Source code

001package org.hl7.fhir.r5.utils;
002
003import java.io.FileInputStream;
004import java.io.FileNotFoundException;
005import java.io.FileOutputStream;
006import java.io.IOException;
007import java.io.InputStream;
008import java.util.ArrayList;
009import java.util.HashMap;
010import java.util.List;
011import java.util.Map;
012
013import org.hl7.fhir.exceptions.FHIRException;
014import org.hl7.fhir.r5.formats.IParser.OutputStyle;
015import org.hl7.fhir.r5.formats.JsonParser;
016import org.hl7.fhir.r5.model.CanonicalResource;
017import org.hl7.fhir.r5.model.ConceptMap;
018import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
019import org.hl7.fhir.r5.model.ConceptMap.OtherElementComponent;
020import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
021import org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent;
022import org.hl7.fhir.r5.model.DateTimeType;
023import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
024import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
025import org.hl7.fhir.r5.model.IdType;
026import org.hl7.fhir.r5.model.StringType;
027import org.hl7.fhir.r5.model.StructureMap;
028import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupComponent;
029import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleComponent;
030import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleDependentComponent;
031import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleSourceComponent;
032import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupRuleTargetComponent;
033import org.hl7.fhir.r5.model.StructureMap.StructureMapTransform;
034import org.hl7.fhir.r5.model.UrlType;
035import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
036import org.hl7.fhir.utilities.CSVReader;
037import org.hl7.fhir.utilities.FileUtilities;
038import org.hl7.fhir.utilities.MarkedToMoveToAdjunctPackage;
039import org.hl7.fhir.utilities.Utilities;
040import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
041
042@MarkedToMoveToAdjunctPackage
043public class MappingSheetParser {
044
045  public class MappingRow {
046    private String sequence;
047    private String identifier;
048    private String name;
049    private String dataType;
050    private String cardinality;
051    private String condition;
052    private String attribute;
053    private String type;
054    private String minMax;
055    private String dtMapping;
056    private String vocabMapping;
057    private String derived;
058    private String derivedMapping;
059    private String comments;
060    public String getSequence() {
061      return sequence;
062    }
063    public String getIdentifier() {
064      return identifier;
065    }
066    public String getName() {
067      return name;
068    }
069    public String getDataType() {
070      return dataType;
071    }
072    public String getCardinality() {
073      return cardinality;
074    }
075    public int getCardinalityMin() {
076      return Integer.parseInt(cardinality.split("\\.")[0]);
077    }
078    public String getCardinalityMax() {
079      return cardinality.split("\\.")[2];
080    }
081    public String getCondition() {
082      return condition;
083    }
084    public String getAttribute() {
085      return attribute;
086    }
087    public String getType() {
088      return type;
089    }
090    public String getMinMax() {
091      return minMax;
092    }
093    public String getDtMapping() {
094      return dtMapping;
095    }
096    public String getVocabMapping() {
097      return vocabMapping;
098    }
099    public String getDerived() {
100      return derived;
101    }
102    public String getDerivedMapping() {
103      return derivedMapping;
104    }
105    public String getComments() {
106      return comments;
107    }
108
109  }
110
111
112  private List<MappingRow> rows = new ArrayList<>();
