Cleaning up validator
This commit is contained in:
markiantorno
parent
a31ce48e6e
commit
0e45efb766
|
|
@ -48,46 +48,12 @@ POSSIBILITY OF SUCH DAMAGE.
|
|||
|
||||
*/
|
||||
|
||||
import java.awt.Desktop;
|
||||
import java.io.File;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Locale;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.UUID;
|
||||
|
||||
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities;
|
||||
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities.CapabilityStatementComparisonOutput;
|
||||
import org.hl7.fhir.r5.conformance.ProfileComparer;
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
|
||||
import org.hl7.fhir.r5.formats.IParser;
|
||||
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.model.Bundle;
|
||||
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.r5.model.CapabilityStatement;
|
||||
import org.hl7.fhir.r5.model.DomainResource;
|
||||
import org.hl7.fhir.r5.model.FhirPublication;
|
||||
import org.hl7.fhir.r5.model.ImplementationGuide;
|
||||
import org.hl7.fhir.r5.model.CanonicalResource;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome;
|
||||
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.r5.utils.KeyGenerator;
|
||||
import org.hl7.fhir.r5.utils.ToolingExtensions;
|
||||
import org.hl7.fhir.validation.ValidationEngine.ScanOutputItem;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.VersionUtilities;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage;
|
||||
import org.hl7.fhir.validation.cliutils.*;
|
||||
|
||||
/**
|
||||
|
|
@ -128,365 +94,67 @@ public class Validator {
|
|||
public static void main(String[] args) throws Exception {
|
||||
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");
|
||||
String proxy = getNamedParam(args, "-proxy");
|
||||
String proxy = getNamedParam(args, Params.PROXY);
|
||||
if (!Utilities.noString(proxy)) {
|
||||
String[] p = proxy.split("\\:");
|
||||
System.setProperty("http.proxyHost", p[0]);
|
||||
System.setProperty("http.proxyPort", p[1]);
|
||||
}
|
||||
|
||||
if (ParamUtils.hasParam(args, "-tests")) {
|
||||
Utils.runValidationEngineTests();
|
||||
} else if (args.length == 0 || ParamUtils.hasParam(args, "help") || ParamUtils.hasParam(args, "?") || ParamUtils.hasParam(args, "-?") || ParamUtils.hasParam(args, "/?")) {
|
||||
DisplayUtils.displayHelpDetails();
|
||||
} else if (ParamUtils.hasParam(args, "-compare")) {
|
||||
DisplayUtils.printCliArgumentsAndInfo(args);
|
||||
String dest = ParamUtils.getParam(args, "-dest");
|
||||
if (Params.hasParam(args, Params.TEST)) {
|
||||
Common.runValidationEngineTests();
|
||||
} else if (args.length == 0 || Params.hasParam(args, Params.HELP) || Params.hasParam(args, "?") || Params.hasParam(args, "-?") || Params.hasParam(args, "/?")) {
|
||||
Display.displayHelpDetails();
|
||||
} else if (Params.hasParam(args, Params.COMPARE)) {
|
||||
Display.printCliArgumentsAndInfo(args);
|
||||
String dest = Params.getParam(args, Params.DESTINATION);
|
||||
if (dest == null)
|
||||
System.out.println("no -dest parameter provided");
|
||||
else if (!new File(dest).isDirectory())
|
||||
System.out.println("Specified destination (-dest parameter) is not valid: \"" + dest + "\")");
|
||||
else {
|
||||
// first, prepare the context
|
||||
String txLog = Utils.getTerminologyServerLog(args);
|
||||
ValidationEngine validator = Utils.getValidationEngine(args, txLog);
|
||||
Utils.checkIGFileReferences(args);
|
||||
ComparisonUtils.doLeftRightComparison(args, dest, validator);
|
||||
String txLog = Common.getTerminologyServerLog(args);
|
||||
ValidationEngine validator = Common.getValidationEngine(args, txLog);
|
||||
Common.checkIGFileReferences(args);
|
||||
Comparison.doLeftRightComparison(args, dest, validator);
|
||||
}
|
||||
} else {
|
||||
DisplayUtils.printCliArgumentsAndInfo(args);
|
||||
|
||||
String map = null;
|
||||
List<String> igs = new ArrayList<String>();
|
||||
List<String> questionnaires = new ArrayList<String>();
|
||||
String txServer = "http://tx.fhir.org";
|
||||
boolean doNative = false;
|
||||
boolean anyExtensionsAllowed = true;
|
||||
boolean hintAboutNonMustSupport = false;
|
||||
boolean recursive = false;
|
||||
Locale locale = null;
|
||||
List<String> profiles = new ArrayList<String>();
|
||||
EngineMode mode = EngineMode.VALIDATION;
|
||||
String output = null;
|
||||
Boolean canDoNative = null;
|
||||
List<String> sources = new ArrayList<String>();
|
||||
Map<String, String> locations = new HashMap<String, String>();
|
||||
String sv = "current";
|
||||
String txLog = null;
|
||||
String mapLog = null;
|
||||
String lang = null;
|
||||
String fhirpath = null;
|
||||
String snomedCT = "900000000000207008";
|
||||
String targetVer = null;
|
||||
boolean doDebug = false;
|
||||
boolean assumeValidRestReferences = false;
|
||||
|
||||
// load the parameters - so order doesn't matter
|
||||
for (int i = 0; i < args.length; i++) {
|
||||
if (args[i].equals("-version")) {
|
||||
sv = args[++i];
|
||||
sv = VersionUtilities.getCurrentPackageVersion(sv);
|
||||
} else if (args[i].equals("-output")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -output without indicating output file");
|
||||
else
|
||||
output = args[++i];
|
||||
} else if (args[i].equals("-proxy")) {
|
||||
i++; // ignore next parameter
|
||||
} else if (args[i].equals("-profile")) {
|
||||
String p = null;
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -profile without indicating profile source");
|
||||
else {
|
||||
p = args[++i];
|
||||
profiles.add(p);
|
||||
}
|
||||
if (p != null && i + 1 < args.length && args[i + 1].equals("@")) {
|
||||
i++;
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -profile with @ without indicating profile location");
|
||||
else
|
||||
locations.put(p, args[++i]);
|
||||
}
|
||||
} else if (args[i].equals("-questionnaire")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -questionnaire without indicating questionnaire file");
|
||||
else
|
||||
questionnaires.add(args[++i]);
|
||||
} else if (args[i].equals("-native")) {
|
||||
doNative = true;
|
||||
} else if (args[i].equals("-assumeValidRestReferences")) {
|
||||
assumeValidRestReferences = true;
|
||||
} else if (args[i].equals("-debug")) {
|
||||
doDebug = true;
|
||||
} else if (args[i].equals("-sct")) {
|
||||
String s = args[++i];
|
||||
snomedCT = SnomedVersion.resolveSnomedCTCode(s);
|
