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

Example 21 with Package

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

the class NPMPackageGenerator method loadFiles.

public void loadFiles(String root, File dir, String... noload) throws IOException {
    for (File f : dir.listFiles()) {
        if (!Utilities.existsInList(f.getName(), noload)) {
            if (f.isDirectory()) {
                loadFiles(root, f);
            } else {
                String path = f.getAbsolutePath().substring(root.length() + 1);
                byte[] content = TextFile.fileToBytes(f);
                if (created.contains(path))
                    System.out.println("Duplicate package file " + path);
                else {
                    created.add(path);
                    TarArchiveEntry entry = new TarArchiveEntry(path);
                    entry.setSize(content.length);
                    tar.putArchiveEntry(entry);
                    tar.write(content);
                    tar.closeArchiveEntry();
                }
            }
        }
    }
}

Example 22 with Package

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

the class BaseWorkerContext method cacheResourceFromPackage.

public void cacheResourceFromPackage(Resource r, PackageVersion packageInfo) throws FHIRException {
    synchronized (lock) {
        if (r.getId() != null) {
            Map<String, ResourceProxy> map = allResourcesById.get(r.fhirType());
            if (map == null) {
                map = new HashMap<String, ResourceProxy>();
                allResourcesById.put(r.fhirType(), map);
            }
            if ((packageInfo == null || !packageInfo.isExamplesPackage()) || !map.containsKey(r.getId())) {
                map.put(r.getId(), new ResourceProxy(r));
            } else {
                logger.logDebugMessage(LogCategory.PROGRESS, "Ignore " + r.fhirType() + "/" + r.getId() + " from package " + packageInfo.toString());
            }
        }
        if (r instanceof CodeSystem || r instanceof NamingSystem) {
            oidCache.clear();
        }
        if (r instanceof CanonicalResource) {
            CanonicalResource m = (CanonicalResource) r;
            String url = m.getUrl();
            if (!allowLoadingDuplicates && hasResource(r.getClass(), url)) {
                // special workaround for known problems with existing packages
                if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
                    return;
                }
                throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url));
            }
            if (r instanceof StructureDefinition) {
                StructureDefinition sd = (StructureDefinition) m;
                if ("1.4.0".equals(version)) {
                    fixOldSD(sd);
                }
                structures.see(sd, packageInfo);
            } else if (r instanceof ValueSet) {
                valueSets.see((ValueSet) m, packageInfo);
            } else if (r instanceof CodeSystem) {
                CodeSystemUtilities.crossLinkCodeSystem((CodeSystem) r);
                codeSystems.see((CodeSystem) m, packageInfo);
            } else if (r instanceof ImplementationGuide) {
                guides.see((ImplementationGuide) m, packageInfo);
            } else if (r instanceof CapabilityStatement) {
                capstmts.see((CapabilityStatement) m, packageInfo);
            } else if (r instanceof Measure) {
                measures.see((Measure) m, packageInfo);
            } else if (r instanceof Library) {
                libraries.see((Library) m, packageInfo);
            } else if (r instanceof SearchParameter) {
                searchParameters.see((SearchParameter) m, packageInfo);
            } else if (r instanceof PlanDefinition) {
                plans.see((PlanDefinition) m, packageInfo);
            } else if (r instanceof OperationDefinition) {
                operations.see((OperationDefinition) m, packageInfo);
            } else if (r instanceof Questionnaire) {
                questionnaires.see((Questionnaire) m, packageInfo);
            } else if (r instanceof ConceptMap) {
                maps.see((ConceptMap) m, packageInfo);
            } else if (r instanceof StructureMap) {
                transforms.see((StructureMap) m, packageInfo);
            } else if (r instanceof NamingSystem) {
                systems.see((NamingSystem) m, packageInfo);
            }
        }
    }
}

Example 23 with Package

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

the class ParsingTests method data.

public static Stream<Arguments> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
    FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
    npm = pcm.loadPackage("hl7.fhir.r5.examples", "5.0.0");
    List<Arguments> objects = new ArrayList<>();
    List<String> names = npm.list("package");
    for (String n : names) {
        if (!n.contains("manifest.json") && !n.contains("xver-") && !n.contains("uml.json") && !n.contains("package-min-ver.json")) {
            objects.add(Arguments.of(n));
        }
    }
    return objects.stream();
}

Example 24 with Package

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

the class StandAloneValidatorFetcher method resolveURL.

