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rework validation output + fix up package loading in validator

This commit is contained in:
Grahame Grieve 2020-08-31 13:24:20 +10:00
parent 3fad39620b
commit ef2ad7ce21
10 changed files with 163 additions and 99 deletions
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33
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/FilesystemPackageCacheManager.java vendored
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@ -90,7 +90,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
// private static final String SECONDARY_SERVER = "http://local.fhir.org:960/packages";
public static final String PACKAGE_REGEX = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+$";
public static final String PACKAGE_VERSION_REGEX = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+\\#[a-z0-9\\-\\_]+(\\.[a-z0-9\\-\\_]+)*$";
public static final String PACKAGE_VERSION_REGEX_OPT = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+(\\#[a-z0-9\\-\\_]+(\\.[a-z0-9\\-\\_]+)*)$";
public static final String PACKAGE_VERSION_REGEX_OPT = "^[a-z][a-z0-9\\_\\-]*(\\.[a-z0-9\\_\\-]+)+(\\#[a-z0-9\\-\\_]+(\\.[a-z0-9\\-\\_]+)*)?$";
private static final Logger ourLog = LoggerFactory.getLogger(FilesystemPackageCacheManager.class);
private static final String CACHE_VERSION = "3"; // second version - see wiki page
private String cacheFolder;
@ -862,7 +862,38 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
}
}
public boolean packageExists(String id, String ver) throws IOException {
if (packageInstalled(id, ver)) {
return true;
}
for (String s : getPackageServers()) {
if (new PackageClient(s).exists(id, ver)) {
return true;
}
}
return false;
}
public boolean packageInstalled(String id, String version) {
for (NpmPackage p : temporaryPackages) {
if (p.name().equals(id) && ("current".equals(version) || "dev".equals(version) || p.version().equals(version))) {
return true;
}
if (p.name().equals(id) && Utilities.noString(version)) {
return true;
}
}
for (String f : sorted(new File(cacheFolder).list())) {
if (f.equals(id + "#" + version) || (Utilities.noString(version) && f.startsWith(id + "#"))) {
return true;
}
}
if ("dev".equals(version))
return packageInstalled(id, "current");
else
return false;
}

10
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageHacker.java vendored
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@ -25,7 +25,7 @@ import com.google.gson.JsonObject;
public class PackageHacker {
public static void main(String[] args) throws FileNotFoundException, IOException {
new PackageHacker().edit("M:\\web\\hl7.org\\fhir\\2020Sep\\hl7.fhir.r5.expansions.tgz");
new PackageHacker().edit("M:\\web\\hl7.org\\fhir\\uv\\cdisc-lab\\package.tgz");
}
private void edit(String name) throws FileNotFoundException, IOException {
@ -57,10 +57,10 @@ public class PackageHacker {
private void change(JsonObject npm, Map<String, byte[]> content) throws FileNotFoundException, IOException {
fixVersions(npm);
// npm.remove("url");
// npm.addProperty("url", url);
npm.remove("version");
npm.addProperty("version", "4.5.0");
npm.remove("url");
npm.addProperty("url", "http://hl7.org/fhir/uv/cdisc-lab/STU1");
npm.remove("name");
npm.addProperty("name", "hl7.fhir.uv.cdisc-lab");
// npm.remove("canonical");
// npm.addProperty("canonical", "http://hl7.org/fhir/us/davinci-drug-formulary");
//// npm.remove("description");

