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