update MIMIC code and reverse testing change (maven said no)

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/CodeableConcept.java

@@ -319,6 +319,25 @@ public class CodeableConcept extends Type implements ICompositeType {
         return super.isEmpty() && ca.uhn.fhir.util.ElementUtil.isEmpty(coding, text);
       }
 
+   // added from java-adornments.txt:
+      
+      public boolean hasCoding(String system, String code) {
+        for (Coding c : getCoding()) {
+          if (system.equals(c.getSystem()) && code.equals(c.getCode()))
+            return true;
+        }
+        return false;
+      } 
+
+      public CodeableConcept(Coding code) {
+        super();
+        addCoding(code);
+      }
+      
+      
+
+    // end addition
+
 
 }
 

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/importers/Mimic14Importer.java

@@ -31,9 +31,14 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.math.BigDecimal;
 import java.nio.charset.Charset;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Map;
+import java.util.Set;
 import java.util.UUID;
 
 import org.fhir.ucum.UcumEssenceService;
@@ -53,6 +58,7 @@ import org.hl7.fhir.r4.model.DocumentReference;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Enumerations.DocumentReferenceStatus;
+import org.hl7.fhir.r4.model.InstantType;
 import org.hl7.fhir.r4.model.MedicationRequest;
 import org.hl7.fhir.r4.model.MedicationRequest.MedicationRequestStatus;
 import org.hl7.fhir.r4.model.Observation;
@@ -61,11 +67,15 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.hl7.fhir.r4.model.PractitionerRole;
+import org.hl7.fhir.r4.model.Procedure;
+import org.hl7.fhir.r4.model.Procedure.ProcedureStatus;
 import org.hl7.fhir.r4.model.Quantity;
 import org.hl7.fhir.r4.model.Quantity.QuantityComparator;
+import org.hl7.fhir.r4.model.Range;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Type;
 import org.hl7.fhir.utilities.CSVReader;
+import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.Utilities;
 
 public class Mimic14Importer {
@@ -96,9 +106,10 @@ public class Mimic14Importer {
   private Date date;
   private Map<String, LabItem> labItems = new HashMap<>();
   private Map<String, Item> items = new HashMap<>();
-//  private Map<String, PractitionerRole> careGivers = new HashMap<>();
+  private Map<String, PractitionerRole> careGivers = new HashMap<>();
   private Map<String, Patient> patients = new HashMap<>();
   private Map<String, Encounter> encounters = new HashMap<>();
+  private IniFile ini;
 
   private UcumService ucum;
   
@@ -116,6 +127,7 @@ public class Mimic14Importer {
     System.out.println("Loading UCUM from "+ucumSrc);
   
    ucum = new UcumEssenceService(ucumSrc);
+   ini = new IniFile(Utilities.path(src, "translations.ini"));
   
    loadItems(Utilities.path(src, "d_items.csv"));
    loadLabItems(Utilities.path(src, "d_labitems.csv"));
@@ -127,7 +139,11 @@ public class Mimic14Importer {
    processMicroEvents(Utilities.path(src, "microbiologyevents.csv"), Utilities.path(dest, "micro-observations.json"));
    processNoteEvents(Utilities.path(src, "noteevents.csv"), Utilities.path(dest, "notes.json"));
    processDiagnoses(Utilities.path(src, "diagnoses_icd.csv"), Utilities.path(dest, "diagnoses.json"));
+   processProcedures(Utilities.path(src, "procedures_icd.csv"), Utilities.path(dest, "procedures.json"));
    processPrescriptions(Utilities.path(src, "prescriptions.csv"), Utilities.path(dest, "prescriptions.json"));
+   processProcedureEvents(Utilities.path(src, "procedureevents_mv.csv"), Utilities.path(dest, "procedure-events.json"));
+   processOutputEvents(Utilities.path(src, "outputevents.csv"), Utilities.path(dest, "outputs.json"));
+   processChartEvents(Utilities.path(src, "chartevents.csv"), Utilities.path(dest, "chartevents.json"));
    
    System.out.println("saving");
    
