Source code

001package org.hl7.fhir.r4.utils;
002
003import java.io.BufferedReader;
004import java.io.IOException;
005import java.io.InputStreamReader;
006import java.net.URISyntaxException;
007import java.util.List;
008
009import org.hl7.fhir.exceptions.FHIRException;
010import org.hl7.fhir.r4.context.SimpleWorkerContext;
011import org.hl7.fhir.r4.fhirpath.FHIRPathEngine;
012import org.hl7.fhir.r4.formats.IParser.OutputStyle;
013import org.hl7.fhir.r4.formats.JsonParser;
014import org.hl7.fhir.r4.model.Base;
015import org.hl7.fhir.r4.model.BooleanType;
016import org.hl7.fhir.r4.model.Bundle;
017import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
018import org.hl7.fhir.r4.model.CapabilityStatement;
019import org.hl7.fhir.r4.model.CodeSystem;
020import org.hl7.fhir.r4.model.CodeType;
021import org.hl7.fhir.r4.model.CodeableConcept;
022import org.hl7.fhir.r4.model.Coding;
023import org.hl7.fhir.r4.model.Condition;
024import org.hl7.fhir.r4.model.DateType;
025import org.hl7.fhir.r4.model.HumanName;
026import org.hl7.fhir.r4.model.Immunization;
027import org.hl7.fhir.r4.model.Parameters;
028import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
029import org.hl7.fhir.r4.model.Patient;
030import org.hl7.fhir.r4.model.Period;
031import org.hl7.fhir.r4.model.Procedure;
032import org.hl7.fhir.r4.model.Property;
033import org.hl7.fhir.r4.model.Resource;
034import org.hl7.fhir.r4.model.StringType;
035import org.hl7.fhir.r4.model.Type;
036import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
037import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
038import org.hl7.fhir.utilities.Utilities;
039import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
040import org.hl7.fhir.utilities.npm.NpmPackage;
041
042@MarkedToMoveToAdjunctPackage
043public class CmdLineApp {
044
045  private FHIRToolingClient client;
046  private String currentId;
047  private Resource currentResource;
048  private SimpleWorkerContext context;
049  private FHIRPathEngine fpe;
050
051  public static void main(String[] args) throws IOException, Exception {
052    new CmdLineApp().execute();
053  }
054
055  private void execute() throws IOException {
056    System.out.print("Loading...");
057    NpmPackage npm = new FilesystemPackageCacheManager.Builder().build().loadPackage("hl7.fhir.r4.core");
058    context = SimpleWorkerContext.fromPackage(npm);
059    fpe = new FHIRPathEngine(context);
060    System.out.println(" Done");
061    BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
062    genMenu();
063    boolean finished = false;
064    do {
065      System.out.print("> ");
066      String cmd = reader.readLine();
067      String[] p = cmd.split("\\s+");
068      try {
069        if (p.length == 1 && p[0].equals("x")) {
070          finished = true;
071        } else if (p.length == 1 && p[0].equals("?")) {
072          genMenu();
073        } else if (p.length == 1 && p[0].equals("?tx")) {
074          genMenuTx();
075        } else if (p.length >= 1 && p[0].equals("c")) {
076          if (p.length == 1) {
077            connectToServer("http://hapi.fhir.org/baseR4");
078          } else {
079            connectToServer(p[1]);
080          }
081        } else if (p.length >= 1 && p[0].equals("imm")) {
082          if (p.length == 1) {
083            if (currentResource == null || !(currentResource instanceof Patient)) {
084              throw new FHIRException("Current resource must be a patient for this command");
085            }
086            getImmunizations();
087          } else {
088            select("Immunization", p[1]);
089          }
090        } else if (p.length >= 1 && p[0].equals("cnd")) {
091          if (p.length == 1) {
092            if (currentResource == null || !(currentResource instanceof Patient)) {
093              throw new FHIRException("Current resource must be a patient for this command");
094            }
095            getConditions();
096          } else {
097            select("Condition", p[1]);
098          }
099        } else if (p.length >= 1 && p[0].equals("prc")) {
100          if (p.length == 1) {
101            if (currentResource == null || !(currentResource instanceof Patient)) {
102              throw new FHIRException("Current resource must be a patient for this command");
103            }
104            getProcedures();
105          } else {
106            select("Procedure", p[1]);
107          }
108        } else if (p.length >= 1 && p[0].equals("v")) {
109          if (p.length == 1) {
110            viewResource();
111          } else {
112            viewResource(p[1]);
113          }
114        } else if (p.length >= 2 && p[0].equals("s")) {
115          search(p);
116        } else if (p.length >= 2 && p[0].equals("p")) {
117          select("Patient", p[1]);
118        } else if (p.length == 3 && p[0].equals("e")) {
119          edit(p[1], p[2]);
120        } else if (p.length > 3 && p[0].equals("tx")) {
121          tx(p);
122        } else {
123          System.out.println("Command unknown or not understood: "+cmd);
124        }
125      } catch (Exception e) {
126        System.out.println("Error executing command "+p[0]+": "+e.getMessage());
127      }