113  private Map<String, String> metadata = new HashMap<>();
114
115  public MappingSheetParser() {
116    super();    
117  }
118    
119  public void  parse(InputStream stream, String name) throws FHIRException, IOException {
120    CSVReader csv = new CSVReader(stream);
121    checkHeaders1(csv, name);
122    checkHeaders2(csv, name);
123    while (csv.line()) {
124      processRow(csv); 
125    }
126  }
127
128  private void checkHeaders1(CSVReader csv, String name) throws FHIRException, IOException {
129    csv.readHeaders();
130    csv.checkColumn(1, "HL7 v2", "Mapping Sheet "+name);
131    csv.checkColumn(6, "Condition (IF True)", "Mapping Sheet "+name);
132    csv.checkColumn(7, "HL7 FHIR", "Mapping Sheet "+name);
133    csv.checkColumn(14, "Comments", "Mapping Sheet "+name);
134    csv.checkColumn(16, "Name", "Mapping Sheet "+name);
135    csv.checkColumn(17, "Value", "Mapping Sheet "+name);
136  }
137
138  private void checkHeaders2(CSVReader csv, String name) throws FHIRException, IOException {
139    csv.readHeaders();
140    csv.checkColumn(1, "Display Sequence", "Mapping Sheet "+name);
141    csv.checkColumn(2, "Identifier", "Mapping Sheet "+name);
142    csv.checkColumn(3, "Name", "Mapping Sheet "+name);
143    csv.checkColumn(4, "Data Type", "Mapping Sheet "+name);
144    csv.checkColumn(5, "Cardinality", "Mapping Sheet "+name);
145    csv.checkColumn(7, "FHIR Attribute", "Mapping Sheet "+name);
146    csv.checkColumn(8, "Data Type", "Mapping Sheet "+name);
147    csv.checkColumn(9, "Cardinality", "Mapping Sheet "+name);
148    csv.checkColumn(10, "Data Type Mapping", "Mapping Sheet "+name);
149    csv.checkColumn(11, "Vocabulary Mapping\n(IS, ID, CE, CNE, CWE)", "Mapping Sheet "+name);
150    csv.checkColumn(12, "Derived Mapping", "Mapping Sheet "+name);
151  }
152
153  private void processRow(CSVReader csv) {
154    MappingRow mr = new MappingRow();
155    mr.sequence = csv.value(1);
156    mr.identifier =  csv.value(2);
157    mr.name = csv.value(3);
158    mr.dataType = csv.value(4);
159    mr.cardinality = csv.value(5);
160    mr.condition = csv.value(6);
161    mr.attribute = csv.value(7);
162    mr.type = csv.value(8);
163    mr.minMax = csv.value(9);
164    mr.dtMapping = csv.value(10);
165    mr.vocabMapping = csv.value(11);
166    mr.derived = csv.value(12);
167    if (!Utilities.noString(mr.derived)) {
168      String[] s = mr.derived.split("\\=");
169      mr.derived = s[0].trim();
170      mr.derivedMapping = s[1].trim();
171    }
172    mr.comments = csv.value(14);
173    rows.add(mr);
174    if (!org.hl7.fhir.utilities.Utilities.noString(csv.value(16)))
175      metadata.put(csv.value(16), csv.value(17));
176  }
177
178  public List<MappingRow> getRows() {
179    return rows;
180  }
181
182  public ConceptMap getConceptMap() throws FHIRException {
183    ConceptMap map = new ConceptMap();
184    loadMetadata(map);
185    if (metadata.containsKey("copyright"))
186      map.setCopyright(metadata.get("copyright"));
187    for (MappingRow row : rows) {
188      SourceElementComponent element = map.getGroupFirstRep().addElement();
189      element.setCode(row.getIdentifier());
190      element.setId(row.getSequence());
191      element.setDisplay(row.getName()+" : "+row.getDataType()+" ["+row.getCardinality()+"]");
192      element.addExtension(ToolingExtensions.EXT_MAPPING_NAME, new StringType(row.getName()));
193      element.addExtension(ToolingExtensions.EXT_MAPPING_TYPE, new StringType(row.getDataType()));
194      element.addExtension(ToolingExtensions.EXT_MAPPING_CARD, new StringType(row.getCardinality()));
195      if ("N/A".equals(row.getAttribute()))
196        element.setNoMap(true);
197      else {
198        element.getTargetFirstRep().setRelationship(ConceptMapRelationship.RELATEDTO);
199        if (row.getCondition() != null)