@Override
public boolean resolveURL(IResourceValidator validator, Object appContext, String path, String url, String type) throws IOException, FHIRException {
    if (!Utilities.isAbsoluteUrl(url)) {
        return false;
    }
    if (url.contains("|")) {
        url = url.substring(0, url.lastIndexOf("|"));
    }
    if (type != null && type.equals("uri") && isMappingUri(url)) {
        return true;
    }
    // if we've got to here, it's a reference to a FHIR URL. We're going to try to resolve it on the fly
    String pid = null;
    String ver = null;
    String base = findBaseUrl(url);
    if (base == null) {
        return !url.startsWith("http://hl7.org/fhir") && !type.equals("canonical");
    }
    // the next operations are expensive. we're going to cache them
    if (urlList.containsKey(url)) {
        return urlList.get(url);
    }
    if (base.equals("http://terminology.hl7.org")) {
        pid = "hl7.terminology";
    } else if (url.startsWith("http://hl7.org/fhir")) {
        pid = pcm.getPackageId(base);
    } else {
        if (pidList.containsKey(base)) {
            pid = pidList.get(base);
        } else {
            pid = pcm.findCanonicalInLocalCache(base);
            pidList.put(base, pid);
        }
    }
    ver = url.contains("|") ? url.substring(url.indexOf("|") + 1) : null;
    if (pid == null && Utilities.startsWithInList(url, "http://hl7.org/fhir", "http://terminology.hl7.org")) {
        urlList.put(url, false);
        return false;
    }
    if (url.startsWith("http://hl7.org/fhir")) {
        // first possibility: it's a reference to a version specific URL http://hl7.org/fhir/X.X/...
        VersionURLInfo vu = VersionUtilities.parseVersionUrl(url);
        if (vu != null) {
            NpmPackage pi = pcm.loadPackage(VersionUtilities.packageForVersion(vu.getVersion()), VersionUtilities.getCurrentVersion(vu.getVersion()));
            boolean res = pi.hasCanonical(vu.getUrl());
            urlList.put(url, res);
            return res;
        }
    }
    // ok maybe it's a reference to a package we know
    if (pid != null) {
        if ("sharedhealth.fhir.ca.common".equals(pid)) {
            // special case - optimise this
            return false;
        }
        NpmPackage pi = null;
        if (pidMap.containsKey(pid + "|" + ver)) {
            pi = pidMap.get(pid + "|" + ver);
        } else if (installer.packageExists(pid, ver)) {
            try {
                installer.loadPackage(pid, ver);
                pi = pcm.loadPackage(pid);
                pidMap.put(pid + "|" + ver, pi);
            } catch (Exception e) {
                pidMap.put(pid + "|" + ver, null);
            }
        } else {
            pidMap.put(pid + "|" + ver, null);
        }
        if (pi != null) {
            context.loadFromPackage(pi, null);
            return pi.hasCanonical(url);
        }
    }
    // we don't bother with urls outside fhir space in the standalone validator - we assume they are valid
    return !url.startsWith("http://hl7.org/fhir") && !type.equals("canonical");
}

Example 25 with Package

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

the class R3TEchnicalCorrectionProcessor method extractToPackageMaster.

private void extractToPackageMaster(List<Resource> list, String root) throws IOException, FHIRFormatError {
    System.out.println("Updating Packages Master");
    String corePath = Utilities.path(root, "hl7.fhir.r3.core", "package");
    String examplesPath = Utilities.path(root, "hl7.fhir.r3.examples", "package");
    String elementsPath = Utilities.path(root, "hl7.fhir.r3.elements", "package");
    int coreTotal = new File(corePath).list().length - 1;
    int examplesTotal = new File(examplesPath).list().length - 1;
    int elementsTotal = new File(elementsPath).list().length - 1;
    int coreCount = 0;
    int examplesCount = 0;
    int elementsCount = 0;
    for (Resource r : list) {
        String n = r.fhirType() + "-" + r.getId() + ".json";
        FileOutputStream dst = null;
        if (n.startsWith("DataElement-")) {
            elementsCount++;
            dst = new FileOutputStream(Utilities.path(elementsPath, n));
            new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
        } else {
            dst = new FileOutputStream(Utilities.path(examplesPath, n));
            new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
            examplesCount++;
            if (isCoreResource(r.fhirType())) {
                coreCount++;
                DomainResource dr = (DomainResource) r;
                dr.setText(null);
                new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(new FileOutputStream(Utilities.path(corePath, n)), r);
            }
        }
    }
    System.out.println("  Core @ " + corePath + ": Replaced " + coreCount + " of " + coreTotal);
    System.out.println("  Examples @ " + examplesPath + ": Replaced " + examplesCount + " of " + examplesTotal);
    System.out.println("  Elements @ " + elementsPath + ": Replaced " + elementsCount + " of " + elementsTotal);
}