128    } while (!finished);
129    
130    System.out.println("Finished!"); 
131  }
132
133  private boolean tx(String[] p) throws IOException {
134    if (p[1].equals("l")) {
135      if (p.length == 4) {
136        return lookup(p[2], p[3]);
137      }
138    } else if (p[1].equals("v")) {
139      if (p.length == 4) {
140        return validate(p[2], p[3], null);
141      } else if (p.length == 5) {
142        return validate(p[2], p[3], p[4]);
143      }
144    }
145    throw new FHIRException("Not understood");
146  }
147
148  private boolean validate(String system, String code, String url) throws IOException {
149    Parameters pin = new Parameters();
150    if (url != null) {
151      pin.addParameter("url", url);
152    }
153    pin.addParameter("system", system);
154    pin.addParameter("code", code);
155    Parameters pout = client.operateType(CodeSystem.class, "validate-code", pin);
156    showParameters("  ", pout.getParameter());
157    return true;
158  }
159
160  private void showParameters(String prefix, List<ParametersParameterComponent> list) {
161    for (ParametersParameterComponent pp : list) {
162      if (pp.hasValue()) {        
163        System.out.println("  "+pp.getName()+": "+pp.getValue().toString());
164      } else if (pp.hasPart()) {
165        showParameters("   ", pp.getPart());
166      }
167    }
168  }
169
170  private boolean lookup(String string, String string2) {
171    throw new FHIRException("Not implemented");
172  }
173
174  private void getImmunizations() throws IOException {
175    Bundle bnd = client.search("Immunization", "?patient="+currentId);
176    System.out.println(""+bnd.getTotal()+" Immunizations found. Printing "+bnd.getEntry().size());
177    
178    for (BundleEntryComponent be : bnd.getEntry()) {
179      Resource imm = be.getResource();
180      System.out.println(summary(imm));
181    } 
182  }
183
184  private void getProcedures() throws IOException {
185
186    Bundle bnd = client.search("Procedure", "?patient="+currentId);
187    System.out.println(""+bnd.getTotal()+" Procedures found. Printing "+bnd.getEntry().size());
188    
189    for (BundleEntryComponent be : bnd.getEntry()) {
190      Resource imm = be.getResource();
191      System.out.println(summary(imm));
192    } 
193  }
194  
195  private void getConditions() throws IOException {
196
197    Bundle bnd = client.search("Condition", "?patient="+currentId);
198    System.out.println(""+bnd.getTotal()+" Conditions found. Printing "+bnd.getEntry().size());
199    
200    for (BundleEntryComponent be : bnd.getEntry()) {
201      Resource imm = be.getResource();
202      System.out.println(summary(imm));
203    } 
204  }
205
206  private void edit(String path, String value) {
207    if (path.contains(".")) {
208      List<Base> list = fpe.evaluate(currentResource, fpe.parse(path.substring(0, path.lastIndexOf("."))));
209      if (list.size() == 1) {
210        path = path.substring(path.lastIndexOf(".")+1);
211        Property p = list.get(0).getNamedProperty(path);
212        Base b = makeValue(p, value);
213        list.get(0).setProperty(path, b);
214      } else {
215        throw new FHIRException("Unable to set value at "+path+": "+list.size()+" matches");
216      }
217    } else {
218      Property p = currentResource.getNamedProperty(path);
219      Base b = makeValue(p, value);
220      currentResource.setProperty(path, b);
221    }
222    currentResource = client.update(currentResource);
223  }
224
225  private Base makeValue(Property p, String value) {
226    switch (p.getTypeCode()) {
227    case "boolean" : return new BooleanType(value);
228    case "code" :  return new CodeType(value);
229    case "string" : return new StringType(value);
230    case "date" : return new DateType(value);
231    }
232    throw new FHIRException("Unhandled type "+p.getTypeCode());
233  }
234
235  private void viewResource(String path) {
236    System.out.println("Current Resource, query = "+path);
237    List<Base> list = fpe.evaluate(currentResource, fpe.parse(path));
238    for (Base b : list) {
239      System.out.println(b.toString());
240    }
241  }
242
243  private void viewResource() throws IOException {
244    System.out.println("Current Resource:");
245    System.out.println(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(currentResource));
246  }
247
248  private void select(String type, String id) throws IOException {
249    if (type.equals("Patient")) {
250      currentResource = client.fetchResource(Patient.class, id);
251    } else if (type.equals("Immunization")) {
252      currentResource = client.fetchResource(Immunization.class, id);
253    } else if (type.equals("Condition")) {
254      currentResource = client.fetchResource(Condition.class, id);
255    } else if (type.equals("Procedure")) {
256      currentResource = client.fetchResource(Procedure.class, id);
257    } else {
258      throw new FHIRException("Unhandled type "+type);
259    }
260    currentId = type+"/"+id;
261    System.out.println("Resource = "+currentId+" "+summary(currentResource));
262  }
263
264  private String summary(Resource r) throws IOException {
265//    return new XmlParser().composeString(r);
266    if (r instanceof Patient) {
267      Patient pat = (Patient) r;
268      return pat.getIdBase()+" "+pat.getGender()+" "+pat.getBirthDateElement().asStringValue()+" "+name(pat);
269    }
270    if (r instanceof Immunization) {
271      Immunization imm = (Immunization) r;
272      return imm.getIdBase()+" "+imm.getOccurrenceDateTimeType().asStringValue()+" "+code(imm.getVaccineCode())+" "+imm.getLotNumber()+" ("+imm.getStatus()+")";
273    }
274    if (r instanceof Condition) {
275      Condition cnd = (Condition) r;
276      return cnd.getIdBase()+" "+code(cnd.getClinicalStatus())+" "+code(cnd.getVerificationStatus())+" "+code(cnd.getCode())+" "+cnd.getRecordedDateElement().asStringValue();
277    }
278    if (r instanceof Procedure) {
279      Procedure prc = (Procedure) r;
280      return prc.getIdBase()+" "+prc.getStatusElement().asStringValue()+" "+code(prc.getCode())+" "+code(prc.getCode())+" "+dt(prc.getPerformed());
281    }
282    return "??";
283  }
284
285  private String dt(Type type) {
286    if (type == null) {
287      return "";
288    }
289    if (type.isPrimitive()) {
290      return type.primitiveValue();
291    }
292    if (type instanceof Period) {
293      Period pd = (Period) type;
294      return pd.getStartElement().asStringValue()+" -> "+pd.getEndElement().asStringValue();
295    }
296    return "??";
297  }
298
299  private String code(CodeableConcept cc) {
300    for (Coding c : cc.getCoding()) {
301      if (c.hasSystem()) {
302        String d = c.hasDisplay() ? " ("+c.getDisplay()+")" : "";
303        if (c.hasCode()) {
304          switch (c.getSystem()) {
305          case "http://hl7.org/fhir/sid/cvx": return "CVX "+c.getCode()+d;
306          case "http://snomed.info/sct": return "SCT "+c.getCode()+d;
307          default:
308            if (Utilities.startsWithInList(c.getSystem(), "http://terminology.hl7.org")) {
309              return c.getCode();
310            } else {
311              throw new FHIRException("Unknown system "+c.getSystem());
312            }
313          }
314        }
315      }
316    }
317    for (Coding c : cc.getCoding()) {
318      if (c.hasCode()) {
319        return c.getCode();
320      }
321    }
322    if (cc.hasText()) {
323      return cc.getText();
324    }
325    return "";
326  }
327
328  private void search(String[] p) throws IOException {
329    if (client == null) {
330      throw new FHIRException("Not connected to to a server");
331    }
332    String search = "?name="+p[1];
333    if (p.length > 2) {
334      search = search +"&gender="+p[2];
335      if (p.length > 3) {
336        search = search +"&birthdate="+p[3];
337      }
338    }
339    Bundle bnd = client.search("Patient", search);
340    System.out.println(""+bnd.getTotal()+" Patients found. Printing "+bnd.getEntry().size());
341    
342    for (BundleEntryComponent be : bnd.getEntry()) {
343      Patient pat = (Patient) be.getResource();
344      System.out.println(summary(pat));
345    } 
346  }
347
348  private String name(Patient pat) {
349    if (pat.getName().size() > 0) {
350      return name(pat.getName().get(0));
351    }
352    return null;
353  }
354
355  private String name(HumanName n) {
356    if (n.hasText()) {
357      return n.getText();
358    }
359    if (n.hasFamily()) {
360      if (n.hasGiven()) {
361        return n.getGiven().get(0)+" "+n.getFamily().toUpperCase();
362      } else {
363        return n.getFamily().toUpperCase();
364      }
365    }
366    return "??";
367  }
368
369  private void connectToServer(String url) throws URISyntaxException {
370    client = new FHIRToolingClient(url, "FHIR-Command-Line-App");
371    CapabilityStatement cs = client.getCapabilitiesStatementQuick();
372    System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+", version "+cs.getFhirVersion().toCode());
373  }
374
375  private void genMenuTx() {
376
377    System.out.println("Simple Client. Commands you can run:");
378    System.out.println(" tx l {system} {code}");
379    System.out.println(" tx v {system} {code} {vs-url}");
380    System.out.println(" ?tx - print this again");    
381    System.out.println(" x - exit");    
382  }
383  
384  private void genMenu() {
385    System.out.println("Simple Client. Commands you can run:");
386    System.out.println(" c {url} - connect to a server");
387    System.out.println(" s {name} [{gender}] {{dob]} - find a patient record");
388    System.out.println(" p {id} - choose a patient record");    
389    System.out.println(" v [{field}] - see a set of field(s) in the current resource, or the whole resource");
390    System.out.println(" e {field} {value} - edit a field in the current resource");
391    System.out.println(" imm [{id}] - get a list of the patient's immunizations, or use the resource for the id (then use e to edit it)");
392    System.out.println(" cnd [{id}] - get a list of the patient's conditions, or use the resource for the id (then use e to edit it)");
393    System.out.println(" prc [{id}] - get a list of the patient's procedures, or use the resource for the id (then use e to edit it)");
394    System.out.println(" ? - print this again");    
395    System.out.println(" x - exit");    
396  }
397}