||||
} else if (args[i].equals("-recurse")) {
|
||||
recursive = true;
|
||||
} else if (args[i].equals("-locale")) {
|
||||
if (i + 1 == args.length) {
|
||||
throw new Error("Specified -locale without indicating locale");
|
||||
} else {
|
||||
locale = new Locale(args[++i]);
|
||||
}
|
||||
} else if (args[i].equals("-strictExtensions")) {
|
||||
anyExtensionsAllowed = false;
|
||||
} else if (args[i].equals("-hintAboutNonMustSupport")) {
|
||||
hintAboutNonMustSupport = true;
|
||||
} else if (args[i].equals("-to-version")) {
|
||||
targetVer = args[++i];
|
||||
mode = EngineMode.VERSION;
|
||||
} else if (args[i].equals("-do-native")) {
|
||||
canDoNative = true;
|
||||
} else if (args[i].equals("-no-native")) {
|
||||
canDoNative = false;
|
||||
} else if (args[i].equals("-transform")) {
|
||||
map = args[++i];
|
||||
mode = EngineMode.TRANSFORM;
|
||||
} else if (args[i].equals("-narrative")) {
|
||||
mode = EngineMode.NARRATIVE;
|
||||
} else if (args[i].equals("-snapshot")) {
|
||||
mode = EngineMode.SNAPSHOT;
|
||||
} else if (args[i].equals("-scan")) {
|
||||
mode = EngineMode.SCAN;
|
||||
} else if (args[i].equals("-tx")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -tx without indicating terminology server");
|
||||
else
|
||||
txServer = "n/a".equals(args[++i]) ? null : args[i];
|
||||
} else if (args[i].equals("-txLog")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -txLog without indicating file");
|
||||
else
|
||||
txLog = args[++i];
|
||||
} else if (args[i].equals("-log")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -log without indicating file");
|
||||
else
|
||||
mapLog = args[++i];
|
||||
} else if (args[i].equals("-language")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -language without indicating language");
|
||||
else
|
||||
lang = args[++i];
|
||||
} else if (args[i].equals("-ig") || args[i].equals("-defn")) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified " + args[i] + " without indicating ig file");
|
||||
else {
|
||||
String s = args[++i];
|
||||
sv = Utils.getVersionFromIGName(null, s);
|
||||
if (sv == null) {
|
||||
igs.add(s);
|
||||
}
|
||||
}
|
||||
} else if (args[i].equals("-map")) {
|
||||
if (map == null) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -map without indicating map file");
|
||||
else
|
||||
map = args[++i];
|
||||
} else {
|
||||
throw new Exception("Can only nominate a single -map parameter");
|
||||
}
|
||||
} else if (args[i].startsWith("-x")) {
|
||||
i++;
|
||||
} else if (args[i].equals("-convert")) {
|
||||
mode = EngineMode.CONVERT;
|
||||
} else if (args[i].equals("-fhirpath")) {
|
||||
mode = EngineMode.FHIRPATH;
|
||||
if (fhirpath == null)
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -fhirpath without indicating a FHIRPath expression");
|
||||
else
|
||||
fhirpath = args[++i];
|
||||
else
|
||||
throw new Exception("Can only nominate a single -fhirpath parameter");
|
||||
} else {
|
||||
sources.add(args[i]);
|
||||
}
|
||||
}
|
||||
if (sources.isEmpty())
|
||||
throw new Exception("Must provide at least one source file");
|
||||
Display.printCliArgumentsAndInfo(args);
|
||||
CliContext cliContext = Params.loadCliContext(args);
|
||||
|
||||
// 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(sv) + "#" + VersionUtilities.getCurrentVersion(sv);
|
||||
System.out.println(" .. FHIR Version " + sv + ", definitions from " + definitions);
|
||||
System.out.println(" .. connect to tx server @ " + txServer);
|
||||
ValidationEngine validator = new ValidationEngine(definitions, txServer, txLog, FhirPublication.fromCode(sv), sv);
|
||||
validator.setDebug(doDebug);
|
||||
System.out.println(" (v" + validator.getContext().getVersion() + ")");
|
||||
for (String src : igs) {
|
||||
System.out.println("+ .. load IG from " + src);
|
||||
validator.loadIg(src, recursive);
|
||||
}
|
||||
validator.setQuestionnaires(questionnaires);
|
||||
validator.setNative(doNative);
|
||||
validator.setHintAboutNonMustSupport(hintAboutNonMustSupport);
|
||||
validator.setAnyExtensionsAllowed(anyExtensionsAllowed);
|
||||
validator.setLanguage(lang);
|
||||
validator.setLocale(locale);
|
||||
validator.setSnomedExtension(snomedCT);
|
||||
validator.setAssumeValidRestReferences(assumeValidRestReferences);
|
||||
String definitions = VersionUtilities.packageForVersion(cliContext.getSv()) + "#" + VersionUtilities.getCurrentVersion(cliContext.getSv());
|
||||
ValidationEngine validator = ValidationUtils.getValidator(cliContext, definitions);
|
||||
|
||||
IParser x;
|
||||
if (output != null && output.endsWith(".json"))
|
||||
x = new JsonParser();
|
||||
else
|
||||
x = new XmlParser();
|
||||
x.setOutputStyle(OutputStyle.PRETTY);
|
||||
|
||||
if (mode == EngineMode.VERSION) {
|
||||
if (sources.size() > 1) {
|
||||
throw new Exception("Can only have one source when converting versions (found " + sources + ")");
|
||||
}
|
||||
if (targetVer == null) {
|
||||
throw new Exception("Must provide a map when converting versions");
|
||||
}
|
||||
if (output == null) {
|
||||
throw new Exception("Must nominate an output when converting versions");
|
||||
}
|
||||
try {
|
||||
if (mapLog != null) {
|
||||
validator.setMapLog(mapLog);
|
||||
}
|
||||
byte[] r = validator.transformVersion(sources.get(0), targetVer, output.endsWith(".json") ? FhirFormat.JSON : FhirFormat.XML, canDoNative);
|
||||
System.out.println(" ...success");
|
||||
TextFile.bytesToFile(r, output);
|
||||
} catch (Exception e) {
|
||||
System.out.println(" ...Failure: " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
}
|
||||
} else if (mode == EngineMode.TRANSFORM) {
|
||||
if (sources.size() > 1)
|
||||
throw new Exception("Can only have one source when doing a transform (found " + sources + ")");
|
||||
if (txServer == null)
|
||||
throw new Exception("Must provide a terminology server when doing a transform");
|
||||
if (map == null)
|
||||
throw new Exception("Must provide a map when doing a transform");
|
||||
try {
|
||||
validator.setMapLog(mapLog);
|
||||
org.hl7.fhir.r5.elementmodel.Element r = validator.transform(sources.get(0), map);
|
||||
System.out.println(" ...success");
|
||||
if (output != null) {
|
||||
FileOutputStream s = new FileOutputStream(output);
|
||||
if (output != null && output.endsWith(".json"))
|
||||
new org.hl7.fhir.r5.elementmodel.JsonParser(validator.getContext()).compose(r, s, OutputStyle.PRETTY, null);