@@ -198,6 +214,7 @@ public class Mimic14Importer {
       t++;
       pr.setId(csv.cell("cgid"));
       pr.addCode().addCoding().setSystem("http://mimic.physionet.org/fhir/CareGiverType").setCode(csv.cell("label")).setDisplay(csv.cell("description"));
+      careGivers.put(pr.getId(), pr);
       bnd.addEntry().setResource(pr);
     }
     System.out.println(Integer.toString(t)+" found");
@@ -232,7 +249,7 @@ public class Mimic14Importer {
       obs.setEffective(readDateTime(csv.cell("charttime")));
       if (item != null) {
         if (!Utilities.noString(item.category)) {
-          obs.addCategory().setText(item.category);
+          obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode(item.category);
         }
         obs.getCode().setText(item.label);
         if (!Utilities.noString(item.fluid)) {
@@ -244,14 +261,7 @@ public class Mimic14Importer {
       }
 
       if (csv.has("valuenum")) {
-        Quantity qty = new Quantity();
+        Quantity qty = parseQuantity(csv.cell("valuenum"), "valueuom"); 
-        qty.setValue(new BigDecimal(csv.cell("valuenum")));
-        String uom = csv.cell("valueuom");
-        qty.setUnit(uom);
-        if (ucum.validate(uom) == null) {
-          qty.setCode(uom);
-          qty.setSystem("http://unitsofmeasure.org");
-        }
         obs.setValue(qty);
       } else {
         obs.setValue(new CodeableConcept().setText(csv.cell("value")));
@@ -306,7 +316,7 @@ public class Mimic14Importer {
         cache.put(cacheId, obs);
         obs.setId(csv.cell("row_id"));
         obs.setStatus(ObservationStatus.FINAL);
-        obs.addCategory().setText("microbiology");
+        obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("microbiology");
         bnd.addEntry().setResource(obs);
  
         
@@ -594,6 +604,41 @@ public class Mimic14Importer {
     new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
   }
 
+  private void processProcedures(String src, String dest) throws FileNotFoundException, IOException {
+    System.out.print("Processing Procedures... ");
+    CSVReader csv = new CSVReader(new FileInputStream(src));
+    Bundle bnd = new Bundle();
+    bnd.setId("procedures");
+    bnd.setType(BundleType.COLLECTION);
+    bnd.setTimestamp(date);    
+    csv.readHeaders();
+    int t = 0;
+    while (csv.line()) {
+      Procedure prc = new Procedure();
+      t++;
+
+      Patient pat = patients.get(csv.cell("subject_id"));
+      Encounter enc = encounters.get(csv.cell("hadm_id"));
+
+      prc.setId(csv.cell("row_id"));
+      prc.setStatus(ProcedureStatus.UNKNOWN);
+      prc.getCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("diagnosis");
+      if (pat != null) {
+        prc.setSubject(new Reference("Patient/"+pat.getId()));
+      }
+      if (enc != null) {
+        prc.setEncounter(new Reference("Encounter/"+enc.getId()));
+        enc.addDiagnosis().setCondition(new Reference("Procedure/"+prc.getId())).setRank(Integer.parseInt(csv.cell("seq_num")));
+      }
+      prc.setCode(new CodeableConcept(new Coding().setCode(csv.cell("icd9_code")).setSystem("http://hl7.org/fhir/sid/icd-9-cm")));
+
+      bnd.addEntry().setResource(prc);
+    }
+    System.out.println(Integer.toString(t)+" found");
+    csv.close();
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
+  }
+
   private void processPrescriptions(String src, String dest) throws FHIRException, FileNotFoundException, IOException {
     System.out.print("Processing Prescriptions... ");
     CSVReader csv = new CSVReader(new FileInputStream(src));
@@ -618,20 +663,238 @@ public class Mimic14Importer {
       if (enc != null) {
         med.setEncounter(new Reference("Encounter/"+enc.getId()));
       }
-      
+      med.getDispenseRequest().getValidityPeriod().setStartElement(readDateTime(csv.cell("startdate")));
-      
+      med.getDispenseRequest().getValidityPeriod().setEndElement(readDateTime(csv.cell("enddate")));
-//      cnd.setCode(new CodeableConcept(new Coding().setCode(csv.cell("icd9_code")).setSystem("http://hl7.org/fhir/sid/icd-9-cm")));
+      med.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode(csv.cell("drug_type"));
+      CodeableConcept cc = new CodeableConcept();
+      cc.setText(csv.cell("drug"));
+      if (csv.has("formulary_drug_cd")) {
+        cc.addCoding().setSystem("http://mimic.physionet.org/fhir/drugs").setCode(csv.cell("formulary_drug_cd"));
+      }
+      med.setMedication(cc);
+//      if (csv.has("gsn")) {
+//        cc.addCoding().setSystem("http://hl7.org/fhir/sid/GSN?").setCode(csv.cell("gsn"));
+//      }
+      if (csv.has("ndc")) {
+        cc.addCoding().setSystem("http://hl7.org/fhir/sid/ndc").setCode(csv.cell("ndc"));
+      }
+
+      //PROD_STRENGTH, DOSE_VAL_RX, DOSE_UNIT_RX - ignore as denomormalizations
+      if (csv.has("dose_val_rx")) {
+        try {
+          med.getDosageInstructionFirstRep().getDoseAndRateFirstRep().setDose(parseQuantityRange(csv.cell("dose_val_rx"), csv.cell("dose_unit_rx")));
+        } catch (Exception e) {
+          med.getDosageInstructionFirstRep().setText(csv.cell("dose_val_rx"));
+        }
+      }
+      if (csv.has("route")) {
+        med.getDosageInstructionFirstRep().getRoute().addCoding().setSystem("http://mimic.physionet.org/fhir/route").setCode(csv.cell("route"));
+      }
 
