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Merge pull request #1590 from hapifhir/2024-04-gg-fixes 

2024 04 gg fixes
This commit is contained in:
Grahame Grieve 2024-04-03 21:46:57 +11:00 committed by GitHub
parent dfcd5ed161 5faa2df2fa
commit aa8d171e10
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
291 changed files with 2980 additions and 2080 deletions
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10
.mvn/wrapper/MavenWrapperDownloader.java vendored
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@ -50,17 +50,17 @@ public class MavenWrapperDownloader {
public static void main(String args[]) {
System.out.println("- Downloader started");
File baseDirectory = new File(args[0]);
File baseDirectory = ManagedFileAccess.file(args[0]);
System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
// If the maven-wrapper.properties exists, read it and check if it contains a custom
// wrapperUrl parameter.
File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
File mavenWrapperPropertyFile = ManagedFileAccess.file(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
String url = DEFAULT_DOWNLOAD_URL;
if(mavenWrapperPropertyFile.exists()) {
FileInputStream mavenWrapperPropertyFileInputStream = null;
try {
mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
mavenWrapperPropertyFileInputStream = ManagedFileAccess.inStream(mavenWrapperPropertyFile);
Properties mavenWrapperProperties = new Properties();
mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
@ -78,7 +78,7 @@ public class MavenWrapperDownloader {
}
System.out.println("- Downloading from: : " + url);
File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
File outputFile = ManagedFileAccess.file(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
if(!outputFile.getParentFile().exists()) {
if(!outputFile.getParentFile().mkdirs()) {
System.out.println(
@ -101,7 +101,7 @@ public class MavenWrapperDownloader {
URL website = new URL(urlString);
ReadableByteChannel rbc;
rbc = Channels.newChannel(website.openStream());
FileOutputStream fos = new FileOutputStream(destination);
FileOutputStream fos = ManagedFileAccess.outStream(destination);
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
fos.close();
rbc.close();

17
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/R2R3ConversionManager.java
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@ -67,6 +67,7 @@ import org.hl7.fhir.dstu3.utils.StructureMapUtilities;
import org.hl7.fhir.dstu3.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
/**
* This class manages conversion from R2 to R3 and vice versa
@ -113,8 +114,8 @@ public class R2R3ConversionManager implements ITransformerServices {
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"));
InputStream src = ManagedFileAccess.inStream(getNamedParam(args, "-src"));
OutputStream dst = ManagedFileAccess.outStream(getNamedParam(args, "-dest"));
self.convert(src, dst, hasParam(args, "-r2"), fmt);
}
}
@ -164,9 +165,9 @@ public class R2R3ConversionManager implements ITransformerServices {
}
public void setR2Definitions(String source) throws IOException, FHIRException {
File f = new File(source);
File f = ManagedFileAccess.file(source);
if (f.exists())
setR2Definitions(new FileInputStream(f));
setR2Definitions(ManagedFileAccess.inStream(f));
else
setR2Definitions(fetch(source));
}
@ -184,9 +185,9 @@ public class R2R3ConversionManager implements ITransformerServices {
}
public void setR3Definitions(String source) throws IOException, FHIRException {
File f = new File(source);
File f = ManagedFileAccess.file(source);
if (f.exists())
setR3Definitions(new FileInputStream(f));
setR3Definitions(ManagedFileAccess.inStream(f));
else
setR3Definitions(fetch(source));
}
@ -201,9 +202,9 @@ public class R2R3ConversionManager implements ITransformerServices {
}
public void setMappingLibrary(String source) throws IOException, FHIRException {
File f = new File(source);
File f = ManagedFileAccess.file(source);
if (f.exists())
setMappingLibrary(new FileInputStream(f));
setMappingLibrary(ManagedFileAccess.inStream(f));
else
setMappingLibrary(fetch(source));
}

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/SpecDifferenceEvaluator.java
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@ -42,6 +42,7 @@ import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.ZipGenerator;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -132,7 +133,7 @@ public class SpecDifferenceEvaluator {
}
private static void loadSD4(Map<String, StructureDefinition> map, String fn) throws FHIRException, IOException {
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(new FileInputStream(fn));
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(ManagedFileAccess.inStream(fn));
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
if (be.getResource() instanceof org.hl7.fhir.r4.model.StructureDefinition) {
org.hl7.fhir.r4.model.StructureDefinition sd = (org.hl7.fhir.r4.model.StructureDefinition) be.getResource();
@ -143,7 +144,7 @@ public class SpecDifferenceEvaluator {
}
private static void loadSD(Map<String, StructureDefinition> map, String fn) throws FHIRFormatError, IOException {
Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(fn));
Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(fn));
for (BundleEntryComponent be : bundle.getEntry()) {
if (be.getResource() instanceof StructureDefinition) {
StructureDefinition sd = (StructureDefinition) be.getResource();
@ -153,7 +154,7 @@ public class SpecDifferenceEvaluator {
}
private static void loadVS4(Map<String, ValueSet> map, String fn) throws FHIRException, IOException {
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(new FileInputStream(fn));
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.XmlParser().parse(ManagedFileAccess.inStream(fn));
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
if (be.getResource() instanceof org.hl7.fhir.r4.model.ValueSet) {
org.hl7.fhir.r4.model.ValueSet sd = (org.hl7.fhir.r4.model.ValueSet) be.getResource();
@ -163,7 +164,7 @@ public class SpecDifferenceEvaluator {
}
private static void loadVS(Map<String, ValueSet> map, String fn) throws FHIRFormatError, IOException {
Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(fn));
Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(fn));
for (BundleEntryComponent be : bundle.getEntry()) {
if (be.getResource() instanceof ValueSet) {
ValueSet sd = (ValueSet) be.getResource();

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
View File

@ -18,6 +18,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -230,14 +231,14 @@ public class PackageVisitor {
String[] p = url.split("\\/");
String repo = "https://build.fhir.org/ig/"+p[0]+"/"+p[1];
JsonObject manifest = JsonParser.parseObjectFromUrl(repo+"/package.manifest.json");
File co = new File(Utilities.path(cache, pid+"."+manifest.asString("date")+".tgz"));
File co = ManagedFileAccess.file(Utilities.path(cache, pid+"."+manifest.asString("date")+".tgz"));
if (!co.exists()) {
SimpleHTTPClient fetcher = new SimpleHTTPClient();
HTTPResult res = fetcher.get(repo+"/package.tgz?nocache=" + System.currentTimeMillis());
res.checkThrowException();
TextFile.bytesToFile(res.getContent(), co);
}
NpmPackage npm = NpmPackage.fromPackage(new FileInputStream(co));
NpmPackage npm = NpmPackage.fromPackage(ManagedFileAccess.inStream(co));
String fv = npm.fhirVersion();
long ms2 = System.currentTimeMillis();

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/BOMRemover.java
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@ -9,11 +9,12 @@ import java.io.InputStreamReader;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class BOMRemover {
public static void main(String[] args) throws FileNotFoundException, IOException {
new BOMRemover().execute(new File(args[0]));
new BOMRemover().execute(ManagedFileAccess.file(args[0]));
}

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/BigCodeSystemGenerator.java
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@ -9,20 +9,21 @@ import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class BigCodeSystemGenerator {
public static void main(String[] args) throws FileNotFoundException, IOException {
new BigCodeSystemGenerator().execute(new File("/Users/grahamegrieve/work/test-cases/tx/big/codesystem-big.json"));
new BigCodeSystemGenerator().execute(ManagedFileAccess.file("/Users/grahamegrieve/work/test-cases/tx/big/codesystem-big.json"));
}
private void execute(File file) throws FHIRFormatError, FileNotFoundException, IOException {
CodeSystem cs = (CodeSystem) new JsonParser().parse(new FileInputStream(file));
CodeSystem cs = (CodeSystem) new JsonParser().parse(ManagedFileAccess.inStream(file));
cs.getConcept().clear();
for (int i = 1; i <= 2000; i++) {
cs.addConcept().setCode("code"+i).setDisplay("Display "+i).setDefinition("This is code "+i);
}
new JsonParser().compose(new FileOutputStream(file), cs);
new JsonParser().compose(ManagedFileAccess.outStream(file), cs);
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CKMImporter.java
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@ -44,6 +44,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -115,9 +116,9 @@ public class CKMImporter {
String src = Utilities.path(Utilities.path("[tmp]"), id + ".xml");
String dst = Utilities.path(dest, id + ".xml");
if (!new File(src).exists())
if (!ManagedFileAccess.file(src).exists())
downloadArchetype(id);
if (cfg != null && new File(cfg).exists())
if (cfg != null && ManagedFileAccess.file(cfg).exists())
ADLImporter.main(new String[]{"-source", src, "-dest", dst, "-config", config, "-info", cfg});
else
ADLImporter.main(new String[]{"-source", src, "-dest", dst, "-config", config});

15
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CPTImporter.java
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@ -32,6 +32,7 @@ import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class CPTImporter {
@ -89,12 +90,12 @@ public class CPTImporter {
System.out.println(c);
System.out.println(k);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dst), cs);
produceDB(Utilities.changeFileExt(dst, ".db"), cs);
cs.setContent(CodeSystemContentMode.FRAGMENT);
cs.getConcept().removeIf(cc -> !Utilities.existsInList(cc.getCode(), "metadata-kinds", "metadata-designations", "99202", "99203", "0001A", "99252", "25", "P1", "1P", "F1", "95"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.changeFileExt(dst, "-fragment.json")), cs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.changeFileExt(dst, "-fragment.json")), cs);
produceDB(Utilities.changeFileExt(dst, "-fragment.db"), cs);
}
@ -146,7 +147,7 @@ public class CPTImporter {
}
private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException {
private void produceDB(String path, CodeSystem cs) throws ClassNotFoundException, SQLException, IOException {
Connection con = connect(path);
Statement stmt = con.createStatement();
@ -185,10 +186,10 @@ public class CPTImporter {
}
private Connection connect(String dest) throws SQLException, ClassNotFoundException {
private Connection connect(String dest) throws SQLException, ClassNotFoundException, IOException {
// Class.forName("com.mysql.jdbc.Driver");
// con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd});
new File(dest).delete();
ManagedFileAccess.file(dest).delete();
Connection con = DriverManager.getConnection("jdbc:sqlite:"+dest);
makeMetadataTable(con);
makeConceptsTable(con);
@ -267,7 +268,7 @@ public class CPTImporter {
}
private int processModifiers(CodeSystem cs, String path) throws FHIRException, FileNotFoundException, IOException {
CSVReader csv = new CSVReader(new FileInputStream(path));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(path));
csv.readHeaders();
int res = 0;
@ -309,7 +310,7 @@ public class CPTImporter {
FileInputStream inputStream = null;
Scanner sc = null;
try {
inputStream = new FileInputStream(path);
inputStream = ManagedFileAccess.inStream(path);
sc = new Scanner(inputStream, "UTF-8");
while (sc.hasNextLine()) {
String line = sc.nextLine();

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CVXImporter.java
View File

@ -24,6 +24,7 @@ import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -58,7 +59,7 @@ public class CVXImporter {
}
private void doUpdate(String source, String dest) throws FHIRFormatError, FileNotFoundException, IOException, ParserConfigurationException, SAXException {
CodeSystem cvx = (CodeSystem) new JsonParser().parse(new FileInputStream(dest));
CodeSystem cvx = (CodeSystem) new JsonParser().parse(ManagedFileAccess.inStream(dest));
String ldate = null;
@ -94,7 +95,7 @@ public class CVXImporter {
Collections.sort(cvx.getConcept(), new CVXSorter());
cvx.setDateElement(new DateTimeType(ldate));
cvx.setVersion(ldate.replace("-", ""));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), cvx);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dest), cvx);
}
private ConceptDefinitionComponent findCVXCode(CodeSystem cvx, String code) {

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CorePackageTools.java
View File

@ -7,6 +7,7 @@ import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -26,12 +27,12 @@ public class CorePackageTools {
private void buildPackage(String path, String output) throws IOException {
NpmPackage npm = NpmPackage.fromFolder(path);
npm.loadAllFiles();
npm.save(new FileOutputStream(output));
npm.save(ManagedFileAccess.outStream(output));
}
private void buildXml(String json, String xml, String version) throws FHIRFormatError, IOException {
for (File f : new File(Utilities.path(json, "package")).listFiles()) {
for (File f : ManagedFileAccess.file(Utilities.path(json, "package")).listFiles()) {
if (f.getName().endsWith(".json")) {
JsonObject j = JsonParser.parseObject(f);
if (j.has("resourceType")) {
@ -39,8 +40,8 @@ public class CorePackageTools {
String n = f.getName();
System.out.println(n);
String xn = Utilities.changeFileExt(n, ".xml");
org.hl7.fhir.dstu2016may.model.Resource r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(f));
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.NORMAL).compose(new FileOutputStream(Utilities.path(xml, "package", xn)), r);
org.hl7.fhir.dstu2016may.model.Resource r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(f));
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(Utilities.path(xml, "package", xn)), r);
}
}
}

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CountryCodesConverter.java
View File

@ -45,6 +45,7 @@ import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -123,10 +124,10 @@ public class CountryCodesConverter {
cs1.setCount(cs1.getConcept().size());
cs2.setCount(cs2.getConcept().size());
throw new Error("Needs revisiting");
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166.json")), cs1);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166.json")), cs1); // format hasn't changed
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "4.0.1", "package", "CodeSstem-iso3166-2.json")), cs2);
// new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "3.0.2", "package", "CodeSstem-iso3166-2.json")), cs2); // format hasn't changed
}
public void setMetadata(Document src, CodeSystem cs, String id, String url, String partName, String partTitle) {
@ -360,7 +361,7 @@ public class CountryCodesConverter {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
return builder.parse(new FileInputStream(source));
return builder.parse(ManagedFileAccess.inStream(source));
}

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/DicomPackageBuilder.java
View File

@ -23,6 +23,7 @@ import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.utils.NPMPackageGenerator;
import org.hl7.fhir.r4.utils.NPMPackageGenerator.Category;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -73,8 +74,8 @@ public class DicomPackageBuilder {
Set<String> ids = new HashSet<>();
ids.add(vs.getId());
for (File f : new File(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
vs = (ValueSet) JsonParser.loadFile(new FileInputStream(f));
for (File f : ManagedFileAccess.file(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
vs = (ValueSet) JsonParser.loadFile(ManagedFileAccess.inStream(f));
vs.setVersion(version);
if (vs.getId().length() > 64) {
vs.setId(vs.getId().substring(0, 64));
@ -133,7 +134,7 @@ public class DicomPackageBuilder {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
Document doc = builder.parse(ManagedFileAccess.inStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
Element rdf = doc.getDocumentElement();
Element d = XMLUtil.getFirstChild(rdf);
version = processVersion(XMLUtil.getNamedChildText(d, "versionInfo"));

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExamplesPackageBuilder.java
View File

@ -10,6 +10,7 @@ import java.util.Set;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -22,9 +23,9 @@ public class ExamplesPackageBuilder {
private void process(String source) throws FHIRFormatError, FileNotFoundException, IOException {
Set<String> set = new HashSet<>();
for (File f : new File(source).listFiles()) {
for (File f : ManagedFileAccess.file(source).listFiles()) {
if (f.getName().endsWith(".json")) {
JsonObject obj = JsonParser.parseObject(new FileInputStream(f));
JsonObject obj = JsonParser.parseObject(ManagedFileAccess.inStream(f));
if (obj.has("resourceType") && obj.has("id")) {
String type = obj.asString("resourceType");
String id = obj.asString("id");

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ExtensionExtractor.java
View File