79
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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@ -38,6 +38,7 @@ import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageI
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.cache.NpmPackage;
@ -351,8 +352,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
context = SimpleWorkerContext.fromNothing();
}
public void setTerminologyServer(String src, String log, FhirPublication version) throws FHIRException, URISyntaxException {
connectToTSServer(src, log, version);
public String setTerminologyServer(String src, String log, FhirPublication version) throws FHIRException, URISyntaxException {
return connectToTSServer(src, log, version);
}
public boolean isHintAboutNonMustSupport() {
@ -382,7 +383,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, String vString) throws FHIRException, IOException, URISyntaxException {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
loadCoreDefinitions(src, false);
loadCoreDefinitions(src, false, null);
context.setCanRunWithoutTerminology(canRunWithoutTerminologyServer);
setTerminologyServer(txsrvr, txLog, version);
this.version = vString;
@ -390,13 +391,20 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, String vString) throws FHIRException, IOException, URISyntaxException {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
loadCoreDefinitions(src, false);
loadCoreDefinitions(src, false, null);
setTerminologyServer(txsrvr, txLog, version);
this.version = vString;
}
public ValidationEngine(String src, FhirPublication version, String vString, TimeTracker tt) throws FHIRException, IOException, URISyntaxException {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
loadCoreDefinitions(src, false, tt);
this.version = vString;
}
public ValidationEngine(String src) throws FHIRException, IOException {
loadCoreDefinitions(src, false);
loadCoreDefinitions(src, false, null);
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
@ -408,7 +416,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
this.language = language;
}
private void loadCoreDefinitions(String src, boolean recursive) throws FHIRException, IOException {
private void loadCoreDefinitions(String src, boolean recursive, TimeTracker tt) throws FHIRException, IOException {
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
@ -427,6 +435,9 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
context.setCacheId(UUID.randomUUID().toString());
context.setAllowLoadingDuplicates(true); // because of Forge
context.setExpansionProfile(makeExpProfile());
if (tt != null) {
context.setClock(tt);
}
NpmPackage npmX = pcm.loadPackage("hl7.fhir.xver-extensions", "0.0.4");
context.loadFromPackage(npmX, null);
}
@ -912,16 +923,17 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
return checkIsResource(TextFile.fileToBytes(path), path);
}
public void connectToTSServer(String url, String log, FhirPublication version) throws URISyntaxException, FHIRException {
public String connectToTSServer(String url, String log, FhirPublication version) throws URISyntaxException, FHIRException {
context.setTlogging(false);
if (url == null) {
context.setCanRunWithoutTerminology(true);
return "n/a: No Terminology Server";
} else {
try {
context.connectToTSServer(TerminologyClientFactory.makeClient(url, version), log);
return context.connectToTSServer(TerminologyClientFactory.makeClient(url, version), log);
} catch (Exception e) {
if (context.isCanRunWithoutTerminology()) {
System.out.println("Running without Terminology Server (error: "+e.getMessage()+")");
return "n/a: Running without Terminology Server (error: "+e.getMessage()+")";
} else
throw e;
}
@ -956,9 +968,16 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
}
}
}
context.loadFromPackage(npm, loaderForVersion(npm.fhirVersion()));
System.out.print(" Load " + src);
if (!src.contains("#")) {
System.out.print("#"+npm.version());
}
int count = context.loadFromPackage(npm, loaderForVersion(npm.fhirVersion()));
System.out.println(" - "+count+" resources ("+context.clock().milestone()+")");
} else {
System.out.print(" Load " + src);
String canonical = null;
int count = 0;
Map<String, byte[]> source = loadIgSource(src, recursive, true);
String version = Constants.VERSION;
if (this.version != null) {
@ -972,6 +991,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
if (!exemptFile(fn)) {
Resource r = loadFileWithErrorChecking(version, t, fn);
if (r != null) {
count++;
context.cacheResource(r);
if (r instanceof ImplementationGuide) {
canonical = ((ImplementationGuide) r).getUrl();
@ -988,6 +1008,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
if (canonical != null) {
grabNatives(source, canonical);
}
System.out.println(" - "+count+" resources ("+context.clock().milestone()+")");
}
}
@ -1247,22 +1268,27 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
}
public Resource validate(List<String> sources, List<String> profiles) throws FHIRException, IOException {
if (profiles.size() > 0) {
System.out.println(" Profiles: "+profiles);
}
List<String> refs = new ArrayList<String>();
boolean asBundle = handleSources(sources, refs);
Bundle results = new Bundle();
results.setType(Bundle.BundleType.COLLECTION);
for (String ref : refs) {
TimeTracker.Session tts = context.clock().start("validation");
context.clock().milestone();
System.out.print(" Validate " + ref);
Content cnt = loadContent(ref, "validate");
if (refs.size() > 1)
System.out.println("Validate "+ref);
try {
OperationOutcome outcome = validate(ref, cnt.focus, cnt.cntType, profiles);
ToolingExtensions.addStringExtension(outcome, ToolingExtensions.EXT_OO_FILE, ref);
if (refs.size() > 1)
produceValidationSummary(outcome);
System.out.println(" " + context.clock().milestone());
results.addEntry().setResource(outcome);
tts.end();
} catch (Exception e) {
System.out.println("Validation Infrastructure fail validating "+ref+": "+e.getMessage());
tts.end();
throw new FHIRException(e);
}
}
@ -1271,14 +1297,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
else
return results.getEntryFirstRep().getResource();
}
private void produceValidationSummary(OperationOutcome oo) {
for (OperationOutcomeIssueComponent iss : oo.getIssue()) {
if (iss.getSeverity() == org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR || iss.getSeverity() == org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.FATAL) {
System.out.println(" "+iss.getSeverity().toCode()+": "+iss.getDetails().getText());
}
}
}
public OperationOutcome validateString(String location, String source, FhirFormat format, List<String> profiles) throws FHIRException, IOException, EOperationOutcome, SAXException {
return validate(location, source.getBytes(), format, profiles);
@ -2361,14 +2380,6 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
return TextFile.streamToBytes(c.getInputStream());
}
public void doneLoading(long loadStart) {
if (showTimes) {
String s = String.format("Load Time (ms): %d", (System.nanoTime() - loadStart) / 1000000);
System.out.println(s);
}
}
public FilesystemPackageCacheManager getPcm() {
return pcm;
}
@ -2377,5 +2388,13 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
return bundleValidationRules;
}
public boolean packageExists(String id, String ver) throws IOException, FHIRException {
return pcm.packageExists(id, ver);
}
public void loadPackage(String id, String ver) throws IOException, FHIRException {
loadIg(id+(ver == null ? "" : "#"+ver), true);
}
}

25
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/Validator.java
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@ -63,6 +63,7 @@ import java.net.URI;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
@ -131,10 +132,11 @@ public class Validator {
}
public static void main(String[] args) throws Exception {
TimeTracker tt = new TimeTracker();
TimeTracker.Session tts = tt.start("Loading");
long loadStart = System.nanoTime();
System.out.println("FHIR Validation tool " + VersionUtil.getVersionString());
System.out.println("Detected Java version: " + System.getProperty("java.version") + " from " + System.getProperty("java.home") + " on " + System.getProperty("os.arch") + " (" + System.getProperty("sun.arch.data.model") + "bit). " + toMB(Runtime.getRuntime().maxMemory()) + "MB available");
System.out.println(" Java: " + System.getProperty("java.version") + " from " + System.getProperty("java.home") + " on " + System.getProperty("os.arch") + " (" + System.getProperty("sun.arch.data.model") + "bit). " + toMB(Runtime.getRuntime().maxMemory()) + "MB available");
String proxy = getNamedParam(args, Params.PROXY);
if (!Utilities.noString(proxy)) {
String[] p = proxy.split("\\:");
@ -146,7 +148,7 @@ public class Validator {
cliContext = Params.loadCliContext(args);
String v = Common.getVersion(args);
String definitions = VersionUtilities.packageForVersion(v) + "#" + v;
ValidationEngine validationEngine = Common.getValidationEngine(v, definitions, cliContext.getTxLog());
ValidationEngine validationEngine = Common.getValidationEngine(v, definitions, cliContext.getTxLog(), null);
ValidatorGui.start(cliContext, validationEngine, true);
} else if (Params.hasParam(args, Params.TEST)) {
Common.runValidationEngineTests();
@ -167,7 +169,7 @@ public class Validator {
}
String v = VersionUtilities.getCurrentVersion(cliContext.getSv());
String definitions = VersionUtilities.packageForVersion(v) + "#" + v;
ValidationEngine validator = ValidationService.getValidator(cliContext, definitions);
ValidationEngine validator = ValidationService.getValidator(cliContext, definitions, tt);
ComparisonService.doLeftRightComparison(args, dest, validator);
}
} else {
@ -178,9 +180,11 @@ public class Validator {
cliContext.setSv(determineVersion(cliContext));
}
System.out.println("Loading");
// Comment this out because definitions filename doesn't necessarily contain version (and many not even be 14 characters long). Version gets spit out a couple of lines later after we've loaded the context
String definitions = VersionUtilities.packageForVersion(cliContext.getSv()) + "#" + VersionUtilities.getCurrentVersion(cliContext.getSv());
ValidationEngine validator = ValidationService.getValidator(cliContext, definitions);
ValidationEngine validator = ValidationService.getValidator(cliContext, definitions, tt);
tts.end();
if (cliContext.getMode() == EngineMode.VERSION) {
ValidationService.transformVersion(cliContext, validator);
@ -194,22 +198,21 @@ public class Validator {
ValidationService.convertSources(cliContext, validator);
} else if (cliContext.getMode() == EngineMode.FHIRPATH) {
ValidationService.evaluateFhirpath(cliContext, validator);
} else {
if (definitions == null) {
throw new Exception("Must provide a defn when doing validation");
}
} else {
for (String s : cliContext.getProfiles()) {
if (!validator.getContext().hasResource(StructureDefinition.class, s) && !validator.getContext().hasResource(ImplementationGuide.class, s)) {
System.out.println("Fetch Profile from " + s);
System.out.println(" Fetch Profile from " + s);
validator.loadProfile(cliContext.getLocations().getOrDefault(s, s));
}
}
System.out.println("Validating");
if (cliContext.getMode() == EngineMode.SCAN) {
ValidationService.validateScan(cliContext, validator);
} else {
ValidationService.validateSources(cliContext, validator, loadStart);
ValidationService.validateSources(cliContext, validator);
}
}
System.out.println("Done. "+tt.report());
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/ValidatorGui.java
View File

@ -28,7 +28,7 @@ public class ValidatorGui {
CliContext cliContext = new CliContext();
String v = Common.getVersion(args);
String definitions = VersionUtilities.packageForVersion(v) + "#" + v;
ValidationEngine validationEngine = Common.getValidationEngine(v, definitions, cliContext.getTxLog());
ValidationEngine validationEngine = Common.getValidationEngine(v, definitions, cliContext.getTxLog(), null);
start(new CliContext(), validationEngine, false);
}

15
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
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@ -22,7 +22,8 @@ import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageI
public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
public interface IPackageInstaller {
public void loadIg(String src, boolean recursive) throws IOException, FHIRException;
public boolean packageExists(String id, String ver) throws IOException, FHIRException;
public void loadPackage(String id, String ver) throws IOException, FHIRException;
}
private BasePackageCacheManager pcm;
@ -63,13 +64,13 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {
// ok maybe it's a reference to a package we know
String base = findBaseUrl(url);
String pid = pcm.getPackageId(base);
if (url.contains("|")) {
pid = pid+"#"+url.substring(url.indexOf("|")+1);
}
String ver = url.contains("|") ? url.substring(url.indexOf("|")+1) : null;
if (pid != null) {
installer.loadIg(pid, false);
NpmPackage pi = pcm.loadPackage(pid);
return pi.hasCanonical(url);
if (installer.packageExists(pid, ver)) {
installer.loadPackage(pid, ver);
NpmPackage pi = pcm.loadPackage(pid);
return pi.hasCanonical(url);
}
}
if (!url.startsWith("http://hl7.org/fhir")) {

58
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -9,6 +9,7 @@ import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
@ -36,7 +37,6 @@ public class ValidationService {
} else {
System.out.println(" .. validate " + request.listSourceFiles());
}
validator.prepare(); // generate any missing snapshots
ValidationResponse response = new ValidationResponse();
for (FileInfo fp : request.getFilesToValidate()) {
@ -62,22 +62,19 @@ public class ValidationService {
ve.scanForVersions(cliContext.getSources(), versions);
return versions;
}
public static void validateSources(CliContext cliContext, ValidationEngine validator, long loadStart) throws Exception {
validator.doneLoading(loadStart);
if (cliContext.getProfiles().size() > 0) {
System.out.println(" .. validate " + cliContext.getSources() + " against " + cliContext.getProfiles().toString());
} else {
System.out.println(" .. validate " + cliContext.getSources());
}
validator.prepare(); // generate any missing snapshots
public static void validateSources(CliContext cliContext, ValidationEngine validator) throws Exception {
Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles());
int ec = 0;
System.out.println("Done. "+validator.getContext().clock().report());
System.out.println();
if (cliContext.getOutput() == null) {
if (r instanceof Bundle)
for (Bundle.BundleEntryComponent e : ((Bundle) r).getEntry())
ec = displayOperationOutcome((OperationOutcome) e.getResource()) + ec;
ec = ec + displayOperationOutcome((OperationOutcome) e.getResource(), ((Bundle) r).getEntry().size() > 1) + ec;
else
ec = displayOperationOutcome((OperationOutcome) r);
ec = displayOperationOutcome((OperationOutcome) r, false);
} else {
IParser x;
if (cliContext.getOutput() != null && cliContext.getOutput().endsWith(".json")) {
@ -193,16 +190,20 @@ public class ValidationService {
}
}
public static ValidationEngine getValidator(CliContext cliContext, String definitions) throws Exception {
System.out.println(" .. FHIR Version " + cliContext.getSv() + ", definitions from " + definitions);
System.out.println(" .. connect to tx server @ " + cliContext.getTxServer());
ValidationEngine validator = new ValidationEngine(definitions, cliContext.getTxServer(), cliContext.getTxLog(), FhirPublication.fromCode(cliContext.getSv()), cliContext.getSv());
public static ValidationEngine getValidator(CliContext cliContext, String definitions, TimeTracker tt) throws Exception {
tt.milestone();
System.out.print(" Load FHIR v" + cliContext.getSv() + " from " + definitions);
FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());
ValidationEngine validator = new ValidationEngine(definitions, ver, cliContext.getSv(), tt);
System.out.println(" - "+validator.getContext().countAllCaches()+" resources ("+tt.milestone()+")");
System.out.print(" Terminology server " + cliContext.getTxServer());
String txver = validator.setTerminologyServer(cliContext.getTxServer(), cliContext.getTxLog(), ver);
System.out.println(" - Version "+txver+" ("+tt.milestone()+")");
validator.setDebug(cliContext.isDoDebug());
System.out.println(" (v" + validator.getContext().getVersion() + ")");
for (String src : cliContext.getIgs()) {
System.out.println("+ .. load IG from " + src);
validator.loadIg(src, cliContext.isRecursive());
}
System.out.print(" Get set... ");
validator.setQuestionnaires(cliContext.getQuestionnaires());
validator.setNative(cliContext.isDoNative());
validator.setHintAboutNonMustSupport(cliContext.isHintAboutNonMustSupport());
@ -218,10 +219,13 @@ public class ValidationService {
validator.setFetcher(new StandAloneValidatorFetcher(validator.getPcm(), validator.getContext(), validator));
validator.getBundleValidationRules().addAll(cliContext.getBundleValidationRules());
TerminologyCache.setNoCaching(cliContext.isNoInternalCaching());
validator.prepare(); // generate any missing snapshots
System.out.println(" go ("+tt.milestone()+")");
return validator;
}
public static int displayOperationOutcome(OperationOutcome oo) {
public static int displayOperationOutcome(OperationOutcome oo, boolean hasMultiples) {
int error = 0;
int warn = 0;
int info = 0;
@ -235,12 +239,24 @@ public class ValidationService {
else
info++;
}
System.out.println((error == 0 ? "Success..." : "*FAILURE* ") + "validating " + file + ": " + " error:" + Integer.toString(error) + " warn:" + Integer.toString(warn) + " info:" + Integer.toString(info));
if (hasMultiples) {
System.out.print("-- ");
System.out.print(file);
System.out.print(" --");
System.out.println(Utilities.padLeft("", '-', Integer.max(38, file.length()+6)));
}
System.out.println((error == 0 ? "Success" : "*FAILURE*") + ": " + Integer.toString(error) + " errors, " + Integer.toString(warn) + " warnings, " + Integer.toString(info)+" notes");
for (OperationOutcome.OperationOutcomeIssueComponent issue : oo.getIssue()) {
System.out.println(getIssueSummary(issue));
}
System.out.println();
if (hasMultiples) {
System.out.print("---");
System.out.print(Utilities.padLeft("", '-', file.length()));
System.out.print("---");
System.out.println(Utilities.padLeft("", '-', Integer.max(38, file.length()+6)));
System.out.println();
}
return error;
}