200          element.getTargetFirstRep().addDependsOn().setAttribute("http://hl7.org/fhirpath").setValue(new StringType(processCondition(row.getCondition())));
201        element.getTargetFirstRep().setCode(row.getAttribute());
202        element.getTargetFirstRep().setDisplay(row.getType()+" : ["+row.getMinMax()+"]");
203        element.getTargetFirstRep().addExtension(ToolingExtensions.EXT_MAPPING_TGTTYPE, new StringType(row.getType()));
204        element.getTargetFirstRep().addExtension(ToolingExtensions.EXT_MAPPING_TGTCARD, new StringType(row.getMinMax()));
205        if (row.getDerived() != null) 
206          element.getTargetFirstRep().getProductFirstRep().setAttribute(row.getDerived()).setValue(new StringType(row.getDerivedMapping()));
207        if (row.getComments() != null)
208          element.getTargetFirstRep().setComment(row.getComments());
209        if (row.getDtMapping() != null)
210          element.getTargetFirstRep().addExtension("http://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping", new UrlType("todo#"+row.getDtMapping()));
211        if (row.getVocabMapping() != null)
212          element.getTargetFirstRep().addExtension("http://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping", new UrlType("todo#"+row.getVocabMapping()));
213      }
214    }
215    return map;    
216  }
217
218  private String processCondition(String condition) {
219    if (condition.startsWith("IF ") && condition.endsWith(" IS VALUED"))
220      return "`"+condition.substring(4, condition.length()-10)+"`.exists()";
221    if (condition.startsWith("IF ") && condition.endsWith(" DOES NOT EXIST"))
222      return "`"+condition.substring(4, condition.length()-15)+"`.exists()";
223    throw new Error("not processed yet: "+condition); 
224  }
225
226  private void loadMetadata(CanonicalResource mr) throws FHIRException {
227    if (metadata.containsKey("id"))
228      mr.setId(metadata.get("id"));
229    if (metadata.containsKey("url"))
230      mr.setUrl(metadata.get("url"));
231    if (metadata.containsKey("name"))
232      mr.setName(metadata.get("name"));
233    if (metadata.containsKey("title"))
234      mr.setTitle(metadata.get("title"));
235    if (metadata.containsKey("version"))
236      mr.setVersion(metadata.get("version"));
237    if (metadata.containsKey("status"))
238      mr.setStatus(PublicationStatus.fromCode(metadata.get("status")));
239    if (metadata.containsKey("date"))
240      mr.setDateElement(new DateTimeType(metadata.get("date")));
241    if (metadata.containsKey("publisher"))
242      mr.setPublisher(metadata.get("publisher"));
243    if (metadata.containsKey("description"))
244      mr.setDescription(metadata.get("description"));
245  }
246
247  public StructureMap getStructureMap() throws FHIRException {
248    StructureMap map = new StructureMap();
249    loadMetadata(map);
250    if (metadata.containsKey("copyright"))
251      map.setCopyright(metadata.get("copyright"));
252    StructureMapGroupComponent grp = map.addGroup();
253    for (MappingRow row : rows) {
254      StructureMapGroupRuleComponent rule = grp.addRule();
255      rule.setName(row.getSequence());
256      StructureMapGroupRuleSourceComponent src = rule.getSourceFirstRep();
257      src.setContext("src");
258      src.setElement(row.getIdentifier());
259      src.setMin(row.getCardinalityMin());
260      src.setMax(row.getCardinalityMax());
261      src.setType(row.getDataType());
262      src.addExtension(ToolingExtensions.EXT_MAPPING_NAME, new StringType(row.getName()));
263      if (row.getCondition() != null) {
264        src.setCheck(processCondition(row.getCondition()));
265      }
266      StructureMapGroupRuleTargetComponent tgt = rule.getTargetFirstRep();
267      tgt.setContext("tgt");
268      tgt.setElement(row.getAttribute());
269      tgt.addExtension(ToolingExtensions.EXT_MAPPING_TGTTYPE, new StringType(row.getType()));
