Merge pull request #1175 from usnistgov/feature/multiple-fixes-pre-de…

…ployment

Feature/multiple fixes pre deployment

bootstrap/src/main/java/gov/nist/hit/hl7/igamt/bootstrap/app/BootstrapApplication.java

@@ -36,7 +36,9 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import ca.uhn.fhir.context.FhirContext;
+import gov.nist.hit.hl7.igamt.bootstrap.data.CodeFixer;
 import gov.nist.hit.hl7.igamt.bootstrap.data.ConformanceStatementFixer;
+import gov.nist.hit.hl7.igamt.bootstrap.data.DynamicMappingFixer;
 import gov.nist.hit.hl7.igamt.bootstrap.data.IgFixer;
 import gov.nist.hit.hl7.igamt.bootstrap.data.TablesFixes;
 import gov.nist.hit.hl7.igamt.bootstrap.factory.BindingCollector;
@@ -133,6 +135,8 @@ public static void main(String[] args) {
 
   @Autowired
   private PredicateRepository predicateRepository;
+  @Autowired
+  DynamicMappingFixer dynamicMappingFixer;
 
   //  @Autowired
   //  RelationShipService testCache;
@@ -176,6 +180,8 @@ public static void main(String[] args) {
 
   @Autowired
   ConformanceStatementFixer conformanceStatementFixer;
+  @Autowired
+  CodeFixer codeFixer;
 
 
   @Bean
@@ -993,4 +999,14 @@ void fixConformanceStatements() throws IGUpdateException, CoConstraintGroupNotFo
 
   }
 
+ // @PostConstruct
+  void addDynamicMappingInfo() {
+    codeFixer.fixTableHL70125();
+    dynamicMappingFixer.processSegments();
+  }
+
+  // @PostConstruct
+   void fixHl70125() throws FileNotFoundException {
+     codeFixer.fixFromCSV();
+   }
 }

bootstrap/src/main/java/gov/nist/hit/hl7/igamt/bootstrap/data/CodeFixer.java

@@ -0,0 +1,106 @@
+/**
+ * This software was developed at the National Institute of Standards and Technology by employees of
+ * the Federal Government in the course of their official duties. Pursuant to title 17 Section 105
+ * of the United States Code this software is not subject to copyright protection and is in the
+ * public domain. This is an experimental system. NIST assumes no responsibility whatsoever for its
+ * use by other parties, and makes no guarantees, expressed or implied, about its quality,
+ * reliability, or any other characteristic. We would appreciate acknowledgement if the software is
+ * used. This software can be redistributed and/or modified freely provided that any derivative
+ * works bear some notice that they are derived from it, and any modified versions bear some notice
+ * that they have been modified.
+ */
+package gov.nist.hit.hl7.igamt.bootstrap.data;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.util.ResourceUtils;
+
+import com.opencsv.CSVReader;
+
+import gov.nist.hit.hl7.igamt.common.base.domain.Scope;
+import gov.nist.hit.hl7.igamt.datatype.repository.DatatypeRepository;
+import gov.nist.hit.hl7.igamt.valueset.domain.Valueset;
+import gov.nist.hit.hl7.igamt.valueset.service.ValuesetService;
+
+/**
+ * @author Abdelghani El Ouakili
+ *
+ */
+@Service
+public class CodeFixer {
+
+  @Autowired
+  private DatatypeRepository datatypeRepository;
+
+  @Autowired
+  private ValuesetService valueSetService;
+
+  public void fixTableHL70125() {
+   List<Valueset> vss = valueSetService.findByDomainInfoScopeAndBindingIdentifier(Scope.HL7STANDARD.toString(), "HL70125");
+
+   for(Valueset vs: vss) {
+     vs.getCodes().removeIf((x) -> !datatypeRepository.existsByNameAndDomainInfoScopeAndDomainInfoVersion(x.getValue(), Scope.HL7STANDARD, vs.getDomainInfo().getVersion()));
+     vs.setNumberOfCodes(vs.getCodes().size());
+     valueSetService.save(vs);
+
+   }
+  }
+
+  public void fixFromCSV() throws FileNotFoundException {
+
+    File file = ResourceUtils.getFile("classpath:deprecatedCodes.csv");
+    System.out.println(file.exists());
+    CSVReader reader = null;
+    Map<String, Set<String>> map = new HashMap<String, Set<String>>();
+    try {
+      reader = new CSVReader(new FileReader(file));
+      String[] line1= reader.readNext();
+      while ((line1 = reader.readNext()) != null) {
+          String id = line1[1]+"V"+line1[0].replaceAll("\\.", "-");
+          if(map.containsKey(id)) {
+            Set<String> codes = map.get(id);
+                if(codes != null) {
+                  codes.add(line1[2]);
+                }
+
+          }else {
+            Set<String> codes = new HashSet<String>();
+            codes.add(line1[2]);
+            map.put(id, codes);         
+          }
+
+      }
+      fix(map);
+    } catch (IOException e) {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * @param map
+   */
+  private void fix(Map<String, Set<String>> map) {
+    // TODO Auto-generated method stub
+   List<Valueset> valuesets= valueSetService.findByIdIn(map.keySet());
+
+   valuesets.forEach(x -> {     
+     x.getCodes().forEach((c) -> {
+       if(map.get(x.getId()).contains(c.getValue())) {
+         c.setDeprecated(true);
+       }     
+     });      
+     valueSetService.save(x);
+   });
+  }
+
+}

