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