       bnd.addEntry().setResource(med);
     }
     System.out.println(Integer.toString(t)+" found");
     csv.close();
     new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
-
-    
   }
 
-  private Type parseQuantity(String cell) {
+  private void processProcedureEvents(String src, String dest) throws FileNotFoundException, IOException {
+    System.out.print("Processing Procedure Events... ");
+    CSVReader csv = new CSVReader(new FileInputStream(src));
+    Bundle bnd = new Bundle();
+    bnd.setId("procedure-events");
+    bnd.setType(BundleType.COLLECTION);
+    bnd.setTimestamp(date);    
+    csv.readHeaders();
+    int t = 0;
+    while (csv.line()) {
+      Procedure prc = new Procedure();
+      t++;
+
+      Patient pat = patients.get(csv.cell("subject_id"));
+      Encounter enc = encounters.get(csv.cell("hadm_id"));
+
+      prc.setId(csv.cell("row_id"));
+      prc.setStatus(ProcedureStatus.UNKNOWN);
+      prc.getCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("diagnosis");
+      if (pat != null) {
+        prc.setSubject(new Reference("Patient/"+pat.getId()));
+      }
+      if (enc != null) {
+        prc.setEncounter(new Reference("Encounter/"+enc.getId()));
+      }
+      prc.getPerformedPeriod().setStartElement(readDateTime(csv.cell("starttime")));
+      prc.getPerformedPeriod().setEndElement(readDateTime(csv.cell("endtime")));
+      Item spec = items.get(csv.cell("itemid"));
+      if (spec != null)
+        prc.setCode(new CodeableConcept(new Coding().setSystem("http://mimic.physionet.org/fhir/procedures").setCode(csv.cell("itemid")).setDisplay(spec.label)));
+      if (csv.has("location"))
+        prc.addBodySite().setText(csv.cell("location"));
+      bnd.addEntry().setResource(prc);
+    }
+    System.out.println(Integer.toString(t)+" found");
+    csv.close();
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
+  }
+
+  private void processOutputEvents(String src, String dest) throws FileNotFoundException, IOException {
+    System.out.print("Processing Output Events... ");
+    CSVReader csv = new CSVReader(new FileInputStream(src));
+    Bundle bnd = new Bundle();
+    bnd.setId("output-events");
+    bnd.setType(BundleType.COLLECTION);
+    bnd.setTimestamp(date);    
+    csv.readHeaders();
+    int t = 0;
+    while (csv.line()) {
+      t++;
+      Patient pat = patients.get(csv.cell("subject_id"));
+      Encounter enc = encounters.get(csv.cell("hadm_id"));
+      Item spec = items.get(csv.cell("itemid"));
+      String loinc = ini.getStringProperty("outputs", csv.cell("itemid"));
+      if (loinc != null) {
+        if (!loinc.equals("n/a")) {
+          String value = null;
+          if (loinc.contains(";")) {
+            String[] p = loinc.split("\\;");
+            value=p[1].trim();
+            loinc = p[0];
+          }
+          Observation obs = new Observation();
+          obs.setId(csv.cell("row_id"));
+          obs.setStatus(ObservationStatus.FINAL);
+          obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("output");
+
+          if (pat != null) {
+            obs.setSubject(new Reference("Patient/"+pat.getId()));
+          }
+          if (enc != null) {
+            obs.setEncounter(new Reference("Encounter/"+enc.getId()));
+          }
+          obs.setEffective(readDateTime(csv.cell("charttime")));
+          if (spec != null) {
+            obs.setCode(new CodeableConcept(loincCoding(loinc)).setText(spec.label));
+            obs.getCode().addCoding().setSystem("http://mimic.physionet.org/fhir/outputs").setCode(csv.cell("itemid"));
+          }
+          if (value != null) {
+            obs.setValue(new CodeableConcept().setText(value)); 
+          } else {
+            Quantity qty = parseQuantity(csv.cell("value"), "valueuom"); 
+            obs.setValue(qty);
+          }
+          obs.setIssuedElement(readInstant(csv.cell("storetime")));
+
+          PractitionerRole prr = careGivers.get(csv.cell("cgid"));
+          if (prr != null)
+            obs.addPerformer().setReference("PractitionerRole/"+prr.getId());
+
+          bnd.addEntry().setResource(obs);
+        }
+      } else {
+        throw new Error("No LOINC code for output event "+csv.cell("itemid")+" ("+(spec == null ? "n/a" : spec.label)+"="+csv.cell("value")+")");
