From c82c71894f87e13ff6bb1c082c0be4fcd04ac66b Mon Sep 17 00:00:00 2001 From: Grahame Grieve Date: Thu, 8 Oct 2020 20:58:28 +1100 Subject: [PATCH] Add UTG version revision engine --- .../convertors/misc/UTGVersionSorter.java | 210 ++++++++++++++++++ .../hl7/fhir/utilities/npm/NpmPackage.java | 5 + 2 files changed, 215 insertions(+) create mode 100644 org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java diff --git a/org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java b/org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java new file mode 100644 index 000000000..8dfa13310 --- /dev/null +++ b/org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java @@ -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 r2l, Map r3l, Map 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 ll, Map 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 ll, Map 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 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 list = new ArrayList<>(); + System.out.println("Loading UTG"); + loadFromSource(list, new File(source)); + + Map r2 = loadPackageR2("hl7.fhir.r2.core"); + Map r3 = loadPackageR3("hl7.fhir.r3.core"); + Map 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 loadPackageR2(String id) throws IOException { + Mapres = 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 loadPackageR3(String id) throws IOException { + Mapres = 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 loadPackageR4(String id) throws IOException { + Mapres = 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 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()); + } + } + } + + } + + + +} diff --git a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java index 5f1415f62..414cb0784 100644 --- a/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java +++ b/org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java @@ -35,6 +35,7 @@ import java.io.BufferedOutputStream; import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.File; +import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStream; @@ -1095,6 +1096,10 @@ public class NpmPackage { public boolean isNotForPublication() { return JSONUtil.bool(npm, "notForPublication"); } + + public InputStream load(PackageResourceInformation p) throws FileNotFoundException { + return new FileInputStream(p.filename); + } } \ No newline at end of file