fix bug converting search parameters
This commit is contained in:
Grahame Grieve
parent
c002d5b5d1
commit
5e6755e422
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@ -54,6 +54,22 @@ public class VersionConvertor_40_50 {
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}
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}
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protected static void copyEnumeration(org.hl7.fhir.r4.model.Enumeration<?> src, org.hl7.fhir.r5.model.Enumeration<?> tgt) throws FHIRException {
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if (src.hasId())
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tgt.setId(src.getId());
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for (org.hl7.fhir.r4.model.Extension e : src.getExtension()) {
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tgt.addExtension(convertExtension(e));
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}
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}
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protected static void copyEnumeration(org.hl7.fhir.r5.model.Enumeration<?> src, org.hl7.fhir.r4.model.Enumeration<?> tgt) throws FHIRException {
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if (src.hasId())
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tgt.setId(src.getId());
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for (org.hl7.fhir.r5.model.Extension e : src.getExtension()) {
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tgt.addExtension(convertExtension(e));
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}
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}
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protected static void copyBackboneElement(org.hl7.fhir.r4.model.BackboneElement src, org.hl7.fhir.r5.model.BackboneElement tgt) throws FHIRException {
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copyElement(src, tgt);
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for (org.hl7.fhir.r4.model.Extension e : src.getModifierExtension()) {
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@ -91,7 +91,7 @@ public class SearchParameter extends VersionConvertor_40_50 {
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for (org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchComparator> t : src.getComparator())
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tgt.addComparator(convertSearchComparator(t.getValue()));
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for (org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode> t : src.getModifier())
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tgt.addModifier(convertSearchModifierCode(t.getValue()));
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tgt.getModifier().add(convertSearchModifierCode(t));
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for (org.hl7.fhir.r4.model.StringType t : src.getChain())
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tgt.getChain().add(convertString(t));
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for (org.hl7.fhir.r4.model.SearchParameter.SearchParameterComponentComponent t : src.getComponent())
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@ -151,7 +151,7 @@ public class SearchParameter extends VersionConvertor_40_50 {
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for (org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchComparator> t : src.getComparator())
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tgt.addComparator(convertSearchComparator(t.getValue()));
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for (org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode> t : src.getModifier())
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tgt.addModifier(convertSearchModifierCode(t.getValue()));
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tgt.getModifier().add(convertSearchModifierCode(t));
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for (org.hl7.fhir.r5.model.StringType t : src.getChain())
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tgt.getChain().add(convertString(t));
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for (org.hl7.fhir.r5.model.SearchParameter.SearchParameterComponentComponent t : src.getComponent())
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@ -219,45 +219,51 @@ public class SearchParameter extends VersionConvertor_40_50 {
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}
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}
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public static org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode convertSearchModifierCode(org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode src) throws FHIRException {
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public static org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode> convertSearchModifierCode(org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode> src) throws FHIRException {
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if (src == null)
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return null;
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switch (src) {
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case MISSING: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.MISSING;
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case EXACT: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.EXACT;
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case CONTAINS: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.CONTAINS;
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case NOT: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NOT;
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case TEXT: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.TEXT;
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case IN: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.IN;
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case NOTIN: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NOTIN;
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case BELOW: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.BELOW;
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case ABOVE: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.ABOVE;
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case TYPE: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.TYPE;
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case IDENTIFIER: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.IDENTIFIER;
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case OFTYPE: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.OFTYPE;
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default: return org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NULL;
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org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode> tgt = new org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode>();
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copyEnumeration(src, tgt);
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switch (src.getValue()) {
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case MISSING: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.MISSING);
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case EXACT: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.EXACT);
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case CONTAINS: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.CONTAINS);
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case NOT: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NOT);
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case TEXT: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.TEXT);
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case IN: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.IN);
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case NOTIN: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NOTIN);
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case BELOW: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.BELOW);
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case ABOVE: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.ABOVE);
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case TYPE: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.TYPE);
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case IDENTIFIER: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.IDENTIFIER);
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case OFTYPE: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.OFTYPE);
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default: tgt.setValue(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode.NULL);
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}
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return tgt;
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}
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}
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public static org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode convertSearchModifierCode(org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode src) throws FHIRException {
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public static org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode> convertSearchModifierCode(org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode> src) throws FHIRException {
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if (src == null)
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return null;
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switch (src) {
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case MISSING: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.MISSING;
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case EXACT: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.EXACT;
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case CONTAINS: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.CONTAINS;
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case NOT: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NOT;
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case TEXT: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.TEXT;
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case IN: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.IN;
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case NOTIN: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NOTIN;
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case BELOW: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.BELOW;
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case ABOVE: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.ABOVE;
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case TYPE: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.TYPE;
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case IDENTIFIER: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.IDENTIFIER;
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case OFTYPE: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.OFTYPE;
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default: return org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NULL;
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org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode> tgt = new org.hl7.fhir.r4.model.Enumeration<org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode>();
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copyEnumeration(src, tgt);
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switch (src.getValue()) {
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case MISSING: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.MISSING);
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case EXACT: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.EXACT);
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case CONTAINS: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.CONTAINS);
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case NOT: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NOT);
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case TEXT: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.TEXT);
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case IN: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.IN);
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case NOTIN: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NOTIN);
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case BELOW: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.BELOW);
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case ABOVE: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.ABOVE);
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case TYPE: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.TYPE);
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case IDENTIFIER: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.IDENTIFIER);
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case OFTYPE: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.OFTYPE);
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default: tgt.setValue( org.hl7.fhir.r4.model.SearchParameter.SearchModifierCode.NULL);
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}
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return tgt;
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}
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}
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public static org.hl7.fhir.r5.model.SearchParameter.SearchParameterComponentComponent convertSearchParameterComponentComponent(org.hl7.fhir.r4.model.SearchParameter.SearchParameterComponentComponent src) throws FHIRException {
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if (src == null)
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@ -0,0 +1,213 @@
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package org.hl7.fhir.r5.utils;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.fhir.ucum.Utilities;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.r5.model.ConceptMap;
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import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
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import org.hl7.fhir.r5.model.DateTimeType;
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import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r5.model.MetadataResource;
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import org.hl7.fhir.r5.model.UrlType;
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import org.hl7.fhir.utilities.CSVReader;
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public class MappingSheetParser {
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public class MappingRow {
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private String sequence;
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private String identifier;
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private String name;
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private String dataType;
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private String cardinality;
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private String condition;
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private String attribute;
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private String type;
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private String minMax;
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private String dtMapping;
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private String vocabMapping;
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private String derived;
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private String derivedMapping;
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private String comments;
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public String getSequence() {
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return sequence;
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}
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public String getIdentifier() {
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return identifier;
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}
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public String getName() {
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return name;
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}
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public String getDataType() {
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return dataType;
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}
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public String getCardinality() {
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return cardinality;
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}
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public String getCondition() {
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return condition;
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}
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public String getAttribute() {
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return attribute;
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}
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public String getType() {
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return type;
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}
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public String getMinMax() {
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return minMax;
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}
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public String getDtMapping() {
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return dtMapping;
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}
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public String getVocabMapping() {
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return vocabMapping;
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}
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public String getDerived() {
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return derived;
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}
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public String getDerivedMapping() {
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return derivedMapping;
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}
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public String getComments() {
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return comments;
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}
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}
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private CSVReader csv;
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private List<MappingRow> rows = new ArrayList<>();
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private Map<String, String> metadata = new HashMap<>();
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public MappingSheetParser(InputStream stream, String name) throws FHIRException, IOException {
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super();
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this.csv = new CSVReader(stream);
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checkHeaders1(name);
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checkHeaders2(name);
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while (csv.line()) {
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processRow();
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}
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}
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private void checkHeaders1(String name) throws FHIRException, IOException {
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csv.readHeaders();
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csv.checkColumn(1, "HL7 v2", "Mapping Sheet "+name);
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csv.checkColumn(6, "Condition (IF True)", "Mapping Sheet "+name);
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csv.checkColumn(7, "HL7 FHIR", "Mapping Sheet "+name);
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csv.checkColumn(14, "Comments", "Mapping Sheet "+name);
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csv.checkColumn(16, "Name", "Mapping Sheet "+name);
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csv.checkColumn(17, "Value", "Mapping Sheet "+name);
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}
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private void checkHeaders2(String name) throws FHIRException, IOException {
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csv.readHeaders();
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csv.checkColumn(1, "Display Sequence", "Mapping Sheet "+name);