+      }
+    }
+    System.out.println(Integer.toString(t)+" found");
+    csv.close();
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
+  }
+
+  private void processChartEvents(String src, String dest) throws FileNotFoundException, IOException {
+    System.out.print("Processing Chart Events... ");
+    CSVReader csv = new CSVReader(new FileInputStream(src));
+    Bundle bnd = new Bundle();
+    bnd.setId("chart-events");
+    bnd.setType(BundleType.COLLECTION);
+    bnd.setTimestamp(date);    
+    csv.readHeaders();
+    int t = 0;
+    while (csv.line()) {
+      t++;
+      Patient pat = patients.get(csv.cell("subject_id"));
+      Encounter enc = encounters.get(csv.cell("hadm_id"));
+      Item spec = items.get(csv.cell("itemid"));
+      if (spec != null) {
+        Observation obs = new Observation();
+        obs.setId(csv.cell("row_id"));
+        obs.setStatus(ObservationStatus.FINAL);
+        obs.addCategory().addCoding().setSystem("http://mimic.physionet.org/fhir/categories").setCode("chart");
+
+        if (pat != null) {
+          obs.setSubject(new Reference("Patient/"+pat.getId()));
+        }
+        if (enc != null) {
+          obs.setEncounter(new Reference("Encounter/"+enc.getId()));
+        }
+        obs.setEffective(readDateTime(csv.cell("charttime")));
+
+        obs.getCode().setText(spec.label).addCoding().setSystem("http://mimic.physionet.org/fhir/outputs").setCode(csv.cell("itemid"));
+        String loinc = ini.getStringProperty("chartevents", csv.cell("itemid"));
+        String value = null;
+        if (!Utilities.noString(loinc)) {
+          if (loinc.contains(";")) {
+            String[] p = loinc.split("\\;");
+            value=p[1].trim();
+            loinc = p[0];
+          }
+          obs.getCode().addCoding(loincCoding(loinc));
+        }
+        if (value != null) {
+          obs.setValue(new CodeableConcept().setText(value));         
+        } else if (csv.has("valuenum")) {
+          Quantity qty = parseQuantity(csv.cell("valuenum"), "valueuom"); 
+          obs.setValue(qty);
+        } else {
+          obs.setValue(new CodeableConcept().setText(csv.cell("value")));
+        }
+        obs.setIssuedElement(readInstant(csv.cell("storetime")));
+
+        PractitionerRole prr = careGivers.get(csv.cell("cgid"));
+        if (prr != null)
+          obs.addPerformer().setReference("PractitionerRole/"+prr.getId());
+
+        bnd.addEntry().setResource(obs);
+      }
+    }
+    System.out.println(Integer.toString(t)+" found");
+    csv.close();
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), bnd);    
+  }
+
+  private Coding loincCoding(String loinc) {
+    Coding c = new Coding();
+    String[] p = loinc.split("\\#");
+    c.setSystem(p[0]);
+    p = p[1].split("\\:");
+    c.setCode(p[0]);
+    c.setDisplay(p[1].trim());
+    return c;
+  }
+
+  private Type parseQuantityRange(String cell, String uom) {
+    if (!Utilities.noString(cell) && cell.contains("-")) {
+      String[] p = cell.split("\\-");
+      Range rng = new Range();
+      rng.setLow(parseQuantity(p[0], uom));
+      rng.setHigh(parseQuantity(p[1], uom));
+      return rng;
+    } else
+      return parseQuantity(cell, uom);
+  }
+  private Quantity parseQuantity(String cell, String uom) {
+    if (Utilities.noString(cell))
+      return null;
+    Quantity qty = parseQuantity(cell);
+    if (!Utilities.noString(uom)) {
+      qty.setUnit(uom);
+      if (ucum.validate(uom) == null) {
+        qty.setCode(uom);
+        qty.setSystem("http://unitsofmeasure.org");
+      }
+    }
+    return qty;
+  }
+  
+  private Quantity parseQuantity(String cell) {
     if (cell.startsWith("<=")) {
       return new Quantity().setComparator(QuantityComparator.LESS_OR_EQUAL).setValue(new BigDecimal(cell.substring(2)));
     }
@@ -645,7 +908,7 @@ public class Mimic14Importer {
       return new Quantity().setComparator(QuantityComparator.GREATER_THAN).setValue(new BigDecimal(cell.substring(2)));
     }
     if (!Utilities.isDecimal(cell, true)) {
-      throw new Error("Not a valid decimal: "+cell);
+      throw new FHIRException("Not a valid decimal: "+cell);
     }
       