|
||||
else
|
||||
new org.hl7.fhir.r5.elementmodel.XmlParser(validator.getContext()).compose(r, s, OutputStyle.PRETTY, null);
|
||||
s.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
System.out.println(" ...Failure: " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
}
|
||||
} else if (mode == EngineMode.NARRATIVE) {
|
||||
DomainResource r = validator.generate(sources.get(0), sv);
|
||||
System.out.println(" ...generated narrative successfully");
|
||||
if (output != null) {
|
||||
validator.handleOutput(r, output, sv);
|
||||
}
|
||||
} else if (mode == EngineMode.SNAPSHOT) {
|
||||
StructureDefinition r = validator.snapshot(sources.get(0), sv);
|
||||
System.out.println(" ...generated snapshot successfully");
|
||||
if (output != null) {
|
||||
validator.handleOutput(r, output, sv);
|
||||
}
|
||||
} else if (mode == EngineMode.CONVERT) {
|
||||
validator.convert(sources.get(0), output);
|
||||
System.out.println(" ...convert");
|
||||
} else if (mode == EngineMode.FHIRPATH) {
|
||||
System.out.println(" ...evaluating " + fhirpath);
|
||||
System.out.println(validator.evaluateFhirPath(sources.get(0), fhirpath));
|
||||
if (cliContext.getMode() == EngineMode.VERSION) {
|
||||
ValidationUtils.transformVersion(cliContext, validator);
|
||||
} else if (cliContext.getMode() == EngineMode.TRANSFORM) {
|
||||
ValidationUtils.transform(cliContext, validator);
|
||||
} else if (cliContext.getMode() == EngineMode.NARRATIVE) {
|
||||
ValidationUtils.generateNarrative(cliContext, validator);
|
||||
} else if (cliContext.getMode() == EngineMode.SNAPSHOT) {
|
||||
ValidationUtils.generateSnapshot(cliContext, validator);
|
||||
} else if (cliContext.getMode() == EngineMode.CONVERT) {
|
||||
ValidationUtils.convertSources(cliContext, validator);
|
||||
} else if (cliContext.getMode() == EngineMode.FHIRPATH) {
|
||||
ValidationUtils.evaluateFhirpath(cliContext, validator);
|
||||
} else {
|
||||
if (definitions == null)
|
||||
if (definitions == null) {
|
||||
throw new Exception("Must provide a defn when doing validation");
|
||||
for (String s : profiles) {
|
||||
}
|
||||
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);
|
||||
validator.loadProfile(locations.getOrDefault(s, s));
|
||||
validator.loadProfile(cliContext.getLocations().getOrDefault(s, s));
|
||||
}
|
||||
}
|
||||
if (mode == EngineMode.SCAN) {
|
||||
if (Utilities.noString(output))
|
||||
throw new Exception("Output parameter required when scanning");
|
||||
if (!(new File(output).isDirectory()))
|
||||
throw new Exception("Output '" + output + "' must be a directory when scanning");
|
||||
System.out.println(" .. scan " + sources + " against loaded IGs");
|
||||
Set<String> urls = new HashSet<>();
|
||||
for (ImplementationGuide ig : validator.getContext().allImplementationGuides()) {
|
||||
if (ig.getUrl().contains("/ImplementationGuide") && !ig.getUrl().equals("http://hl7.org/fhir/ImplementationGuide/fhir"))
|
||||
urls.add(ig.getUrl());
|
||||
}
|
||||
List<ScanOutputItem> res = validator.validateScan(sources, urls);
|
||||
validator.genScanOutput(output, res);
|
||||
System.out.println("Done. output in " + Utilities.path(output, "scan.html"));
|
||||
if (cliContext.getMode() == EngineMode.SCAN) {
|
||||
ValidationUtils.validateScan(cliContext, validator);
|
||||
} else {
|
||||
if (profiles.size() > 0)
|
||||
System.out.println(" .. validate " + sources + " against " + profiles.toString());
|
||||
else
|
||||
System.out.println(" .. validate " + sources);
|
||||
validator.prepare(); // generate any missing snapshots
|
||||
Resource r = validator.validate(sources, profiles);
|
||||
int ec = 0;
|
||||
if (output == null) {
|
||||
if (r instanceof Bundle)
|
||||
for (BundleEntryComponent e : ((Bundle) r).getEntry())
|
||||
ec = displayOO((OperationOutcome) e.getResource()) + ec;
|
||||
else
|
||||
ec = displayOO((OperationOutcome) r);
|
||||
} else {
|
||||
FileOutputStream s = new FileOutputStream(output);
|
||||
x.compose(s, r);
|
||||
s.close();
|
||||
}
|
||||
System.exit(ec > 0 ? 1 : 0);
|
||||
ValidationUtils.validateSources(cliContext, validator);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static String getGitBuild() {
|
||||
return "??";
|
||||
}
|
||||
|
||||
private static int displayOO(OperationOutcome oo) {
|
||||
int error = 0;
|
||||
int warn = 0;
|
||||
int info = 0;
|
||||
String file = ToolingExtensions.readStringExtension(oo, ToolingExtensions.EXT_OO_FILE);
|
||||
|
||||
for (OperationOutcomeIssueComponent issue : oo.getIssue()) {
|
||||
if (issue.getSeverity() == OperationOutcome.IssueSeverity.FATAL || issue.getSeverity() == OperationOutcome.IssueSeverity.ERROR)
|
||||
error++;
|
||||
else if (issue.getSeverity() == OperationOutcome.IssueSeverity.WARNING)
|
||||
warn++;
|
||||
else
|
||||
info++;
|
||||
}
|
||||
|
||||
System.out.println((error == 0 ? "Success..." : "*FAILURE* ") + "validating " + file + ": " + " error:" + Integer.toString(error) + " warn:" + Integer.toString(warn) + " info:" + Integer.toString(info));
|
||||
for (OperationOutcomeIssueComponent issue : oo.getIssue()) {
|
||||
System.out.println(getIssueSummary(issue));
|
||||
}
|
||||
System.out.println();
|
||||
return error;
|
||||
}
|
||||
|
||||
private static String getIssueSummary(OperationOutcomeIssueComponent issue) {
|
||||
String loc = null;
|
||||
if (issue.hasExpression()) {
|
||||
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
|
||||
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
|
||||
loc = issue.getExpression().get(0).asStringValue() + (line >= 0 && col >= 0 ? " (line " + Integer.toString(line) + ", col" + Integer.toString(col) + ")" : "");
|
||||
} else if (issue.hasLocation()) {
|
||||
loc = issue.getLocation().get(0).asStringValue();
|
||||
} else {
|
||||
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
|
||||
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
|
||||
loc = (line >= 0 && col >= 0 ? "line " + Integer.toString(line) + ", col" + Integer.toString(col) : "??");
|
||||
}
|
||||
return " " + issue.getSeverity().getDisplay() + " @ " + loc + " : " + issue.getDetails().getText();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,6 +4,9 @@ import org.hl7.fhir.validation.Validator;
|
|||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* A POJO for storing the flags/values for the CLI validator.