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csv.checkColumn(2, "Identifier", "Mapping Sheet "+name);
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csv.checkColumn(3, "Name", "Mapping Sheet "+name);
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csv.checkColumn(4, "Data Type", "Mapping Sheet "+name);
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csv.checkColumn(5, "Cardinality", "Mapping Sheet "+name);
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csv.checkColumn(7, "FHIR Attribute", "Mapping Sheet "+name);
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csv.checkColumn(8, "Data Type", "Mapping Sheet "+name);
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csv.checkColumn(9, "Cardinality", "Mapping Sheet "+name);
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csv.checkColumn(10, "Data Type Mapping", "Mapping Sheet "+name);
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csv.checkColumn(11, "Vocabulary Mapping\n(IS, ID, CE, CNE, CWE)", "Mapping Sheet "+name);
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csv.checkColumn(12, "Derived Mapping", "Mapping Sheet "+name);
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}
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private void processRow() {
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MappingRow mr = new MappingRow();
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mr.sequence = csv.value(1);
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mr.identifier = csv.value(2);
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mr.name = csv.value(3);
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mr.dataType = csv.value(4);
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mr.cardinality = csv.value(5);
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mr.condition = csv.value(6);
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mr.attribute = csv.value(7);
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mr.type = csv.value(8);
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mr.minMax = csv.value(9);
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mr.dtMapping = csv.value(10);
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mr.vocabMapping = csv.value(11);
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mr.derived = csv.value(12);
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if (!Utilities.noString(mr.derived)) {
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String[] s = mr.derived.split("\\=");
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mr.derived = s[0].trim();
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mr.derivedMapping = s[1].trim();
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}
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mr.comments = csv.value(14);
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rows.add(mr);
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if (!org.hl7.fhir.utilities.Utilities.noString(csv.value(16)))
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metadata.put(csv.value(16), csv.value(17));
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}
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public List<MappingRow> getRows() {
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return rows;
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}
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public ConceptMap getConceptMap() throws FHIRException {
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ConceptMap map = new ConceptMap();
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loadMetadata(map);
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if (metadata.containsKey("copyright"))
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map.setCopyright(metadata.get("copyright"));
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for (MappingRow row : rows) {
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SourceElementComponent element = map.getGroupFirstRep().addElement();
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element.setCode(row.getIdentifier());
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element.setId(row.getSequence());
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element.setDisplay(row.getName()+" : "+row.getDataType()+" ["+row.getCardinality()+"]");
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if (row.getCondition() != null)
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element.getTargetFirstRep().addDependsOn().setProperty("http://hl7.org/fhirpath").setValue(processCondition(row.getCondition()));
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element.getTargetFirstRep().setCode(row.getAttribute());
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element.getTargetFirstRep().setDisplay(row.getType()+" : ["+row.getMinMax()+"]");
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if (row.getDerived() != null)
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element.getTargetFirstRep().getProductFirstRep().setProperty(row.getDerived()).setValue(row.getDerivedMapping());
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if (row.getComments() != null)
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element.getTargetFirstRep().setComment(row.getComments());
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if (row.getDtMapping() != null)
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element.getTargetFirstRep().addExtension("htp://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping", new UrlType("todo#"+row.getDtMapping()));
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if (row.getVocabMapping() != null)
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element.getTargetFirstRep().addExtension("htp://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping", new UrlType("todo#"+row.getVocabMapping()));
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}
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return map;
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}
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private String processCondition(String condition) {
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if (condition.startsWith("IF ") && condition.endsWith(" IS VALUED"))
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return "`"+condition.substring(4, condition.length()-10)+".exists()";
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if (condition.startsWith("IF ") && condition.endsWith(" DOES NOT EXIST"))
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return "`"+condition.substring(4, condition.length()-15)+".exists()";
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throw new Error("not processed yet: "+condition);
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}
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private void loadMetadata(MetadataResource mr) throws FHIRException {
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if (metadata.containsKey("id"))
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mr.setId(metadata.get("id"));
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if (metadata.containsKey("url"))
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mr.setUrl(metadata.get("url"));
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if (metadata.containsKey("name"))
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mr.setName(metadata.get("name"));
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if (metadata.containsKey("title"))
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mr.setTitle(metadata.get("title"));
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if (metadata.containsKey("version"))
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mr.setVersion(metadata.get("version"));
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if (metadata.containsKey("status"))
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mr.setStatus(PublicationStatus.fromCode(metadata.get("status")));
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if (metadata.containsKey("date"))
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mr.setDateElement(new DateTimeType(metadata.get("date")));
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if (metadata.containsKey("publisher"))
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mr.setPublisher(metadata.get("publisher"));
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if (metadata.containsKey("description"))
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mr.setDescription(metadata.get("description"));
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}
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public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
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MappingSheetParser parser = new MappingSheetParser(new FileInputStream("c:\\temp\\v2-pid.csv"), "v2-pid.csv");
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ConceptMap cm = parser.getConceptMap();
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}
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}
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@ -191,4 +191,21 @@ public class CSVReader extends InputStreamReader {
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}
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public void checkColumn(int i, String name, String desc) throws FHIRException {
|
||||
if (cols.length < i)
|
||||
throw new FHIRException("Error parsing "+desc+": expected column "+name+" at col "+i+" but only found "+cols.length+" cols");
|
||||
if (!cols[i-1].equals(name))
|
||||
throw new FHIRException("Error parsing "+desc+": expected column "+name+" at col "+i+" but found '"+cols[i-1]+"'");
|
||||
}
|
||||
|
||||
|
||||
public String value(int i) {
|
||||
if (i > cells.length)
|
||||
return null;
|
||||
if (Utilities.noString(cells[i-1]))
|
||||
return null;
|
||||
return cells[i-1];
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -745,4 +745,14 @@ public class PackageCacheManager {
|
|||
return res;
|
||||
}
|
||||
|
||||
|
||||
public void clear() throws IOException {
|
||||
for (File f : new File(cacheFolder).listFiles()) {
|
||||
if (f.isDirectory()) {
|
||||
Utilities.clearDirectory(f.getAbsolutePath());
|
||||
f.delete();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
24
release.bat
24
release.bat
|
|
@ -1,28 +1,30 @@
|
|||
REM replace versions before running
|
||||
REM make sure you are committed
|
||||
|
||||
@echo off
|
||||
|
||||
set oldver=3.8.3
|
||||
set newver=3.8.4
|
||||
|
||||
echo ..
|
||||
echo =====================================================================
|
||||
echo upgrade and release fhir.core from 3.8.3-SNAPSHOT to 3.8.4-SNAPSHOT
|
||||
echo upgrade and release fhir.core from %oldver%-SNAPSHOT to %newver%-SNAPSHOT
|
||||
echo =====================================================================
|
||||
echo ..
|
||||
echo check versions and make sure committed...
|
||||
pause
|
||||
|
||||
call mvn versions:set -DnewVersion=3.8.4-SNAPSHOT
|
||||
call mvn versions:set -DnewVersion=%newver%-SNAPSHOT
|
||||
call git commit -a -m "Release new version"
|
||||
call git push origin master
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.java" --includeSubDirectories --find "3.8.3-SNAPSHOT" --replace "3.8.4-SNAPSHOT"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\fhir-ig-publisher" --fileMask "*.xml" --includeSubDirectories --find "3.8.3-SNAPSHOT" --replace "3.8.4-SNAPSHOT"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.xml" --find "3.8.3-SNAPSHOT" --replace "3.8.4-SNAPSHOT"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.java" --includeSubDirectories --find "%oldver%-SNAPSHOT" --replace "%newver%-SNAPSHOT"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\build" --fileMask "*.xml" --find "%oldver%-SNAPSHOT" --replace "%newver%-SNAPSHOT"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\latest-ig-publisher" --fileMask "*.html" --find "%oldver%" --replace "%newver%"
|
||||
call "C:\tools\fnr.exe" --cl --dir "C:\work\org.hl7.fhir\latest-ig-publisher" --fileMask "*.json" --find "%oldver%" --replace "%newver%"
|
||||
call mvn deploy
|
||||
copy org.hl7.fhir.validation.cli\target\org.hl7.fhir.validation.cli-3.8.4-SNAPSHOT.jar ..\latest-ig-publisher\org.hl7.fhir.validator.jar
|
||||
copy org.hl7.fhir.validation.cli\target\org.hl7.fhir.validation.cli-%newver%-SNAPSHOT.jar ..\latest-ig-publisher\org.hl7.fhir.validator.jar
|
||||
cd ..\latest-ig-publisher
|
||||
call git commit -a -m "Release new version 3.8.4-SNAPSHOT"
|
||||
call git commit -a -m "Release new version %newver%-SNAPSHOT"
|
||||
call git push origin master
|
||||
cd ..\org.hl7.fhir.core
|
||||
call python c:\tools\zulip-api\zulip\zulip\send.py --stream committers/notification --subject "java core" -m "New Java Core v3.8.4-SNAPSHOT released. New Validator at https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=3.8.4-SNAPSHOT&e=jar, and also deployed at https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar" --config-file zuliprc
|
||||
call python c:\tools\zulip-api\zulip\zulip\send.py --stream committers/notification --subject "java core" -m "New Java Core v%newver%-SNAPSHOT released. New Validator at https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots&g=ca.uhn.hapi.fhir&a=org.hl7.fhir.validation.cli&v=%newver%-SNAPSHOT&e=jar, and also deployed at https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.validator.jar" --config-file zuliprc
|
||||
|
||||
echo ===============================================================
|
||||
echo all done
|
||||
|
|
|
|||
Loading…
Reference in New Issue