Examples with Source org.hl7.fhir.utilities.validation.ValidationMessage.Source used on opensource projects

Example 36 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class R2R3ConversionManager method main.

public static void main(String[] args) throws IOException, FHIRException {
    if (args.length == 0 || !hasParam(args, "-d2") || !hasParam(args, "-d3") || !hasParam(args, "-maps") || !hasParam(args, "-src") || !hasParam(args, "-dest") || (!hasParam(args, "-r2") && !hasParam(args, "-r3"))) {
        System.out.println("R2 <--> R3 Convertor");
        System.out.println("====================");
        System.out.println();
        System.out.println("parameters: -d2 [r2 definitions] -d3 [r3 definitions] -maps [map source] -src [source] -dest [dest] -r2/3 - fmt [format]");
        System.out.println();
        System.out.println("d2: definitions from http://hl7.org/fhir/DSTU2/downloads.html");
        System.out.println("d3: definitions from http://hl7.org/fhir/STU3/downloads.html");
        System.out.println("maps: R2/R3 maps from http://hl7.org/fhir/r2r3maps.zip");
        System.out.println("src: filename for source to convert");
        System.out.println("dest: filename for destination of conversion");
        System.out.println("-r2: source is r2, convert to r3");
        System.out.println("-r3: source is r3, convert to r2");
        System.out.println("-fmt: xml | json (xml is default)");
    } else {
        R2R3ConversionManager self = new R2R3ConversionManager();
        self.setR2Definitions(getNamedParam(args, "-d2"));
        self.setR3Definitions(getNamedParam(args, "-d3"));
        self.setMappingLibrary(getNamedParam(args, "-maps"));
        FhirFormat fmt = hasParam(args, "-fmt") ? getNamedParam(args, "-fmt").equalsIgnoreCase("json") ? FhirFormat.JSON : FhirFormat.XML : FhirFormat.XML;
        InputStream src = new FileInputStream(getNamedParam(args, "-src"));
        OutputStream dst = new FileOutputStream(getNamedParam(args, "-dest"));
        self.convert(src, dst, hasParam(args, "-r2"), fmt);
    }
}

Example 37 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class PhinVadsImporter method process.

private void process(String source, String dest) {
    for (File f : new File(source).listFiles()) {
        try {
            System.out.println("Process " + f.getName());
            ValueSet vs = importValueSet(TextFile.fileToBytes(f));
            if (vs.getId() != null) {
                new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

Example 38 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class PhinVadsImporter method importValueSet.

private ValueSet importValueSet(byte[] source) throws FHIRException, IOException, ParseException {
    // first thing do is split into 2
    List<byte[]> parts = Utilities.splitBytes(source, "\r\n\r\n".getBytes());
    if (parts.size() < 2) {
        TextFile.bytesToFile(source, Utilities.path("[tmp]", "phinvads.txt"));
        throw new FHIRException("Unable to parse phinvads value set: " + parts.size() + " parts found");
    }
    CSVReader rdr = new CSVReader(new ByteArrayInputStream(parts.get(0)));
    rdr.setDelimiter('\t');
    rdr.setMultiline(true);
    rdr.readHeaders();
    rdr.line();
    ValueSet vs = new ValueSet();
    vs.setId(rdr.cell("Value Set OID"));
    vs.setUrl("http://phinvads.cdc.gov/fhir/ValueSet/" + vs.getId());
    vs.getMeta().setSource("https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=" + vs.getId());
    vs.setVersion(rdr.cell("Value Set Version"));
    vs.setTitle(rdr.cell("Value Set Name"));
    vs.setName(rdr.cell("Value Set Code"));
    vs.setDescription(rdr.cell("Value Set Definition"));
    if ("Published".equals(rdr.cell("Value Set Status"))) {
        vs.setStatus(PublicationStatus.ACTIVE);
    } else {
        vs.setStatus(PublicationStatus.DRAFT);
    }
    if (rdr.has("VS Last Updated Date")) {
        vs.setDate(new SimpleDateFormat("mm/dd/yyyy").parse(rdr.cell("VS Last Updated Date")));
    }
    rdr = new CSVReader(new ByteArrayInputStream(parts.get(parts.size() - 1)));
    rdr.setMultiline(true);
    rdr.setDelimiter('\t');
    rdr.readHeaders();
    while (rdr.line()) {
        String code = rdr.cell("Concept Code");
        String display = rdr.cell("Preferred Concept Name");
        String csoid = rdr.cell("Code System OID");
        String csver = rdr.cell("Code System Version");
        String url = context.oid2Uri(csoid);
        if (url == null) {
            url = "urn:oid:" + csoid;
        }
        csver = fixVersionforSystem(url, csver);
        ConceptSetComponent inc = getInclude(vs, url, csver);
        inc.addConcept().setCode(code).setDisplay(display);
    }
    return vs;
}

Example 39 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class VSACImporter method process.

private void process(String source, String dest, String username, String password) throws FHIRException, IOException, URISyntaxException {
    CSVReader csv = new CSVReader(new FileInputStream(source));
    csv.readHeaders();
    FHIRToolingClient fhirToolingClient = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", "fhir/vsac");
    fhirToolingClient.setUsername(username);
    fhirToolingClient.setPassword(password);
    int i = 0;
    while (csv.line()) {
        String oid = csv.cell("OID");
        try {
            ValueSet vs = fhirToolingClient.read(ValueSet.class, oid);
            new JsonParser().compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
            i++;
            if (i % 100 == 0) {
                System.out.println(i);
            }
        } catch (Exception e) {
            System.out.println("Unable to fetch OID " + oid + ": " + e.getMessage());
        }
    }
    System.out.println("Done. " + i + " ValueSets");
}

Example 40 with Source

use of org.hl7.fhir.utilities.validation.ValidationMessage.Source in project org.hl7.fhir.core by hapifhir.

the class ExamplesPackageBuilder method process.

private void process(String source) throws FHIRFormatError, FileNotFoundException, IOException {
    Set<String> set = new HashSet<>();
    for (File f : new File(source).listFiles()) {
        if (f.getName().endsWith(".json")) {
            JsonObject obj = JsonTrackingParser.parseJson(new FileInputStream(f));
            if (obj.has("resourceType") && obj.has("id")) {
                String type = obj.get("resourceType").getAsString();
                String id = obj.get("id").getAsString();
                byte[] content = TextFile.fileToBytes(f);
                if (type.equals("ConceptMap")) {
                    System.out.println("convert " + f.getName());
                    content = r5ToR4B(content);
                    TextFile.bytesToFile(content, f);
                }
            // TextFile.bytesToFile(content, Utilities.path(dest2, type+"-"+id+".json"));
            // if (!set.contains(type+"/"+id)) {
            // set.add(type+"/"+id);
            // pck.addFile(Category.RESOURCE, type+"-"+id+".json", content);
            // }
            }
        }
    }
// pck.finish();
// 
}