     return new Quantity().setValue(new BigDecimal(cell));
@@ -734,15 +997,26 @@ public class Mimic14Importer {
 
 
   private DateType readDate(String cell) {
+    if (Utilities.noString(cell))
+      return null;
     String src = cell.substring(0, 10);
     return new DateType(src);
   }
 
   private DateTimeType readDateTime(String cell) {
+    if (Utilities.noString(cell))
+      return null;
     String src = cell.replace(" ", "T");
     if (src.endsWith("00:00:00"))
       src = cell.substring(0, 10);
     return new DateTimeType(src);
   }
 
+  private InstantType readInstant(String cell) {
+    if (Utilities.noString(cell))
+      return null;
+    String src = cell.replace(" ", "T");
+    return new InstantType(src);
+  }
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestingUtilities.java

@@ -1,4 +1,4 @@
-package org.hl7.fhir.r5.test;
+package org.hl7.fhir.r5.test.utils;
 
 /*-
  * #%L

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java

@@ -17,6 +17,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.utilities.cache.PackageCacheManager;
 import org.hl7.fhir.utilities.cache.ToolsVersion;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRMappingLanguageTests.java

@@ -26,6 +26,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r5.model.StructureMap;
 import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.StructureMapUtilities;
 import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
 import org.hl7.fhir.utilities.TextFile;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java

@@ -25,6 +25,7 @@ import org.hl7.fhir.r5.model.Quantity;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLEngineTests.java