|
||||
*/
|
||||
public class CliContext {
|
||||
|
||||
private String map = null;
|
||||
|
|
@ -26,8 +29,261 @@ public class CliContext {
|
|||
private String mapLog = null;
|
||||
private String lang = null;
|
||||
private String fhirpath = null;
|
||||
private String snomedCT = "900000000000207008";
|
||||
private String snomedCT = SnomedVersion.INTL.getCode();
|
||||
private String targetVer = null;
|
||||
private boolean doDebug = false;
|
||||
private boolean assumeValidRestReferences = false;
|
||||
|
||||
public String getMap() {
|
||||
return map;
|
||||
}
|
||||
|
||||
public CliContext setMap(String map) {
|
||||
this.map = map;
|
||||
return this;
|
||||
}
|
||||
|
||||
public List<String> getIgs() {
|
||||
return igs;
|
||||
}
|
||||
|
||||
public CliContext setIgs(List<String> igs) {
|
||||
this.igs = igs;
|
||||
return this;
|
||||
}
|
||||
|
||||
public CliContext addIg(String ig) {
|
||||
if (this.igs == null) {
|
||||
this.igs = new ArrayList<>();
|
||||
}
|
||||
this.igs.add(ig);
|
||||
return this;
|
||||
}
|
||||
|
||||
public List<String> getQuestionnaires() {
|
||||
return questionnaires;
|
||||
}
|
||||
|
||||
public CliContext setQuestionnaires(List<String> questionnaires) {
|
||||
this.questionnaires = questionnaires;
|
||||
return this;
|
||||
}
|
||||
|
||||
public CliContext addQuestionnaire(String questionnaire) {
|
||||
if (this.questionnaires == null) {
|
||||
this.questionnaires = new ArrayList<>();
|
||||
}
|
||||
this.questionnaires.add(questionnaire);
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getTxServer() {
|
||||
return txServer;
|
||||
}
|
||||
|
||||
public CliContext setTxServer(String txServer) {
|
||||
this.txServer = txServer;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isDoNative() {
|
||||
return doNative;
|
||||
}
|
||||
|
||||
public CliContext setDoNative(boolean doNative) {
|
||||
this.doNative = doNative;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isAnyExtensionsAllowed() {
|
||||
return anyExtensionsAllowed;
|
||||
}
|
||||
|
||||
public CliContext setAnyExtensionsAllowed(boolean anyExtensionsAllowed) {
|
||||
this.anyExtensionsAllowed = anyExtensionsAllowed;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isHintAboutNonMustSupport() {
|
||||
return hintAboutNonMustSupport;
|
||||
}
|
||||
|
||||
public CliContext setHintAboutNonMustSupport(boolean hintAboutNonMustSupport) {
|
||||
this.hintAboutNonMustSupport = hintAboutNonMustSupport;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isRecursive() {
|
||||
return recursive;
|
||||
}
|
||||
|
||||
public CliContext setRecursive(boolean recursive) {
|
||||
this.recursive = recursive;
|
||||
return this;
|
||||
}
|
||||
|
||||
public Locale getLocale() {
|
||||
return locale;
|
||||
}
|
||||
|
||||
public CliContext setLocale(Locale locale) {
|
||||
this.locale = locale;
|
||||
return this;
|
||||
}
|
||||
|
||||
public List<String> getProfiles() {
|
||||
return profiles;
|
||||
}
|
||||
|
||||
public CliContext setProfiles(List<String> profiles) {
|
||||
this.profiles = profiles;
|
||||
return this;
|
||||
}
|
||||
|
||||
public CliContext addProfile(String profile) {
|
||||
if (this.profiles == null) {
|
||||
this.profiles = new ArrayList<>();
|
||||
}
|
||||
this.profiles.add(profile);
|
||||
return this;
|
||||
}
|
||||
|
||||
public Validator.EngineMode getMode() {
|
||||
return mode;
|
||||
}
|
||||
|
||||
public CliContext setMode(Validator.EngineMode mode) {
|
||||
this.mode = mode;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getOutput() {
|
||||
return output;
|
||||
}
|
||||
|
||||
public CliContext setOutput(String output) {
|
||||
this.output = output;
|
||||
return this;
|
||||
}
|
||||
|
||||
public Boolean getCanDoNative() {
|
||||
return canDoNative;
|
||||
}
|
||||
|
||||
public CliContext setCanDoNative(Boolean canDoNative) {
|
||||
this.canDoNative = canDoNative;
|
||||
return this;
|
||||
}
|
||||
|
||||
public List<String> getSources() {
|
||||
return sources;
|
||||
}
|
||||
|
||||
public CliContext setSources(List<String> sources) {
|
||||
this.sources = sources;
|
||||
return this;
|
||||
}
|
||||
|
||||
public CliContext addSource(String source) {
|
||||
if (this.sources == null) {
|
||||
this.sources = new ArrayList<>();
|
||||
}
|
||||
this.sources.add(source);
|
||||
return this;
|
||||
}
|
||||
|
||||
public Map<String, String> getLocations() {
|
||||
return locations;
|
||||
}
|
||||
|
||||
public CliContext setLocations(Map<String, String> locations) {
|
||||
this.locations = locations;
|
||||
return this;
|
||||
}
|
||||
|
||||
public CliContext addLocation(String profile, String location) {
|
||||
this.locations.put(profile, location);
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getSv() {
|
||||
return sv;
|
||||
}
|
||||
|
||||
public CliContext setSv(String sv) {
|
||||
this.sv = sv;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getTxLog() {
|
||||
return txLog;
|
||||
}
|
||||
|
||||
public CliContext setTxLog(String txLog) {
|
||||
this.txLog = txLog;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getMapLog() {
|
||||
return mapLog;
|
||||
}
|
||||
|
||||
public CliContext setMapLog(String mapLog) {
|
||||
this.mapLog = mapLog;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getLang() {
|
||||
return lang;
|
||||
}
|
||||
|
||||
public CliContext setLang(String lang) {
|
||||
this.lang = lang;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getFhirpath() {
|
||||
return fhirpath;
|
||||
}
|
||||
|
||||
public CliContext setFhirpath(String fhirpath) {
|
||||
this.fhirpath = fhirpath;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getSnomedCT() {
|
||||
return snomedCT;
|
||||
}
|
||||
|
||||
public CliContext setSnomedCT(String snomedCT) {
|
||||
this.snomedCT = SnomedVersion.resolveSnomedCTCode(snomedCT);
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getTargetVer() {
|
||||
return targetVer;
|
||||
}
|
||||
|
||||
public CliContext setTargetVer(String targetVer) {
|
||||
this.targetVer = targetVer;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isDoDebug() {
|
||||
return doDebug;
|
||||
}
|
||||
|
||||
public CliContext setDoDebug(boolean doDebug) {
|
||||
this.doDebug = doDebug;
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean isAssumeValidRestReferences() {
|
||||
return assumeValidRestReferences;
|
||||
}
|
||||
|
||||
public CliContext setAssumeValidRestReferences(boolean assumeValidRestReferences) {
|
||||
this.assumeValidRestReferences = assumeValidRestReferences;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,19 +1,16 @@
|
|||
package org.hl7.fhir.validation.cliutils;
|
||||
|
||||
import org.hl7.fhir.r5.context.SimpleWorkerContext;
|
||||
import org.hl7.fhir.r5.model.Constants;
|
||||
import org.hl7.fhir.r5.model.FhirPublication;
|
||||
import org.hl7.fhir.r5.model.Resource;
|
||||
import org.hl7.fhir.utilities.VersionUtilities;
|
||||
import org.hl7.fhir.validation.ValidationEngine;
|
||||
|
||||
import java.io.File;
|
||||
|
||||
public class Utils {
|
||||
|
||||
public class Common {
|
||||
|
||||
public static String getVersion(String[] args) {
|
||||
String v = ParamUtils.getParam(args, "-version");
|
||||
String v = Params.getParam(args, "-version");
|
||||
if (v == null) {
|
||||
v = "current";
|
||||
for (int i = 0; i < args.length; i++) {
|
||||
|
|
@ -22,7 +19,7 @@ public class Utils {
|
|||
throw new Error("Specified -ig without indicating ig file");
|
||||
else {
|
||||
String n = args[i + 1];
|
||||
v = Utils.getVersionFromIGName(v, n);
|
||||
v = Common.getVersionFromIGName(v, n);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -42,11 +39,11 @@ public class Utils {
|
|||
|
||||
/**
|
||||
* Evaluates the current implementation guide file name and sets the current version accordingly.
|
||||
*
|
||||
* <p>
|
||||
* If igFileName is not one of the known patterns, will return whatever value is passed in as default.
