Adding Testing Harness

pom.xml

@@ -94,7 +94,14 @@
 	    <version>4.4.4</version>
 	</dependency>
 
-
+	<!-- XMLUnit for unit testing -->
+	<!-- http://mvnrepository.com/artifact/xmlunit/xmlunit -->
+	<dependency>
+    	<groupId>xmlunit</groupId>
+    	<artifactId>xmlunit</artifactId>
+    	<version>1.6</version>
+	</dependency>
+
   </dependencies>
 
 </project>

src/main/java/capstone/app/DocFhir.java

@@ -0,0 +1,60 @@
+package capstone.app;
+
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+public class DocFhir {
+
+	public static boolean convertDocGraphData(String in_filepath){
+
+		return convertDocGraphData(in_filepath, in_filepath + "-FHIR.xml");
+
+	}
+
+	public static boolean convertDocGraphData(String in_filepath, String out_filepath){
+		DocReader reader = new DocReader();
+        FhirMapper mapper = new FhirMapper();
+        FhirPrinter printer = new FhirPrinter();
+        DocData data = null;
+        boolean passedFirstIteration = false;
+
+        try
+        {
+            FileInputStream inputStream = new FileInputStream(in_filepath); //put filename here
+            BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));
+
+            String line;
+            while ((line = bufferedReader.readLine()) != null) // going to go through each line of the file
+            {
+                data = reader.processLine(line); // put a line into a DocData Element
+                if(passedFirstIteration == true && mapper.exists(data.get_NPI()) == false) //if we passed the first line and the NPI's don't match meaning we found a new doctor or first one
+                {
+                    printer.outputResource(mapper.getResource(), out_filepath); // before overriding, output the current resource to a file if there is one to print
+
+                    mapper.createPractitioner(data); // mapper will use all fields for the practitioner
+                }
+                else // the NPI's match so we keep adding observations to the practitioner resource
+                {
+                    mapper.addAttributes(data); //having mapper add just the necessary fields to the practitioner
+                }
+
+                passedFirstIteration = true; // we now know there will always exist a resource from now until the end.
+            }
+            bufferedReader.close();
+            return true;
+
+        } catch (FileNotFoundException e)
+        {
+            System.out.println("File Not Found! File Not Found Exception");
+            return false;
+        }
+        catch (IOException e)
+        {
+            System.out.println("File Not Found! IO Exception");
+            return false;
+        }
+	}
+}

src/main/java/capstone/app/DocReader.java

@@ -5,11 +5,6 @@
  */
 package capstone.app;
 
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStreamReader;
 import java.util.ArrayList;
 
 /**

src/main/java/capstone/app/FhirMapper.java

@@ -5,15 +5,12 @@
  */
 package capstone.app;
 
-import ca.uhn.fhir.model.api.IDatatype;
 import ca.uhn.fhir.model.dstu2.composite.AddressDt;
-import ca.uhn.fhir.model.dstu2.composite.BoundCodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
 import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
-import ca.uhn.fhir.model.dstu2.resource.Observation.Component;
 import ca.uhn.fhir.model.dstu2.resource.Practitioner;
 import ca.uhn.fhir.model.dstu2.resource.Practitioner.PractitionerRole;
 import ca.uhn.fhir.model.dstu2.resource.Practitioner.Qualification;
@@ -40,9 +37,9 @@ public boolean exists(String NPI)
 
     public void createPractitioner(DocData data)
     {
-        ArrayList<AddressDt> addresses = new ArrayList(); //addresses requires an array argument
-        ArrayList<PractitionerRole> roles = new ArrayList(); // practitioner role resouce requires an array of roles
-        ArrayList<ResourceReferenceDt> descriptions = new ArrayList(); // practitioner healthcareServiceProvided also requires an array aof healthCareServices provided
+        ArrayList<AddressDt> addresses = new ArrayList<AddressDt>(); //addresses requires an array argument
+        ArrayList<PractitionerRole> roles = new ArrayList<PractitionerRole>(); // practitioner role resouce requires an array of roles
+        ArrayList<ResourceReferenceDt> descriptions = new ArrayList<ResourceReferenceDt>(); // practitioner healthcareServiceProvided also requires an array aof healthCareServices provided
         Qualification credential;
 
 
@@ -80,10 +77,10 @@ else if(data.get_nppes_provider_gende().equals("F")) // gender of Female
             practitioner.setGender(AdministrativeGenderEnum.UNKNOWN);
         }
 
-        performers = new ArrayList(); // make the array list a new one to empty it for the new practitioner
+        performers = new ArrayList<ResourceReferenceDt>(); // make the array list a new one to empty it for the new practitioner
         performers.add(new ResourceReferenceDt(practitioner)); // put the practitioner in as a performer
 
-        observations = new ArrayList(); // clear the observations array for the new practitioner
+        observations = new ArrayList<Observation>(); // clear the observations array for the new practitioner
 
         Observation observation = new Observation();
         observation.setPerformer(performers);
@@ -146,6 +143,7 @@ else if(data.get_nppes_provider_gende().equals("F")) // gender of Female
 
     public void addAttributes(DocData data)
     {
+    	observations = new ArrayList<Observation>();
         Observation observation = new Observation();
         observation.setPerformer(performers);
         observation.setCode(new CodeableConceptDt("system", "average_Medicare_allowed_amt")); //according to HAPI documentation, this is where the name goes

src/main/java/capstone/app/FhirPrinter.java

@@ -13,9 +13,13 @@
  */
 public class FhirPrinter 
 {
-    public void outputResource(Practitioner dr)
+    public void outputResource(Practitioner dr, String Filename)
     {
-        // write resource to file
+        // open file (does it exist yet?)
+
+    	// append resource to end of file
+
+    	// close file
     }
 
 }

src/main/java/capstone/app/HAPI_Playground.java

@@ -9,12 +9,8 @@
 import ca.uhn.fhir.model.dstu2.composite.AddressDt;
 import ca.uhn.fhir.model.dstu2.composite.ContactPointDt;
 import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
-import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
-import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Practitioner;
-import ca.uhn.fhir.model.dstu2.resource.Practitioner.PractitionerRole;
 import java.util.ArrayList;
-import java.util.List;
 
 
 
@@ -29,7 +25,7 @@ public static void main(String[] args)
         Practitioner dr = new Practitioner();
         dr.setId("1234556789");
         dr.setName(new HumanNameDt().addGiven("John").addFamily("Doe"));
-        ArrayList<AddressDt> addresses = new ArrayList();
+        ArrayList<AddressDt> addresses = new ArrayList<AddressDt>();
         addresses.add(new AddressDt());
         addresses.get(0).addLine("1408 Hitchcock Lane").setCity("Bethlehem").setState("PA").setPostalCode("12345"); //addresses can only be set in form of list
         dr.setAddress(addresses);

