honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

update extension extractor

This commit is contained in:
Grahame Grieve 2023-02-01 14:48:48 +11:00
parent f9b386d5b2
commit 107fa0e3a2
18 changed files with 58 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
View File

@ -17,7 +17,6 @@ import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonElement;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv30_40/resources30_40/Immunization30_40.java
View File

@ -10,7 +10,6 @@ import org.hl7.fhir.convertors.conv30_40.datatypes30_40.primitivetypes30_40.Bool
import org.hl7.fhir.convertors.conv30_40.datatypes30_40.primitivetypes30_40.Date30_40;
import org.hl7.fhir.convertors.conv30_40.datatypes30_40.primitivetypes30_40.DateTime30_40;
import org.hl7.fhir.convertors.conv30_40.datatypes30_40.primitivetypes30_40.String30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Immunization;

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv30_50/resources30_50/CompartmentDefinition30_50.java
View File

@ -3,7 +3,6 @@ package org.hl7.fhir.convertors.conv30_50.resources30_50;
import org.hl7.fhir.convertors.context.ConversionContext30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.ContactDetail30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.UsageContext30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.complextypes30_50.CodeableConcept30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Boolean30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Code30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.DateTime30_50;

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv30_50/resources30_50/GraphDefinition30_50.java
View File

@ -5,9 +5,7 @@ import org.hl7.fhir.convertors.conv30_50.datatypes30_50.ContactDetail30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.UsageContext30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.complextypes30_50.CodeableConcept30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Boolean30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Code30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.DateTime30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Integer30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.MarkDown30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.String30_50;
import org.hl7.fhir.convertors.conv30_50.datatypes30_50.primitivetypes30_50.Uri30_50;

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/datatypes40_50/primitive40_50/DateTime40_50.java
View File

@ -1,7 +1,6 @@
package org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50;
import org.hl7.fhir.convertors.context.ConversionContext40_50;
import org.hl7.fhir.convertors.context.ConversionContext43_50;
import org.hl7.fhir.exceptions.FHIRException;
public class DateTime40_50 {

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/datatypes40_50/special40_50/Reference40_50.java
View File

@ -1,13 +1,10 @@
package org.hl7.fhir.convertors.conv40_50.datatypes40_50.special40_50;
import org.hl7.fhir.convertors.context.ConversionContext30_50;
import org.hl7.fhir.convertors.context.ConversionContext40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.general40_50.Identifier40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.String40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Uri40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeableReference;
public class Reference40_50 {

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/GraphDefinition40_50.java
View File

@ -5,10 +5,7 @@ import org.hl7.fhir.convertors.conv40_50.datatypes40_50.general40_50.CodeableCon
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.metadata40_50.ContactDetail40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.metadata40_50.UsageContext40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Boolean40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Canonical40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Code40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.DateTime40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Integer40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.MarkDown40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.String40_50;
import org.hl7.fhir.convertors.conv40_50.datatypes40_50.primitive40_50.Uri40_50;

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv43_50/datatypes43_50/special43_50/Reference43_50.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.convertors.conv43_50.datatypes43_50.special43_50;
import org.hl7.fhir.convertors.context.ConversionContext40_50;
import org.hl7.fhir.convertors.context.ConversionContext43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.general43_50.Identifier43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.String43_50;

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv43_50/resources43_50/GraphDefinition43_50.java
View File

@ -5,10 +5,7 @@ import org.hl7.fhir.convertors.conv43_50.datatypes43_50.general43_50.CodeableCon
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.metadata43_50.ContactDetail43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.metadata43_50.UsageContext43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.Boolean43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.Canonical43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.Code43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.DateTime43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.Integer43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.MarkDown43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.String43_50;
import org.hl7.fhir.convertors.conv43_50.datatypes43_50.primitive43_50.Uri43_50;

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R5ToR5Loader.java
View File

@ -47,12 +47,10 @@ import org.hl7.fhir.r5.model.CanonicalType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.Enumerations.BindingStrength;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.utils.ToolingExtensions;
public class R5ToR5Loader extends BaseLoaderR5 {

56
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionExtractor.java
View File