|
||||
*
|
||||
* @param defaultValue Version to return if no associated version can be determined from passed in igFileName
|
||||
* @param igFileName Name of the implementation guide
|
||||
* @param igFileName Name of the implementation guide
|
||||
* @return
|
||||
*/
|
||||
public static String getVersionFromIGName(String defaultValue, String igFileName) {
|
||||
|
|
@ -82,15 +79,15 @@ public class Utils {
|
|||
|
||||
public static String getTerminologyServerLog(String[] args) {
|
||||
String txLog = null;
|
||||
if (ParamUtils.hasParam(args, "-txLog")) {
|
||||
txLog = ParamUtils.getParam(args, "-txLog");
|
||||
if (Params.hasParam(args, "-txLog")) {
|
||||
txLog = Params.getParam(args, "-txLog");
|
||||
new File(txLog).delete();
|
||||
}
|
||||
return txLog;
|
||||
}
|
||||
|
||||
public static ValidationEngine getValidationEngine(String[] args, String txLog) throws Exception {
|
||||
String v = Utils.getVersion(args);
|
||||
String v = Common.getVersion(args);
|
||||
String definitions = VersionUtilities.packageForVersion(v) + "#" + v;
|
||||
System.out.println("Loading (v = " + v + ", tx server http://tx.fhir.org)");
|
||||
return new ValidationEngine(definitions, "http://tx.fhir.org", txLog, FhirPublication.fromCode(v), v);
|
||||
|
|
@ -110,21 +107,4 @@ public class Utils {
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static Resource loadResource(String[] args, String param, SimpleWorkerContext context) {
|
||||
String resString = ParamUtils.getParam(args, param);
|
||||
Resource resource = context.fetchResource(Resource.class, resString);
|
||||
if (resource == null) {
|
||||
System.out.println("Unable to locate resource for " + param + ", " + resString);
|
||||
}
|
||||
return resource;
|
||||
}
|
||||
|
||||
public static Resource getRightResource(String[] args, SimpleWorkerContext context) {
|
||||
return loadResource(args, "-right", context);
|
||||
}
|
||||
|
||||
public static Resource getLeftResource(String[] args, SimpleWorkerContext context) {
|
||||
return loadResource(args, "-left", context);
|
||||
}
|
||||
}
|
||||
|
|
@ -21,27 +21,27 @@ import java.io.FileOutputStream;
|
|||
import java.io.IOException;
|
||||
import java.util.UUID;
|
||||
|
||||
public class ComparisonUtils {
|
||||
public class Comparison {
|
||||
|
||||
public static void doLeftRightComparison(String[] args, String dest, ValidationEngine validator) throws IOException {
|
||||
// ok now set up the comparison
|
||||
String left = ParamUtils.getParam(args, "-left");
|
||||
String right = ParamUtils.getParam(args, "-right");
|
||||
String left = Params.getParam(args, Params.LEFT);
|
||||
String right = Params.getParam(args, Params.RIGHT);
|
||||
|
||||
Resource resLeft = validator.getContext().fetchResource(Resource.class, left);
|
||||
Resource resLeft = validator.getContext().fetchResource(Resource.class, left);
|
||||
Resource resRight = validator.getContext().fetchResource(Resource.class, right);
|
||||
if (resLeft == null) {
|
||||
System.out.println("Unable to locate left resource " +left);
|
||||
System.out.println("Unable to locate left resource " + left);
|
||||
}
|
||||
if (resRight == null) {
|
||||
System.out.println("Unable to locate right resource " +right);
|
||||
System.out.println("Unable to locate right resource " + right);
|
||||
}
|
||||
|
||||
if (resLeft != null && resRight != null) {
|
||||
if (resLeft instanceof StructureDefinition && resRight instanceof StructureDefinition) {
|
||||
ComparisonUtils.compareStructureDefinitions(dest, validator, left, right, (StructureDefinition) resLeft, (StructureDefinition) resRight);
|
||||
Comparison.compareStructureDefinitions(dest, validator, left, right, (StructureDefinition) resLeft, (StructureDefinition) resRight);
|
||||
} else if (resLeft instanceof CapabilityStatement && resRight instanceof CapabilityStatement) {
|
||||
ComparisonUtils.compareCapabilityStatements(args, dest, validator, left, right, (CanonicalResource) resLeft, (CanonicalResource) resRight);
|
||||
Comparison.compareCapabilityStatements(args, dest, validator, left, right, (CanonicalResource) resLeft, (CanonicalResource) resRight);
|
||||
} else
|
||||
System.out.println("Unable to compare left resource " + left + " (" + resLeft.fhirType() + ") with right resource " + right + " (" + resRight.fhirType() + ")");
|
||||
}
|
||||
|
|
@ -90,7 +90,7 @@ public class ComparisonUtils {
|
|||
}
|
||||
|
||||
private static String chooseName(String[] args, String name, CanonicalResource mr) {
|
||||
String s = ParamUtils.getParam(args, "-" + name);
|
||||
String s = Params.getParam(args, "-" + name);
|
||||
if (Utilities.noString(s))
|
||||
s = mr.present();
|
||||
return s;
|
||||
|
|
@ -7,7 +7,7 @@ import org.hl7.fhir.utilities.cache.ToolsVersion;
|
|||
|
||||
import java.io.IOException;
|
||||
|
||||
public class DisplayUtils {
|
||||
public class Display {
|
||||
|
||||
public static void printCliArgumentsAndInfo(String[] args) throws IOException {
|
||||
System.out.print("Arguments:");
|
||||
|
|
@ -27,8 +27,8 @@ public class DisplayUtils {
|
|||
System.out.println("");
|
||||
System.out.println("The FHIR validation tool validates a FHIR resource or bundle.");
|
||||
System.out.println("Schema and schematron checking is performed, then some additional checks are performed. ");
|
||||
System.out.println("* XML & Json (FHIR versions 1.0, 1.4, 3.0, 4.0, "+ Constants.VERSION_MM+")");
|
||||
System.out.println("* Turtle (FHIR versions 3.0, 4.0, "+Constants.VERSION_MM+")");
|
||||
System.out.println("* XML & Json (FHIR versions 1.0, 1.4, 3.0, 4.0, " + Constants.VERSION_MM + ")");
|
||||
System.out.println("* Turtle (FHIR versions 3.0, 4.0, " + Constants.VERSION_MM + ")");
|
||||
System.out.println("");
|
||||
System.out.println("If requested, instances will also be verified against the appropriate schema");
|
||||
System.out.println("W3C XML Schema, JSON schema or ShEx, as appropriate");
|
||||
|
|
@ -43,8 +43,8 @@ public class DisplayUtils {
|
|||
System.out.println(" Patterns are limited to a directory followed by a filename with an embedded");
|
||||
System.out.println(" asterisk. E.g. foo*-examples.xml or someresource.*, etc.");
|
||||
System.out.println("-version [ver]: The FHIR version to use. This can only appear once. ");
|
||||
System.out.println(" valid values 1.0 | 1.4 | 3.0 | "+ VersionUtilities.CURRENT_VERSION+" or 1.0.2 | 1.4.0 | 3.0.2 | 4.0.1 | "+VersionUtilities.CURRENT_FULL_VERSION);
|
||||
System.out.println(" Default value is "+VersionUtilities.CURRENT_VERSION);
|
||||
System.out.println(" valid values 1.0 | 1.4 | 3.0 | " + VersionUtilities.CURRENT_VERSION + " or 1.0.2 | 1.4.0 | 3.0.2 | 4.0.1 | " + VersionUtilities.CURRENT_FULL_VERSION);
|
||||
System.out.println(" Default value is " + VersionUtilities.CURRENT_VERSION);
|
||||
System.out.println("-ig [package|file|folder|url]: an IG or profile definition to load. Can be ");
|
||||
System.out.println(" the URL of an implementation guide or a package ([id]-[ver]) for");
|
||||
System.out.println(" a built implementation guide or a local folder that contains a");
|
||||
|
|
@ -1,81 +0,0 @@
|
|||
package org.hl7.fhir.validation.cliutils;