bootstrap/src/main/java/gov/nist/hit/hl7/igamt/bootstrap/data/DynamicMappingFixer.java

@@ -0,0 +1,103 @@
+/**
+ * This software was developed at the National Institute of Standards and Technology by employees of
+ * the Federal Government in the course of their official duties. Pursuant to title 17 Section 105
+ * of the United States Code this software is not subject to copyright protection and is in the
+ * public domain. This is an experimental system. NIST assumes no responsibility whatsoever for its
+ * use by other parties, and makes no guarantees, expressed or implied, about its quality,
+ * reliability, or any other characteristic. We would appreciate acknowledgement if the software is
+ * used. This software can be redistributed and/or modified freely provided that any derivative
+ * works bear some notice that they are derived from it, and any modified versions bear some notice
+ * that they have been modified.
+ */
+package gov.nist.hit.hl7.igamt.bootstrap.data;
+
+import java.util.List;
+import java.util.Optional;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import gov.nist.hit.hl7.igamt.common.base.domain.Scope;
+import gov.nist.hit.hl7.igamt.common.base.domain.ValuesetBinding;
+import gov.nist.hit.hl7.igamt.common.binding.domain.StructureElementBinding;
+import gov.nist.hit.hl7.igamt.datatype.domain.Datatype;
+import gov.nist.hit.hl7.igamt.datatype.service.DatatypeService;
+import gov.nist.hit.hl7.igamt.segment.domain.DynamicMappingInfo;
+import gov.nist.hit.hl7.igamt.segment.domain.DynamicMappingItem;
+import gov.nist.hit.hl7.igamt.segment.domain.Segment;
+import gov.nist.hit.hl7.igamt.segment.service.SegmentService;
+import gov.nist.hit.hl7.igamt.valueset.domain.Code;
+import gov.nist.hit.hl7.igamt.valueset.domain.Valueset;
+import gov.nist.hit.hl7.igamt.valueset.service.ValuesetService;
+
+/**
+ * @author Abdelghani El Ouakili
+ *
+ */
+@Service
+public class DynamicMappingFixer {
+
+  @Autowired
+  SegmentService segmentsService;
+
+  @Autowired
+  ValuesetService valueSetService;
+
+  @Autowired
+  DatatypeService datatypeService;
+
+
+  public void processSegments() {
+    List<Segment> obxs = segmentsService.findByName("OBX");
+    obxs.forEach((x) -> {processSegment(x);});
+  }
+
+
+  /**
+   * @param x
+   */
+  private void processSegment(Segment s) {
+    // TODO Auto-generated method stub
+    s.setDynamicMappingInfo(new DynamicMappingInfo("2", "5", null));
+    String vsId =  findObx2VsId(s);
+
+    if(vsId != null) {
+      Valueset vs = valueSetService.findById(vsId);
+      for(Code c : vs.getCodes()) {
+        if(c.getValue() !=null) {
+         Datatype d = datatypeService.findOneByNameAndVersionAndScope(c.getValue(),s.getDomainInfo().getVersion(), Scope.HL7STANDARD.toString());
+         if(d != null) {
+           s.getDynamicMappingInfo().addItem(new DynamicMappingItem(d.getId(), c.getValue()));
+         }
+        }
+      }
+    }
+    segmentsService.save(s);  
+  }
+
+
+  /**
+   * @param s
+   * @return
+   */
+  private String findObx2VsId(Segment s) {
+    // TODO Auto-generated method stub
+    if(s.getBinding() != null && s.getBinding().getChildren() != null) {
+     for(StructureElementBinding child : s.getBinding().getChildren()) {
+       if(child.getLocationInfo() != null && child.getLocationInfo().getPosition() ==2) {
+         if(child.getValuesetBindings() != null) {
+           Optional<ValuesetBinding> vs = child.getValuesetBindings().stream().findAny();
+           if(vs.isPresent() && vs.get().getValueSets() !=null && !vs.get().getValueSets().isEmpty()) {
+            return vs.get().getValueSets().get(0);
+           }
+
+         }
+       }
+     }
+    }
+
+    return null;
+  }
+
+
+}