                Console.WriteLine("\tID: " + annotationPage.ID);
+                Console.WriteLine("\tPrefLabel: " + annotationPage.PrefLabel);
+                Console.WriteLine("\tOntology: " + annotationPage.Links?.Ontology);
+
+                Console.WriteLine("Annotation details"); 
+                foreach(Annotation annotation in annotationResult.Annotations)
+                {
+                    Console.WriteLine("\tFrom: " + annotation.From);
+                    Console.WriteLine("\tTo: " + annotation.To);
+                    Console.WriteLine("\tMatch type: " + annotation.MatchType); 
+                }
+
+                if(annotationResult.Hierarchy!=null && annotationResult.Hierarchy.Count > 0)
+                {
+                    Console.WriteLine("Hierachy Annotations"); 
+                    foreach (AnnotatedClass annotatedClass in annotationResult.Hierarchy)
+                    {
+                        AnnotationPage annotationHierarchyPage =
+                            Network.GetResponseAs<AnnotationPage>(annotationResult.AnnotatedClass.Link.Self);
+
+                        Console.WriteLine("\tClass details");
+                        Console.WriteLine("\t\tID: " + annotationHierarchyPage.ID);
+                        Console.WriteLine("\t\tPrefLabel: " + annotationHierarchyPage.PrefLabel);
+                        Console.WriteLine("\t\tOntology: " + annotationHierarchyPage.Links.Ontology);
+                        Console.WriteLine("\t\tDistance from originally annotated class: : " + annotatedClass.Distance);
+                    }
+                }
+
+                Console.WriteLine("===="); 
+            }
+        }
+
+        public static void DoIt()
+        {
+            string textToAnnotate =
+                "Melanoma is a malignant tumor of melanocytes which are found " + 
+                 "predominantly in skin but also in the bowel and the eye.";
+
+            AnnotationResult[] annotationResults = 
+                Network.GetResponseAs<AnnotationResult[]>(Constants.BaseUrl + "/annotator?text=" + textToAnnotate);
+
+            PrintAnnotations(annotationResults); 
+        }
+    }
+}
+