Enable bulk -snapshot and -convert on multiple/wildcard -source (#945)
* initial R4B and 4.3.0 fixes * Add support for loading ig-folder for R4b. Using R4 stuff for now. Otherwise missing classes and methods * undo CRLF edits * enable snapshot generation on multiple sources * String.valueOf(i) * Update help.txt * enable convert generation on multiple sources * correction in help.txt * optimize loops * outfilename to include sourcefilename as prefix * updated help.txt * polish-up help.txt * Tests and add new parameter * -output XOR -outputSuffix logic * fix typo * fixing the logic * updated help.txt Co-authored-by: Cees de Jonge <c.de.jonge@philips.com> Co-authored-by: dotasek <david.otasek@smilecdr.com>
This commit is contained in:
David Simons
GitHub
parent
3f93d7532a
commit
50f61901fa
|
|
@ -212,7 +212,7 @@ else
|
|||
if [ "$MVNW_VERBOSE" = true ]; then
|
||||
echo "Couldn't find .mvn/wrapper/maven-wrapper.jar, downloading it ..."
|
||||
fi
|
||||
jarUrl="http://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
|
||||
jarUrl="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
|
||||
while IFS="=" read key value; do
|
||||
case "$key" in (wrapperUrl) jarUrl="$value"; break ;;
|
||||
esac
|
||||
|
|
|
|||
|
|
@ -120,7 +120,7 @@ SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe"
|
|||
set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar"
|
||||
set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
|
||||
|
||||
set DOWNLOAD_URL="http://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
|
||||
set DOWNLOAD_URL="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
|
||||
FOR /F "tokens=1,2 delims==" %%A IN (%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties) DO (
|
||||
IF "%%A"=="wrapperUrl" SET DOWNLOAD_URL=%%B
|
||||
)
|
||||
|
|
|
|||
|
|
@ -55,6 +55,8 @@ public class CliContext {
|
|||
private String map = null;
|
||||
@JsonProperty("output")
|
||||
private String output = null;
|
||||
@JsonProperty("outputSuffix")
|
||||
private String outputSuffix;
|
||||
@JsonProperty("htmlOutput")
|
||||
private String htmlOutput = null;
|
||||
@JsonProperty("txServer")
|
||||
|
|
@ -122,7 +124,8 @@ public class CliContext {
|
|||
|
||||
@JsonProperty("jurisdiction")
|
||||
private String jurisdiction = JurisdictionUtilities.getJurisdictionFromLocale(Locale.getDefault().getCountry());
|
||||
|
||||
|
||||
|
||||
@JsonProperty("map")
|
||||
public String getMap() {
|
||||
return map;
|
||||
|
|
@ -321,6 +324,17 @@ public class CliContext {
|
|||
return this;
|
||||
}
|
||||
|
||||
@JsonProperty("outputSuffix")
|
||||
public String getOutputSuffix() {
|
||||
return outputSuffix;
|
||||
}
|
||||
|
||||
@JsonProperty("outputSuffix")
|
||||
public CliContext setOutputSuffix(String outputSuffix) {
|
||||
this.outputSuffix = outputSuffix;
|
||||
return this;
|
||||
}
|
||||
|
||||
@JsonProperty("htmlOutput")
|
||||
public String getHtmlOutput() {
|
||||
return htmlOutput;
|
||||
|
|
@ -630,6 +644,7 @@ public class CliContext {
|
|||
Objects.equals(extensions, that.extensions) &&
|
||||
Objects.equals(map, that.map) &&
|
||||
Objects.equals(output, that.output) &&
|
||||
Objects.equals(outputSuffix, that.outputSuffix) &&
|
||||
Objects.equals(htmlOutput, that.htmlOutput) &&
|
||||
Objects.equals(txServer, that.txServer) &&
|
||||
Objects.equals(sv, that.sv) &&
|
||||
|
|
@ -659,7 +674,7 @@ public class CliContext {
|
|||
@Override
|
||||
public int hashCode() {
|
||||
return Objects.hash(doNative, extensions, hintAboutNonMustSupport, recursive, doDebug, assumeValidRestReferences, canDoNative, noInternalCaching,
|
||||
noExtensibleBindingMessages, noInvariants, wantInvariantsInMessages, map, output, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, fhirpath, snomedCT,
|
||||
noExtensibleBindingMessages, noInvariants, wantInvariantsInMessages, map, output, outputSuffix, htmlOutput, txServer, sv, txLog, txCache, mapLog, lang, fhirpath, snomedCT,
|
||||
targetVer, igs, questionnaireMode, level, profiles, sources, mode, locale, locations, crumbTrails, forPublication, showTimes, allowExampleUrls, outputStyle, jurisdiction, noUnicodeBiDiControlChars);
|
||||
}
|
||||
|
||||
|
|
@ -680,6 +695,7 @@ public class CliContext {
|
|||
", wantInvariantsInMessages=" + wantInvariantsInMessages +
|
||||
", map='" + map + '\'' +
|
||||
", output='" + output + '\'' +
|
||||
", outputSuffix='" + output + '\'' +
|
||||
", htmlOutput='" + htmlOutput + '\'' +
|
||||
", txServer='" + txServer + '\'' +
|
||||
", sv='" + sv + '\'' +
|
||||
|
|
|
|||
|
|
@ -210,8 +210,25 @@ public class ValidationService {
|
|||
}
|
||||
|
||||
public void convertSources(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
System.out.println(" ...convert");
|
||||
validator.convert(cliContext.getSources().get(0), cliContext.getOutput());
|
||||
|
||||
if (!((cliContext.getOutput() == null) ^ (cliContext.getOutputSuffix() == null))) {
|
||||
throw new Exception("Convert requires one of {-output, -outputSuffix} parameter to be set");
|
||||
}
|
||||
|
||||
List<String> sources = cliContext.getSources();
|
||||
if ((sources.size() == 1) && (cliContext.getOutput() != null)) {
|
||||
System.out.println(" ...convert");
|
||||
validator.convert(sources.get(0), cliContext.getOutput());
|
||||
} else {
|
||||
if (cliContext.getOutputSuffix() == null) {
|
||||
throw new Exception("Converting multiple/wildcard sources requires a -outputSuffix parameter to be set");
|
||||
}
|
||||
for (int i = 0; i < sources.size(); i++) {
|
||||
String output = sources.get(i) + "." + cliContext.getOutputSuffix();
|
||||
validator.convert(sources.get(i), output);
|
||||
System.out.println(" ...convert [" + i + "] (" + sources.get(i) + " to " + output + ")");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public void evaluateFhirpath(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
|
|
@ -220,11 +237,28 @@ public class ValidationService {
|
|||
}
|
||||
|
||||
public 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());
|
||||
}
|
||||
|
||||
if (!((cliContext.getOutput() == null) ^ (cliContext.getOutputSuffix() == null))) {
|
||||
throw new Exception("Snapshot generation requires one of {-output, -outputSuffix} parameter to be set");
|
||||
}
|
||||
|
||||
List<String> sources = cliContext.getSources();
|
||||
if ((sources.size() == 1) && (cliContext.getOutput() != null)) {
|
||||
StructureDefinition r = validator.snapshot(sources.get(0), cliContext.getSv());
|
||||
System.out.println(" ...generated snapshot successfully");
|
||||
validator.handleOutput(r, cliContext.getOutput(), cliContext.getSv());
|
||||
} else {
|
||||
if (cliContext.getOutputSuffix() == null) {
|
||||
throw new Exception("Snapshot generation for multiple/wildcard sources requires a -outputSuffix parameter to be set");
|
||||
}
|
||||
for (int i = 0; i < sources.size(); i++) {
|
||||
StructureDefinition r = validator.snapshot(sources.get(i), cliContext.getSv());
|
||||
String output = sources.get(i) + "." + cliContext.getOutputSuffix();
|
||||
validator.handleOutput(r, output, cliContext.getSv());
|
||||
System.out.println(" ...generated snapshot [" + i + "] successfully (" + sources.get(i) + " to " + output + ")");
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public void generateNarrative(CliContext cliContext, ValidationEngine validator) throws Exception {
|
||||
|
|
|
|||
|
|
@ -15,6 +15,8 @@ public class Params {
|
|||
|
||||
public static final String VERSION = "-version";
|
||||
public static final String OUTPUT = "-output";
|
||||
|
||||
public static final String OUTPUT_SUFFIX = "-outputSuffix";
|
||||
public static final String LEVEL = "-level";
|
||||
public static final String HTML_OUTPUT = "-html-output";
|
||||
public static final String PROXY = "-proxy";
|
||||
|
|
@ -119,7 +121,13 @@ public class Params {
|
|||
throw new Error("Specified -output without indicating output file");
|
||||
else
|
||||
cliContext.setOutput(args[++i]);
|
||||
} else if (args[i].equals(HTML_OUTPUT)) {
|
||||
} else if (args[i].equals(OUTPUT_SUFFIX)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -outputSuffix without indicating output suffix");
|
||||
else
|
||||
cliContext.setOutputSuffix(args[++i]);
|
||||
}
|
||||
else if (args[i].equals(HTML_OUTPUT)) {
|
||||
if (i + 1 == args.length)
|
||||
throw new Error("Specified -html-output without indicating output file");
|
||||
else
|
||||
|
|
|
|||
|
|
@ -73,6 +73,8 @@ The following parameters are supported:
|
|||
number of times
|
||||
-output [file]: a filename for the results (OperationOutcome)
|
||||
Default: results are sent to the std out.
|
||||
-outputSuffix [string]: used in -convert and -snapshot to deal with
|
||||
one or more result files (where -output can only have one)
|
||||
-debug
|
||||
Produce additional information about the loading/validation process
|
||||
-recurse
|
||||
|
|
@ -148,8 +150,14 @@ you must provide a specific parameter:
|
|||
|
||||
-convert
|
||||
|
||||
-convert requires the parameters -source and -output. ig may be used to provide
|
||||
a logical model
|
||||
-convert requires the parameters -source and one of {-output, -outputSuffix}.
|
||||
-ig may be used to provide a logical model.
|
||||
|
||||
If the -source maps to one or more resources, e.g. when using a wildcard,
|
||||
use -outputSuffix <suffix>, to obtain multiple result files with a
|
||||
`<sourcefilename>.<suffix>` filename.
|
||||
Example: `-source *.xml -convert -outputSuffix convert.json` outputs:
|
||||
`source1.xml.convert.json`, `source2.xml.convert.json`, etc. .
|
||||
|
||||
FHIRPath
|
||||
========
|
||||
|
|
@ -172,8 +180,17 @@ must provide a specific parameter:
|
|||
|
||||
-snapshot
|
||||
|
||||
-snapshot requires the parameters -defn, -txserver, -source, and -output. ig may
|
||||
be used to provide necessary base profiles
|
||||
-snapshot requires the parameters -defn, -txserver, -source, and
|
||||
one of {-output, -outputSuffix}.
|
||||
-ig may be used to provide necessary base profiles.
|
||||
|
||||
The -output/-outputSuffic filetype (xml, json) may imply a conversion.
|
||||
|
||||
If the -source maps to one or more profiles, e.g. when using a wildcard,
|
||||
use -outputSuffix <suffix>, to obtain multiple result files with a
|
||||
`<sourcefilename>.<suffix>` filename.
|
||||
Example: `-source *.xml -snapshot -outputSuffix snapshot.json` outputs:
|
||||
`source1.xml.snapshot.json`, `source2.xml.snapshot.json`, etc. .
|
||||
|
||||
Tests
|
||||
=====
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ package org.hl7.fhir.validation.cli.services;
|
|||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.hl7.fhir.r5.elementmodel.Manager;
|
||||
import org.hl7.fhir.r5.model.StructureDefinition;
|
||||
import org.hl7.fhir.validation.ValidationEngine;
|
||||
import org.hl7.fhir.validation.cli.model.CliContext;
|
||||
import org.hl7.fhir.validation.cli.model.FileInfo;
|
||||
|
|
@ -13,15 +14,24 @@ import org.mockito.Mockito;
|
|||
|
||||
import java.io.InputStream;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.*;
|
||||
|
||||
import static org.hl7.fhir.validation.tests.utilities.TestUtilities.getTerminologyCacheDirectory;
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
import static org.mockito.AdditionalMatchers.and;
|
||||
import static org.mockito.ArgumentMatchers.*;
|
||||
import static org.mockito.Mockito.*;
|
||||
|
||||
class ValidationServiceTest {
|
||||
|
||||
final String DUMMY_SOURCE = "dummySource";
|
||||
final String DUMMY_SOURCE1 = "dummySource1";
|
||||
final String DUMMY_SOURCE2 = "dummySource2";
|
||||
final String DUMMY_SOURCE3 = "dummySource3";
|
||||
final String DUMMY_OUTPUT = "dummyOutput";
|
||||
|
||||
final String DUMMY_SV = "1.2.3";
|
||||
|
||||
@Test
|
||||
void validateSources() throws Exception {
|
||||
SessionCache sessionCache = Mockito.spy(new SessionCache());
|
||||
|
|
@ -34,7 +44,7 @@ class ValidationServiceTest {
|
|||
ValidationRequest request = new ValidationRequest().setCliContext(new CliContext().setTxCache(getTerminologyCacheDirectory("validationService"))).setFilesToValidate(filesToValidate);
|
||||
// Validation run 1...nothing cached yet
|
||||
myService.validateSources(request);
|
||||
Mockito.verify(sessionCache, Mockito.times(1)).cacheSession(ArgumentMatchers.any(ValidationEngine.class));
|
||||