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Common.java
View File

@ -2,6 +2,7 @@ package org.hl7.fhir.validation.cli.utils;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine;
@ -80,13 +81,15 @@ public class Common {
/**
* Default validation engine will point to "http://tx.fhir.org" terminology server.
*/
public static ValidationEngine getValidationEngine(String version, String definitions, String txLog) throws Exception {
return getValidationEngine(version, DEFAULT_TX_SERVER, definitions, txLog);
public static ValidationEngine getValidationEngine(String version, String definitions, String txLog, TimeTracker tt) throws Exception {
return getValidationEngine(version, DEFAULT_TX_SERVER, definitions, txLog, tt);
}
public static ValidationEngine getValidationEngine(String version, String txServer, String definitions, String txLog) throws Exception {
public static ValidationEngine getValidationEngine(String version, String txServer, String definitions, String txLog, TimeTracker tt) throws Exception {
System.out.println("Loading (v = " + version + ", tx server -> " + txServer + ")");
return new ValidationEngine(definitions, txServer, txLog, FhirPublication.fromCode(version), version);
ValidationEngine ve = new ValidationEngine(definitions, FhirPublication.fromCode(version), version, tt);
ve.connectToTSServer(txServer, txLog, FhirPublication.fromCode(version));
return ve;
}
}

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
View File

@ -15,12 +15,12 @@ import java.io.IOException;
public class Display {
public static void printCliArgumentsAndInfo(String[] args) throws IOException {
System.out.print("Arguments:");
System.out.println(" Paths: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).getFolder());
System.out.print(" Params:");
for (String s : args) {
System.out.print(s.contains(" ") ? " \"" + s + "\"" : " " + s);
}
System.out.println();
System.out.println("Directories: Current = " + System.getProperty("user.dir") + ", Package Cache = " + new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).getFolder());
}
public static void displayHelpDetails() {

25
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ValidatorHostContext.java
View File

@ -4,16 +4,21 @@ import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Stack;
public class ValidatorHostContext {
private Object appContext;
private Element container; // bundle, or parameters
private Element resource;
// the resource we are actually validating right now
private Element resource;
// the resource that is the scope of id resolution - either the same as resource, or the resource the contains that resource. This can only be one level deep.
private Element rootResource;
private StructureDefinition profile; // the profile that contains the content being validated
private boolean checkSpecials = true;
private Map<String, List<ValidationMessage>> sliceRecords;
@ -26,6 +31,7 @@ public class ValidatorHostContext {
this.appContext = appContext;
this.resource = element;
this.rootResource = element;
// no container
}
public Object getAppContext() {
@ -37,15 +43,6 @@ public class ValidatorHostContext {
return this;
}
public Element getContainer() {
return container;
}
public ValidatorHostContext setContainer(Element container) {
this.container = container;
return this;
}
public ValidatorHostContext setResource(Element resource) {
this.resource = resource;
return this;
@ -98,7 +95,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.rootResource = resource;
res.resource = element;
res.container = resource;
res.profile = profile;
return res;
}
@ -107,7 +103,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.rootResource = element;
res.resource = element;
res.container = resource;
res.profile = profile;
return res;
}
@ -116,7 +111,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.resource = resource;
res.rootResource = rootResource;
res.container = container;
res.profile = profile;
res.sliceRecords = sliceRecords != null ? sliceRecords : new HashMap<String, List<ValidationMessage>>();
return res;
@ -126,7 +120,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.resource = resource;
res.rootResource = resource;
res.container = container;
res.profile = profile;
res.checkSpecials = false;
return res;
@ -136,7 +129,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.resource = resource;
res.rootResource = resource;
res.container = resource;
res.profile = profile;
res.checkSpecials = false;
return res;
@ -146,7 +138,6 @@ public class ValidatorHostContext {
ValidatorHostContext res = new ValidatorHostContext(appContext);
res.resource = resource;
res.rootResource = resource;
res.container = resource;
res.profile = profile;
res.checkSpecials = false;
res.sliceRecords = new HashMap<String, List<ValidationMessage>>();