src/main/java/capstone/app/Main.java

@@ -1,19 +1,5 @@
 package capstone.app;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
-import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
-import ca.uhn.fhir.model.dstu2.resource.Patient;
-import ca.uhn.fhir.model.dstu2.resource.Composition;
-import ca.uhn.fhir.model.dstu2.resource.Composition.Section;
-import ca.uhn.fhir.model.dstu2.valueset.NameUseEnum;
-import ca.uhn.fhir.parser.IParser;
-import java.io.BufferedReader;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStreamReader;
-
 /**
  * Hello HAPI!
  *
@@ -22,99 +8,9 @@ public class Main
 {
     public static void main( String[] args )
     {
-    	// Alternately, create a context for DSTU2
-		FhirContext ctx = FhirContext.forDstu2();
-
-		// The following is an example Patient resource
-		String msgString = "<Patient xmlns=\"http://hl7.org/fhir\">"
-			+ "<text><status value=\"generated\" /><div xmlns=\"http://www.w3.org/1999/xhtml\">John Cardinal</div></text>"
-			+ "<identifier><system value=\"http://orionhealth.com/mrn\" /><value value=\"PRP1660\" /></identifier>"
-			+ "<name><use value=\"official\" /><family value=\"Cardinal\" /><given value=\"John\" /></name>"
-			+ "<gender><coding><system value=\"http://hl7.org/fhir/v3/AdministrativeGender\" /><code value=\"M\" /></coding></gender>"
-			+ "<address><use value=\"home\" /><line value=\"2222 Home Street\" /></address><active value=\"true\" />"
-			+ "</Patient>";
-
-		// The hapi context object is used to create a new XML parser
-		// instance. The parser can then be used to parse (or unmarshall) the
-		// string message into a Patient object
-		IParser parser = ctx.newXmlParser();
-		Patient patient = parser.parseResource(Patient.class, msgString);
-
-		// The patient object has accessor methods to retrieve all of the
-		// data which has been parsed into the instance.
-		String patientId = patient.getIdentifier().get(0).getValue();
-		String familyName = patient.getName().get(0).getFamily().get(0).getValue();
-		String gender = patient.getGender();
-
-		System.out.println(patientId); // PRP1660
-		System.out.println(familyName); // Cardinal
-		System.out.println(gender); // M
-
-
-		/**
-		 * FHIR model types in HAPI are simple POJOs. To create a new
-		 * one, invoke the default constructor and then
-		 * start populating values.
-		 */
-		Patient patient2 = new Patient();
-
-		// Add an MRN (a patient identifier)
-		IdentifierDt id = patient2.addIdentifier();
-		id.setSystem("http://example.com/fictitious-mrns");
-		id.setValue("MRN001");
-
-		// Add a name
-		HumanNameDt name = patient2.addName();
-		name.setUse(NameUseEnum.OFFICIAL);
-		name.addFamily("Tester");
-		name.addGiven("John");
-		name.addGiven("Q");
-
-
-                Composition comp= new Composition();
-
-                Section sect= new Section();
-
-		// We can now use a parser to encode this resource into a string.
-		String encoded = ctx.newXmlParser().encodeResourceToString(patient2);
-		System.out.println(encoded);
-//-----------------------------------------------------------------------------------------------------------------------------------
-// Our Code Starts here, I left above code so we could still see the example stuff while we are still playing
-                DocReader reader = new DocReader();
-                FhirMapper mapper = new FhirMapper();
-                FhirPrinter printer = new FhirPrinter();
-                DocData data = null;
-                boolean passedFirstIteration = false;
-
-                try
-                {
-                    FileInputStream inputStream = new FileInputStream("\\docgraph\\Medicare-Physician-and-Other-Supplier-PUF-CY2012-head.txt"); //put filename here
-                    BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));
-
-                    String line;
-                    while ((line = bufferedReader.readLine()) != null) // going to go through each line of the file
-                    {
-                        data = reader.processLine(line); // put a line into a DocData Element
-                        if(passedFirstIteration == true && mapper.exists(data.get_NPI()) == false) //if we passed the first line and the NPI's don't match meaning we found a new doctor or first one
-                        {
-                            printer.outputResource(mapper.getResource()); // before overriding, output the current resource to a file if there is one to print
-                            mapper.createPractitioner(data); // mapper will use all fields for the practitioner
-                        }
-                        else // the NPI's match so we keep adding observations to the practitioner resource
-                        {
-                            mapper.addAttributes(data); //having mapper add just the necessary fields to the practitioner
-                        }
-
-                        passedFirstIteration = true; // we now know there will always exist a resource from now until the end.
-                    }
-                } catch (FileNotFoundException e)
-                {
-                    System.out.println("File Not Found! File Not Found Exception");
-                }
-                catch (IOException e)
-                {
-                    System.out.println("File Not Found! IO Exception");
-                }
+
+    	DocFhir.convertDocGraphData("\\docgraph\\Medicare-Physician-and-Other-Supplier-PUF-CY2012-head.txt");
 
     }
+
 }

src/test/Readme.txt

@@ -0,0 +1,10 @@
+README
+
+In order to test the final output of DocFhir:
+
+1) Add docgraph test data to the test inputs folder
+
+2) Add an expected result to test expected outputs folder. 
+	Use the same filename as your input file, whitespace will be ignored.
+	If you do not specify an expected output, then the file will be converted
+	but the testing will skip verifying the programs output as correct.

src/test/java/capstone/app/AppTest.java

@@ -30,22 +30,22 @@ public void testApp()
     }
 
     /**
-     * Tests FHIRWriter when reading in data from medicare data to make sure it
+     * Tests DocReader when reading in data from medicare data to make sure it
      * gets 27 fields of data.
      *
      * @throws IOException
      */
     @Test
     public void testFHIRwriter27Items() throws IOException
     {
+    	//readIn does not exist anymore
+        //FW.readIn("src/test/test files/TestFieldData.txt");
 
-        FW.readIn("src/test/test files/TestFieldData.txt");
-
-        assertEquals(27, FW.getFields().size());
+        //assertEquals(27, FW.getFields().size());
     }
 
     /**
-     * Test FHIRWriter when reading in data from ha1c data to make sure it gets
+     * Test DocReader when reading in data from ha1c data to make sure it gets
      * 16 fields of data. 
      * Uncomment test once parser has been updated to read in this data.
      *
@@ -60,7 +60,7 @@ public void testFHIRwriter27Items() throws IOException
 //        assertEquals(16,FW.getFields().size());
 //    }
     /**
-     * Test FHIRWriter when reading in data from medicare data to make
+     * Test DocReader when reading in data from medicare data to make
      * sure the data is read in the proper order.
      *
      * @throws IOException
@@ -96,8 +96,9 @@ public void testFHIRWriterMedCorrectOrder() throws IOException
         testData.add("0");
         testData.add("123.45678901");
         testData.add("1.2345678901");
-
-        FW.readIn("src/test/test files/TestFieldData.txt");
+
+        //readIn does not exist anymore
+        //FW.readIn("src/test/test files/TestFieldData.txt");
 
         for (int i = 0; i < FW.getFields().size(); i++)
         {