@ -23,6 +23,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -131,7 +132,7 @@ public class ExtensionExtractor {
save(cs, dst,s, ids);
}
deleteMatchingResources(ids, new File("/Users/grahamegrieve/work/r5/source"));
deleteMatchingResources(ids, ManagedFileAccess.file("/Users/grahamegrieve/work/r5/source"));
}
private void deleteMatchingResources(Set<String> ids, File folder) {
@ -172,9 +173,9 @@ public class ExtensionExtractor {
ids.add(cr.getId());
String fn = Utilities.path(dst, folder, cr.fhirType()+"-"+cr.getId()+".xml");
cr.setUserData("folder", folder);
if (!new File(fn).exists()) {
if (!ManagedFileAccess.file(fn).exists()) {
Utilities.createDirectory(Utilities.getDirectoryForFile(fn));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), cr);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(fn), cr);
}
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/GenValueSetExpansionConvertor.java
View File

@ -43,13 +43,14 @@ import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class GenValueSetExpansionConvertor {
public static void main(String[] args) throws FHIRFormatError, IOException {
String src = args[0];
String tgt = args[1];
Bundle bundle = (Bundle) new XmlParser().parse(new FileInputStream(src));
Bundle bundle = (Bundle) new XmlParser().parse(ManagedFileAccess.inStream(src));
for (BundleEntryComponent be : bundle.getEntry()) {
Resource res = be.getResource();
if (res != null) {
@ -58,7 +59,7 @@ public class GenValueSetExpansionConvertor {
id = tail(((ValueSet) res).getUrl());
String dst = Utilities.path(tgt, res.fhirType() + "-" + id + ".json");
System.out.println(dst);
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(new FileOutputStream(dst), res);
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(dst), res);
}
}
}

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICD11Generator.java
View File

@ -28,6 +28,7 @@ import org.hl7.fhir.r4.utils.ToolingExtensions;
import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonElement;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -49,7 +50,7 @@ public class ICD11Generator {
processMMSEntity(cs, base, child.asString(), cs.addConcept(), dest);
System.out.println();
}
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "icd-11-mms.xml")), cs);
makeFullVs(dest, cs);
cs = makeEntityCodeSystem();
@ -62,7 +63,7 @@ public class ICD11Generator {
processEntity(cs, ids, base, tail(child.asString()), dest);
System.out.println();
}
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "icd-11-foundation.xml")), cs);
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "icd-11-foundation.xml")), cs);
makeFullVs2(dest, cs);
System.out.println("finished");
}
@ -153,7 +154,7 @@ public class ICD11Generator {
vs.setStatus(cs.getStatus());
ConceptSetComponent inc = vs.getCompose().addInclude();
inc.setSystem(cs.getUrl());
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-all-MMS.xml")), vs);
}
private void makeFullVs2(String dest, CodeSystem cs) throws IOException {
@ -172,7 +173,7 @@ public class ICD11Generator {
vs.setStatus(cs.getStatus());
ConceptSetComponent inc = vs.getCompose().addInclude();
inc.setSystem(cs.getUrl());
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-all-foundation.xml")), vs);
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-all-foundation.xml")), vs);
}
private void processMMSEntity(CodeSystem cs, String base, String ref, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String dest) throws IOException {
@ -281,7 +282,7 @@ public class ICD11Generator {
for (JsonElement e : o.getJsonArray("scaleEntity")) {
inc.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue(tail(e.asString()));
}
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "vs-" + id + ".xml")), vs);
new XmlParser(XmlVersion.V1_1).setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "vs-" + id + ".xml")), vs);
return url;
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICFImporter.java
View File

@ -19,6 +19,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.PropertyType;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class ICFImporter {
@ -28,7 +29,7 @@ public class ICFImporter {
}
private void doImport(String src, String dst) throws FHIRException, FileNotFoundException, IOException {
CSVReader csv = new CSVReader(new FileInputStream(src));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
csv.setDelimiter('\t');
csv.readHeaders();
@ -98,7 +99,7 @@ public class ICFImporter {
}
csv.close();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dst), cs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dst), cs);
}
//
// private String processLink(String cell) {

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ICPC2Importer.java
View File

@ -53,6 +53,7 @@ import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.terminologies.CodeSystemUtilities;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -122,7 +123,7 @@ public class ICPC2Importer {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(false);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(sourceFileName));
Document doc = builder.parse(ManagedFileAccess.inStream(sourceFileName));
ValueSet vs = new ValueSet();
vs.setUrl("http://hl7.org/fhir/sid/icpc2/vs");
@ -170,8 +171,8 @@ public class ICPC2Importer {
XmlParser xml = new XmlParser();
xml.setOutputStyle(OutputStyle.PRETTY);
xml.compose(new FileOutputStream(targetFileNameVS), vs);
xml.compose(new FileOutputStream(targetFileNameCS), cs);
xml.compose(ManagedFileAccess.outStream(targetFileNameVS), vs);
xml.compose(ManagedFileAccess.outStream(targetFileNameCS), cs);
}
private void processClass(Element cls, Map<String, ConceptDefinitionComponent> concepts, CodeSystem define) throws FHIRFormatError {

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IEEE11073Convertor.java
View File

@ -68,6 +68,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class IEEE11073Convertor {
@ -113,7 +114,7 @@ public class IEEE11073Convertor {
g.setSource("urn:iso:std:iso:11073:10101");
g.setTarget("http://loinc.org");
CSVReader csv = new CSVReader(new FileInputStream(src));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
csv.readHeaders();
while (csv.line()) {
SourceElementComponent e = g.addElement();
@ -124,13 +125,13 @@ public class IEEE11073Convertor {
t.setCode(csv.cell("LOINC_NUM"));
t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
}
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
System.out.println("Done");
return cm;
}
public static CodeSystem generateMDC(String src, String dst, UcumService ucum) throws IOException, FHIRException {
CSVReader csv = new CSVReader(new FileInputStream(src));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(src));
csv.readHeaders();
CodeSystem cs = new CodeSystem();
Map<String, String> ucumIssues = new HashMap<String, String>();
@ -206,7 +207,7 @@ public class IEEE11073Convertor {
}
}
csv.close();
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
System.out.println(errorCount + "UCUM errors");
for (String u : sorted(ucumIssues.keySet()))

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IGPackConverter102.java
View File

@ -49,6 +49,7 @@ import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class IGPackConverter102 extends BaseAdvisor_10_30 {
@ -60,21 +61,21 @@ public class IGPackConverter102 extends BaseAdvisor_10_30 {
private void process() throws IOException, FHIRException {
initCSList();
for (String s : new File(Utilities.path("[tmp]", "igpack2")).list()) {
for (String s : ManagedFileAccess.file(Utilities.path("[tmp]", "igpack2")).list()) {
if (s.endsWith(".xml") && !s.startsWith("z-") && !Utilities.existsInList(s, "expansions.xml", "v3-codesystems.xml", "v2-tables.xml")) {
System.out.println("process " + s);
org.hl7.fhir.dstu2.formats.XmlParser xp = new org.hl7.fhir.dstu2.formats.XmlParser();
org.hl7.fhir.dstu2.model.Resource r10 = xp.parse(new FileInputStream(Utilities.path("[tmp]", "igpack2\\" + s)));
org.hl7.fhir.dstu2.model.Resource r10 = xp.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "igpack2\\" + s)));
org.hl7.fhir.dstu3.model.Resource r17 = VersionConvertorFactory_10_30.convertResource(r10, this);
org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
xc.setOutputStyle(OutputStyle.PRETTY);
xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack2\\" + s)), r17);
xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack2\\" + s)), r17);
}
}
System.out.println("save codesystems");
org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
xc.setOutputStyle(OutputStyle.PRETTY);
xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack2\\codesystems.xml")), cslist);
xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack2\\codesystems.xml")), cslist);
System.out.println("done");
}

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/IGPackConverter140.java
View File

@ -37,20 +37,21 @@ import java.io.FileOutputStream;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_30;
import org.hl7.fhir.dstu3.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class IGPackConverter140 {
public static void main(String[] args) throws Exception {
for (String s : new File(Utilities.path("[tmp]", "igpack")).list()) {
for (String s : ManagedFileAccess.file(Utilities.path("[tmp]", "igpack")).list()) {
// if (s.endsWith(".xml") && !s.contains("z-")) {
if (s.equals("expansions.xml")) {
System.out.println("process " + s);
org.hl7.fhir.dstu2016may.formats.XmlParser xp = new org.hl7.fhir.dstu2016may.formats.XmlParser();
org.hl7.fhir.dstu2016may.model.Resource r14 = xp.parse(new FileInputStream(Utilities.path("[tmp]", "igpack\\" + s)));
org.hl7.fhir.dstu2016may.model.Resource r14 = xp.parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "igpack\\" + s)));
org.hl7.fhir.dstu3.model.Resource r17 = VersionConvertorFactory_14_30.convertResource(r14);
org.hl7.fhir.dstu3.formats.XmlParser xc = new org.hl7.fhir.dstu3.formats.XmlParser();
xc.setOutputStyle(OutputStyle.PRETTY);
xc.compose(new FileOutputStream(Utilities.path("[tmp]", "igpack\\z-" + s)), r17);
xc.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "igpack\\z-" + s)), r17);
}
}
System.out.println("done");

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/JsonProcessor.java
View File

@ -3,6 +3,7 @@ package org.hl7.fhir.convertors.misc;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -15,7 +16,7 @@ public class JsonProcessor {
private void process(String source) throws IOException {
JsonObject json = JsonParser.parseObjectFromFile(source);
process(json);
JsonParser.compose(json, new FileOutputStream(source), true);
JsonParser.compose(json, ManagedFileAccess.outStream(source), true);
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/LoincToDEConvertor.java
View File

@ -50,6 +50,7 @@ import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.InstantType;
import org.hl7.fhir.r5.model.Meta;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -151,12 +152,12 @@ public class LoincToDEConvertor {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
xml = builder.parse(new FileInputStream(definitions));
xml = builder.parse(ManagedFileAccess.inStream(definitions));
}
private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
XmlParser xml = new XmlParser();
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
xml.compose(s, bundle, true);
s.close();
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/NUCCConvertor.java
View File

@ -48,6 +48,7 @@ import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class NUCCConvertor {
@ -56,7 +57,7 @@ public class NUCCConvertor {
}
public void execute() throws IOException, FHIRException {
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path("[tmp]", "nucc.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path("[tmp]", "nucc.csv")));
CodeSystem cs = new CodeSystem();
cs.setId("nucc-provider-taxonomy");
cs.setUrl("http://nucc.org/provider-taxonomy");
@ -79,7 +80,7 @@ public class NUCCConvertor {
}
csv.close();
cs.sort();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "nucc.json")), cs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "nucc.json")), cs);
}
private void processLine(CodeSystem cs, String[] values) throws FHIRFormatError {

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/NpmPackageVersionConverter.java
View File

@ -39,6 +39,7 @@ import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -80,7 +81,7 @@ public class NpmPackageVersionConverter {
}
public void execute() throws IOException {
Map<String, byte[]> content = loadContentMap(new FileInputStream(source));
Map<String, byte[]> content = loadContentMap(ManagedFileAccess.inStream(source));
Map<String, byte[]> output = new HashMap<>();
output.put("package/package.json", convertPackage(content.get("package/package.json")));
@ -141,7 +142,7 @@ public class NpmPackageVersionConverter {
tar.write(cnt);
tar.closeArchiveEntry();
cnt = TextFile.fileToBytes(e.getValue().getDbFilename());
new File(e.getValue().getDbFilename()).delete();
ManagedFileAccess.file(e.getValue().getDbFilename()).delete();
entry = new TarArchiveEntry(e.getKey() + "/.index.db");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);

26
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/OIDAssigner.java
View File

@ -3,10 +3,12 @@ package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class OIDAssigner {
@ -15,9 +17,9 @@ public class OIDAssigner {
new OIDAssigner().execute(args[0], args[1], args[2]);
}
private void execute(String oidSource, String folder, String version) {
private void execute(String oidSource, String folder, String version) throws IOException {
IniFile oids = new IniFile(oidSource);
File f = new File(folder);
File f = ManagedFileAccess.file(folder);
process(oids, f, version);
}
@ -47,7 +49,7 @@ public class OIDAssigner {
org.hl7.fhir.dstu2.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.dstu2.formats.JsonParser() : new org.hl7.fhir.dstu2.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.dstu2.model.Resource r = parser.parse(new FileInputStream(f));
org.hl7.fhir.dstu2.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof org.hl7.fhir.dstu2.model.ValueSet) {
org.hl7.fhir.dstu2.model.ValueSet vs = (org.hl7.fhir.dstu2.model.ValueSet) r;
boolean hasOid = isOid(vs.getIdentifier());
@ -81,7 +83,7 @@ public class OIDAssigner {
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@ -93,7 +95,7 @@ public class OIDAssigner {
org.hl7.fhir.dstu3.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.dstu3.formats.JsonParser() : new org.hl7.fhir.dstu3.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.dstu3.model.Resource r = parser.parse(new FileInputStream(f));
org.hl7.fhir.dstu3.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
org.hl7.fhir.dstu3.model.CodeSystem cs = (org.hl7.fhir.dstu3.model.CodeSystem) r;
boolean hasOid = isOid(cs.getIdentifier());
@ -141,7 +143,7 @@ public class OIDAssigner {
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@ -153,7 +155,7 @@ public class OIDAssigner {
org.hl7.fhir.r4.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r4.formats.JsonParser() : new org.hl7.fhir.r4.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r4.model.Resource r = parser.parse(new FileInputStream(f));
org.hl7.fhir.r4.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof org.hl7.fhir.r4.model.CodeSystem) {
org.hl7.fhir.r4.model.CodeSystem cs = (org.hl7.fhir.r4.model.CodeSystem) r;
boolean hasOid = false;
@ -206,7 +208,7 @@ public class OIDAssigner {
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@ -217,7 +219,7 @@ public class OIDAssigner {
org.hl7.fhir.r4b.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r4b.formats.JsonParser() : new org.hl7.fhir.r4b.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r4b.model.Resource r = parser.parse(new FileInputStream(f));
org.hl7.fhir.r4b.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof org.hl7.fhir.r4b.model.CanonicalResource) {
org.hl7.fhir.r4b.model.CanonicalResource cs = (org.hl7.fhir.r4b.model.CanonicalResource) r;
boolean hasOid = false;
@ -233,7 +235,7 @@ public class OIDAssigner {
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r4b.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(org.hl7.fhir.r4b.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());
@ -245,7 +247,7 @@ public class OIDAssigner {
org.hl7.fhir.r5.formats.IParser parser = fmt == FhirFormat.JSON ? new org.hl7.fhir.r5.formats.JsonParser() : new org.hl7.fhir.r5.formats.XmlParser();
try {
boolean save = false;
org.hl7.fhir.r5.model.Resource r = parser.parse(new FileInputStream(f));
org.hl7.fhir.r5.model.Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof org.hl7.fhir.r5.model.CanonicalResource) {
org.hl7.fhir.r5.model.CanonicalResource cs = (org.hl7.fhir.r5.model.CanonicalResource) r;
boolean hasOid = false;
@ -261,7 +263,7 @@ public class OIDAssigner {
}
}
if (save) {
parser.setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
} catch (Exception e) {
System.out.println("Erro processing "+f.getAbsolutePath()+": "+e.getMessage());

39
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/OMOPImporter.java
View File

@ -15,6 +15,7 @@ import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class OMOPImporter {
@ -107,15 +108,15 @@ public class OMOPImporter {
}
private void connect(String dest) throws SQLException, ClassNotFoundException {
private void connect(String dest) throws SQLException, ClassNotFoundException, IOException {
// Class.forName("com.mysql.jdbc.Driver");
// con = DriverManager.getConnection("jdbc:mysql://localhost:3306/omop?useSSL=false","root",{pwd});
new File("/Users/grahamegrieve/temp/omop/omop.db").delete();
ManagedFileAccess.file("/Users/grahamegrieve/temp/omop/omop.db").delete();
con = DriverManager.getConnection("jdbc:sqlite:"+dest);
}
private void processRelationships(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
Tracker t = new Tracker("Relationships", 700);
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "RELATIONSHIP.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "RELATIONSHIP.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -147,7 +148,7 @@ public class OMOPImporter {
stmt.execute("Create Index `RelationshipsId` on Relationships (`relationship_id`)");
stmt.execute("Create Index`RelationshipsReverse` on Relationships (`reverse_relationship_id`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "RELATIONSHIP.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "RELATIONSHIP.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -182,7 +183,7 @@ public class OMOPImporter {
private void processVocabularies(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
Tracker t = new Tracker("Vocabularies", 60);
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "VOCABULARY.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "VOCABULARY.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -217,7 +218,7 @@ public class OMOPImporter {
"\r\n");
stmt.execute("CREATE INDEX `VocabulariesId` on Vocabularies (`vocabulary_id`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "VOCABULARY.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "VOCABULARY.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -244,7 +245,7 @@ public class OMOPImporter {
private void processDomains(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
Tracker t = new Tracker("Domains", 50);
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DOMAIN.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DOMAIN.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -275,7 +276,7 @@ public class OMOPImporter {
stmt.execute("CREATE INDEX `DomainId` on Domains (`domain_id`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DOMAIN.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DOMAIN.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -299,7 +300,7 @@ public class OMOPImporter {
private void processConceptClasses(String folder, boolean process) throws FHIRException, FileNotFoundException, IOException, SQLException {
Tracker t = new Tracker("ConceptClasses", 400);
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -325,7 +326,7 @@ public class OMOPImporter {
" PRIMARY KEY (`concept_class_concept_id`)\r\n"+
") \r\n"+
"\r\n");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_CLASS.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -356,7 +357,7 @@ public class OMOPImporter {
return;
}
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -398,7 +399,7 @@ public class OMOPImporter {
" PRIMARY KEY (`drug_concept_id`,`ingredient_concept_id`)\r\n"+
") \r\n"+
"\r\n");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "DRUG_STRENGTH.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -446,7 +447,7 @@ public class OMOPImporter {
return;
}
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -485,7 +486,7 @@ public class OMOPImporter {
stmt.execute("CREATE INDEX `ConceptVocabulary` on Concepts (`vocabulary_id`,`concept_code`)");
stmt.execute("CREATE INDEX `ConceptClass` on Concepts (`concept_class_id`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -523,7 +524,7 @@ public class OMOPImporter {
}
t.scan();
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -545,7 +546,7 @@ public class OMOPImporter {
stmt.execute("CREATE INDEX `SynonymId` on ConceptSynonyms (`concept_id`)");
stmt.execute("CREATE INDEX `SynonymLang` on ConceptSynonyms (`language_concept_id`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_SYNONYM.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -575,7 +576,7 @@ public class OMOPImporter {
}
t.process();
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_ANCESTOR.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_ANCESTOR.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -614,7 +615,7 @@ public class OMOPImporter {
}
t.scan();
CSVReader csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);
@ -641,7 +642,7 @@ public class OMOPImporter {
// stmt.execute("CREATE INDEX `type1` on ConceptRelationships (`relationship_id`,`concept_id_1`,`concept_id_2`)");
// stmt.execute("CREATE INDEX `type2` on ConceptRelationships (`relationship_id`,`concept_id_2`,`concept_id_1`)");
csv = new CSVReader(new FileInputStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
csv = new CSVReader(ManagedFileAccess.inStream(Utilities.path(folder, "CONCEPT_RELATIONSHIP.csv")));
csv.setDelimiter('\t');
csv.readHeaders();
csv.setDoingQuotes(false);

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ObservationStatsBuilder.java
View File

@ -51,6 +51,7 @@ import org.hl7.fhir.dstu3.model.Type;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class ObservationStatsBuilder {
@ -78,7 +79,7 @@ public class ObservationStatsBuilder {
vitals(b, base, 130, 95, 133, 97, 37.2);
vitals(b, base, 150, 85, 125, 98, 37.1);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "vitals.xml")), b);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "vitals.xml")), b);
}
private static void vitals(Bundle b, Calendar base, int minutes, int diastolic, int systolic, int sat, double temp) throws FHIRFormatError {
@ -202,7 +203,7 @@ public class ObservationStatsBuilder {
addAge(b, 10, 0, "31.9");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "obs.xml")), b);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "obs.xml")), b);
}
private static void addAge(Bundle b, int y, int m, String v) throws FHIRException {

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PackageMaintainer.java
View File

@ -7,6 +7,7 @@ import java.util.List;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -67,15 +68,15 @@ public class PackageMaintainer {
System.out.println("Examples contains " + s + " but core doesn't");
}
}
strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
if (!ver.equals("r2b"))
strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
strip(ManagedFileAccess.file(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
}
private List<String> listResources(String dir) {
File folder = new File(dir);
private List<String> listResources(String dir) throws IOException {
File folder = ManagedFileAccess.file(dir);
List<String> res = new ArrayList<>();
for (String fn : folder.list()) {
if (fn.endsWith(".json") && fn.contains("-")) {

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PackageMinifier.java
View File

@ -7,6 +7,7 @@ import java.io.IOException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.utils.ResourceMinifier;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
@ -33,7 +34,7 @@ public class PackageMinifier {
}
}
}
tgt.save(new FileOutputStream(target));
tgt.save(ManagedFileAccess.outStream(target));
}
}

12
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PackagePreparer.java
View File

@ -3,6 +3,7 @@ package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
/*
Copyright (c) 2011+, HL7, Inc.
@ -38,6 +39,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_40;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
/*
* load reosurces in xml format, and sve them in package format (json, with correct name
@ -48,10 +50,10 @@ import org.hl7.fhir.utilities.Utilities;
public class PackagePreparer {
public static void main(String[] args) {
for (File f : new File("C:\\work\\fhirserver\\resources\\mihin").listFiles()) {
public static void main(String[] args) throws IOException {
for (File f : ManagedFileAccess.file("C:\\work\\fhirserver\\resources\\mihin").listFiles()) {
try {
org.hl7.fhir.dstu3.model.Resource r = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(f));
org.hl7.fhir.dstu3.model.Resource r = new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(f));
if (r instanceof Bundle) {
Bundle b = (Bundle) r;
for (BundleEntryComponent be : b.getEntry()) {
@ -60,7 +62,7 @@ public class PackagePreparer {
if (r4.getId().startsWith(r4.fhirType() + "-"))
be.getResource().setId(r4.getId().substring(r4.fhirType().length() + 1));
if (be.getResource().hasId())
new org.hl7.fhir.r4.formats.JsonParser().compose(new FileOutputStream(Utilities.path("C:\\work\\fhirserver\\resources\\fhir.test.data\\3.5.0\\package", be.getResource().fhirType() + "-" + be.getResource().getId() + ".json")), r4);
new org.hl7.fhir.r4.formats.JsonParser().compose(ManagedFileAccess.outStream(Utilities.path("C:\\work\\fhirserver\\resources\\fhir.test.data\\3.5.0\\package", be.getResource().fhirType() + "-" + be.getResource().getId() + ".json")), r4);
else
System.out.println(f.getName() + " bundle entry has no id");
} catch (Exception e) {
@ -68,7 +70,7 @@ public class PackagePreparer {
}
}
} else if (r.hasId())
new org.hl7.fhir.r4.formats.JsonParser().compose(new FileOutputStream(Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), r.fhirType() + "-" + r.getId() + ".json")), VersionConvertorFactory_30_40.convertResource(r));
new org.hl7.fhir.r4.formats.JsonParser().compose(ManagedFileAccess.outStream(Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), r.fhirType() + "-" + r.getId() + ".json")), VersionConvertorFactory_30_40.convertResource(r));
else
System.out.println(f.getName() + " has no id");
} catch (Exception e) {

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/PhinVadsImporter.java
View File

@ -18,6 +18,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class PhinVadsImporter extends OIDBasedValueSetImporter {
@ -32,13 +33,13 @@ public class PhinVadsImporter extends OIDBasedValueSetImporter {
self.process(args[0], args[1]);
}
private void process(String source, String dest) {
for (File f : new File(source).listFiles()) {
private void process(String source, String dest) throws IOException {
for (File f : ManagedFileAccess.file(source).listFiles()) {
try {
System.out.println("Process " + f.getName());
ValueSet vs = importValueSet(TextFile.fileToBytes(f));
if (vs.getId() != null) {
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + vs.getId() + ".json")), vs);
}
} catch (Exception e) {
e.printStackTrace();

3
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/ResourceDependencyPackageBuilder.java
View File

@ -23,6 +23,7 @@ import org.hl7.fhir.r5.utils.ResourceDependencyWalker;
import org.hl7.fhir.r5.utils.ResourceDependencyWalker.IResourceDependencyNotifier;
import org.hl7.fhir.r5.utils.ResourceMinifier;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.JsonException;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@ -47,7 +48,7 @@ public class ResourceDependencyPackageBuilder {
new ResourceDependencyWalker(ctxt, pckBuilder).walk(ctxt.fetchResource(CapabilityStatement.class, args[2]));
pckBuilder.npm.save(new FileOutputStream(args[4]));
pckBuilder.npm.save(ManagedFileAccess.outStream(args[4]));
}
private static NpmPackage makeNpm(String vid, String version) throws JsonException, IOException {

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/SPDXImporter.java
View File

@ -13,6 +13,7 @@ import org.hl7.fhir.r4.terminologies.CodeSystemUtilities;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -27,7 +28,7 @@ public class SPDXImporter {
public void generate(String[] args) throws Exception {
JsonObject json = JsonParser.parseObjectFromUrl("https://raw.githubusercontent.com/spdx/license-list-data/main/json/licenses.json");
CodeSystem cs = (CodeSystem) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(args[0]));
CodeSystem cs = (CodeSystem) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(args[0]));
cs.getConcept().clear();
cs.getProperty().clear();
cs.addProperty().setCode("reference").setType(PropertyType.STRING);
@ -58,7 +59,7 @@ public class SPDXImporter {
}
}
CodeSystemUtilities.sortAllCodes(cs);
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(args[1]), cs);
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(args[1]), cs);
b = new StringBuilder();
generateEnum("SPDXLicense", cs);
TextFile.stringToFile(b.toString(), Utilities.changeFileExt(args[1], ".java"));

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/Test.java
View File

@ -45,6 +45,7 @@ import org.hl7.fhir.dstu3.formats.JsonParser;
import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class Test {
public final static String DEF_TS_SERVER = "http://fhir-dev.healthintersections.com.au/open";
@ -58,13 +59,13 @@ public class Test {
public static void main(String[] args) {
try {
CCDAConverter c = new CCDAConverter(new UcumEssenceService(UCUM_PATH), SimpleWorkerContext.fromPack(Utilities.path(SRC_PATH, "validation.zip")));
Bundle a = c.convert(new FileInputStream(DEF_PATH + "ccda.xml"));
Bundle a = c.convert(ManagedFileAccess.inStream(DEF_PATH + "ccda.xml"));
String fx = DEF_PATH + "output.xml";
IParser x = new XmlParser().setOutputStyle(OutputStyle.PRETTY);
x.compose(new FileOutputStream(fx), a);
x.compose(ManagedFileAccess.outStream(fx), a);
String fj = DEF_PATH + "output.json";
IParser j = new JsonParser().setOutputStyle(OutputStyle.PRETTY);
j.compose(new FileOutputStream(fj), a);
j.compose(ManagedFileAccess.outStream(fj), a);
System.out.println("done. save as " + fx + " and " + fj);
} catch (Exception e) {
e.printStackTrace();

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
View File

@ -30,6 +30,7 @@ import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r4.terminologies.JurisdictionUtilities;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.model.JsonProperty;
@ -47,7 +48,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
}
private void process(String source, String dest, String apiKey, boolean onlyNew) throws FHIRException, IOException, URISyntaxException {
CSVReader csv = new CSVReader(new FileInputStream(source));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream(source));
csv.readHeaders();
Map<String, String> errs = new HashMap<>();
@ -59,13 +60,13 @@ public class VSACImporter extends OIDBasedValueSetImporter {
CapabilityStatement cs = fhirToolingClient.getCapabilitiesStatement();
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "vsac-capability-statmenet.json")), cs);
json.setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "vsac-capability-statmenet.json")), cs);
System.out.println("Loading");
List<String> oids = new ArrayList<>();
while (csv.line()) {
String oid = csv.cell("OID");
if (!onlyNew || !(new File(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
if (!onlyNew || !(ManagedFileAccess.file(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
oids.add(oid);
}
}
@ -99,7 +100,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
for (String oid : errs.keySet()) {
oo.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.EXCEPTION).setDiagnostics(errs.get(oid)).addLocation(oid);
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
System.out.println("Done. " + i + " ValueSets in "+Utilities.describeDuration(System.currentTimeMillis() - tt));
}
@ -164,7 +165,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
}
vs.setName(makeValidName(vs.getName()));
JurisdictionUtilities.setJurisdictionCountry(vs.getJurisdiction(), "US");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
return true;
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/XMLPackageConvertor.java
View File

@ -4,6 +4,7 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.model.JsonProperty;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -11,7 +12,7 @@ import org.hl7.fhir.utilities.npm.NpmPackage;
public class XMLPackageConvertor {
public static void main(String[] args) throws IOException {
new XMLPackageConvertor().process(new File("C:\\web\\hl7.org\\fhir"));
new XMLPackageConvertor().process(ManagedFileAccess.file("C:\\web\\hl7.org\\fhir"));
}
private void process(File folder) throws IOException {
@ -21,7 +22,7 @@ public class XMLPackageConvertor {
} else {
if (f.getName().endsWith(".tgz")) {
System.out.println("Package " + f.getAbsolutePath());
NpmPackage p = NpmPackage.fromPackage(new FileInputStream(f));
NpmPackage p = NpmPackage.fromPackage(ManagedFileAccess.inStream(f));
if (p.getNpm().has("dependencies")) {
JsonObject dep = p.getNpm().getJsonObject("dependencies");
if (dep.getProperties().isEmpty()) {

13
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/XVerPackegeFixer.java
View File

@ -19,6 +19,7 @@ import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.model.StructureDefinition.StructureDefinitionSnapshotComponent;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.xml.sax.SAXException;
@ -66,7 +67,7 @@ public class XVerPackegeFixer {
public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
modCount = 0;
for (File f : new File(args[0]).listFiles()) {
for (File f : ManagedFileAccess.file(args[0]).listFiles()) {
if (f.getName().startsWith("xver-") && f.getName().contains("1.0")) {
JsonObject j = JsonTrackingParser.parseJson(f);
fixUp(j, f.getName());
@ -164,7 +165,7 @@ public class XVerPackegeFixer {
if (map5.containsKey(tn)) {
sd = map5.get(tn);
} else {
sd = (org.hl7.fhir.r5.model.StructureDefinition) new org.hl7.fhir.r5.formats.JsonParser().parse(new FileInputStream(Utilities.path(R5_FOLDER, "StructureDefinition-"+tn+".json")));
sd = (org.hl7.fhir.r5.model.StructureDefinition) new org.hl7.fhir.r5.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R5_FOLDER, "StructureDefinition-"+tn+".json")));
map5.put(tn, sd);
}
for (org.hl7.fhir.r5.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@ -220,7 +221,7 @@ public class XVerPackegeFixer {
if (map4.containsKey(tn)) {
sd = map4.get(tn);
} else {
sd = (org.hl7.fhir.r4.model.StructureDefinition) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(Utilities.path(R4_FOLDER, "StructureDefinition-"+tn+".json")));
sd = (org.hl7.fhir.r4.model.StructureDefinition) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R4_FOLDER, "StructureDefinition-"+tn+".json")));
map4.put(tn, sd);
}
for (org.hl7.fhir.r4.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@ -277,7 +278,7 @@ public class XVerPackegeFixer {
if (map3.containsKey(tn)) {
sd = map3.get(tn);
} else {
sd = (org.hl7.fhir.dstu3.model.StructureDefinition) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(Utilities.path(R3_FOLDER, "StructureDefinition-"+tn+".json")));
sd = (org.hl7.fhir.dstu3.model.StructureDefinition) new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R3_FOLDER, "StructureDefinition-"+tn+".json")));
map3.put(tn, sd);
}
for (org.hl7.fhir.dstu3.model.ElementDefinition ed : sd.getSnapshot().getElement()) {
@ -383,7 +384,7 @@ public class XVerPackegeFixer {
if (map2.containsKey(tn)) {
sd = map2.get(tn);
} else {
sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
sd = (org.hl7.fhir.dstu2.model.StructureDefinition) new org.hl7.fhir.dstu2.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R2_FOLDER, "StructureDefinition-"+tn+".json")));
map2.put(tn, sd);
}
return sd;
@ -431,7 +432,7 @@ public class XVerPackegeFixer {
if (map2b.containsKey(tn)) {
sd = map2b.get(tn);
} else {
sd = (org.hl7.fhir.dstu2016may.model.StructureDefinition) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(Utilities.path(R2B_FOLDER, "StructureDefinition-"+tn+".json")));
sd = (org.hl7.fhir.dstu2016may.model.StructureDefinition) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path(R2B_FOLDER, "StructureDefinition-"+tn+".json")));
map2b.put(tn, sd);
}
for (org.hl7.fhir.dstu2016may.model.ElementDefinition ed : sd.getSnapshot().getElement()) {

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/adl/ADLImporter.java
View File

@ -46,6 +46,7 @@ import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.ElementDefinition;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Element;
@ -91,11 +92,11 @@ public class ADLImporter {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
adlConfig = builder.parse(ManagedFileAccess.inStream(config)).getDocumentElement();
// load ADL
builder = factory.newDocumentBuilder();
adl = builder.parse(new FileInputStream(source)).getDocumentElement();
adl = builder.parse(ManagedFileAccess.inStream(source)).getDocumentElement();
check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
@ -150,7 +151,7 @@ public class ADLImporter {
genElements(sd, root.getName(), root);
// save
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(dest), sd);
System.out.println("done. saved as " + dest);
}

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/argonaut/ArgonautConverter.java
View File

@ -110,6 +110,7 @@ import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.dstu3.utils.ResourceUtilities;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.ZipGenerator;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.xhtml.NodeType;
@ -178,7 +179,7 @@ public class ArgonautConverter extends ConverterBase {
}
public void convert(String sourceFolder, Coding clss) throws Exception {
File source = new File(sourceFolder);
File source = ManagedFileAccess.file(sourceFolder);
for (String f : source.list()) {
convert(sourceFolder, f, clss);
}
@ -221,13 +222,13 @@ public class ArgonautConverter extends ConverterBase {
}
private void convert(String sourceFolder, String filename, Coding clss) throws IOException {
if (new File(Utilities.path(sourceFolder, filename)).length() == 0)
if (ManagedFileAccess.file(Utilities.path(sourceFolder, filename)).length() == 0)
return;
CDAUtilities cda;
try {
System.out.println("Process " + Utilities.path(sourceFolder, filename));
cda = new CDAUtilities(new FileInputStream(Utilities.path(sourceFolder, filename)));
cda = new CDAUtilities(ManagedFileAccess.inStream(Utilities.path(sourceFolder, filename)));
zipJ = new ZipGenerator(Utilities.path(destFolder, "json/doc", Utilities.changeFileExt(filename, ".json.zip")));
zipX = new ZipGenerator(Utilities.path(destFolder, "xml/doc", Utilities.changeFileExt(filename, ".xml.zip")));
Element doc = cda.getElement();
@ -1320,7 +1321,7 @@ public class ArgonautConverter extends ConverterBase {
Binary binary = new Binary();
binary.setId(context.getBaseId() + "-binary");
binary.setContentType("application/hl7-v3+xml");
binary.setContent(IOUtils.toByteArray(new FileInputStream(Utilities.path(sourceFolder, filename))));
binary.setContent(IOUtils.toByteArray(ManagedFileAccess.inStream(Utilities.path(sourceFolder, filename))));
saveResource(binary);
}

7
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/iso21090/ISO21090Importer.java
View File

@ -59,6 +59,7 @@ import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -125,7 +126,7 @@ public class ISO21090Importer {
addParentProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getParent(), false, true);
produceProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getProperties(), false, true);
ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\StructureDefinition-" + dt.getName() + ".xml")), sd);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "iso21090\\StructureDefinition-" + dt.getName() + ".xml")), sd);
}
private void addParentProperties(List<ElementDefinition> elements, String name, String parent, boolean attrMode, boolean snapshot) throws FHIRFormatError {
@ -176,7 +177,7 @@ public class ISO21090Importer {
for (String code : evs.getCodes()) {
inc.addConcept().setCode(code);
}
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\ValueSet-" + evs.getName() + ".xml")), vs);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "iso21090\\ValueSet-" + evs.getName() + ".xml")), vs);
}
private void processDataTypes() {
@ -319,7 +320,7 @@ public class ISO21090Importer {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(false);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream("C:\\work\\projects\\org.hl7.v3.dt\\iso\\iso-21090-datatypes.xsd"));
Document doc = builder.parse(ManagedFileAccess.inStream("C:\\work\\projects\\org.hl7.v3.dt\\iso\\iso-21090-datatypes.xsd"));
schema = doc.getDocumentElement();
}

13
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/searchparam/SearchParameterProcessor.java
View File

@ -49,6 +49,7 @@ import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class SearchParameterProcessor {
@ -120,7 +121,7 @@ public class SearchParameterProcessor {
e.addTarget().setCode(d).setRelationship(ConceptMapRelationship.RELATEDTO);
}
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(ROOT, "ConceptMap-" + map.getId() + ".json")), map);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(ROOT, "ConceptMap-" + map.getId() + ".json")), map);
}
private SourceElementComponent makeElement(String code, ConceptMapGroupComponent group) {
@ -208,7 +209,7 @@ public class SearchParameterProcessor {
}
private void load4() throws FHIRFormatError, IOException {
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp4.json")));
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp4.json")));
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.r4.model.SearchParameter sp = (org.hl7.fhir.r4.model.SearchParameter) be.getResource();
for (org.hl7.fhir.r4.model.CodeType br : sp.getBase()) {
@ -221,7 +222,7 @@ public class SearchParameterProcessor {
}
private void load3() throws FHIRFormatError, IOException {
org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp3.json")));
org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp3.json")));
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.SearchParameter sp = (org.hl7.fhir.dstu3.model.SearchParameter) be.getResource();
for (org.hl7.fhir.dstu3.model.CodeType br : sp.getBase()) {
@ -234,7 +235,7 @@ public class SearchParameterProcessor {
}
private void load2() throws FHIRFormatError, IOException {
org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp2.json")));
org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp2.json")));
for (org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu2.model.SearchParameter sp = (org.hl7.fhir.dstu2.model.SearchParameter) be.getResource();
String br = sp.getBase();
@ -246,7 +247,7 @@ public class SearchParameterProcessor {
}
private void load2b() throws FHIRFormatError, IOException {
org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(Utilities.path("[tmp]", "sp2b.json")));
org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(Utilities.path("[tmp]", "sp2b.json")));
for (org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu2016may.model.SearchParameter sp = (org.hl7.fhir.dstu2016may.model.SearchParameter) be.getResource();
String br = sp.getBase();
@ -258,7 +259,7 @@ public class SearchParameterProcessor {
}
private void loadCsv() throws IOException, FHIRException {
CSVReader csv = new CSVReader(new FileInputStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
CSVReader csv = new CSVReader(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
csv.readHeaders();
while (csv.line()) {
String r4 = csv.cell("R4");

9
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGCaseSensitivePopulator.java
View File

@ -21,11 +21,12 @@ import org.hl7.fhir.r4.model.Provenance;
import org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class UTGCaseSensitivePopulator {
public static void main(String[] args) throws FileNotFoundException, IOException {
new UTGCaseSensitivePopulator().process(new File(args[0]));
new UTGCaseSensitivePopulator().process(ManagedFileAccess.file(args[0]));
}
@ -35,7 +36,7 @@ public class UTGCaseSensitivePopulator {
bundle.setId("hxutg1-1-0-12");
scanFolders(root, bundle);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(root.getAbsolutePath(), "input", "sourceOfTruth", "history", "utgrel1hx-1-0-12.json")), bundle);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(root.getAbsolutePath(), "input", "sourceOfTruth", "history", "utgrel1hx-1-0-12.json")), bundle);
System.out.println("Done");
}
@ -60,10 +61,10 @@ public class UTGCaseSensitivePopulator {
private void processFile(File f, Bundle bundle, IParser parser, Date d, Date dt) {
try {
Resource r = parser.parse(new FileInputStream(f));
Resource r = parser.parse(ManagedFileAccess.inStream(f));
if (r instanceof CodeSystem) {
if (processCodeSystem((CodeSystem) r, bundle, d, dt)) {
parser.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
parser.setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
}
} catch (Exception e) {

11
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGVersionSorter.java
View File

@ -29,6 +29,7 @@ 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.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
@ -47,7 +48,7 @@ public class UTGVersionSorter {
private void execute(String source) throws IOException {
List<CanonicalResourceAnalysis> list = new ArrayList<>();
System.out.println("Loading UTG");
loadFromSource(list, new File(source));
loadFromSource(list, ManagedFileAccess.file(source));
Map<String, CanonicalResource> r2 = loadPackageR2("hl7.fhir.r2.core");
Map<String, CanonicalResource> r3 = loadPackageR3("hl7.fhir.r3.core");
@ -58,7 +59,7 @@ public class UTGVersionSorter {
cr.analyse(r2, r3, r4);
}
Bundle b = (Bundle) new JsonParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"));
Bundle b = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"));
System.out.println("Summary");
for (CanonicalResourceAnalysis cr : list) {
@ -79,10 +80,10 @@ public class UTGVersionSorter {
pa.getWho().setDisplay("Vocabulary WG");
CanonicalResource res = cr.resource;
res.setVersion(cr.recommendation);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(cr.filename), res);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(cr.filename), res);
}
System.out.println();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"), b);
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"), b);
System.out.println("Done");
}
@ -134,7 +135,7 @@ public class UTGVersionSorter {
loadFromSource(list, f);
} else if (f.getName().endsWith(".xml")) {
try {
Resource r = new XmlParser().parse(new FileInputStream(f));
Resource r = new XmlParser().parse(ManagedFileAccess.inStream(f));
if (r instanceof CanonicalResource) {
CanonicalResource cr = (CanonicalResource) r;
cr.setWebPath(f.getAbsolutePath());

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/xver/CorePackageVersionConvertor.java
View File

@ -15,6 +15,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.parser.JsonParser;
@ -479,7 +480,7 @@ public class CorePackageVersionConvertor {
// build a new package
System.out.println("Convert "+packageSource+" to "+versionTarget);
NpmPackage src = NpmPackage.fromPackage(new FileInputStream(packageSource));
NpmPackage src = NpmPackage.fromPackage(ManagedFileAccess.inStream(packageSource));
IContentConvertor conv = contentConvertorFactory(src.fhirVersion(), versionTarget);
NpmPackage dst = NpmPackage.empty();
@ -510,7 +511,7 @@ public class CorePackageVersionConvertor {
}
}
}
dst.save(new FileOutputStream(Utilities.changeFileExt(packageSource, ".as."+VersionUtilities.getNameForVersion(versionTarget).toLowerCase()+".tgz")));
dst.save(ManagedFileAccess.outStream(Utilities.changeFileExt(packageSource, ".as."+VersionUtilities.getNameForVersion(versionTarget).toLowerCase()+".tgz")));
}
private IContentConvertor contentConvertorFactory(String fhirVersion, String versionTarget) throws Exception {

4
org.hl7.fhir.core.generator/configuration/tests/RoundTripTests.java
View File

@ -33,7 +33,7 @@ public class RoundTripTests {
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
File dir = new File(EXAMPLES_DIR);
File dir = ManagedFileAccess.file(EXAMPLES_DIR);
String[] list = dir.list();
List<Object[]> objects = new ArrayList<Object[]>(list.length);
@ -77,7 +77,7 @@ public class RoundTripTests {
}
private void save(byte[] src, String path) throws IOException {
File f = new File(path);
File f = ManagedFileAccess.file(path);
if (f.exists()) {
f.delete();
}

2
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/Configuration.java
View File

@ -23,7 +23,7 @@ public class Configuration {
public Configuration(String path) throws FileNotFoundException, IOException {
license = TextFile.fileToString(Utilities.path(path, "license.txt"));
ini = new IniFile(Utilities.path(path, "configuration.ini"));
for (File jfn : new File(path).listFiles()) {
for (File jfn : ManagedFileAccess.file(path).listFiles()) {
if (jfn.getName().endsWith(".java")) {
adornments.put(Utilities.changeFileExt(jfn.getName(), ""), TextFile.fileToString(jfn));
}

2
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaResourceGenerator.java
View File

@ -483,7 +483,7 @@ public class JavaResourceGenerator extends JavaBaseGenerator {
//// write(" }\r\n");
////
//// // now, generate the implementation
//// JavaPatternImplGenerator jrg = new JavaPatternImplGenerator(new FileOutputStream(javaPatternDir+jn+namenn+"Impl.java"), definitions, adornments, enumInfo);
//// JavaPatternImplGenerator jrg = new JavaPatternImplGenerator(ManagedFileAccess.outStream(javaPatternDir+jn+namenn+"Impl.java"), definitions, adornments, enumInfo);
//// jrg.generate(resourceDefn.getRoot(), jn, JavaGenClass.Resource, null, genDate, version, false, null, null, namenn, root);
//// jrg.close();
////

4
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/extensions/JavaExtensionsGenerator.java
View File

@ -58,9 +58,9 @@ public class JavaExtensionsGenerator {
}
}
JavaExtensionsFactoryGenerator gen = new JavaExtensionsFactoryGenerator(new FileOutputStream(Utilities.path(path, "Extensions.java")), master, config, version, date, jid, elementInfo, genClassList);
JavaExtensionsFactoryGenerator gen = new JavaExtensionsFactoryGenerator(ManagedFileAccess.outStream(Utilities.path(path, "Extensions.java")), master, config, version, date, jid, elementInfo, genClassList);
gen.start();
JavaConstantsGenerator cgen = new JavaConstantsGenerator(new FileOutputStream(Utilities.path(path, "ExtensionConstants.java")), master, config, version, date, jid);
JavaConstantsGenerator cgen = new JavaConstantsGenerator(ManagedFileAccess.outStream(Utilities.path(path, "ExtensionConstants.java")), master, config, version, date, jid);
cgen.start();
for (String url : urls) {
StructureDefinition sd = extensions.get(url);

16
org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/engine/JavaCoreGenerator.java
View File

@ -89,19 +89,19 @@ public class JavaCoreGenerator {
System.out.println("Generate Model in "+dest);
System.out.println(" .. Constants");
JavaConstantsGenerator cgen = new JavaConstantsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Constants.java")), master, config, date, npm.version(), jid);
JavaConstantsGenerator cgen = new JavaConstantsGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Constants.java")), master, config, date, npm.version(), jid);
cgen.generate();
cgen.close();
System.out.println(" .. Enumerations");
JavaEnumerationsGenerator egen = new JavaEnumerationsGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Enumerations.java")), master, config, date, npm.version(), jid);
JavaEnumerationsGenerator egen = new JavaEnumerationsGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "Enumerations.java")), master, config, date, npm.version(), jid);
egen.generate();
egen.close();
JavaFactoryGenerator fgen = new JavaFactoryGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceFactory.java")), master, config, date, npm.version(), jid);
JavaTypeGenerator tgen = new JavaTypeGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceType.java")), master, config, date, npm.version(), jid);
JavaParserJsonGenerator jgen = new JavaParserJsonGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "JsonParser.java")), master, config, date, npm.version(), jid);
JavaParserXmlGenerator xgen = new JavaParserXmlGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "XmlParser.java")), master, config, date, npm.version(), jid);
JavaParserRdfGenerator rgen = new JavaParserRdfGenerator(new FileOutputStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "RdfParser.java")), master, config, date, npm.version(), jid);
JavaFactoryGenerator fgen = new JavaFactoryGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceFactory.java")), master, config, date, npm.version(), jid);
JavaTypeGenerator tgen = new JavaTypeGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", "ResourceType.java")), master, config, date, npm.version(), jid);
JavaParserJsonGenerator jgen = new JavaParserJsonGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "JsonParser.java")), master, config, date, npm.version(), jid);
JavaParserXmlGenerator xgen = new JavaParserXmlGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "XmlParser.java")), master, config, date, npm.version(), jid);
JavaParserRdfGenerator rgen = new JavaParserRdfGenerator(ManagedFileAccess.outStream(Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "formats", "RdfParser.java")), master, config, date, npm.version(), jid);
if (VersionUtilities.isR4BVer(version)) {
StructureDefinition sd = master.getStructures().get("http://hl7.org/fhir/StructureDefinition/Element");
@ -206,7 +206,7 @@ public class JavaCoreGenerator {
Analysis analysis = jca.analyse(sd, elementInfo);
String fn = Utilities.path(dest, "src", "main", "java", "org", "hl7", "fhir", jid, "model", name+".java");
JavaResourceGenerator gen = new JavaResourceGenerator(new FileOutputStream(fn), master, config, date, npm.version(), jid);
JavaResourceGenerator gen = new JavaResourceGenerator(ManagedFileAccess.outStream(fn), master, config, date, npm.version(), jid);
gen.generate(analysis);
gen.close();
jgen.seeClass(analysis);

5
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/terminologies/LoincToDEConvertor.java
View File

@ -54,6 +54,7 @@ import org.hl7.fhir.dstu2.model.Meta;
import org.hl7.fhir.dstu2.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -165,12 +166,12 @@ public class LoincToDEConvertor {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
xml = builder.parse(new FileInputStream(definitions));
xml = builder.parse(ManagedFileAccess.inStream(definitions));
}
private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
XmlParser xml = new XmlParser();
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
xml.compose(s, bundle, true);
s.close();
}

7
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/terminologies/ValueSetExpansionCache.java
View File

@ -75,6 +75,7 @@ import org.hl7.fhir.dstu2.utils.IWorkerContext;
import org.hl7.fhir.dstu2.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@ -91,7 +92,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
// well, we'll see if the designated server can expand it, and if it can, we'll
// cache it locally
vso = context.expandVS(source, false);
FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
s.close();
}
@ -125,10 +126,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
}
private void loadCache() throws FHIRFormatError, IOException {
File[] files = new File(cacheFolder).listFiles();
File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
for (File f : files) {
if (f.getName().endsWith(".xml")) {
final FileInputStream is = new FileInputStream(f);
final FileInputStream is = ManagedFileAccess.inStream(f);
try {
Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
if (r instanceof OperationOutcome) {

5
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/BatchLoader.java
View File

@ -47,6 +47,7 @@ import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class BatchLoader {
@ -66,7 +67,7 @@ public class BatchLoader {
throw new FHIRException("Unimplemented file type " + file);
} else if (file.endsWith(".zip")) {
LoadZipFile(server, file, p, size, 0, -1);
} else if (new File(file).isDirectory()) {
} else if (ManagedFileAccess.file(file).isDirectory()) {
LoadDirectory(server, file, p, size);
} else
throw new FHIRException("Unknown file type " + file);
@ -99,7 +100,7 @@ public class BatchLoader {
Bundle b = new Bundle();
b.setType(BundleType.COLLECTION);
b.setId(UUID.randomUUID().toString().toLowerCase());
ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
ZipEntry entry;
while ((entry = zip.getNextEntry()) != null) {
try {

2
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/SimpleWorkerContext.java
View File

@ -60,8 +60,8 @@ import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
import org.hl7.fhir.dstu2.utils.validation.IResourceValidator;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;

2
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/Translations.java
View File

@ -38,7 +38,7 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

5
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/Unbundler.java
View File

@ -42,6 +42,7 @@ import org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.model.ValueSet;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class Unbundler {
@ -51,7 +52,7 @@ public class Unbundler {
private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
String folder = Utilities.getDirectoryForFile(src);
Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
for (BundleEntryComponent be : bnd.getEntry()) {
Resource r = be.getResource();
if (r != null) {
@ -61,7 +62,7 @@ public class Unbundler {
}
if (!StringUtils.isBlank(r.getId())) {
String tgt = Utilities.path(folder, r.fhirType() + "-" + r.getId() + ".json");
new JsonParser().compose(new FileOutputStream(tgt), r);
new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
}
}
}

3
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/FluentPathTests.java
View File

@ -7,6 +7,7 @@ import org.hl7.fhir.dstu2.utils.FHIRPathEngine;
import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.*;
import org.junit.jupiter.params.ParameterizedTest;
@ -55,7 +56,7 @@ public class FluentPathTests {
fp.check(null, null, null, node);
else {
res = new XmlParser()
.parse(new FileInputStream(Utilities.path("C:\\work\\org.hl7.fhir.dstu2\\build\\publish", input)));
.parse(ManagedFileAccess.inStream(Utilities.path("C:\\work\\org.hl7.fhir.dstu2\\build\\publish", input)));
fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
}
outcome = fp.evaluate(res, node);

5
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/NarrativeGeneratorTests.java
View File

@ -11,6 +11,7 @@ import org.hl7.fhir.dstu2.utils.NarrativeGenerator;
import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
@ -40,9 +41,9 @@ public class NarrativeGeneratorTests {
private void process(String path) throws IOException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
}

17
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ProfileUtilitiesTests.java
View File

@ -24,8 +24,9 @@ import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -85,11 +86,11 @@ public class ProfileUtilitiesTests {
for (ProfileComparison outcome : comp.getComparisons()) {
if (outcome.getSubset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(
new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")),
ManagedFileAccess.outStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")),
outcome.getSubset());
if (outcome.getSuperset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(
new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
ManagedFileAccess.outStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and "
+ outcome.getRight().getUrl());
@ -115,9 +116,9 @@ public class ProfileUtilitiesTests {
System.out.println("Compare " + fn1 + " to " + fn2);
System.out.println(" .. load");
StructureDefinition left = (StructureDefinition) new XmlParser()
.parse(new FileInputStream(Utilities.path(root, fn1)));
.parse(ManagedFileAccess.inStream(Utilities.path(root, fn1)));
StructureDefinition right = (StructureDefinition) new XmlParser()
.parse(new FileInputStream(Utilities.path(root, fn2)));
.parse(ManagedFileAccess.inStream(Utilities.path(root, fn2)));
System.out.println(" .. compare");
comp.compareProfiles(left, right);
@ -918,16 +919,16 @@ public class ProfileUtilitiesTests {
// focus.setDifferential(null);
String f1 = Utilities.path("c:", "temp", "base.xml");
String f2 = Utilities.path("c:", "temp", "derived.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f1), base);
;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f2), focus);
;
String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
List<String> command = new ArrayList<String>();
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}

10
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/QuestionnaireBuilderTester.java
View File

@ -2,27 +2,29 @@ package org.hl7.fhir.dstu2.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import org.hl7.fhir.dstu2.formats.XmlParser;
import org.hl7.fhir.dstu2.model.StructureDefinition;
import org.hl7.fhir.dstu2.utils.QuestionnaireBuilder;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class QuestionnaireBuilderTester {
private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
// private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
public static void main(String[] args) {
public static void main(String[] args) throws IOException {
QuestionnaireBuilder b = new QuestionnaireBuilder(null);
for (String f : new File(TEST_PROFILE_DIR).list()) {
for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
if (f.endsWith(".profile.xml") && !f.contains("type-")) {
System.out.println("process " + f);
try {
StructureDefinition p = (StructureDefinition) new XmlParser()
.parse(new FileInputStream(TEST_PROFILE_DIR + "\\" + f));
.parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR + "\\" + f));
// Questionnaire q = b.buildQuestionnaire(p);
// new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
// new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
throw new FHIRException("test");
} catch (Exception e) {
e.printStackTrace();

9
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ResourceTest.java
View File

@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2.formats.JsonParser;
import org.hl7.fhir.dstu2.formats.XmlParser;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class ResourceTest {
@ -61,18 +62,18 @@ public class ResourceTest {
p = new JsonParser();
else
p = new XmlParser(false);
Resource rf = p.parse(new FileInputStream(source));
Resource rf = p.parse(ManagedFileAccess.inStream(source));
FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.json");
JsonParser json1 = new JsonParser();
json1.setOutputStyle(OutputStyle.PRETTY);
json1.compose(out, rf);
out.close();
JsonParser json = new JsonParser();
rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile() + ".out.json"));
out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.xml");
XmlParser atom = new XmlParser();
atom.setOutputStyle(OutputStyle.PRETTY);
atom.compose(out, rf, true);

4
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/SingleTest.java
View File

@ -30,6 +30,8 @@ package org.hl7.fhir.dstu2.test;
import java.io.File;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class SingleTest {
/**
@ -38,7 +40,7 @@ public class SingleTest {
public static void main(String[] args) {
try {
ResourceTest r = new ResourceTest();
r.setSource(new File("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
r.test();
System.out.println("Completed OK");
} catch (Exception e) {

9
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/TestingUtilities.java
View File

@ -13,9 +13,10 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.hl7.fhir.dstu2.utils.IWorkerContext;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
@ -41,7 +42,7 @@ public class TestingUtilities {
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}
@ -154,7 +155,7 @@ public class TestingUtilities {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
return builder.parse(new FileInputStream(fn));
return builder.parse(ManagedFileAccess.inStream(fn));
}
public static String checkJsonIsSame(String f1, String f2)
@ -166,7 +167,7 @@ public class TestingUtilities {
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}

57
org.hl7.fhir.dstu2/src/test/java/org/hl7/fhir/dstu2/test/ToolsHelper.java
View File

@ -55,10 +55,11 @@ import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserException;
import org.xmlpull.v1.XmlPullParserFactory;
@ -103,7 +104,7 @@ public class ToolsHelper {
private void executeExamples(String[] args) throws IOException {
try {
@SuppressWarnings("unchecked")
List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
String srcDir = lines.get(0);
lines.remove(0);
processExamples(srcDir, lines);
@ -179,7 +180,7 @@ public class ToolsHelper {
// } else
if (definitions.startsWith("https:") || definitions.startsWith("http:")) {
defn = loadFromUrl(definitions);
} else if (new File(definitions).exists()) {
} else if (ManagedFileAccess.file(definitions).exists()) {
defn = loadFromFile(definitions);
} else
throw new FHIRException("Unable to find FHIR validation Pack (source = " + definitions + ")");
@ -193,7 +194,7 @@ public class ToolsHelper {
}
private byte[] loadFromFile(String src) throws IOException {
FileInputStream in = new FileInputStream(src);
FileInputStream in = ManagedFileAccess.inStream(src);
byte[] b = new byte[in.available()];
in.read(b);
in.close();
@ -220,10 +221,10 @@ public class ToolsHelper {
public void executeFragments(String[] args) throws IOException {
try {
File source = new CSFile(args[1]);
File source = ManagedFileAccess.csfile(args[1]);
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
XmlPullParser xpp = loadXml(new FileInputStream(source));
XmlPullParser xpp = loadXml(ManagedFileAccess.inStream(source));
nextNoWhitespace(xpp);
if (!xpp.getName().equals("tests"))
throw new FHIRFormatError("Unable to parse file - starts with " + xpp.getName());
@ -269,8 +270,8 @@ public class ToolsHelper {
public void executeRoundTrip(String[] args) throws IOException, FHIRException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
if (args.length >= 4) {
Utilities.copyFile(args[1], args[3]);
}
@ -288,17 +289,17 @@ public class ToolsHelper {
json.close();
TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
new XmlParser().compose(s, rf, true);
s.close();
}
public String executeJson(String[] args) throws IOException, FHIRException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
File destt = new CSFile(args[2] + ".tmp");
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
File destc = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".canonical.json"));
File destt = ManagedFileAccess.csfile(args[2] + ".tmp");
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@ -307,16 +308,16 @@ public class ToolsHelper {
Resource rf = p.parse(in);
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
json.compose(s, rf);
s.close();
json.setOutputStyle(OutputStyle.CANONICAL);
s = new FileOutputStream(destc);
s = ManagedFileAccess.outStream(destc);
json.compose(s, rf);
s.close();
json.setSuppressXhtml("Snipped for Brevity");
json.setOutputStyle(OutputStyle.PRETTY);
s = new FileOutputStream(destt);
s = ManagedFileAccess.outStream(destt);
json.compose(s, rf);
s.close();
return TextFile.fileToString(destt.getAbsolutePath());
@ -324,8 +325,8 @@ public class ToolsHelper {
public void executeCanonicalXml(String[] args) throws FHIRException, IOException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@ -334,7 +335,7 @@ public class ToolsHelper {
Resource rf = p.parse(in);
XmlParser cxml = new XmlParser();
cxml.setOutputStyle(OutputStyle.NORMAL);
cxml.compose(new FileOutputStream(dest), rf);
cxml.compose(ManagedFileAccess.outStream(dest), rf);
}
private void executeVersion(String[] args) throws IOException {
@ -347,7 +348,7 @@ public class ToolsHelper {
String filename = rootDir + n + ".xml";
// 1. produce canonical XML
CSFileInputStream source = new CSFileInputStream(filename);
FileOutputStream dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.xml"));
FileOutputStream dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.xml"));
XmlParser p = new XmlParser();
Resource r = p.parse(source);
XmlParser cxml = new XmlParser();
@ -356,14 +357,14 @@ public class ToolsHelper {
// 2. produce JSON
source = new CSFileInputStream(filename);
dest = new FileOutputStream(Utilities.changeFileExt(filename, ".json"));
dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".json"));
r = p.parse(source);
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
json.compose(dest, r);
json = new JsonParser();
json.setOutputStyle(OutputStyle.CANONICAL);
dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.json"));
dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.json"));
json.compose(dest, r);
} catch (Exception e) {
e.printStackTrace();
@ -383,23 +384,23 @@ public class ToolsHelper {
String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
FileInputStream in = new FileInputStream(source);
FileInputStream in = ManagedFileAccess.inStream(source);
XmlParser xp = new XmlParser();
Resource r = xp.parse(in);
System.err.print(".");
JsonParser jp = new JsonParser();
FileOutputStream out = new FileOutputStream(tmp);
FileOutputStream out = ManagedFileAccess.outStream(tmp);
jp.setOutputStyle(OutputStyle.PRETTY);
jp.compose(out, r);
out.close();
r = null;
System.err.print(".");
in = new FileInputStream(tmp);
in = ManagedFileAccess.inStream(tmp);
System.err.print(",");
r = jp.parse(in);
System.err.print(".");
out = new FileOutputStream(dest);
out = ManagedFileAccess.outStream(dest);
new XmlParser().compose(out, r, true);
System.err.println("!");
out.close();
@ -415,7 +416,7 @@ public class ToolsHelper {
private void executeTest(String[] args) throws Throwable {
try {
@SuppressWarnings("unchecked")
List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
String srcDir = lines.get(0);
lines.remove(0);
String dstDir = lines.get(0).trim();

15
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/metamodel/Tester.java
View File

@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
@ -52,21 +53,21 @@ public class Tester {
.fromPack(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", "validation-min.xml.zip"));
int t = 0;
int ok = 0;
for (String f : new File("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire")
&& new File("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".ttl")).exists()) {
&& ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".ttl")).exists()) {
// if (f.equals("account-questionnaire.xml")) {
System.out.print("convert " + f);
// Manager.convert(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML,
// new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
// Manager.convert(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML,
// ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
// String src = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
// String tgt = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + f),
Element e = Manager.parse(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + f),
FhirFormat.XML);
Manager.compose(context, e,
new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl")),
ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl")),
FhirFormat.TURTLE, OutputStyle.PRETTY, null);
Manager.compose(context, e, new FileOutputStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML,
Manager.compose(context, e, ManagedFileAccess.outStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML,
OutputStyle.PRETTY, null);
String src = TextFile
.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\" + Utilities.changeFileExt(f, ".mm.ttl"));

7
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/ICPC2Importer.java
View File

@ -49,6 +49,7 @@ import org.hl7.fhir.dstu2016may.model.Enumerations.ConformanceResourceStatus;
import org.hl7.fhir.dstu2016may.model.Identifier;
import org.hl7.fhir.dstu2016may.model.ValueSet;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -118,7 +119,7 @@ public class ICPC2Importer {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(false);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(sourceFileName));
Document doc = builder.parse(ManagedFileAccess.inStream(sourceFileName));
ValueSet vs = new ValueSet();
vs.setUrl("http://hl7.org/fhir/sid/icpc2/vs");
@ -167,8 +168,8 @@ public class ICPC2Importer {
XmlParser xml = new XmlParser();
xml.setOutputStyle(OutputStyle.PRETTY);
xml.compose(new FileOutputStream(targetFileNameVS), vs);
xml.compose(new FileOutputStream(targetFileNameCS), cs);
xml.compose(ManagedFileAccess.outStream(targetFileNameVS), vs);
xml.compose(ManagedFileAccess.outStream(targetFileNameCS), cs);
}
private void processClass(Element cls, Map<String, ConceptDefinitionComponent> concepts, CodeSystem define) {

5
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/LoincToDEConvertor.java
View File

@ -54,6 +54,7 @@ import org.hl7.fhir.dstu2016may.model.Meta;
import org.hl7.fhir.dstu2016may.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -165,12 +166,12 @@ public class LoincToDEConvertor {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
xml = builder.parse(new FileInputStream(definitions));
xml = builder.parse(ManagedFileAccess.inStream(definitions));
}
private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
XmlParser xml = new XmlParser();
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
xml.compose(s, bundle, true);
s.close();
}

7
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/terminologies/ValueSetExpansionCache.java
View File

@ -75,6 +75,7 @@ import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
import org.hl7.fhir.dstu2016may.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@ -91,7 +92,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
// well, we'll see if the designated server can expand it, and if it can, we'll
// cache it locally
vso = context.expandVS(source, false);
FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
s.close();
}
@ -125,10 +126,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
}
private void loadCache() throws FHIRFormatError, IOException {
File[] files = new File(cacheFolder).listFiles();
File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
for (File f : files) {
if (f.getName().endsWith(".xml")) {
final FileInputStream is = new FileInputStream(f);
final FileInputStream is = ManagedFileAccess.inStream(f);
try {
Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
if (r instanceof OperationOutcome) {

5
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/BatchLoader.java
View File

@ -47,6 +47,7 @@ import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class BatchLoader {
@ -66,7 +67,7 @@ public class BatchLoader {
throw new FHIRException("Unimplemented file type " + file);
} else if (file.endsWith(".zip")) {
LoadZipFile(server, file, p, size, 0, -1);
} else if (new File(file).isDirectory()) {
} else if (ManagedFileAccess.file(file).isDirectory()) {
LoadDirectory(server, file, p, size);
} else
throw new FHIRException("Unknown file type " + file);
@ -99,7 +100,7 @@ public class BatchLoader {
Bundle b = new Bundle();
b.setType(BundleType.COLLECTION);
b.setId(UUID.randomUUID().toString().toLowerCase());
ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
ZipEntry entry;
while ((entry = zip.getNextEntry()) != null) {
try {

7
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/SimpleWorkerContext.java
View File

@ -71,9 +71,10 @@ import org.hl7.fhir.dstu2016may.utils.client.FHIRToolingClient;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -425,7 +426,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
public void loadFromFolder(String folder) throws FileNotFoundException, Exception {
for (String n : new File(folder).list()) {
for (String n : ManagedFileAccess.file(folder).list()) {
if (n.endsWith(".json"))
loadFromFile(Utilities.path(folder, n), new JsonParser());
else if (n.endsWith(".xml"))
@ -436,7 +437,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private void loadFromFile(String filename, IParser p) throws FileNotFoundException, Exception {
Resource r;
try {
r = p.parse(new FileInputStream(filename));
r = p.parse(ManagedFileAccess.inStream(filename));
if (r.getResourceType() == ResourceType.Bundle) {
for (BundleEntryComponent e : ((Bundle) r).getEntry()) {
seeResource(null, e.getResource());

10
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Transformer.java
View File

@ -32,6 +32,7 @@ package org.hl7.fhir.dstu2016may.utils;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@ -45,6 +46,7 @@ import org.hl7.fhir.dstu2016may.model.Bundle;
import org.hl7.fhir.dstu2016may.model.StructureMap;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class Transformer {
@ -117,7 +119,7 @@ public class Transformer {
loadMaps(folder);
}
System.out.println(" .. load source from " + source);
Element e = Manager.parse(context, new FileInputStream(source), FhirFormat.XML);
Element e = Manager.parse(context, ManagedFileAccess.inStream(source), FhirFormat.XML);
Bundle bundle = new Bundle();
StructureMap map = scu.getLibrary().get(mapUri);
@ -125,7 +127,7 @@ public class Transformer {
throw new Error("Unable to find map " + mapUri + " (Known Maps = "
+ Utilities.listCanonicalUrls(scu.getLibrary().keySet()) + ")");
scu.transform(null, e, map, bundle);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(output), bundle);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(output), bundle);
return true;
} catch (Exception e) {
e.printStackTrace();
@ -134,8 +136,8 @@ public class Transformer {
}
}
private void loadMaps(String folder) {
for (String f : new File(folder).list()) {
private void loadMaps(String folder) throws IOException {
for (String f : ManagedFileAccess.file(folder).list()) {
try {
StructureMap map = scu.parse(TextFile.fileToString(Utilities.path(folder, f)));
scu.getLibrary().put(map.getUrl(), map);

2
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Translations.java
View File

@ -38,7 +38,7 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

5
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/Unbundler.java
View File

@ -42,6 +42,7 @@ import org.hl7.fhir.dstu2016may.model.Bundle;
import org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class Unbundler {
@ -51,7 +52,7 @@ public class Unbundler {
private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
String folder = Utilities.getDirectoryForFile(src);
Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
for (BundleEntryComponent be : bnd.getEntry()) {
Resource r = be.getResource();
if (r != null) {
@ -61,7 +62,7 @@ public class Unbundler {
}
if (!StringUtils.isBlank(r.getId())) {
String tgt = Utilities.path(folder, r.fhirType() + "-" + r.getId() + ".json");
new JsonParser().compose(new FileOutputStream(tgt), r);
new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
}
}
}

15
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/FluentPathTests.java
View File

@ -25,6 +25,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -46,35 +47,35 @@ public class FluentPathTests {
private Patient patient() throws FHIRFormatError, FileNotFoundException, IOException {
if (patient == null)
patient = (Patient) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/patient-example.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/patient-example.json"));
return patient;
}
private Appointment appointment() throws FHIRFormatError, FileNotFoundException, IOException {
if (appointment == null)
appointment = (Appointment) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/appointment-example-request.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/appointment-example-request.json"));
return appointment;
}
private Questionnaire questionnaire() throws FHIRFormatError, FileNotFoundException, IOException {
if (questionnaire == null)
questionnaire = (Questionnaire) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example.json"));
return questionnaire;
}
private ValueSet valueset() throws FHIRFormatError, FileNotFoundException, IOException {
if (valueset == null)
valueset = (ValueSet) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/valueset-example-expansion.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/valueset-example-expansion.json"));
return valueset;
}
private Observation observation() throws FHIRFormatError, FileNotFoundException, IOException {
if (observation == null)
observation = (Observation) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/observation-example.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/observation-example.json"));
return observation;
}
@ -929,7 +930,7 @@ public class FluentPathTests {
@Test
public void testQuestionnaire() throws FileNotFoundException, IOException, FHIRException {
Questionnaire q = (Questionnaire) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example-gcs.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/questionnaire-example-gcs.json"));
for (QuestionnaireItemComponent qi : q.getItem()) {
testQItem(qi);
}
@ -943,7 +944,7 @@ public class FluentPathTests {
@Test
public void testExtensionDefinitions() throws FileNotFoundException, IOException, FHIRException {
Bundle b = (Bundle) new JsonParser()
.parse(new FileInputStream("C:/work/org.hl7.fhir.2016May/build/publish/extension-definitions.json"));
.parse(ManagedFileAccess.inStream("C:/work/org.hl7.fhir.2016May/build/publish/extension-definitions.json"));
for (BundleEntryComponent be : b.getEntry()) {
testStructureDefinition((StructureDefinition) be.getResource());
}

5
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/NarrativeGeneratorTests.java
View File

@ -7,6 +7,7 @@ import org.hl7.fhir.dstu2016may.utils.NarrativeGenerator;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -41,9 +42,9 @@ public class NarrativeGeneratorTests {
private void process(String path)
throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
}

28
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ParserTests.java
View File

@ -12,7 +12,7 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -32,7 +32,7 @@ public class ParserTests {
@Test
public void testAll() throws Exception {
String examples = Utilities.path(root, "examples");
for (String fn : new File(examples).list()) {
for (String fn : ManagedFileAccess.file(examples).list()) {
if (fn.endsWith(".xml")) {
testRoundTrip(Utilities.path(examples, fn), fn);
}
@ -41,50 +41,50 @@ public class ParserTests {
private void testRoundTrip(String filename, String name) throws Exception {
System.out.println(name);
Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new FileInputStream(filename));
Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(ManagedFileAccess.inStream(filename));
String fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(fn), r);
.compose(ManagedFileAccess.outStream(fn), r);
String msg = TestingUtilities.checkXMLIsSame(filename, fn);
Assertions.assertNull(msg, name + ": " + msg);
String j1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(j1), r);
.compose(ManagedFileAccess.outStream(j1), r);
if (TestingUtilities.context == null) {
TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation-min.xml.zip"));
}
Element re = Manager.parse(TestingUtilities.context, new FileInputStream(filename), FhirFormat.XML);
Element re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(filename), FhirFormat.XML);
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(filename, fn);
Assertions.assertNull(msg, name + ": " + msg);
String j2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, j2);
Assertions.assertNull(msg, name + ": " + msg);
// ok, we've produced equivalent JSON by both methods.
// now, we're going to reverse the process
r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(j2)); // crossover too
r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(j2)); // crossover too
fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(fn), r);
.compose(ManagedFileAccess.outStream(fn), r);
msg = TestingUtilities.checkJsonIsSame(j2, fn);
Assertions.assertNull(msg, name + ": " + msg);
String x1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(x1), r);
.compose(ManagedFileAccess.outStream(x1), r);
re = Manager.parse(TestingUtilities.context, new FileInputStream(j1), FhirFormat.JSON);
re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(j1), FhirFormat.JSON);
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, fn);
Assertions.assertNull(msg, name + ": " + msg);
String x2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(x1, x2);
Assertions.assertNull(msg, name + ": " + msg);

10
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/QuestionnaireBuilderTester.java
View File

@ -2,27 +2,29 @@ package org.hl7.fhir.dstu2016may.test;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import org.hl7.fhir.dstu2016may.formats.XmlParser;
import org.hl7.fhir.dstu2016may.model.StructureDefinition;
import org.hl7.fhir.dstu2016may.utils.QuestionnaireBuilder;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class QuestionnaireBuilderTester {
private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
// private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
public static void main(String[] args) {
public static void main(String[] args) throws IOException {
QuestionnaireBuilder b = new QuestionnaireBuilder(null);
for (String f : new File(TEST_PROFILE_DIR).list()) {
for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
if (f.endsWith(".profile.xml") && !f.contains("type-")) {
System.out.println("process " + f);
try {
StructureDefinition p = (StructureDefinition) new XmlParser()
.parse(new FileInputStream(TEST_PROFILE_DIR + "\\" + f));
.parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR + "\\" + f));
// Questionnaire q = b.buildQuestionnaire(p);
// new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
// new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
throw new FHIRException("test");
} catch (Exception e) {
e.printStackTrace();

9
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ResourceTest.java
View File

@ -40,6 +40,7 @@ import org.hl7.fhir.dstu2016may.formats.JsonParser;
import org.hl7.fhir.dstu2016may.formats.XmlParser;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class ResourceTest {
@ -61,18 +62,18 @@ public class ResourceTest {
p = new JsonParser();
else
p = new XmlParser(false);
Resource rf = p.parse(new FileInputStream(source));
Resource rf = p.parse(ManagedFileAccess.inStream(source));
FileOutputStream out = new FileOutputStream(source.getAbsoluteFile() + ".out.json");
FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.json");
JsonParser json1 = new JsonParser();
json1.setOutputStyle(OutputStyle.PRETTY);
json1.compose(out, rf);
out.close();
JsonParser json = new JsonParser();
rf = json.parse(new FileInputStream(source.getAbsoluteFile() + ".out.json"));
rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile() + ".out.json"));
out = new FileOutputStream(source.getAbsoluteFile() + ".out.xml");
out = ManagedFileAccess.outStream(source.getAbsoluteFile() + ".out.xml");
XmlParser atom = new XmlParser();
atom.setOutputStyle(OutputStyle.PRETTY);
atom.compose(out, rf, true);

27
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/RoundTripTest.java
View File

@ -16,6 +16,7 @@ import org.hl7.fhir.dstu2016may.metamodel.Manager.FhirFormat;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
@ -29,7 +30,7 @@ public class RoundTripTest {
public static Stream<Arguments> getFiles() throws IOException {
List<Arguments> params = new ArrayList();
String examples = Utilities.path(root, "examples");
for (File f : new File(examples).listFiles()) {
for (File f : ManagedFileAccess.file(examples).listFiles()) {
if (f.getName().endsWith(".xml")) {
params.add(Arguments.of(f));
}
@ -48,50 +49,50 @@ public class RoundTripTest {
@SuppressWarnings("deprecation")
public void test(File file) throws Exception {
System.out.println(file.getName());
Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new FileInputStream(file));
Resource r = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(ManagedFileAccess.inStream(file));
String fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(fn), r);
.compose(ManagedFileAccess.outStream(fn), r);
String msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
String j1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(j1), r);
.compose(ManagedFileAccess.outStream(j1), r);
if (TestingUtilities.context == null) {
TestingUtilities.context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation-min.xml.zip"));
}
Element re = Manager.parse(TestingUtilities.context, new FileInputStream(file), FhirFormat.XML);
Element re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(file), FhirFormat.XML);
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(file.getAbsolutePath(), fn);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
String j2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(j2), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, j2);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
// ok, we've produced equivalent JSON by both methods.
// now, we're going to reverse the process
r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream(j2)); // crossover too
r = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(ManagedFileAccess.inStream(j2)); // crossover too
fn = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(fn), r);
.compose(ManagedFileAccess.outStream(fn), r);
msg = TestingUtilities.checkJsonIsSame(j2, fn);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
String x1 = makeTempFilename();
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(x1), r);
.compose(ManagedFileAccess.outStream(x1), r);
re = Manager.parse(TestingUtilities.context, new FileInputStream(j1), FhirFormat.JSON);
re = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(j1), FhirFormat.JSON);
fn = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(fn), FhirFormat.JSON, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkJsonIsSame(j1, fn);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);
String x2 = makeTempFilename();
Manager.compose(TestingUtilities.context, re, new FileOutputStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, re, ManagedFileAccess.outStream(x2), FhirFormat.XML, OutputStyle.PRETTY, null);
msg = TestingUtilities.checkXMLIsSame(x1, x2);
Assertions.assertTrue(msg == null, file.getName() + ": " + msg);

4
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/SingleTest.java
View File

@ -30,6 +30,8 @@ package org.hl7.fhir.dstu2016may.test;
import java.io.File;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class SingleTest {
/**
@ -38,7 +40,7 @@ public class SingleTest {
public static void main(String[] args) {
try {
ResourceTest r = new ResourceTest();
r.setSource(new File("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\patient-example.xml"));
r.test();
System.out.println("Completed OK");
} catch (Exception e) {

15
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/StructureMapTests.java
View File

@ -21,6 +21,7 @@ import org.hl7.fhir.dstu2016may.utils.StructureMapUtilities;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -86,16 +87,16 @@ public class StructureMapTests {
StructureMapUtilities scu = new StructureMapUtilities(TestingUtilities.context, maps, null);
for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA").list()) {
for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA").list()) {
try {
StructureDefinition sd = (StructureDefinition) new XmlParser()
.parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA\\" + f));
.parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\CDA\\" + f));
((SimpleWorkerContext) TestingUtilities.context).seeResource(sd.getUrl(), sd);
} catch (Exception e) {
}
}
for (String f : new File("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps").list()) {
for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps").list()) {
try {
StructureMap map = scu.parse(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\maps\\" + f));
maps.put(map.getUrl(), map);
@ -104,17 +105,17 @@ public class StructureMapTests {
}
Element cda = Manager.parse(TestingUtilities.context,
new FileInputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.xml"), FhirFormat.XML);
ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.xml"), FhirFormat.XML);
Manager.compose(TestingUtilities.context, cda,
new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.json"), FhirFormat.JSON,
ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.json"), FhirFormat.JSON,
OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, cda,
new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.xml"), FhirFormat.XML,
ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\guides\\ccda\\Example\\ccd.out.xml"), FhirFormat.XML,
OutputStyle.PRETTY, null);
Bundle bundle = new Bundle();
scu.transform(null, cda, maps.get("http://hl7.org/fhir/StructureMap/cda"), bundle);
new XmlParser().setOutputStyle(OutputStyle.PRETTY)
.compose(new FileOutputStream(Utilities.path("[tmp]", "bundle.xml")), bundle);
.compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "bundle.xml")), bundle);
}
}

9
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/TestingUtilities.java
View File

@ -13,9 +13,10 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
@ -41,7 +42,7 @@ public class TestingUtilities {
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}
@ -154,7 +155,7 @@ public class TestingUtilities {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
return builder.parse(new FileInputStream(fn));
return builder.parse(ManagedFileAccess.inStream(fn));
}
public static String checkJsonIsSame(String f1, String f2)
@ -166,7 +167,7 @@ public class TestingUtilities {
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}

63
org.hl7.fhir.dstu2016may/src/test/java/org/hl7/fhir/dstu2016may/test/ToolsHelper.java
View File

@ -57,10 +57,11 @@ import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.utils.SimpleWorkerContext;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.xmlpull.v1.XmlPullParser;
import org.xmlpull.v1.XmlPullParserException;
import org.xmlpull.v1.XmlPullParserFactory;
@ -105,7 +106,7 @@ public class ToolsHelper {
private void executeExamples(String[] args) throws IOException {
try {
@SuppressWarnings("unchecked")
List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
String srcDir = lines.get(0);
lines.remove(0);
processExamples(srcDir, lines);
@ -183,7 +184,7 @@ public class ToolsHelper {
// } else
if (definitions.startsWith("https:") || definitions.startsWith("http:")) {
defn = loadFromUrl(definitions);
} else if (new File(definitions).exists()) {
} else if (ManagedFileAccess.file(definitions).exists()) {
defn = loadFromFile(definitions);
} else
throw new FHIRException("Unable to find FHIR validation Pack (source = " + definitions + ")");
@ -197,7 +198,7 @@ public class ToolsHelper {
}
private byte[] loadFromFile(String src) throws IOException {
FileInputStream in = new FileInputStream(src);
FileInputStream in = ManagedFileAccess.inStream(src);
byte[] b = new byte[in.available()];
in.read(b);
in.close();
@ -224,10 +225,10 @@ public class ToolsHelper {
public void executeFragments(String[] args) throws IOException {
try {
File source = new CSFile(args[1]);
File source = ManagedFileAccess.csfile(args[1]);
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
XmlPullParser xpp = loadXml(new FileInputStream(source));
XmlPullParser xpp = loadXml(ManagedFileAccess.inStream(source));
nextNoWhitespace(xpp);
if (!xpp.getName().equals("tests"))
throw new FHIRFormatError("Unable to parse file - starts with " + xpp.getName());
@ -273,8 +274,8 @@ public class ToolsHelper {
public void executeRoundTrip(String[] args) throws IOException, FHIRException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
if (args.length >= 4) {
Utilities.copyFile(args[1], args[3]);
}
@ -292,18 +293,18 @@ public class ToolsHelper {
json.close();
TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
new XmlParser().compose(s, rf, true);
s.close();
}
public String executeJson(String[] args) throws IOException, FHIRException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File destc = new CSFile(Utilities.changeFileExt(args[2], ".canonical.json"));
File destt = new CSFile(args[2] + ".tmp");
File destr = new CSFile(Utilities.changeFileExt(args[2], ".ttl"));
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
File destc = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".canonical.json"));
File destt = ManagedFileAccess.csfile(args[2] + ".tmp");
File destr = ManagedFileAccess.csfile(Utilities.changeFileExt(args[2], ".ttl"));
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@ -312,21 +313,21 @@ public class ToolsHelper {
Resource rf = p.parse(in);
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
json.compose(s, rf);
s.close();
json.setOutputStyle(OutputStyle.CANONICAL);
s = new FileOutputStream(destc);
s = ManagedFileAccess.outStream(destc);
json.compose(s, rf);
s.close();
json.setSuppressXhtml("Snipped for Brevity");
json.setOutputStyle(OutputStyle.PRETTY);
s = new FileOutputStream(destt);
s = ManagedFileAccess.outStream(destt);
json.compose(s, rf);
s.close();
RdfParserBase rdf = new RdfParser();
s = new FileOutputStream(destr);
s = ManagedFileAccess.outStream(destr);
rdf.compose(s, rf);
s.close();
@ -335,8 +336,8 @@ public class ToolsHelper {
public void executeCanonicalXml(String[] args) throws FHIRException, IOException {
FileInputStream in;
File source = new CSFile(args[1]);
File dest = new CSFile(args[2]);
File source = ManagedFileAccess.csfile(args[1]);
File dest = ManagedFileAccess.csfile(args[2]);
if (!source.exists())
throw new FHIRException("Source File \"" + source.getAbsolutePath() + "\" not found");
@ -345,7 +346,7 @@ public class ToolsHelper {
Resource rf = p.parse(in);
XmlParser cxml = new XmlParser();
cxml.setOutputStyle(OutputStyle.NORMAL);
cxml.compose(new FileOutputStream(dest), rf);
cxml.compose(ManagedFileAccess.outStream(dest), rf);
}
private void executeVersion(String[] args) throws IOException {
@ -358,7 +359,7 @@ public class ToolsHelper {
String filename = rootDir + n + ".xml";
// 1. produce canonical XML
CSFileInputStream source = new CSFileInputStream(filename);
FileOutputStream dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.xml"));
FileOutputStream dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.xml"));
XmlParser p = new XmlParser();
Resource r = p.parse(source);
XmlParser cxml = new XmlParser();
@ -367,18 +368,18 @@ public class ToolsHelper {
// 2. produce JSON
source = new CSFileInputStream(filename);
dest = new FileOutputStream(Utilities.changeFileExt(filename, ".json"));
dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".json"));
r = p.parse(source);
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
json.compose(dest, r);
json = new JsonParser();
json.setOutputStyle(OutputStyle.CANONICAL);
dest = new FileOutputStream(Utilities.changeFileExt(filename, ".canonical.json"));
dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".canonical.json"));
json.compose(dest, r);
// 2. produce JSON
dest = new FileOutputStream(Utilities.changeFileExt(filename, ".ttl"));
dest = ManagedFileAccess.outStream(Utilities.changeFileExt(filename, ".ttl"));
RdfParserBase rdf = new RdfParser();
rdf.compose(dest, r);
} catch (Exception e) {
@ -399,23 +400,23 @@ public class ToolsHelper {
String tmp = tmpDir + n.replace(File.separator, "-") + ".tmp";
String dest = tmpDir + n.replace(File.separator, "-") + ".java.xml";
FileInputStream in = new FileInputStream(source);
FileInputStream in = ManagedFileAccess.inStream(source);
XmlParser xp = new XmlParser();
Resource r = xp.parse(in);
System.err.print(".");
JsonParser jp = new JsonParser();
FileOutputStream out = new FileOutputStream(tmp);
FileOutputStream out = ManagedFileAccess.outStream(tmp);
jp.setOutputStyle(OutputStyle.PRETTY);
jp.compose(out, r);
out.close();
r = null;
System.err.print(".");
in = new FileInputStream(tmp);
in = ManagedFileAccess.inStream(tmp);
System.err.print(",");
r = jp.parse(in);
System.err.print(".");
out = new FileOutputStream(dest);
out = ManagedFileAccess.outStream(dest);
new XmlParser().compose(out, r, true);
System.err.println("!");
out.close();
@ -431,7 +432,7 @@ public class ToolsHelper {
private void executeTest(String[] args) throws Throwable {
try {
@SuppressWarnings("unchecked")
List<String> lines = FileUtils.readLines(new File(args[1]), "UTF-8");
List<String> lines = FileUtils.readLines(ManagedFileAccess.file(args[1]), "UTF-8");
String srcDir = lines.get(0);
lines.remove(0);
String dstDir = lines.get(0).trim();

13
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/context/BaseWorkerContext.java
View File

@ -94,6 +94,7 @@ import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@ -323,7 +324,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
String cacheFn = null;
if (cache != null) {
cacheFn = Utilities.path(cache, determineCacheId(vs, heirarchical) + ".json");
if (new File(cacheFn).exists()) {
if (ManagedFileAccess.file(cacheFn).exists()) {
return loadFromCache(vs.copy(), cacheFn);
}
}
@ -335,8 +336,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
.expand(vs, expProfile.setExcludeNested(!heirarchical));
if (vse.getValueset() != null) {
if (cache != null) {
FileOutputStream s = new FileOutputStream(cacheFn);
newJsonParser().compose(new FileOutputStream(cacheFn), vse.getValueset());
FileOutputStream s = ManagedFileAccess.outStream(cacheFn);
newJsonParser().compose(ManagedFileAccess.outStream(cacheFn), vse.getValueset());
s.close();
}
}
@ -368,7 +369,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
private ValueSetExpansionOutcome loadFromCache(ValueSet vs, String cacheFn)
throws FileNotFoundException, Exception {
JsonParser parser = new JsonParser();
Resource r = parser.parse(new FileInputStream(cacheFn));
Resource r = parser.parse(ManagedFileAccess.inStream(cacheFn));
if (r instanceof OperationOutcome) {
return new ValueSetExpansionOutcome(
((OperationOutcome) r).getIssue().get(0).getDetails().getText(),
@ -382,7 +383,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
private void saveToCache(Resource res, String cacheFn) throws FileNotFoundException, Exception {
JsonParser parser = new JsonParser();
parser.compose(new FileOutputStream(cacheFn), res);
parser.compose(ManagedFileAccess.outStream(cacheFn), res);
}
private String determineCacheId(ValueSet vs, boolean heirarchical) throws Exception {
@ -715,7 +716,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if (fn == null) {
return null;
}
if (!(new File(fn).exists())) {
if (!(ManagedFileAccess.file(fn).exists())) {
return null;
}
String cnt = TextFile.fileToString(fn);

7
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/context/SimpleWorkerContext.java
View File

@ -86,9 +86,10 @@ import org.hl7.fhir.dstu3.utils.validation.IResourceValidator;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
@ -676,7 +677,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public void loadFromFolder(String folder) throws FileNotFoundException, Exception {
for (String n : new File(folder).list()) {
for (String n : ManagedFileAccess.file(folder).list()) {
if (n.endsWith(".json"))
loadFromFile(Utilities.path(folder, n), new JsonParser());
else if (n.endsWith(".xml"))
@ -687,7 +688,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private void loadFromFile(String filename, IParser p) throws FileNotFoundException, Exception {
Resource r;
try {
r = p.parse(new FileInputStream(filename));
r = p.parse(ManagedFileAccess.inStream(filename));
if (r.getResourceType() == ResourceType.Bundle) {
for (BundleEntryComponent e : ((Bundle) r).getEntry()) {
seeResource(null, e.getResource());

15
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/elementmodel/Tester.java
View File

@ -32,6 +32,7 @@ package org.hl7.fhir.dstu3.elementmodel;
import java.io.File;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.Map.Entry;
@ -53,17 +54,17 @@ public class Tester {
IWorkerContext context = SimpleWorkerContext.fromPack(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", "validation-min.xml.zip"));
int t = 0;
int ok = 0;
for (String f : new File("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire") && new File("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl")).exists()) {
for (String f : ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish").list()) {
if (f.endsWith(".xml") && !f.endsWith(".canonical.xml") && !f.contains("profile") && !f.contains("questionnaire") && ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl")).exists()) {
// if (f.equals("account-questionnaire.xml")) {
System.out.print("convert "+f);
// Manager.convert(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML,
// new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
// Manager.convert(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML,
// ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")), FhirFormat.JSON, OutputStyle.PRETTY);
// String src = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.json")));
// String tgt = normalise(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".json")));
Element e = Manager.parse(context, new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML);
Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl")), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
Manager.compose(context, e, new FileOutputStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML, OutputStyle.PRETTY, null);
Element e = Manager.parse(context, ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+f), FhirFormat.XML);
Manager.compose(context, e, ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl")), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
Manager.compose(context, e, ManagedFileAccess.outStream(Utilities.path("[tmp]", "resource.xml")), FhirFormat.XML, OutputStyle.PRETTY, null);
String src = TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".mm.ttl"));
String tgt = TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\"+Utilities.changeFileExt(f, ".ttl"));
t++;

5
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/LoincToDEConvertor.java
View File

@ -56,6 +56,7 @@ import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -157,12 +158,12 @@ public class LoincToDEConvertor {
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
xml = builder.parse(new FileInputStream(definitions));
xml = builder.parse(ManagedFileAccess.inStream(definitions));
}
private void saveBundle() throws FHIRFormatError, IOException, XmlPullParserException {
XmlParser xml = new XmlParser();
FileOutputStream s = new FileOutputStream(dest);
FileOutputStream s = ManagedFileAccess.outStream(dest);
xml.compose(s, bundle, true);
s.close();
}

7
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpansionCache.java
View File

@ -79,6 +79,7 @@ import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcom
import org.hl7.fhir.dstu3.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
public class ValueSetExpansionCache implements ValueSetExpanderFactory {
@ -96,7 +97,7 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
// well, we'll see if the designated server can expand it, and if it can, we'll cache it locally
vso = context.expandVS(source, false, profile == null || !profile.getExcludeNested());
if (cacheFolder != null) {
FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path(cacheFolder, makeFile(source.getUrl())));
context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
s.close();
}
@ -136,10 +137,10 @@ public class ValueSetExpansionCache implements ValueSetExpanderFactory {
}
private void loadCache() throws FHIRFormatError, IOException {
File[] files = new File(cacheFolder).listFiles();
File[] files = ManagedFileAccess.file(cacheFolder).listFiles();
for (File f : files) {
if (f.getName().endsWith(".xml")) {
final FileInputStream is = new FileInputStream(f);
final FileInputStream is = ManagedFileAccess.inStream(f);
try {
Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
if (r instanceof OperationOutcome) {

7
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/BatchLoader.java
View File