|
||||
|
||||
public enum ParamArg {
|
||||
VERSION("-version"),
|
||||
OUTPUT("-output"),
|
||||
PROXY("-proxy"),
|
||||
PROFILE("-profile"),
|
||||
QUESTIONNAIRE("-questionnaire"),
|
||||
NATIVE("-native"),
|
||||
ASSUME_VALID_REST_REF("-assumeValidRestReferences"),
|
||||
DEBUG("-debug"),
|
||||
SCT("-sct"),
|
||||
RECURSE("-recurse"),
|
||||
LOCALE("-locale"),
|
||||
STRICT_EXTENSIONS("-strictExtensions"),
|
||||
HINT_ABOUT_NON_MUST_SUPPORT("-hintAboutNonMustSupport"),
|
||||
TO_VERSION("-to-version"),
|
||||
DO_NATIVE("-do-native"),
|
||||
NO_NATIVE("-no-native"),
|
||||
TRANSFORM("-transform"),
|
||||
NARRATIVE("-narrative"),
|
||||
SNAPSHOT("-snapshot"),
|
||||
SCAN("-scan"),
|
||||
TERMINOLOGY("-tx"),
|
||||
TERMINOLOGY_LOG("-txLog");
|
||||
|
||||
private final String code;
|
||||
|
||||
ParamArg(String code) {
|
||||
this.code = code;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
// } else if (args[i].equals("-log")) {
|
||||
// if (i + 1 == args.length)
|
||||
// throw new Error("Specified -log without indicating file");
|
||||
// else
|
||||
// mapLog = args[++i];
|
||||
// } else if (args[i].equals("-language")) {
|
||||
// if (i + 1 == args.length)
|
||||
// throw new Error("Specified -language without indicating language");
|
||||
// else
|
||||
// lang = args[++i];
|
||||
// } else if (args[i].equals("-ig") || args[i].equals("-defn")) {
|
||||
// if (i + 1 == args.length)
|
||||
// throw new Error("Specified " + args[i] + " without indicating ig file");
|
||||
// else {
|
||||
// String s = args[++i];
|
||||
// sv = Utils.getVersionFromIGName(null, s);
|
||||
// if (sv == null) {
|
||||
// igs.add(s);
|
||||
// }
|
||||
// }
|
||||
// } else if (args[i].equals("-map")) {
|
||||
// if (map == null) {
|
||||
// if (i + 1 == args.length)
|
||||
// throw new Error("Specified -map without indicating map file");
|
||||
// else
|
||||
// map = args[++i];
|
||||
// } else {
|
||||
// throw new Exception("Can only nominate a single -map parameter");
|
||||
// }
|
||||
// } else if (args[i].startsWith("-x")) {
|
||||
// i++;
|
||||
// } else if (args[i].equals("-convert")) {
|
||||
// mode = EngineMode.CONVERT;
|
||||
// } else if (args[i].equals("-fhirpath")) {
|
||||
// mode = EngineMode.FHIRPATH;
|
||||
// if (fhirpath == null)
|
||||
// if (i + 1 == args.length)
|
||||
// throw new Error("Specified -fhirpath without indicating a FHIRPath expression");
|
||||
// else
|
||||
// fhirpath = args[++i];
|
||||
// else
|
||||
// throw new Exception("Can only nominate a single -fhirpath parameter");
|
||||
// } else {
|
||||
// sources.add(args[i]);
|
||||
// }
|
||||
// }
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
package org.hl7.fhir.validation.cliutils;
|
||||
|
||||
import java.util.Arrays;
|
||||
|
||||
public class ParamUtils {
|
||||
|
||||
/**
|
||||
* Checks the list of passed in params to see if it contains the passed in param.
|
||||
*
|
||||
* @param args Array of params to search.
|
||||
* @param param {@link String} param to search for.
|
||||
* @return {@link Boolean#TRUE} if the list contains the given param.
|
||||
*/
|
||||
public static boolean hasParam(String[] args, String param) {
|
||||
return Arrays.asList(args).contains(param);
|
||||
}
|
||||
|
||||
/**
|
||||
* Fetches the vlaue for the passed in param from the provided list of params.
|
||||
*
|
||||
* @param args Array of params to search.
|
||||
* @param param {@link String} param keyword to search for.
|
||||
* @return {@link String} value for the provided param.
|
||||
*/
|
||||
public static String getParam(String[] args, String param) {
|
||||
for (int i = 0; i < args.length - 1; i++)
|
||||
if (args[i].equals(param))
|
||||
return args[i + 1];
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,210 @@
|
|||
package org.hl7.fhir.validation.cliutils;
|
||||
|
||||
import org.hl7.fhir.utilities.VersionUtilities;
|
||||
import org.hl7.fhir.validation.Validator;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Locale;
|
||||
|
||||
public class Params {
|
||||
|
||||
public static final String VERSION = "-version";
|
||||
public static final String OUTPUT = "-output";
|
||||
public static final String PROXY = "-proxy";
|
||||
public static final String PROFILE = "-profile";
|
||||
public static final String QUESTIONNAIRE = "-questionnaire";
|
||||
public static final String NATIVE = "-native";
|
||||
public static final String ASSUME_VALID_REST_REF = "-assumeValidRestReferences";
|
||||
public static final String DEBUG = "-debug";
|
||||
public static final String SCT = "-sct";
|
||||
public static final String RECURSE = "-recurse";
|
||||
public static final String LOCALE = "-locale";
|
||||
public static final String STRICT_EXTENSIONS = "-strictExtensions";
|
||||
public static final String HINT_ABOUT_NON_MUST_SUPPORT = "-hintAboutNonMustSupport";
|
||||
public static final String TO_VERSION = "-to-version";
|
||||
public static final String DO_NATIVE = "-do-native";
|
||||
public static final String NO_NATIVE = "-no-native";
|
||||
public static final String TRANSFORM = "-transform";
|
||||
public static final String NARRATIVE = "-narrative";
|
||||
public static final String SNAPSHOT = "-snapshot";
|
||||
public static final String SCAN = "-scan";
|
||||
public static final String TERMINOLOGY = "-tx";
|
||||
public static final String TERMINOLOGY_LOG = "-txLog";
|
||||
public static final String LOG = "-log";
|
||||
public static final String LANGUAGE = "-language";
|
||||
public static final String IMPLEMENTATION_GUIDE = "-ig";
|
||||
public static final String DEFINITION = "defn";
|
||||
public static final String MAP = "-map";
|
||||
public static final String X = "-x";
|
||||
public static final String CONVERT = "-convert";
|
||||
public static final String FHIRPATH = "-fhirpath";
|
||||
public static final String TEST = "-tests";
|
||||
public static final String HELP = "help";
|
||||
public static final String COMPARE = "-compare";
|
||||
public static final String DESTINATION = "-dest";
|
||||
public static final String LEFT = "-left";
|
||||
public static final String RIGHT = "-right";
|
||||
|
||||
/**
|
||||
* Checks the list of passed in params to see if it contains the passed in param.
|
||||
*
|
||||
* @param args Array of params to search.
|
||||
* @param param {@link String} param to search for.
|
||||
* @return {@link Boolean#TRUE} if the list contains the given param.
|
||||
*/
|
||||
public static boolean hasParam(String[] args, String param) {
|
||||
return Arrays.asList(args).contains(param);
|
||||
}
|
||||
|
||||
/**
|
||||
* Fetches the vlaue for the passed in param from the provided list of params.
|
||||
*
|
||||
* @param args Array of params to search.
|
||||
* @param param {@link String} param keyword to search for.
|
||||
* @return {@link String} value for the provided param.
|
||||
*/
|
||||
public static String getParam(String[] args, String param) {
|
||||
for (int i = 0; i < args.length - 1; i++)
|
||||
if (args[i].equals(param))
|
||||
return args[i + 1];
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* TODO Don't do this all in one for loop.