@@ -9,6 +9,7 @@ import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
 import org.hl7.fhir.r5.model.Bundle.SearchEntryMode;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.model.DomainResource;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.utils.GraphQLEngine;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLParserTests.java

@@ -7,6 +7,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.graphql.EGraphEngine;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/LiquidEngineTests.java

@@ -14,6 +14,7 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.LiquidEngine;
 import org.hl7.fhir.r5.utils.LiquidEngine.ILiquidEngineIcludeResolver;
 import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGeneratorTests.java

@@ -11,6 +11,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.DomainResource;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.r5.utils.NarrativeGenerator;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/OpenApiGeneratorTest.java

@@ -11,6 +11,7 @@ import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.openapi.OpenApiGenerator;
 import org.hl7.fhir.r5.openapi.Writer;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.Test;
 import org.w3c.dom.Document;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java

@@ -16,6 +16,7 @@ import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceRoundTripTests.java

@@ -19,6 +19,7 @@ import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.DomainResource;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.r5.utils.NarrativeGenerator;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.r5.conformance.ShExGenerator;
 import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.TextFile;
 import org.junit.Test;
 

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java

@@ -43,6 +43,7 @@ import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
 import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
 import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
 import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestFetchMode;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.CodingUtilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java

@@ -12,6 +12,7 @@ import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.StructureMap;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.EOperationOutcome;
 import org.hl7.fhir.r5.utils.StructureMapUtilities;
 import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/TurtleTests.java

@@ -3,6 +3,7 @@ package org.hl7.fhir.r5.test;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.formats.Turtle;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/misc/ResourceTest.java

@@ -44,7 +44,7 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Resource;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 
 public class ResourceTest {
 

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/misc/StructureMapTests.java

@@ -12,7 +12,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.model.StructureMap;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.StructureMapUtilities;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageHacker.java

@@ -22,7 +22,7 @@ import com.google.gson.JsonObject;
 public class PackageHacker {
 
   public static void main(String[] args) throws FileNotFoundException, IOException {
-    new PackageHacker().edit("C:\\web\\hl7.org\\fhir\\us\\qicore\\STU2\\package.tgz");
+    new PackageHacker().edit("C:\\work\\fhir.org\\web-source\\source\\guides\\argonaut\\questionnaire\\package.tgz");
   }
 
   private void edit(String name) throws FileNotFoundException, IOException {
@@ -54,8 +54,8 @@ public class PackageHacker {
   }
 
   private void change(JsonObject npm, Map<String, byte[]> content) {
-    npm.remove("version");
+    npm.remove("name");
-    npm.addProperty("version", "2.0.0");
+    npm.addProperty("name", "fhir.argonaut.questionnaire");
 //    JsonArray fhirVersions = new JsonArray();
 //    fhirVersions.add("1.9.0");
 //    npm.add("fhirVersions", fhirVersions);

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/CDAValidationTestCase.java

@@ -1,7 +1,7 @@
 package org.hl7.fhir.validation.tests;
 
 import org.hl7.fhir.r4.context.SimpleWorkerContext;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.validation.Validator;
 import org.hl7.fhir.validation.tests.utilities.TestUtilities;
 import org.junit.Test;

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/NativeHostServiceTester.java

@@ -1,6 +1,6 @@
 package org.hl7.fhir.validation.tests;
 
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.validation.NativeHostServices;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.validation.tests.utilities.TestUtilities;

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ProfileComparisonTests.java

@@ -10,7 +10,7 @@ import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.utils.KeyGenerator;
 import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.validation.ValidationEngine;
 import org.hl7.fhir.validation.tests.utilities.TestUtilities;
 import org.junit.Assert;

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java

@@ -9,7 +9,7 @@ import org.hl7.fhir.r5.model.FhirPublication;
 import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.validation.ValidationEngine;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.validation.tests.utilities.TestUtilities;

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java

@@ -21,7 +21,7 @@ import org.hl7.fhir.r5.elementmodel.ObjectConverter;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.*;
-import org.hl7.fhir.r5.test.TestingUtilities;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher;