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org.hl7.fhir.core
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updates for packages changes

This commit is contained in:
Grahame Grieve 2019-11-26 18:56:52 +11:00
parent 45df4708d7
commit 60703efdd4
9 changed files with 214 additions and 61 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_50.java
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@ -13960,7 +13960,7 @@ public class VersionConvertor_30_50 {
private static org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus> convertMedicationDispenseStatus(org.hl7.fhir.dstu3.model.Enumeration<org.hl7.fhir.dstu3.model.MedicationDispense.MedicationDispenseStatus> src) throws FHIRException {
if (src == null)
return null;
org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus> tgt = new org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus>();
org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus> tgt = new org.hl7.fhir.r5.model.Enumeration<org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus>(new org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatusEnumFactory());
copyElement(src, tgt);
switch (src.getValue()) {
case PREPARATION: tgt.setValue(org.hl7.fhir.r5.model.MedicationDispense.MedicationDispenseStatus.PREPARATION); break;

16
org.hl7.fhir.r4/src/test/resources/logback-test.xml Normal file
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@ -0,0 +1,16 @@
<configuration scan="true" scanPeriod="30 seconds">
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<root level="info">
<appender-ref ref="STDOUT" />
</root>
</configuration>

40
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -835,35 +835,45 @@ public class ProfileUtilities extends TranslatingUtilities {
}
int ndl = findEndOfElement(differential, ndc);
// the first element is setting up the slicing
if (diffMatches.get(0).getSlicing().hasRules())
if (diffMatches.get(0).getSlicing().getRules() != SlicingRules.CLOSED)
throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.rules != closed");
if (diffMatches.get(0).getSlicing().hasOrdered())
if (diffMatches.get(0).getSlicing().getOrdered())
if (diffMatches.get(0).getSlicing().hasRules()) {
// this rule revoked at DevDays Amsterdam 2019 - discussion between Grahame Lloyd Alexander Ardon
// if (diffMatches.get(0).getSlicing().getRules() != SlicingRules.CLOSED) {
// throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.rules != closed");
// }
}
if (diffMatches.get(0).getSlicing().hasOrdered()) {
if (diffMatches.get(0).getSlicing().getOrdered()) {
throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.ordered = true");
}
}
if (diffMatches.get(0).getSlicing().hasDiscriminator()) {
if (diffMatches.get(0).getSlicing().getDiscriminator().size() != 1)
if (diffMatches.get(0).getSlicing().getDiscriminator().size() != 1) {
throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.discriminator.count() > 1");
if (!"$this".equals(diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getPath()))
}
if (!"$this".equals(diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getPath())) {
throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.discriminator.path != '$this'");
if (diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getType() != DiscriminatorType.TYPE)
}
if (diffMatches.get(0).getSlicing().getDiscriminatorFirstRep().getType() != DiscriminatorType.TYPE) {
throw new FHIRException("Error at path "+cpath+" in "+url+": Type slicing with slicing.discriminator.type != 'type'");
}
}
// check the slice names too while we're at it...
for (TypeSlice ts : typeList)
for (TypeSlice ts : typeList) {
if (ts.type != null) {
String tn = rootName(cpath)+Utilities.capitalize(ts.type);
if (!ts.defn.hasSliceName())
if (!ts.defn.hasSliceName()) {
ts.defn.setSliceName(tn);
else if (!ts.defn.getSliceName().equals(tn))
} else if (!ts.defn.getSliceName().equals(tn)) {
throw new FHIRException("Error at path "+(!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath)+": Slice name must be '"+tn+"' but is '"+ts.defn.getSliceName()+"'");
if (!ts.defn.hasType())
} if (!ts.defn.hasType()) {
ts.defn.addType().setCode(ts.type);
else if (ts.defn.getType().size() > 1)
} else if (ts.defn.getType().size() > 1) {
throw new FHIRException("Error at path "+(!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath)+": Slice for type '"+tn+"' has more than one type '"+ts.defn.typeSummary()+"'");
else if (!ts.defn.getType().get(0).getCode().equals(ts.type))
throw new FHIRException("Error at path "+(!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath)+": Slice for type '"+tn+"' has wrong type '"+ts.defn.typeSummary()+"'");
} else if (!ts.defn.getType().get(0).getCode().equals(ts.type)) {
throw new FHIRException("Error at path "+(!Utilities.noString(contextPathSrc) ? contextPathSrc : cpath)+": Slice for type '"+tn+"' has wrong type '"+ts.defn.typeSummary()+"'");
}
}
}
// ok passed the checks.
// copy the root diff, and then process any children it has

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -289,6 +289,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
for (String s : pi.listResources(types)) {
loadDefinitionItem(s, pi.load("package", s), loader);
}
// todogg
version = pi.version();
}
@ -469,6 +470,9 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
generateSnapshot(sd);
} catch (Exception e) {
System.out.println("Unable to generate snapshot for "+sd.getUrl()+" because "+e.getMessage());
if (true) {
e.printStackTrace();
}
}
result.add(sd);
set.add(sd);
@ -586,6 +590,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
ProfileUtilities pu = new ProfileUtilities(this, msgs, this);
pu.setThrowException(false);
pu.sortDifferential(sd, p, p.getUrl(), errors);
pu.setDebug(false);
for (String err : errors)
msgs.add(new ValidationMessage(Source.ProfileValidator, IssueType.EXCEPTION, p.getUserString("path"), "Error sorting Differential: "+err, ValidationMessage.IssueSeverity.ERROR));
pu.generateSnapshot(sd, p, p.getUrl(), Utilities.extractBaseUrl(sd.getUserString("path")), p.getName());

77
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/NpmPackage.java vendored
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@ -48,6 +48,7 @@ import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
@ -250,10 +251,18 @@ public class NpmPackage {
if (f.exists() && f.isDirectory())
for (String s : f.list())
res.add(s);
f = new File(Utilities.path(path, "package", folder));
if (f.exists() && f.isDirectory())
for (String s : f.list())
res.add(s);
} else {
for (String s : content.keySet()) {
if (s.startsWith(folder+"/") && !s.substring(folder.length()+2).contains("/"))
if (s.startsWith(folder+"/") && !s.substring(folder.length()+2).contains("/")) {
res.add(s.substring(folder.length()+1));
}
if (s.startsWith("package/"+folder+"/")) {
res.add(s.substring(folder.length()+9));
}
}
}
return res;
@ -325,10 +334,15 @@ public class NpmPackage {
* @throws IOException
*/
public InputStream load(String folder, String file) throws IOException {
if (content.containsKey(folder+"/"+file))
if (content.containsKey(folder+"/"+file)) {
return new ByteArrayInputStream(content.get(folder+"/"+file));
else {
} else if (content.containsKey("package/"+folder+"/"+file)) {
return new ByteArrayInputStream(content.get(folder+"/"+file));
} else {
File f = new File(Utilities.path(path, folder, file));
if (f.exists())
return new FileInputStream(f);
f = new File(Utilities.path(path, "package", folder, file));
if (f.exists())
return new FileInputStream(f);
throw new IOException("Unable to find the file "+folder+"/"+file+" in the package "+name());
@ -534,14 +548,26 @@ public class NpmPackage {
bufferedOutputStream = new BufferedOutputStream(OutputStream);
gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
tar = new TarArchiveOutputStream(gzipOutputStream);
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
indexer.start();
Map<String, NpmPackageIndexBuilder> indexers = new HashMap<>();
for (String s : content.keySet()) {
byte[] b = content.get(s);
if (s.startsWith("package/")) {
indexer.seeFile(tail(s), b);
if (s.startsWith("package/")) {
String n = s.substring(8);
String dir = null;
if (n.contains("/")) {
dir = n.substring(0, n.lastIndexOf("/"));
n = n.substring(n.lastIndexOf("/")+1);
}
if (!indexers.containsKey(dir)) {
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
indexer.start();
indexers.put(dir, indexer);
}
indexers.get(dir).seeFile(n, b);
} else {
throw new IOException("The package has an illegal file path "+s);
}
if (!s.endsWith(".index.json") && !s.equals("package/package.json")) {
TarArchiveEntry entry = new TarArchiveEntry(s);
@ -558,12 +584,14 @@ public class NpmPackage {
tar.write(cnt);
tar.closeArchiveEntry();
cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
entry = new TarArchiveEntry("package/.index.json");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);
tar.write(cnt);
tar.closeArchiveEntry();
for (String s : indexers.keySet()) {
cnt = indexers.get(s).build().getBytes(Charset.forName("UTF-8"));
entry = s == null ? new TarArchiveEntry("package/.index.json") : new TarArchiveEntry("package/"+s+"/.index.json");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);
tar.write(cnt);
tar.closeArchiveEntry();
}
tar.finish();
tar.close();
@ -640,6 +668,27 @@ public class NpmPackage {
return ver.matches("^[0-9]+\\.[0-9]+\\.[0-9]+$");
}
public String fhirVersionList() {
if (npm.has("fhirVersions")) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (JsonElement n : npm.getAsJsonArray("fhirVersions")) {
b.append(n.getAsString());
}
return b.toString();
} else
return "";
}
public String dependencySummary() {
if (npm.has("dependencies")) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (Entry<String, JsonElement> e : npm.getAsJsonObject("dependencies").entrySet()) {
b.append(e.getKey()+"#"+e.getValue().getAsString());
}
return b.toString();
} else
return "";
}
}

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java vendored
View File

@ -188,7 +188,9 @@ public class PackageCacheManager {
int c = 0;
File[] packages = new File(Utilities.path(dir, "package")).listFiles();
for (File f : packages) {
indexer.seeFile(f.getName(), TextFile.fileToBytes(f));
if (!f.isDirectory()) {
indexer.seeFile(f.getName(), TextFile.fileToBytes(f));
}
i++;
if (progress && i % 50 == 0) {
c++;
@ -289,6 +291,7 @@ public class PackageCacheManager {
public boolean initUrlMaps(IniFile ini, boolean save) {
save = checkIniHasMapping("hl7.fhir.core", "http://hl7.org/fhir", ini) || save;
save = checkIniHasMapping("hl7.fhir.pubpack", "http://fhir.org/packages/hl7.fhir.pubpack", ini) || save;
save = checkIniHasMapping("hl7.fhir.r2.core", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.core.tgz", ini) || save;
save = checkIniHasMapping("hl7.fhir.r2.examples", "http://hl7.org/fhir/DSTU2/hl7.fhir.r2.examples.tgz", ini) || save;
@ -644,7 +647,13 @@ public class PackageCacheManager {
try {
json = fetchJson(pu);
} catch (Exception e) {
throw new FHIRException("Error fetching package list for "+id+" from "+pu+": "+e.getMessage(), e);
String pv = Utilities.pathURL(url, v, "package.tgz");
try {
InputStream stream = fetchFromUrlSpecific(pv, true);
return addPackageToCache(id, v, stream, pv);
} catch (Exception e1) {
throw new FHIRException("Error fetching package directly ("+pv+"), or fetching package list for "+id+" from "+pu+": "+e1.getMessage(), e1);
}
}
if (!id.equals(JSONUtil.str(json, "package-id")))
throw new FHIRException("Package ids do not match in "+pu+": "+id+" vs "+JSONUtil.str(json, "package-id"));

90
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageScanner.java vendored
View File

@ -7,11 +7,16 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;
import org.hl7.fhir.utilities.CSVWriter;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
public class PackageScanner {
public static void main(String[] args) throws FileNotFoundException, IOException {
new PackageScanner().scan(new File("C:\\web\\hl7.org\\fhir"), "c:\\temp\\package-scan.csv", "http://hl7.org/fhir");
@ -19,8 +24,8 @@ public class PackageScanner {
private void scan(File folder, String dest, String url) throws IOException {
CSVWriter csv = new CSVWriter(new FileOutputStream(dest));
csv.line("path", "error", "name", "version", "fhir-version", "canonical", "homepage",
"url", "type", "#types", "#urls");
csv.line("path", "error", "name", "version", "fhir-version", "fhir-version-explicit", "canonical", "homepage",
"url", "type", "#types", "#urls", "dependencies");
scanFolders(folder, csv, folder.getAbsolutePath(), url);
csv.close();
System.out.println("done");
@ -40,9 +45,9 @@ public class PackageScanner {
private void processPackage(File file, CSVWriter csv, String root, String url) {
try {
NpmPackage npm = NpmPackage.fromPackage(new FileInputStream(file));
// fix(npm, file.getAbsolutePath(), root, url);
csv.line(file.getAbsolutePath(), "", npm.name(), npm.version(), npm.fhirVersion(), npm.canonical(), npm.homepage(),
npm.url(), npm.type(), Integer.toString(npm.getTypes().size()), Integer.toString(npm.getUrls().size()));
fix(npm, file, root, url);
csv.line(file.getAbsolutePath(), "", npm.name(), npm.version(), npm.fhirVersion(), npm.fhirVersionList(), npm.canonical(), npm.homepage(),
npm.url(), npm.type(), Integer.toString(npm.getTypes().size()), Integer.toString(npm.getUrls().size()), npm.dependencySummary());
} catch (Exception e) {
try {
csv.line(file.getAbsolutePath(), e.getMessage() == null ? "NPE" : e.getMessage());
@ -54,25 +59,74 @@ public class PackageScanner {
}
private void fix(NpmPackage npm, String filename, String root, String url) throws FileNotFoundException, IOException {
String u = Utilities.pathURL(url, Utilities.getDirectoryForFile(filename).substring(root.length()).replace("\\", "/"));
if (Utilities.getDirectoryForFile(filename).equals("C:\\web\\hl7.org\\fhir")) {
private void fix(NpmPackage npm, File file, String root, String url) throws FileNotFoundException, IOException {
String u = Utilities.pathURL(url, Utilities.getDirectoryForFile(file.getAbsolutePath()).substring(root.length()).replace("\\", "/"));
if (Utilities.getDirectoryForFile(file.getAbsolutePath()).equals("C:\\web\\hl7.org\\fhir")) {
u = "http://hl7.org/fhir/R4";
}
boolean save = false;
if (npm.url() == null || !npm.url().equals(u)) {
npm.getNpm().remove("url");
npm.getNpm().addProperty("url", u);
save = true;
}
if (!npm.canonical().startsWith("http://hl7.org")) {
npm.getNpm().remove("canonical");
npm.getNpm().addProperty("canonical", "http://hl7.org/fhir/smart-app-launch");
save = true;
List<String> names = new ArrayList<>();
names.addAll(npm.getContent().keySet());
for (String s : names) {
if (!s.startsWith("package/")) {
save = true;
String n = "package/"+s;
npm.getContent().put(n, npm.getContent().get(s));
npm.getContent().remove(s);
}
}
if (!npm.getNpm().has("fhirVersions")) {
JsonArray fv = new JsonArray();
fv.add(npm.fhirVersion());
npm.getNpm().add("fhirVersions", fv);
save = true;
}
if (npm.getNpm().has("dependencies")) {
JsonObject dep = npm.getNpm().getAsJsonObject("dependencies");
for (Entry<String, JsonElement> e : dep.entrySet()) {
if ("current".equals(e.getValue().getAsString())) {
save = true;
if ("hl7.fhir.us.core.r4".equals(e.getKey())) {
dep.remove("hl7.fhir.us.core.r4");
dep.addProperty("hl7.fhir.us.core", "3.0.1");
} else if ("hl7.fhir.us.davinci-pas".equals(e.getKey())) {
dep.remove("hl7.fhir.us.davinci-pas");
dep.addProperty("hl7.fhir.us.davinci-pas", "0.1.0");
} else if ("hl7.fhir.uv.sdc".equals(e.getKey())) {
dep.remove("hl7.fhir.uv.sdc");
if ("0.1.0".equals(npm.version()))
dep.addProperty("hl7.fhir.uv.sdc", "2.5.0");
else
dep.addProperty("hl7.fhir.uv.sdc", "2.7.0");
} else if ("hl7.fhir.us.core".equals(e.getKey())) {
dep.remove("hl7.fhir.us.core");
dep.addProperty("hl7.fhir.us.core", "3.0.1");
} else if ("hl7.fhir.us.ccda.r4".equals(e.getKey())) {
dep.remove("hl7.fhir.us.ccda.r4");
dep.addProperty("hl7.fhir.us.ccda", "1.0.0");
}
}
}
}
// if (npm.url() == null || !npm.url().equals(u)) {
// npm.getNpm().remove("url");
// npm.getNpm().addProperty("url", u);
// save = true;
// }
// if (!npm.canonical().startsWith("http://hl7.org")) {
// npm.getNpm().remove("canonical");
// npm.getNpm().addProperty("canonical", "http://hl7.org/fhir/smart-app-launch");
// save = true;
// }
//
if (save) {
npm.save(new FileOutputStream(filename));
File bck = new File(Utilities.changeFileExt(file.getAbsolutePath(), ".bcknpm"));
if (bck.exists()) {
bck.delete();
}
file.renameTo(bck);
npm.save(new FileOutputStream(file));
}
}

30
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
View File

@ -794,16 +794,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
for (Entry<String, byte[]> t : source.entrySet()) {
String fn = t.getKey();
if (!exemptFile(fn)) {
if (debug)
System.out.print("* load file: "+fn);
Resource r = null;
try {
r = loadResourceByVersion(version, t.getValue(), fn);
if (debug)
System.out.println(" .. success");
} catch (Exception e) {
System.out.println(" - ignored due to error: "+e.getMessage());
}
Resource r = loadFileWithErrorChecking(version, t, fn);
if (r != null) {
context.cacheResource(r);
if (r instanceof ImplementationGuide) {
@ -821,6 +812,25 @@ public class ValidationEngine implements IValidatorResourceFetcher {
grabNatives(source, canonical);
}
public Resource loadFileWithErrorChecking(String version, Entry<String, byte[]> t, String fn) {
if (debug)
System.out.print("* load file: "+fn);
Resource r = null;
try {
r = loadResourceByVersion(version, t.getValue(), fn);
if (debug)
System.out.println(" .. success");
} catch (Exception e) {
if (!debug) {
System.out.print("* load file: "+fn);
}
System.out.println(" - ignored due to error: "+(e.getMessage() == null ? " (null - NPE)" : e.getMessage()));
if (debug)
e.printStackTrace();
}
return r;
}
public Resource loadResourceByVersion(String version, byte[] content, String fn) throws IOException, Exception {
Resource r;
if (version.startsWith("3.0")) {

2
pom.xml
View File

@ -17,7 +17,7 @@
<properties>
<hapi_fhir_version>4.1.0</hapi_fhir_version>
<validator_test_case_version>1.0.6-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.0.7-SNAPSHOT</validator_test_case_version>
</properties>
<artifactId>org.hl7.fhir.core</artifactId>