@ -52,6 +52,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class BatchLoader {
@ -68,7 +69,7 @@ public class BatchLoader {
throw new FHIRException("Unimplemented file type "+file);
// } else if (file.endsWith(".zip")) {
// LoadZipFile(server, file, p, size, 0, -1);
} else if (new File(file).isDirectory()) {
} else if (ManagedFileAccess.file(file).isDirectory()) {
LoadDirectory(server, file, size);
} else
throw new FHIRException("Unknown file type "+file);
@ -81,7 +82,7 @@ public class BatchLoader {
System.out.println("Done");
IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));
for (File f : new File(folder).listFiles()) {
for (File f : ManagedFileAccess.file(folder).listFiles()) {
if (f.getName().endsWith(".json") || f.getName().endsWith(".xml")) {
if (!ini.getBooleanProperty("finished", f.getName())) {
sendFile(client, f, size, ini);
@ -145,7 +146,7 @@ public class BatchLoader {
// Bundle b = new Bundle();
// b.setType(BundleType.COLLECTION);
// b.setId(UUID.randomUUID().toString().toLowerCase());
// ZipInputStream zip = new ZipInputStream(new FileInputStream(file));
// ZipInputStream zip = new ZipInputStream(ManagedFileAccess.inStream(file));
// ZipEntry entry;
// while((entry = zip.getNextEntry())!=null)
// {

43
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/R3TEchnicalCorrectionProcessor.java
View File

@ -19,6 +19,7 @@ import org.hl7.fhir.dstu3.model.DomainResource;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class R3TEchnicalCorrectionProcessor {
@ -31,10 +32,10 @@ public class R3TEchnicalCorrectionProcessor {
System.out.println("Loading resources from "+src);
List<Resource> resources = new ArrayList<>();
Map<String, Resource> definitions = new HashMap<>();
for (File f : new File(src).listFiles()) {
for (File f : ManagedFileAccess.file(src).listFiles()) {
if (f.getName().endsWith(".xml") && !(f.getName().endsWith("warnings.xml") || f.getName().endsWith(".diff.xml"))) {
try {
Resource r = new XmlParser().parse(new FileInputStream(f));
Resource r = new XmlParser().parse(ManagedFileAccess.inStream(f));
if (f.getName().contains("canonical")) {
resources.add(r);
}
@ -43,17 +44,17 @@ public class R3TEchnicalCorrectionProcessor {
definitions.put(f.getName(), r);
}
r.setUserData("path", f.getName().substring(0, f.getName().indexOf(".")));
// FileUtils.copyFile(f, new File(f.getAbsolutePath()+"1"));
// FileUtils.copyFile(f, new File(f.getAbsolutePath()+"2"));
// FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"1"));
// FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"2"));
} catch (Exception e) {
System.out.println("Unable to load "+f.getName()+": "+e.getMessage());
}
}
if (f.getName().endsWith(".json") && !(f.getName().endsWith("schema.json") || f.getName().endsWith(".diff.json"))) {
try {
// new JsonParser().parse(new FileInputStream(f));
// FileUtils.copyFile(f, new File(f.getAbsolutePath()+"1"));
// FileUtils.copyFile(f, new File(f.getAbsolutePath()+"2"));
// new JsonParser().parse(ManagedFileAccess.inStream(f));
// FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"1"));
// FileUtils.copyFile(f, ManagedFileAccess.file(f.getAbsolutePath()+"2"));
} catch (Exception e) {
System.out.println("Unable to load "+f.getName()+": "+e.getMessage());
}
@ -79,15 +80,15 @@ public class R3TEchnicalCorrectionProcessor {
private void produceDefinitionsXml(Map<String, Resource> definitions, String dest) throws IOException {
for (String n : definitions.keySet()) {
File f = new File(Utilities.path(dest, "definitions.xml", n));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), definitions.get(n));
File f = ManagedFileAccess.file(Utilities.path(dest, "definitions.xml", n));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), definitions.get(n));
}
}
private void produceDefinitionsJson(Map<String, Resource> definitions, String dest) throws IOException {
for (String n : definitions.keySet()) {
File f = new File(Utilities.path(dest, "definitions.json", Utilities.changeFileExt(n, ".json")));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), definitions.get(n));
File f = ManagedFileAccess.file(Utilities.path(dest, "definitions.json", Utilities.changeFileExt(n, ".json")));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), definitions.get(n));
}
}
@ -97,8 +98,8 @@ public class R3TEchnicalCorrectionProcessor {
if (!r.getId().equals(r.getUserString("path"))) {
n = n+"("+r.getId()+")";
}
File f = new File(Utilities.path(dest, "examples-json", n+".json"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
File f = ManagedFileAccess.file(Utilities.path(dest, "examples-json", n+".json"));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
}
@ -109,8 +110,8 @@ public class R3TEchnicalCorrectionProcessor {
if (!r.getId().equals(r.getUserString("path"))) {
n = n+"("+r.getId()+")";
}
File f = new File(Utilities.path(dest, "examples", n+".xml"));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
File f = ManagedFileAccess.file(Utilities.path(dest, "examples", n+".xml"));
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f), r);
}
}
@ -119,9 +120,9 @@ public class R3TEchnicalCorrectionProcessor {
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 coreTotal = ManagedFileAccess.file(corePath).list().length-1;
int examplesTotal = ManagedFileAccess.file(examplesPath).list().length-1;
int elementsTotal = ManagedFileAccess.file(elementsPath).list().length-1;
int coreCount = 0;
int examplesCount = 0;
@ -131,17 +132,17 @@ public class R3TEchnicalCorrectionProcessor {
FileOutputStream dst = null;
if (n.startsWith("DataElement-")) {
elementsCount++;
dst = new FileOutputStream(Utilities.path(elementsPath, n));
dst = ManagedFileAccess.outStream(Utilities.path(elementsPath, n));
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(dst, r);
} else {
dst = new FileOutputStream(Utilities.path(examplesPath, n));
dst = ManagedFileAccess.outStream(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);
new JsonParser().setOutputStyle(OutputStyle.NORMAL).compose(ManagedFileAccess.outStream(Utilities.path(corePath, n)), r);
}
}
}

2
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/Translations.java
View File

@ -40,7 +40,7 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;

5
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/Unbundler.java
View File

@ -42,6 +42,7 @@ import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class Unbundler {
@ -51,12 +52,12 @@ public class Unbundler {
private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
String folder = Utilities.getDirectoryForFile(src);
Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
Bundle bnd = (Bundle) new JsonParser().parse(ManagedFileAccess.inStream(src));
for (BundleEntryComponent be : bnd.getEntry()) {
Resource r = be.getResource();
if (r != null) {
String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json");
new JsonParser().compose(new FileOutputStream(tgt), r);
new JsonParser().compose(ManagedFileAccess.outStream(tgt), r);
}
}
}

3
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/FluentPathTests.java
View File

@ -19,6 +19,7 @@ import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
@ -59,7 +60,7 @@ public class FluentPathTests {
if (Utilities.noString(input))
fp.check(null, null, node);
else {
res = new XmlParser().parse(new FileInputStream(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", input)));
res = new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path("C:\\work\\org.hl7.fhir\\build\\publish", input)));
fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);
}
outcome = fp.evaluate(res, node);

5
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/NarrativeGeneratorTests.java
View File

@ -12,6 +12,7 @@ import org.hl7.fhir.dstu3.utils.EOperationOutcome;
import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
@ -41,9 +42,9 @@ public class NarrativeGeneratorTests {
private void process(String path) throws FileNotFoundException, IOException, XmlPullParserException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
DomainResource r = (DomainResource) p.parse(ManagedFileAccess.inStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
FileOutputStream s = ManagedFileAccess.outStream(Utilities.path("[tmp]", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();

21
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ProfileUtilitiesTests.java
View File

@ -26,8 +26,9 @@ import org.hl7.fhir.dstu3.utils.EOperationOutcome;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.CSFile;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -45,8 +46,8 @@ public class ProfileUtilitiesTests {
public static void main(String[] args) throws EOperationOutcome, Exception {
// new ProfileUtilitiesTests().execute(args);
new ProfileUtilitiesTests("C:\\work\\org.hl7.fhir\\build\\publish").testSnapshotGeneration();
// StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\publish\\lipid-report-cholesterol.profile.xml"));
// new ProfileUtilities(context, messages, null).generateSchematrons(new FileOutputStream(Utilities.path("[tmp]", "test.sch"), p);
// StructureDefinition p = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\publish\\lipid-report-cholesterol.profile.xml"));
// new ProfileUtilities(context, messages, null).generateSchematrons(ManagedFileAccess.outStream(Utilities.path("[tmp]", "test.sch"), p);
}
public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
@ -76,9 +77,9 @@ public class ProfileUtilitiesTests {
System.out.println("processing output");
for (ProfileComparison outcome : comp.getComparisons()) {
if (outcome.getSubset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-"+outcome.getId()+".xml")), outcome.getSubset());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "intersection-"+outcome.getId()+".xml")), outcome.getSubset());
if (outcome.getSuperset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-"+outcome.getId()+".xml")), outcome.getSuperset());
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path("[tmp]", "union-"+outcome.getId()+".xml")), outcome.getSuperset());
System.out.println("\r\n"+outcome.getId()+": Comparison of "+outcome.getLeft().getUrl()+" and "+outcome.getRight().getUrl());
for (ValidationMessage vm : outcome.getMessages())
@ -101,8 +102,8 @@ public class ProfileUtilitiesTests {
private void compare(String fn1, String fn2) throws FHIRFormatError, FileNotFoundException, IOException, DefinitionException {
System.out.println("Compare "+fn1+" to "+fn2);
System.out.println(" .. load");
StructureDefinition left = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn1)));
StructureDefinition right = (StructureDefinition) new XmlParser().parse(new FileInputStream(Utilities.path(root, fn2)));
StructureDefinition left = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path(root, fn1)));
StructureDefinition right = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(Utilities.path(root, fn2)));
System.out.println(" .. compare");
comp.compareProfiles(left, right);
@ -893,14 +894,14 @@ public class ProfileUtilitiesTests {
// focus.setDifferential(null);
String f1 = Utilities.path("c:", "temp", "base.xml");
String f2 = Utilities.path("c:", "temp", "derived.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f1), base);;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(f2), focus);;
String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
List<String> command = new ArrayList<String>();
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile(Utilities.path("[tmp]")));
builder.directory(ManagedFileAccess.csfile(Utilities.path("[tmp]")));
builder.start();
}

10
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/QuestionnaireBuilderTester.java
View File

@ -1,7 +1,9 @@
package org.hl7.fhir.dstu3.test;
import java.io.File;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import java.io.FileInputStream;
import java.io.IOException;
import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.StructureDefinition;
@ -13,15 +15,15 @@ public class QuestionnaireBuilderTester {
private static final String TEST_PROFILE_DIR = "C:\\work\\org.hl7.fhir\\build\\publish";
// private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
public static void main(String[] args) {
public static void main(String[] args) throws IOException {
QuestionnaireBuilder b = new QuestionnaireBuilder(null);
for (String f : new File(TEST_PROFILE_DIR).list()) {
for (String f : ManagedFileAccess.file(TEST_PROFILE_DIR).list()) {
if (f.endsWith(".profile.xml") && !f.contains("type-")) {
System.out.println("process "+f);
try {
StructureDefinition p = (StructureDefinition) new XmlParser().parse(new FileInputStream(TEST_PROFILE_DIR+"\\"+f));
StructureDefinition p = (StructureDefinition) new XmlParser().parse(ManagedFileAccess.inStream(TEST_PROFILE_DIR+"\\"+f));
// Questionnaire q = b.buildQuestionnaire(p);
// new XmlComposer().compose(new FileOutputStream(TEST_DEST+f), q, true);
// new XmlComposer().compose(ManagedFileAccess.outStream(TEST_DEST+f), q, true);
throw new FHIRException("test");
} catch (Exception e) {
e.printStackTrace();

5
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ResourceRoundTripTests.java
View File

@ -14,6 +14,7 @@ import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.dstu3.utils.EOperationOutcome;
import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@ -24,9 +25,9 @@ public class ResourceRoundTripTests {
public void test() throws FileNotFoundException, IOException, FHIRException, EOperationOutcome {
if (TestingUtilities.context == null)
TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip");
Resource res = new XmlParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.xml"));
Resource res = new XmlParser().parse(ManagedFileAccess.inStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.xml"));
new NarrativeGenerator("", "", TestingUtilities.context).generate((DomainResource) res);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.out.xml"), res);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream("C:\\work\\org.hl7.fhir\\build\\tests\\resources\\unicode.out.xml"), res);
}
}

15
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/ResourceTest.java
View File

@ -45,6 +45,7 @@ import org.hl7.fhir.dstu3.formats.XmlParser;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.test.support.TestingUtilities;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
public class ResourceTest {
@ -66,18 +67,18 @@ public class ResourceTest {
p = new JsonParser();
else
p = new XmlParser(false);
Resource rf = p.parse(new FileInputStream(source));
Resource rf = p.parse(ManagedFileAccess.inStream(source));
FileOutputStream out = new FileOutputStream(source.getAbsoluteFile()+".out.json");
FileOutputStream out = ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json");
JsonParser json1 = new JsonParser();
json1.setOutputStyle(OutputStyle.PRETTY);
json1.compose(out, rf);
out.close();
JsonParser json = new JsonParser();
rf = json.parse(new FileInputStream(source.getAbsoluteFile()+".out.json"));
rf = json.parse(ManagedFileAccess.inStream(source.getAbsoluteFile()+".out.json"));
out = new FileOutputStream(source.getAbsoluteFile()+".out.xml");
out = ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.xml");
XmlParser atom = new XmlParser();
atom.setOutputStyle(OutputStyle.PRETTY);
atom.compose(out, rf, true);
@ -89,9 +90,9 @@ public class ResourceTest {
public Element testEM() throws Exception {
if (TestingUtilities.context == null)
TestingUtilities.context = SimpleWorkerContext.fromPack("C:\\work\\org.hl7.fhir\\build\\publish\\definitions.xml.zip");
Element resource = Manager.parse(TestingUtilities.context, new FileInputStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.context, resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, resource, new FileOutputStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
Element resource = Manager.parse(TestingUtilities.context, ManagedFileAccess.inStream(source), isJson() ? FhirFormat.JSON : FhirFormat.XML);
Manager.compose(TestingUtilities.context, resource, ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
Manager.compose(TestingUtilities.context, resource, ManagedFileAccess.outStream(source.getAbsoluteFile()+".out.json"), FhirFormat.XML, OutputStyle.PRETTY, null);
return resource;
}

3
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SingleTest.java
View File

@ -30,6 +30,7 @@ package org.hl7.fhir.dstu3.test;
import java.io.File;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Disabled;
@Disabled
@ -41,7 +42,7 @@ public class SingleTest {
public static void main(String[] args) {
try {
ResourceTest r = new ResourceTest();
r.setSource(new File("C:\\work\\org.hl7.fhir\\fhir-test-cases\\r3\\ActivityDefinition-referralPrimaryCareMentalHealth.json"));
r.setSource(ManagedFileAccess.file("C:\\work\\org.hl7.fhir\\fhir-test-cases\\r3\\ActivityDefinition-referralPrimaryCareMentalHealth.json"));
r.test();
System.out.println("Completed OK");
} catch (Exception e) {

3
org.hl7.fhir.dstu3/src/test/java/org/hl7/fhir/dstu3/test/SnapShotGenerationTests.java
View File

@ -37,6 +37,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.filesystem.ManagedFileAccess;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.params.ParameterizedTest;
@ -89,7 +90,7 @@ public class SnapShotGenerationTests {
context.fixtures.put(op.getResponseId(), output);
context.snapshots.put(output.getUrl(), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(Utilities.path("[tmp]"), op.getResponseId() + ".xml")), output);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(ManagedFileAccess.outStream(Utilities.path(Utilities.path("[tmp]"), op.getResponseId() + ".xml")), output);
//ok, now the asserts:
for (int i = 1; i < test.getAction().size(); i++) {
SetupActionAssertComponent a = test.getAction().get(i).getAssert();

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