@ -1,5 +1,6 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@ -7,8 +8,10 @@ import java.util.ArrayList;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.CanonicalResourceManager;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingAdditionalComponent;
@ -21,8 +24,6 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import ca.uhn.fhir.model.api.IStreamingDatatype;
public class ExtensionExtractor {
public static void main(String[] args) throws FHIRFormatError, FileNotFoundException, IOException {
@ -57,9 +58,16 @@ public class ExtensionExtractor {
for (String r : r5.listResources("StructureDefinition")) {
StructureDefinition sd = (StructureDefinition) new JsonParser().parse(r5.load(r));
if (sd.getType().equals("Extension") && sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
seeBinding(ed.getBinding().getValueSet(), vslist, "ext", sd);
for (ElementDefinitionBindingAdditionalComponent ab : ed.getBinding().getAdditional()) {
seeBinding(ab.getValueSet(), vslist, "ext", sd);
}
}
sd.setSnapshot(null);
String fn;
if (sd.getContext().size() == 0) {
fn = Utilities.path(dst, "null", sd.getId()+".json");
save(sd, dst,"none");
} else if (sd.getContext().size() > 1) {
boolean dt = true;
for (StructureDefinitionContextComponent x : sd.getContext()) {
@ -67,24 +75,16 @@ public class ExtensionExtractor {
dt = dt && isDataType(s);
}
if (dt) {
fn = Utilities.path(dst, "datatypes", "multiple", sd.getId()+".xml");
save(sd, dst,"datatypes");
} else {
fn = Utilities.path(dst, "multiple", sd.getId()+".xml");
save(sd, dst,"multiple");
}
} else {
String s = extractType(sd.getContextFirstRep().getExpression());
if (isDataType(s)) {
fn = Utilities.path(dst, "datatypes", s, sd.getId()+".xml");
save(sd, dst,"datatypes");
} else {
fn = Utilities.path(dst, s, sd.getId()+".xml");
}
Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
new XmlParser().compose(new FileOutputStream(fn), sd);
}
for (ElementDefinition ed : sd.getSnapshot().getElement()) {
seeBinding(ed.getBinding().getValueSet(), vslist, "ext", sd);
for (ElementDefinitionBindingAdditionalComponent ab : ed.getBinding().getAdditional()) {
seeBinding(ab.getValueSet(), vslist, "ext", sd);
save(sd, dst,s);
}
}
} else {
@ -97,13 +97,13 @@ public class ExtensionExtractor {
}
}
for (ValueSet vs : vslist.getList()) {
if (vs.hasUserData("core") || !vs.hasUserData("ext")) {
if (vs.hasUserData("core") || !vs.hasUserData("ext") || vs.getUrl().startsWith("http://terminology.")) {
vslist.drop(vs.getId());
}
}
for (CodeSystem cs : cslist.getList()) {
boolean keep = false;
if (cs.hasUserData("vsl" )) {
if (cs.hasUserData("vsl") && !cs.getUrl().startsWith("http://terminology.")) {
keep = true;
for (ValueSet vs : (ArrayList<ValueSet>) cs.getUserData("vsl")) {
if (!vslist.has(vs.getUrl())) {
@ -116,10 +116,28 @@ public class ExtensionExtractor {
}
}
for (ValueSet vs : vslist.getList()) {
System.out.println(vs.getUrl());
StructureDefinition sd = (StructureDefinition) vs.getUserData("ext");
String s = sd.getUserString("folder");
save(vs, dst, s);
}
for (CodeSystem cs : cslist.getList()) {
System.out.println(cs.getUrl());
ValueSet vs = ((ArrayList<ValueSet>) cs.getUserData("vsl")).get(0);
String s = vs.getUserString("folder");
save(cs, dst,s);
}
}
private void save(CanonicalResource cr, String dst, String folder) throws IOException {
// TODO Auto-generated method stub
cr.setText(null);
if (!cr.hasTitle()) {
cr.setTitle(Utilities.unCamelCase(cr.getName()));
}
String fn = Utilities.path(dst, folder, cr.fhirType()+"-"+cr.getId()+".xml");
cr.setUserData("folder", folder);
if (!new File(fn).exists()) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), cr);
}
}

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/JsonProcessor.java
View File

@ -1,6 +1,5 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/NpmPackageVersionConverter.java
View File

@ -1,6 +1,10 @@
package org.hl7.fhir.convertors.misc;
import java.io.*;
import java.io.BufferedOutputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashMap;
@ -8,6 +12,8 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import javax.annotation.Nonnull;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
@ -35,9 +41,6 @@ import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.NpmPackageIndexBuilder;
import com.google.common.base.Charsets;
import javax.annotation.Nonnull;
public class NpmPackageVersionConverter {
private static final int BUFFER_SIZE = 1024;

1
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/XMLPackageConvertor.java
View File

@ -3,7 +3,6 @@ package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Map.Entry;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.model.JsonProperty;

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/xver/CorePackageVersionConvertor.java
View File

@ -3,7 +3,6 @@ package org.hl7.fhir.convertors.misc.xver;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_30;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_40;
@ -14,7 +13,6 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.misc.xver.CorePackageVersionConvertor.BaseConvertor;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.model.JsonArray;

15
org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/conv30_40/Immunization30_40Test.java
View File

@ -1,17 +1,16 @@
package org.hl7.fhir.convertors.conv30_40;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.io.IOException;
import java.io.InputStream;
import java.util.stream.Stream;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
public class Immunization30_40Test {
private org.hl7.fhir.r4.formats.JsonParser r4Parser = new org.hl7.fhir.r4.formats.JsonParser();

10
org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/conv40_50/StructureDefinition40_50Test.java
View File

@ -1,20 +1,14 @@
package org.hl7.fhir.convertors.conv40_50;
import static org.junit.jupiter.api.Assertions.assertArrayEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.text.StringEscapeUtils;
import javax.annotation.Nullable;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import javax.annotation.Nullable;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

11
org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/misc/NpmPackageVersionConverterTests.java
View File

@ -1,17 +1,16 @@
package org.hl7.fhir.convertors.misc;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.tests.ResourceLoaderTests;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Map;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import org.hl7.fhir.utilities.tests.ResourceLoaderTests;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class NpmPackageVersionConverterTests implements ResourceLoaderTests {
@org.junit.jupiter.api.Test