|
||||
*
|
||||
* @param args
|
||||
* @return
|
||||
* @throws Exception
|
||||
*/
|
||||
public static CliContext loadCliContext(String[] args) throws Exception {
|
||||
CliContext cliContext = new CliContext();
|
||||
|
||||
// load the parameters - so order doesn't matter
|
||||
for (int i = 0; i < args.length; i++) {
|
||||
if (args[i].equals(VERSION)) {
|
||||
cliContext.setSv(VersionUtilities.getCurrentPackageVersion(args[++i]));
|
||||
} else if (args[i].equals(OUTPUT)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -output without indicating output file");
|
||||
else
|
||||
cliContext.setOutput(args[++i]);
|
||||
} else if (args[i].equals(PROXY)) {
|
||||
i++; // ignore next parameter
|
||||
} else if (args[i].equals(PROFILE)) {
|
||||
String p = null;
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -profile without indicating profile source");
|
||||
else {
|
||||
p = args[++i];
|
||||
cliContext.addProfile(args[++i]);
|
||||
}
|
||||
if (p != null && i + 1 < args.length && args[i + 1].equals("@")) {
|
||||
i++;
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -profile with @ without indicating profile location");
|
||||
else
|
||||
cliContext.addLocation(p, args[++i]);
|
||||
}
|
||||
} else if (args[i].equals(QUESTIONNAIRE)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -questionnaire without indicating questionnaire file");
|
||||
else
|
||||
cliContext.addQuestionnaire(args[++i]);
|
||||
} else if (args[i].equals(NATIVE)) {
|
||||
cliContext.setDoNative(true);
|
||||
} else if (args[i].equals(ASSUME_VALID_REST_REF)) {
|
||||
cliContext.setAssumeValidRestReferences(true);
|
||||
} else if (args[i].equals(DEBUG)) {
|
||||
cliContext.setDoDebug(true);
|
||||
} else if (args[i].equals(SCT)) {
|
||||
cliContext.setSnomedCT(args[++i]);
|
||||
} else if (args[i].equals(RECURSE)) {
|
||||
cliContext.setRecursive(true);
|
||||
} else if (args[i].equals(LOCALE)) {
|
||||
if (i + 1 == args.length) {
|
||||
throw new Error("Specified -locale without indicating locale");
|
||||
} else {
|
||||
cliContext.setLocale(new Locale(args[++i]));
|
||||
}
|
||||
} else if (args[i].equals(STRICT_EXTENSIONS)) {
|
||||
cliContext.setAnyExtensionsAllowed(false);
|
||||
} else if (args[i].equals(HINT_ABOUT_NON_MUST_SUPPORT)) {
|
||||
cliContext.setHintAboutNonMustSupport(true);
|
||||
} else if (args[i].equals(TO_VERSION)) {
|
||||
cliContext.setTargetVer(args[++i]);
|
||||
cliContext.setMode(Validator.EngineMode.VERSION);
|
||||
} else if (args[i].equals(DO_NATIVE)) {
|
||||
cliContext.setCanDoNative(true);
|
||||
} else if (args[i].equals(NO_NATIVE)) {
|
||||
cliContext.setCanDoNative(false);
|
||||
} else if (args[i].equals(TRANSFORM)) {
|
||||
cliContext.setMap(args[++i]);
|
||||
cliContext.setMode(Validator.EngineMode.TRANSFORM);
|
||||
} else if (args[i].equals(NARRATIVE)) {
|
||||
cliContext.setMode(Validator.EngineMode.NARRATIVE);
|
||||
} else if (args[i].equals(SNAPSHOT)) {
|
||||
cliContext.setMode(Validator.EngineMode.SNAPSHOT);
|
||||
} else if (args[i].equals(SCAN)) {
|
||||
cliContext.setMode(Validator.EngineMode.SCAN);
|
||||
} else if (args[i].equals(TERMINOLOGY)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -tx without indicating terminology server");
|
||||
else
|
||||
cliContext.setTxServer("n/a".equals(args[++i]) ? null : args[i]);
|
||||
} else if (args[i].equals(TERMINOLOGY_LOG)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -txLog without indicating file");
|
||||
else
|
||||
cliContext.setTxLog(args[++i]);
|
||||
} else if (args[i].equals(LOG)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -log without indicating file");
|
||||
else
|
||||
cliContext.setMapLog(args[++i]);
|
||||
} else if (args[i].equals(LANGUAGE)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -language without indicating language");
|
||||
else
|
||||
cliContext.setLang(args[++i]);
|
||||
} else if (args[i].equals(IMPLEMENTATION_GUIDE) || args[i].equals(DEFINITION)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified " + args[i] + " without indicating ig file");
|
||||
else {
|
||||
String s = args[++i];
|
||||
cliContext.setSv(Common.getVersionFromIGName(null, s));
|
||||
if (cliContext.getSv() == null) {
|
||||
cliContext.addIg(s);
|
||||
}
|
||||
}
|
||||
} else if (args[i].equals(MAP)) {
|
||||
if (cliContext.getMap() == null) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -map without indicating map file");
|
||||
else
|
||||
cliContext.setMap(args[++i]);
|
||||
} else {
|
||||
throw new Exception("Can only nominate a single -map parameter");
|
||||
}
|
||||
} else if (args[i].startsWith(X)) {
|
||||
i++;
|
||||
} else if (args[i].equals(CONVERT)) {
|
||||
cliContext.setMode(Validator.EngineMode.CONVERT);
|
||||
} else if (args[i].equals(FHIRPATH)) {
|
||||
cliContext.setMode(Validator.EngineMode.FHIRPATH);
|
||||
if (cliContext.getFhirpath() == null)
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -fhirpath without indicating a FHIRPath expression");
|
||||
else
|
||||
cliContext.setFhirpath(args[++i]);
|
||||
else
|
||||
throw new Exception("Can only nominate a single -fhirpath parameter");
|
||||
} else {
|
||||
cliContext.addSource(args[i]);
|
||||
}
|
||||
}
|
||||
if (cliContext.getSources().isEmpty())
|
||||
throw new Exception("Must provide at least one source file");
|
||||
return cliContext;
|
||||
}
|
||||
}
|
||||
|
|
@ -24,6 +24,14 @@ public enum SnomedVersion {
|
|||
this.code = code;
|
||||
}
|
||||
|
||||
public String getLang() {
|
||||
return lang;
|
||||
}
|
||||
|
||||
public String getCode() {
|
||||
return code;
|
||||
}
|
||||
|
||||
public static String resolveSnomedCTCode(String s) {
|
||||
String foundCode;
|
||||
Optional<SnomedVersion> opt = Arrays.stream(values())
|
||||
|
|
|
|||
|
|
@ -0,0 +1,198 @@
|
|||
package org.hl7.fhir.validation.cliutils;
|
||||
|
||||
import org.hl7.fhir.r5.elementmodel.Manager;
|
||||
import org.hl7.fhir.r5.formats.IParser;
|
||||
import org.hl7.fhir.r5.formats.JsonParser;
|
||||
import org.hl7.fhir.r5.formats.XmlParser;
|
||||
import org.hl7.fhir.r5.model.*;
|
||||
import org.hl7.fhir.r5.utils.ToolingExtensions;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.validation.ValidationEngine;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileOutputStream;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
public class ValidationUtils {
|
||||
public static void validateSources(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
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
|
||||
Resource r = validator.validate(cliContext.getSources(), cliContext.getProfiles());
|
||||
int ec = 0;
|
||||
if (cliContext.getOutput() == null) {
|
||||
if (r instanceof Bundle)
|
||||
for (Bundle.BundleEntryComponent e : ((Bundle) r).getEntry())
|
||||
ec = displayOperationOutcome((OperationOutcome) e.getResource()) + ec;
|
||||
else
|
||||
ec = displayOperationOutcome((OperationOutcome) r);
|
||||
} else {
|
||||
IParser x;
|
||||
if (cliContext.getOutput() != null && cliContext.getOutput().endsWith(".json")) {
|
||||
x = new JsonParser();
|
||||
} else {
|
||||
x = new XmlParser();
|
||||
}
|
||||
x.setOutputStyle(IParser.OutputStyle.PRETTY);
|
||||
FileOutputStream s = new FileOutputStream(cliContext.getOutput());
|
||||
x.compose(s, r);
|
||||
s.close();
|
||||
}
|
||||
System.exit(ec > 0 ? 1 : 0);
|
||||
}
|
||||
|
||||
public static void validateScan(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