270      tgt.addExtension(ToolingExtensions.EXT_MAPPING_TGTCARD, new StringType(row.getMinMax()));
271      if (row.getDtMapping() != null) {
272        src.setVariable("s");
273        tgt.setVariable("t");
274        tgt.setTransform(StructureMapTransform.CREATE);
275        StructureMapGroupRuleDependentComponent dep = rule.addDependent();
276        dep.setName(row.getDtMapping());
277        dep.addParameter().setValue(new IdType("s"));
278        dep.addParameter().setValue(new IdType("t"));
279      } else if (row.getVocabMapping() != null) {
280        tgt.setTransform(StructureMapTransform.TRANSLATE);
281        tgt.addParameter().setValue(new StringType(row.getVocabMapping()));
282        tgt.addParameter().setValue(new IdType("src"));
283      } else {
284        tgt.setTransform(StructureMapTransform.COPY);
285      }
286      rule.setDocumentation(row.getComments());
287      if (row.getDerived() != null) { 
288        tgt = rule.addTarget();
289        tgt.setContext("tgt");
290        tgt.setElement(row.getDerived());
291        tgt.setTransform(StructureMapTransform.COPY);
292        tgt.addParameter().setValue(new StringType(row.getDerivedMapping()));
293      }
294    }
295    return map;
296  }
297
298  public boolean isSheet(ConceptMap cm) {
299    if (cm.getGroup().size() != 1)
300      return false;
301    ConceptMapGroupComponent grp = cm.getGroupFirstRep();
302    for (SourceElementComponent e : grp.getElement()) {
303      if (!e.hasExtension(ToolingExtensions.EXT_MAPPING_TYPE))
304        return false;
305    }
306    return true;
307  }
308
309  public String genSheet(ConceptMap cm) throws FHIRException {
310    StringBuilder b = new StringBuilder();
311    readConceptMap(cm);
312    b.append("<table class=\"grid\">\r\n");
313    addHeaderRow1(b);
314    addHeaderRow2(b);
315    for (MappingRow row : rows) 
316      addRow(b, row);
317    b.append("</table>\r\n");
318    return b.toString();
319  }
320
321  private void addRow(StringBuilder b, MappingRow row) {
322    b.append(" <tr>");
323    b.append("<td>"+Utilities.escapeXml(nn(row.sequence))+"</td>");
324    b.append("<td>"+Utilities.escapeXml(nn(row.identifier))+"</td>");
325    b.append("<td>"+Utilities.escapeXml(nn(row.name))+"</td>");
326    b.append("<td>"+Utilities.escapeXml(nn(row.dataType))+"</td>");
327    b.append("<td>"+Utilities.escapeXml(nn(row.cardinality))+"</td>");
328    b.append("<td>"+Utilities.escapeXml(nn(row.condition))+"</td>");
329    b.append("<td>"+Utilities.escapeXml(nn(row.attribute))+"</td>");
330    b.append("<td>"+Utilities.escapeXml(nn(row.type))+"</td>");
331    b.append("<td>"+Utilities.escapeXml(nn(row.minMax))+"</td>");
332    b.append("<td>"+Utilities.escapeXml(nn(row.dtMapping))+"</td>");
333    b.append("<td>"+Utilities.escapeXml(nn(row.vocabMapping))+"</td>");
334    if (row.derived != null)
335      b.append("<td>"+Utilities.escapeXml(nn(row.derived+"="+row.derivedMapping))+"</td>");
336    else
337      b.append("<td></td>");
338    b.append("<td>"+Utilities.escapeXml(nn(row.comments))+"</td>");
339    b.append("</tr>\r\n");   
340    
341  }
342
343  private String nn(String s) {
344    return s == null ? "" : s;
345  }
346
347  private void addHeaderRow1(StringBuilder b) {
348    b.append(" <tr>");
349    b.append("<td colspan=\"5\" style=\"background-color: lightgreen\"><b>v2</b></td>");
350    b.append("<td colspan=\"1\"><b>Condition</b></td>");
351    b.append("<td colspan=\"6\" style=\"background-color: orange\"><b>FHIR</b></td>");
352    b.append("<td colspan=\"1\"><b>Comments</b></td>");
353    b.append("</tr>\r\n");
354  }
355
356  private void addHeaderRow2(StringBuilder b) {
357    b.append(" <tr>");
358    b.append("<td style=\"background-color: lightgreen\"><b>Display Sequence</b></td>");
359    b.append("<td style=\"background-color: lightgreen\"><b>Identifier</b></td>");
360    b.append("<td style=\"background-color: lightgreen\"><b>Name</b></td>");
361    b.append("<td style=\"background-color: lightgreen\"><b>Data Type</b></td>");
362    b.append("<td style=\"background-color: lightgreen\"><b>Cardinality</b></td>");
363    b.append("<td><b></b></td>");
364    b.append("<td style=\"background-color: orange\"><b>FHIR Attribute</b></td>");
365    b.append("<td style=\"background-color: orange\"><b>Data Type</b></td>");
366    b.append("<td style=\"background-color: orange\"><b>Cardinality</b></td>");
367    b.append("<td style=\"background-color: orange\"><b>Data Type Mapping</b></td>");
368    b.append("<td style=\"background-color: orange\"><b>Vocabulary Mapping</b></td>");
369    b.append("<td style=\"background-color: orange\"><b>Derived Mapping</b></td>");
370    b.append("<td><b></b></td>");
371    b.append("</tr>\r\n");   
372  }
373
374  private void readConceptMap(ConceptMap cm) throws FHIRException {
375    for (ConceptMapGroupComponent g : cm.getGroup()) {
376      for (SourceElementComponent e : g.getElement()) {
377        if (e.hasId() && e.getTarget().size() == 1 && e.hasExtension(ToolingExtensions.EXT_MAPPING_TYPE)) {
378          TargetElementComponent t = e.getTargetFirstRep();
379          MappingRow row = new MappingRow();
380          row.sequence = e.getId();
381          row.identifier = e.getCode();
382          row.name = e.getExtensionString(ToolingExtensions.EXT_MAPPING_NAME);
383          row.dataType = e.getExtensionString(ToolingExtensions.EXT_MAPPING_TYPE);
384          row.cardinality = e.getExtensionString(ToolingExtensions.EXT_MAPPING_CARD);
385          if (e.getNoMap() == true) {
386            row.attribute = "N/A";            
387          } else {
388            OtherElementComponent dep = getDependency(t, "http://hl7.org/fhirpath");
389            if (dep != null)
390              row.condition = dep.getValue().primitiveValue();
391            row.attribute = t.getCode();
392            row.type = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTTYPE);
393            row.minMax = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTCARD);
394            row.dtMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping");
395            row.vocabMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping");
396            if (t.getProduct().size() > 0) {
397              row.derived = t.getProductFirstRep().getAttribute();
398              row.derivedMapping = t.getProductFirstRep().getValue().primitiveValue();
399            }
400          }
401          row.comments = t.getComment();
402          rows.add(row);
403        }
404      }
405    }
406  }
407
408
409  private OtherElementComponent getDependency(TargetElementComponent t, String prop) {
410    for (OtherElementComponent dep : t.getDependsOn()) {
411      if (prop.equals(dep.getAttribute()))
412        return dep;
413    }
414    return null;
415  }
416
417  private static final String PFX = "<html><link rel=\"stylesheet\" href=\"file:c:\\work\\org.hl7.fhir\\build\\publish\\fhir.css\"/></head><body>\r\n";
418  private static final String SFX = "<body></html>";
419  public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
420    MappingSheetParser parser = new MappingSheetParser();
421    parser.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "v2-pid.csv")), "v2-pid.csv");
422    ConceptMap cm = parser.getConceptMap();
423    StructureMap sm = parser.getStructureMap();
424    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "sm.json")), sm);
425    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "cm.json")), cm);
426    FileUtilities.stringToFile(StructureMapUtilities.render(sm), Utilities.path("[tmp]", "sm.txt"));
427    FileUtilities.stringToFile(PFX+parser.genSheet(cm)+SFX, Utilities.path("[tmp]", "map.html"));
428  }
429
430}