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Add UTG version revision engine

This commit is contained in:
Grahame Grieve 2020-10-08 20:58:28 +11:00
parent c19f892687
commit c82c71894f
2 changed files with 215 additions and 0 deletions
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210
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java Normal file
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@ -0,0 +1,210 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.exceptions.FHIRException;
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.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class UTGVersionSorter {
private FilesystemPackageCacheManager pcm;
public class CanonicalResourceAnalysis {
private CanonicalResource resource;
private CanonicalResource r2;
private CanonicalResource r3;
private CanonicalResource r4;
private String fmm;
private boolean normative;
private String recommendation;
public CanonicalResourceAnalysis(CanonicalResource cr) {
this.resource = cr;
}
public String summary() {
// return "Relevant: "+resource.getUrl()+" [r2: "+r2Ver+"/"+r2Fmm+"]"+" [r3: "+r3Ver+"/"+r3Fmm+"]"+" [r4: "+r4Ver+"/"+r4Fmm+"/"+r4Normative+"] ---> "+recommendation;
return resource.getUrl()+" ---> "+recommendation;
}
public void analyse(Map<String, CanonicalResource> r2l, Map<String, CanonicalResource> r3l, Map<String, CanonicalResource> r4l) {
r2 = findMatch(r2l);
r3 = findMatch(r3l);
r4 = findMatch(r4l);
fmm = r4 != null ? ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_FMM_LEVEL) : null;
normative = (r4 != null) && ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_NORMATIVE_VERSION) != null;
if (normative) {
recommendation = "1.0.0";
} else if (Utilities.existsInList(fmm,"3", "4", "5")) {
recommendation = "0.5.0";
} else {
int i = 1;
if (r2 != null && r3 != null && !match(r2, r3, r2l, r3l)) {
i++;
}
if (r3 != null && r4 != null && !match(r3, r4, r3l, r4l)) {
i++;
}
recommendation = "0."+i+".0";
}
}
private boolean match(CanonicalResource l, CanonicalResource r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l instanceof CodeSystem && r instanceof CodeSystem) {
return matchCS((CodeSystem) l, (CodeSystem) r);
} else if (l instanceof ValueSet && r instanceof ValueSet) {
return matchVS((ValueSet) l, (ValueSet) r, ll, rl);
} else {
return false;
}
}
private boolean matchVS(ValueSet l, ValueSet r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l.getCompose().getInclude().size() == 1 && l.getCompose().getExclude().isEmpty() && l.getCompose().getIncludeFirstRep().hasSystem() && !l.getCompose().getIncludeFirstRep().hasConcept() && !l.getCompose().getIncludeFirstRep().hasFilter() &&
r.getCompose().getInclude().size() == 1 && r.getCompose().getExclude().isEmpty() && r.getCompose().getIncludeFirstRep().hasSystem() && !r.getCompose().getIncludeFirstRep().hasConcept() && !r.getCompose().getIncludeFirstRep().hasFilter()) {
CodeSystem lc = (CodeSystem) ll.get(l.getCompose().getIncludeFirstRep().getSystem());
CodeSystem rc = (CodeSystem) rl.get(l.getCompose().getIncludeFirstRep().getSystem());
if (lc != null && rc != null) {
return matchCS(lc, rc);
}
}
return false;
}
private boolean matchCS(CodeSystem l, CodeSystem r) {
return Base.compareDeep(l.getConcept(), r.getConcept(), false);
}
public CanonicalResource findMatch(Map<String, CanonicalResource> r2) {
CanonicalResource r = r2.get(resource.getUrl());
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/", "http://hl7.org/fhir/"));
}
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/CodeSystem", "http://hl7.org/fhir/"));
}
return r;
}
}
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException, URISyntaxException {
new UTGVersionSorter().execute("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth");
}
private void execute(String source) throws IOException {
List<CanonicalResourceAnalysis> list = new ArrayList<>();
System.out.println("Loading UTG");
loadFromSource(list, new File(source));
Map<String, CanonicalResource> r2 = loadPackageR2("hl7.fhir.r2.core");
Map<String, CanonicalResource> r3 = loadPackageR3("hl7.fhir.r3.core");
Map<String, CanonicalResource> r4 = loadPackageR4("hl7.fhir.r4.core");
System.out.println("Processing");
for (CanonicalResourceAnalysis cr : list) {
cr.analyse(r2,r3,r4);
}
System.out.println("Summary");
for (CanonicalResourceAnalysis cr : list) {
System.out.println(cr.summary());
}
System.out.println();
System.out.println("Done");
}
private Map<String, CanonicalResource> loadPackageR2(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR3(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(npm.load(p)), false);
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR4(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private void loadFromSource(List<CanonicalResourceAnalysis> list, File source) {
for (File f : source.listFiles()) {
if (f.isDirectory()) {
loadFromSource(list, f);
} else if (f.getName().endsWith(".xml")) {
try {
Resource r = new XmlParser().parse(new FileInputStream(f));
if (r instanceof CanonicalResource) {
CanonicalResource cr = (CanonicalResource) r;
cr.setUserData("path", f.getAbsolutePath());
if (cr.hasVersion() && cr.getVersion().startsWith("4.")) {
list.add(new CanonicalResourceAnalysis(cr));
}
}
} catch (Exception e) {
System.out.println(f.getAbsolutePath()+" not a resource? "+e.getMessage());
}
}
}
}
}

5
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
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@ -35,6 +35,7 @@ import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
import java.io.File; import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
@ -1095,6 +1096,10 @@ public class NpmPackage {
public boolean isNotForPublication() { public boolean isNotForPublication() {
return JSONUtil.bool(npm, "notForPublication"); return JSONUtil.bool(npm, "notForPublication");
} }
public InputStream load(PackageResourceInformation p) throws FileNotFoundException {
return new FileInputStream(p.filename);
}
} }