add Java checks

PACTCare · Jun 18, 2019 · 546e3a8 · 546e3a8
1 parent e2013a1
commit 546e3a8
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Showing 8 changed files with 90 additions and 5 deletions.
diff --git a/Synthea.Iota.Core/Exception/JavaHomeNotSetException.cs b/Synthea.Iota.Core/Exception/JavaHomeNotSetException.cs
@@ -0,0 +1,8 @@
+namespace Synthea.Iota.Core.Exception
+{
+  using System;
+
+  public class JavaHomeNotSetException : Exception
+  {
+  }
+}
diff --git a/Synthea.Iota.Core/Exception/JavaNotInstalledException.cs b/Synthea.Iota.Core/Exception/JavaNotInstalledException.cs
@@ -0,0 +1,8 @@
+namespace Synthea.Iota.Core.Exception
+{
+  using System;
+
+  public class JavaNotInstalledException : Exception
+  {
+  }
+}
diff --git a/Synthea.Iota.Core/Services/FhirInteractor.cs b/Synthea.Iota.Core/Services/FhirInteractor.cs
@@ -19,7 +19,7 @@ public static ParsedResource CreateResource(ParsedResource resource)
       var patientRepository = new SqlLitePatientRepository();
       var referencedResource = patientRepository.GetResource(resource.PatientId);
 
-      if (resource.TypeName != "Patient" && !referencedResource.IsIotaResource)
+      if ((referencedResource == null && resource.TypeName != "Patient") || (resource.TypeName != "Patient" && referencedResource != null && !referencedResource.IsIotaResource))
       {
         throw new MissingReferenceException();
       }

diff --git a/Synthea.Iota.Core/Services/SyntheaInstaller.cs b/Synthea.Iota.Core/Services/SyntheaInstaller.cs
@@ -4,11 +4,15 @@
   using System.IO;
   using System.IO.Compression;
 
+  using Microsoft.Win32;
+
   using Newtonsoft.Json;
 
   using RestSharp;
   using RestSharp.Extensions;
 
+  using Synthea.Iota.Core.Exception;
+
   public static class SyntheaInstaller
   {
     public static event EventHandler DownloadLatest;
@@ -26,6 +30,8 @@ public static string InstallOrUpdate()
         Directory.CreateDirectory("Synthea");
       }
 
+      CheckJavaInstallation();
+
       VersionCheck?.Invoke("SyntheaInstaller", EventArgs.Empty);
       var client = new RestClient("https://github.com/synthetichealth/synthea");
 
@@ -40,9 +46,12 @@ public static string InstallOrUpdate()
       }
 
       DownloadLatest?.Invoke("SyntheaInstaller", EventArgs.Empty);
-      client.DownloadData(new RestRequest($"/archive/{tag}.zip")).SaveAs("synthea.zip");
-      ZipFile.ExtractToDirectory("synthea.zip", "Synthea");
-      File.Delete("synthea.zip");
+      client.DownloadData(new RestRequest($"/archive/{tag}.zip")).SaveAs("synthea.temp");
+      ZipFile.ExtractToDirectory("synthea.temp", "Synthea");
+      if (File.Exists("synthea.temp"))
+      {
+        File.Delete("synthea.temp");
+      }
 
       InstallLatest?.Invoke("SyntheaInstaller", EventArgs.Empty);
       var synthea = SyntheaRunner.StartSynthea("-p 1", currentVersion);
@@ -54,5 +63,13 @@ public static string InstallOrUpdate()
       SetupComplete?.Invoke("SyntheaInstaller", EventArgs.Empty);
       return currentVersion;
     }
+
+    private static void CheckJavaInstallation()
+    {
+      if (string.IsNullOrEmpty(Environment.GetEnvironmentVariable("JAVA_HOME")))
+      {
+        throw new JavaHomeNotSetException();
+      }
+    }
   }
 }
diff --git a/Synthea.Iota.Core/Services/SyntheaRunner.cs b/Synthea.Iota.Core/Services/SyntheaRunner.cs
@@ -101,6 +101,11 @@ private static List<ParsedPatient> ParseSyntheaData(string currentVersion)
     {
       var outputDirectory = $"{GetSyntheaDirectory(currentVersion)}\\output\\fhir";
       var parsedPatients = ParsePatientFromFiles(Directory.GetFiles(outputDirectory));
+      parsedPatients.ForEach(p => p.Resources.ForEach(r =>
+        {
+          r.Id = r.Resource.Id;
+          r.PatientId = p.Resources[0].Resource.Id;
+        }));
 
       Directory.Delete(outputDirectory, true);
       return parsedPatients;

diff --git a/Synthea.Iota.Core/Synthea.Iota.Core.csproj b/Synthea.Iota.Core/Synthea.Iota.Core.csproj
@@ -132,6 +132,8 @@
   <ItemGroup>
     <Compile Include="Entity\ParsedPatient.cs" />
     <Compile Include="Entity\ParsedResource.cs" />
+    <Compile Include="Exception\JavaHomeNotSetException.cs" />
+    <Compile Include="Exception\JavaNotInstalledException.cs" />
     <Compile Include="Exception\MissingReferenceException.cs" />
     <Compile Include="Exception\ResourceException.cs" />
     <Compile Include="Extensions\ResourceExtensions.cs" />

diff --git a/Synthea.Iota.Ui/MainWindow.xaml.cs b/Synthea.Iota.Ui/MainWindow.xaml.cs
@@ -9,6 +9,7 @@
   using Microsoft.Win32;
 
   using Synthea.Iota.Core.Entity;
+  using Synthea.Iota.Core.Exception;
   using Synthea.Iota.Core.Services;
   using Synthea.Iota.Ui;
   using Synthea.Iota.Ui.Services;
@@ -66,7 +67,49 @@ private void InitializeSynthea()
                 }));
         };
 
-      Task.Run(() => ApplicationManager.CurrentSyntheaVersion = SyntheaInstaller.InstallOrUpdate());
+      Task.Run(() =>
+        {
+          try
+          {
+            ApplicationManager.CurrentSyntheaVersion = SyntheaInstaller.InstallOrUpdate();
+          }
+          catch (JavaNotInstalledException)
+          {
+            this.Dispatcher.BeginInvoke(
+              new Action(
+                () =>
+                  {
+                    MessageBox.Show(
+                      "Synthea needs the Java 1.8 JDK or higher to be installed. Please go to https://www.oracle.com/technetwork/java/javase/downloads/index.html and install the latest JDK version.",
+                      "Java not installed or incorrect version!");
+
+                    Application.Current.Shutdown();
+                  }));
+          }
+          catch (JavaHomeNotSetException)
+          {
+            this.Dispatcher.BeginInvoke(
+              new Action(
+                () =>
+                  {
+                    MessageBox.Show(
+                      "Please set the java home variable to your JDK installation (see https://www.google.com/search?q=how+to+set+java_home&oq=how+to+set+java)",
+                      "Java path (JAVA_HOME) not set!");
+
+                    Application.Current.Shutdown();
+                  }));
+          }
+          catch (Exception exception)
+          {
+            this.Dispatcher.BeginInvoke(
+              new Action(
+                () =>
+                  {
+                    MessageBox.Show(exception.StackTrace, exception.Message);
+                    Application.Current.Shutdown();
+                  }));
+          }
+        });
     }
 
     private void GeneratePatients_OnClick(object sender, RoutedEventArgs e)

diff --git a/Synthea.Iota.Ui/PatientList.xaml.cs b/Synthea.Iota.Ui/PatientList.xaml.cs
@@ -86,6 +86,7 @@ private void UploadResource(TreeViewItem treeViewItem, ParsedResource resource)
         var spinner = new LoadingSpinner();
         spinner.SetText("Creating resource on Tangle");
         ApplicationManager.SetContent(spinner);
+        ApplicationManager.MainWindow.MainMenu.IsEnabled = false;
 
         spinner.Start();
 
@@ -159,6 +160,7 @@ private void UploadResource(TreeViewItem treeViewItem, ParsedResource resource)
                   new Action(
                     () =>
                       {
+                        ApplicationManager.MainWindow.MainMenu.IsEnabled = true;
                         ApplicationManager.SetContent(this);
                       }));
               }