if (Utilities.noString(cliContext.getOutput()))
|
||||
throw new Exception("Output parameter required when scanning");
|
||||
if (!(new File(cliContext.getOutput()).isDirectory()))
|
||||
throw new Exception("Output '" + cliContext.getOutput() + "' must be a directory when scanning");
|
||||
System.out.println(" .. scan " + cliContext.getSources() + " against loaded IGs");
|
||||
Set<String> urls = new HashSet<>();
|
||||
for (ImplementationGuide ig : validator.getContext().allImplementationGuides()) {
|
||||
if (ig.getUrl().contains("/ImplementationGuide") && !ig.getUrl().equals("http://hl7.org/fhir/ImplementationGuide/fhir"))
|
||||
urls.add(ig.getUrl());
|
||||
}
|
||||
List<ValidationEngine.ScanOutputItem> res = validator.validateScan(cliContext.getSources(), urls);
|
||||
validator.genScanOutput(cliContext.getOutput(), res);
|
||||
System.out.println("Done. output in " + Utilities.path(cliContext.getOutput(), "scan.html"));
|
||||
}
|
||||
|
||||
public static void convertSources(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
validator.convert(cliContext.getSources().get(0), cliContext.getOutput());
|
||||
System.out.println(" ...convert");
|
||||
}
|
||||
|
||||
public static void evaluateFhirpath(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
System.out.println(" ...evaluating " + cliContext.getFhirpath());
|
||||
System.out.println(validator.evaluateFhirPath(cliContext.getSources().get(0), cliContext.getFhirpath()));
|
||||
}
|
||||
|
||||
public static void generateSnapshot(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
StructureDefinition r = validator.snapshot(cliContext.getSources().get(0), cliContext.getSv());
|
||||
System.out.println(" ...generated snapshot successfully");
|
||||
if (cliContext.getOutput() != null) {
|
||||
validator.handleOutput(r, cliContext.getOutput(), cliContext.getSv());
|
||||
}
|
||||
}
|
||||
|
||||
public static void generateNarrative(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
DomainResource r = validator.generate(cliContext.getSources().get(0), cliContext.getSv());
|
||||
System.out.println(" ...generated narrative successfully");
|
||||
if (cliContext.getOutput() != null) {
|
||||
validator.handleOutput(r, cliContext.getOutput(), cliContext.getSv());
|
||||
}
|
||||
}
|
||||
|
||||
public static void transform(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
if (cliContext.getSources().size() > 1)
|
||||
throw new Exception("Can only have one source when doing a transform (found " + cliContext.getSources() + ")");
|
||||
if (cliContext.getTxServer() == null)
|
||||
throw new Exception("Must provide a terminology server when doing a transform");
|
||||
if (cliContext.getMap() == null)
|
||||
throw new Exception("Must provide a map when doing a transform");
|
||||
try {
|
||||
validator.setMapLog(cliContext.getMapLog());
|
||||
org.hl7.fhir.r5.elementmodel.Element r = validator.transform(cliContext.getSources().get(0), cliContext.getMap());
|
||||
System.out.println(" ...success");
|
||||
if (cliContext.getOutput() != null) {
|
||||
FileOutputStream s = new FileOutputStream(cliContext.getOutput());
|
||||
if (cliContext.getOutput() != null && cliContext.getOutput().endsWith(".json"))
|
||||
new org.hl7.fhir.r5.elementmodel.JsonParser(validator.getContext()).compose(r, s, IParser.OutputStyle.PRETTY, null);
|
||||
else
|
||||
new org.hl7.fhir.r5.elementmodel.XmlParser(validator.getContext()).compose(r, s, IParser.OutputStyle.PRETTY, null);
|
||||
s.close();
|
||||
}
|
||||
} catch (Exception e) {
|
||||
System.out.println(" ...Failure: " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
public static void transformVersion(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
if (cliContext.getSources().size() > 1) {
|
||||
throw new Exception("Can only have one source when converting versions (found " + cliContext.getSources() + ")");
|
||||
}
|
||||
if (cliContext.getTargetVer() == null) {
|
||||
throw new Exception("Must provide a map when converting versions");
|
||||
}
|
||||
if (cliContext.getOutput() == null) {
|
||||
throw new Exception("Must nominate an output when converting versions");
|
||||
}
|
||||
try {
|
||||
if (cliContext.getMapLog() != null) {
|
||||
validator.setMapLog(cliContext.getMapLog());
|
||||
}
|
||||
byte[] r = validator.transformVersion(cliContext.getSources().get(0), cliContext.getTargetVer(), cliContext.getOutput().endsWith(".json") ? Manager.FhirFormat.JSON : Manager.FhirFormat.XML, cliContext.getCanDoNative());
|
||||
System.out.println(" ...success");
|
||||
TextFile.bytesToFile(r, cliContext.getOutput());
|
||||
} catch (Exception e) {
|
||||
System.out.println(" ...Failure: " + e.getMessage());
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
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());
|
||||
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());
|
||||
}
|
||||
validator.setQuestionnaires(cliContext.getQuestionnaires());
|
||||
validator.setNative(cliContext.isDoNative());
|
||||
validator.setHintAboutNonMustSupport(cliContext.isHintAboutNonMustSupport());
|
||||
validator.setAnyExtensionsAllowed(cliContext.isAnyExtensionsAllowed());
|
||||
validator.setLanguage(cliContext.getLang());
|
||||
validator.setLocale(cliContext.getLocale());
|
||||
validator.setSnomedExtension(cliContext.getSnomedCT());
|
||||
validator.setAssumeValidRestReferences(cliContext.isAssumeValidRestReferences());
|
||||
return validator;
|
||||
}
|
||||
|
||||
public static int displayOperationOutcome(OperationOutcome oo) {
|
||||
int error = 0;
|
||||
int warn = 0;
|
||||
int info = 0;
|
||||
String file = ToolingExtensions.readStringExtension(oo, ToolingExtensions.EXT_OO_FILE);
|
||||
|
||||
for (OperationOutcome.OperationOutcomeIssueComponent issue : oo.getIssue()) {
|
||||
if (issue.getSeverity() == OperationOutcome.IssueSeverity.FATAL || issue.getSeverity() == OperationOutcome.IssueSeverity.ERROR)
|
||||
error++;
|
||||
else if (issue.getSeverity() == OperationOutcome.IssueSeverity.WARNING)
|
||||
warn++;
|
||||
else
|
||||
info++;
|
||||
}
|
||||
|
||||
System.out.println((error == 0 ? "Success..." : "*FAILURE* ") + "validating " + file + ": " + " error:" + Integer.toString(error) + " warn:" + Integer.toString(warn) + " info:" + Integer.toString(info));
|
||||
for (OperationOutcome.OperationOutcomeIssueComponent issue : oo.getIssue()) {
|
||||
System.out.println(getIssueSummary(issue));
|
||||
}
|
||||
System.out.println();
|
||||
return error;
|
||||
}
|
||||
|
||||
private static String getIssueSummary(OperationOutcome.OperationOutcomeIssueComponent issue) {
|
||||
String loc = null;
|
||||
if (issue.hasExpression()) {
|
||||
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
|
||||
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
|
||||
loc = issue.getExpression().get(0).asStringValue() + (line >= 0 && col >= 0 ? " (line " + Integer.toString(line) + ", col" + Integer.toString(col) + ")" : "");
|
||||
} else if (issue.hasLocation()) {
|
||||
loc = issue.getLocation().get(0).asStringValue();
|
||||
} else {
|
||||
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
|
||||
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
|
||||
loc = (line >= 0 && col >= 0 ? "line " + Integer.toString(line) + ", col" + Integer.toString(col) : "??");
|
||||
}
|
||||
return " " + issue.getSeverity().getDisplay() + " @ " + loc + " : " + issue.getDetails().getText();
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue