Examples with Package org.hl7.fhir.utilities.graphql.Package used on opensource projects

Example 51 with Package

use of org.hl7.fhir.utilities.graphql.Package in project redmatch by aehrc.

the class RedmatchGrammarCodeSystemGenerator method main.

public static void main(String[] args) {
    if (args.length != 3) {
        System.out.println("Three arguments are required: FHIR package name, FHIR package version, output file.");
        System.exit(0);
    }
    FhirContext ctx = FhirContext.forR4();
    RedmatchGrammarCodeSystemGenerator generator = new RedmatchGrammarCodeSystemGenerator(new Gson(), ctx);
    CodeSystem cs = null;
    try {
        cs = generator.createCodeSystem(new VersionedFhirPackage(args[0], args[1]));
    } catch (IOException e) {
        e.printStackTrace();
    }
    try (FileWriter fw = new FileWriter(args[2])) {
        ctx.newJsonParser().setPrettyPrint(true).encodeResourceToWriter(cs, fw);
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 52 with Package

use of org.hl7.fhir.utilities.graphql.Package in project redmatch by aehrc.

the class RedmatchGrammarCodeSystemGenerator method createCodeSystem.

/**
 * Creates a validation code system for a version of FHIR or an implementation guide.
 *
 * @param fhirPackage The NPM package of a version of FHIR or implementation guide, e.g., hl7.fhir.r4.core.
 * @param progressReporter An object to report progress. Can be null.
 * @return A code system that can be used for validation.
 * @throws IOException If there are issues reading the files.
 */
public CodeSystem createCodeSystem(VersionedFhirPackage fhirPackage, ProgressReporter progressReporter) throws IOException {
    if (progressReporter != null) {
        progressReporter.reportProgress(Progress.reportStart("Creating code system for FHIR package " + fhirPackage));
    }
    // Create a set with all the FHIR packages required
    Set<VersionedFhirPackage> packages = new HashSet<>();
    packages.add(fhirPackage);
    packages.addAll(getDependencies(fhirPackage));
    for (VersionedFhirPackage pack : packages) {
        FhirUtils.getStructureDefinitions(ctx, pack).forEach(e -> {
            structureDefinitionsMapByCode.put(e.getId().replace("StructureDefinition/", ""), e);
            structureDefinitionsMapByUrl.put(e.getUrl(), e);
        });
    }
    Set<StructureDefinition> complexTypes = structureDefinitionsMapByCode.values().stream().filter(e -> e.hasDerivation() && e.getDerivation().equals(StructureDefinition.TypeDerivationRule.SPECIALIZATION) && e.hasKind() && e.getKind().equals(StructureDefinition.StructureDefinitionKind.COMPLEXTYPE)).collect(Collectors.toSet());
    log.info("Found " + complexTypes.size() + " complex types");
    Set<StructureDefinition> resourceProfiles = structureDefinitionsMapByCode.values().stream().filter(e -> e.hasDerivation() && e.getDerivation().equals(StructureDefinition.TypeDerivationRule.CONSTRAINT) && e.hasKind() && e.getKind().equals(StructureDefinition.StructureDefinitionKind.RESOURCE)).collect(Collectors.toSet());
    log.info("Found " + resourceProfiles.size() + " resource profiles");
    Set<StructureDefinition> resources = structureDefinitionsMapByCode.values().stream().filter(e -> e.hasDerivation() && e.getDerivation().equals(StructureDefinition.TypeDerivationRule.SPECIALIZATION) && e.hasKind() && e.getKind().equals(StructureDefinition.StructureDefinitionKind.RESOURCE)).collect(Collectors.toSet());
    log.info("Found " + resources.size() + " resources");
    int total = complexTypes.size() + resourceProfiles.size() + resources.size();
    double div = total / 100.0;
    // Initialise profile children map
    resourceProfiles.forEach(sd -> profileChildrenMap.put(sd.getUrl(), new HashSet<>()));
    resources.forEach(sd -> profileChildrenMap.put(sd.getUrl(), new HashSet<>()));
    // Create temporary profile parents map
    Map<String, Set<String>> profileParentsMap = new HashMap<>();
    resourceProfiles.forEach(sd -> {
        Set<String> parentUrls = new HashSet<>();
        profileParentsMap.put(sd.getUrl(), parentUrls);
        StructureDefinition baseDefinition = structureDefinitionsMapByUrl.get(sd.getBaseDefinition());
        while (baseDefinition != null && baseDefinition.getDerivation() == StructureDefinition.TypeDerivationRule.CONSTRAINT) {
            parentUrls.add(baseDefinition.getUrl());
            baseDefinition = structureDefinitionsMapByUrl.get(baseDefinition.getBaseDefinition());
        }
        // The parent resource will be a specialization
        if (baseDefinition != null) {
            parentUrls.add(baseDefinition.getUrl());
        }
    });
    // Use the temporary map to populate the children map
    profileParentsMap.keySet().forEach(key -> {
        Set<String> parents = profileParentsMap.get(key);
        if (parents != null) {
            parents.forEach(val -> profileChildrenMap.get(val).add(key));
        }
    });
    CodeSystem codeSystem = createBaseCodeSystem(fhirPackage);
    int i = 0;
    for (StructureDefinition structureDefinition : complexTypes) {
        processStructureDefinition(codeSystem, structureDefinition, false, "");
        i++;
        if (progressReporter != null) {
            progressReporter.reportProgress(Progress.reportProgress((int) Math.floor(i / div)));
        }
    }
    for (StructureDefinition structureDefinition : resourceProfiles) {
        processStructureDefinition(codeSystem, structureDefinition, false, "");
        i++;
        if (progressReporter != null) {
            progressReporter.reportProgress(Progress.reportProgress((int) Math.floor(i / div)));
        }
    }
    for (StructureDefinition structureDefinition : resources) {
        processStructureDefinition(codeSystem, structureDefinition, false, "");
        i++;
        if (progressReporter != null) {
            progressReporter.reportProgress(Progress.reportProgress((int) Math.floor(i / div)));
        }
    }
    if (progressReporter != null) {
        progressReporter.reportProgress(Progress.reportEnd());
    }
    return codeSystem;
}

Example 53 with Package

use of org.hl7.fhir.utilities.graphql.Package in project org.hl7.fhir.core by hapifhir.

the class NpmPackageVersionConverter method execute.

public void execute() throws IOException {
    GzipCompressorInputStream gzipIn;
    try {
        gzipIn = new GzipCompressorInputStream(new FileInputStream(source));
    } catch (Exception e) {
        throw new IOException("Error reading " + source + ": " + e.getMessage(), e);
    }
    Map<String, byte[]> content = new HashMap<>();
    try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
        TarArchiveEntry entry;
        while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
            String n = entry.getName();
            if (!entry.isDirectory()) {
                int count;
                byte[] data = new byte[BUFFER_SIZE];
                ByteArrayOutputStream fos = new ByteArrayOutputStream();
                try (BufferedOutputStream dest = new BufferedOutputStream(fos, BUFFER_SIZE)) {
                    while ((count = tarIn.read(data, 0, BUFFER_SIZE)) != -1) {
                        dest.write(data, 0, count);
                    }
                }
                fos.close();
                content.put(n, fos.toByteArray());
            }
        }
    }
    Map<String, byte[]> output = new HashMap<>();
    output.put("package/package.json", convertPackage(content.get("package/package.json")));
    for (Entry<String, byte[]> e : content.entrySet()) {
        if (!e.getKey().equals("package/package.json")) {
            byte[] cnv = e.getValue();
            try {
                JsonObject json = JsonTrackingParser.parseJson(e.getValue());
                if (json.has("resourceType")) {
                    cnv = convertResource(e.getKey(), e.getValue());
                }
            } catch (Exception ex) {
            }
            if (cnv != null && cnv.length > 0) {
                output.put(e.getKey(), cnv);
            }
        }
    }
    TarArchiveOutputStream tar;
    ByteArrayOutputStream OutputStream;
    BufferedOutputStream bufferedOutputStream;
    GzipCompressorOutputStream gzipOutputStream;
    OutputStream = new ByteArrayOutputStream();
    bufferedOutputStream = new BufferedOutputStream(OutputStream);
    gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
    tar = new TarArchiveOutputStream(gzipOutputStream);
    Map<String, NpmPackageIndexBuilder> indexers = new HashMap<>();
    for (Entry<String, byte[]> e : output.entrySet()) {
        String n = e.getKey().substring(0, e.getKey().lastIndexOf("/"));
        String s = e.getKey().substring(n.length() + 1);
        byte[] b = e.getValue();
        NpmPackageIndexBuilder indexer = indexers.get(n);
        if (indexer == null) {
            indexer = new NpmPackageIndexBuilder();
            indexer.start();
            indexers.put(n, indexer);
        }
        indexer.seeFile(s, b);
        if (!s.equals(".index.json") && !s.equals("package.json")) {
            TarArchiveEntry entry = new TarArchiveEntry(e.getKey());
            entry.setSize(b.length);
            tar.putArchiveEntry(entry);
            tar.write(b);
            tar.closeArchiveEntry();
        }
    }
    for (Entry<String, NpmPackageIndexBuilder> e : indexers.entrySet()) {
        byte[] cnt = e.getValue().build().getBytes(StandardCharsets.UTF_8);
        TarArchiveEntry entry = new TarArchiveEntry(e.getKey() + "/.index.json");
        entry.setSize(cnt.length);
        tar.putArchiveEntry(entry);
        tar.write(cnt);
        tar.closeArchiveEntry();
    }
    byte[] cnt = output.get("package/package.json");
    TarArchiveEntry entry = new TarArchiveEntry("package/package.json");
    entry.setSize(cnt.length);
    tar.putArchiveEntry(entry);
    tar.write(cnt);
    tar.closeArchiveEntry();
    tar.finish();
    tar.close();
    gzipOutputStream.close();
    bufferedOutputStream.close();
    OutputStream.close();
    byte[] b = OutputStream.toByteArray();
    TextFile.bytesToFile(b, dest);
}

Example 54 with Package

use of org.hl7.fhir.utilities.graphql.Package in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeImplementationGuideImplementationGuidePageComponent.

protected void composeImplementationGuideImplementationGuidePageComponent(Complex parent, String parentType, String name, ImplementationGuide.ImplementationGuidePageComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "page", name, element, index);
    if (element.hasSourceElement())
        composeUri(t, "ImplementationGuide", "source", element.getSourceElement(), -1);
    if (element.hasNameElement())
        composeString(t, "ImplementationGuide", "name", element.getNameElement(), -1);
    if (element.hasKindElement())
        composeEnum(t, "ImplementationGuide", "kind", element.getKindElement(), -1);
    for (int i = 0; i < element.getType().size(); i++) composeCode(t, "ImplementationGuide", "type", element.getType().get(i), i);
    for (int i = 0; i < element.getPackage().size(); i++) composeString(t, "ImplementationGuide", "package", element.getPackage().get(i), i);
    if (element.hasFormatElement())
        composeCode(t, "ImplementationGuide", "format", element.getFormatElement(), -1);
    for (int i = 0; i < element.getPage().size(); i++) composeImplementationGuideImplementationGuidePageComponent(t, "ImplementationGuide", "page", element.getPage().get(i), i);
}

Example 55 with Package

use of org.hl7.fhir.utilities.graphql.Package in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeMedicationMedicationPackageComponent.

protected void composeMedicationMedicationPackageComponent(Complex parent, String parentType, String name, Medication.MedicationPackageComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "package", name, element, index);
    if (element.hasContainer())
        composeCodeableConcept(t, "Medication", "container", element.getContainer(), -1);
    for (int i = 0; i < element.getContent().size(); i++) composeMedicationMedicationPackageContentComponent(t, "Medication", "content", element.getContent().get(i), i);
    for (int i = 0; i < element.getBatch().size(); i++) composeMedicationMedicationPackageBatchComponent(t, "Medication", "batch", element.getBatch().get(i), i);
}