verify(sessionCache, Mockito.times(1)).cacheSession(ArgumentMatchers.any(ValidationEngine.class));
|
||||
|
||||
Set<String> sessionIds = sessionCache.getSessionIds();
|
||||
if (sessionIds.stream().findFirst().isPresent()) {
|
||||
|
|
@ -42,7 +52,7 @@ class ValidationServiceTest {
|
|||
Assertions.assertEquals(1, sessionIds.size());
|
||||
myService.validateSources(request);
|
||||
// Verify that the cache has been called on once with the id created in the first run
|
||||
Mockito.verify(sessionCache, Mockito.times(1)).fetchSessionValidatorEngine(sessionIds.stream().findFirst().get());
|
||||
verify(sessionCache, Mockito.times(1)).fetchSessionValidatorEngine(sessionIds.stream().findFirst().get());
|
||||
} else {
|
||||
// If no sessions exist within the cache after a run, we auto-fail.
|
||||
fail();
|
||||
|
|
@ -61,4 +71,132 @@ class ValidationServiceTest {
|
|||
return inputStream;
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void convertSingleSource() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextSingleSource();
|
||||
validationService.convertSources(cliContext.setOutput(DUMMY_OUTPUT),validationEngine);
|
||||
|
||||
verify(validationEngine).convert(DUMMY_SOURCE, DUMMY_OUTPUT);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void convertSingleSourceNoOutput() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextSingleSource();
|
||||
Exception exception = assertThrows( Exception.class, () -> {
|
||||
validationService.convertSources(cliContext,validationEngine);
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
public void convertMultipleSourceNoSuffix() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextMultipleSource();
|
||||
assertThrows( Exception.class, () -> {
|
||||
validationService.convertSources(cliContext,validationEngine);
|
||||
}
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void convertMultipleSource() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextMultipleSource();
|
||||
validationService.convertSources(cliContext.setOutputSuffix(DUMMY_OUTPUT),validationEngine);
|
||||
verify(validationEngine).convert(eq(DUMMY_SOURCE1), and(startsWith(DUMMY_SOURCE1), endsWith(DUMMY_OUTPUT)));
|
||||
verify(validationEngine).convert(eq(DUMMY_SOURCE2), and(startsWith(DUMMY_SOURCE2), endsWith(DUMMY_OUTPUT)));
|
||||
verify(validationEngine).convert(eq(DUMMY_SOURCE3), and(startsWith(DUMMY_SOURCE3), endsWith(DUMMY_OUTPUT)));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void generateSnapshotSingleSource() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
StructureDefinition structureDefinition = mock(StructureDefinition.class);
|
||||
when(validationEngine.snapshot(DUMMY_SOURCE, DUMMY_SV)).thenReturn(structureDefinition);
|
||||
CliContext cliContext = getCliContextSingleSource();
|
||||
validationService.generateSnapshot(cliContext.setOutput(DUMMY_OUTPUT).setSv(DUMMY_SV),validationEngine);
|
||||
|
||||
verify(validationEngine).snapshot(DUMMY_SOURCE, DUMMY_SV);
|
||||
verify(validationEngine).handleOutput(structureDefinition, DUMMY_OUTPUT, DUMMY_SV);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void generateSnapshotSingleSourceNoOutput() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextSingleSource();
|
||||
Exception exception = assertThrows( Exception.class, () -> {
|
||||
validationService.generateSnapshot(cliContext.setOutput(DUMMY_OUTPUT).setSv(DUMMY_SV),validationEngine);
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void generateSnapshotMultipleSourceNoSuffix() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
CliContext cliContext = getCliContextMultipleSource();
|
||||
assertThrows( Exception.class, () -> {
|
||||
validationService.generateSnapshot(cliContext.setOutput(DUMMY_OUTPUT).setSv(DUMMY_SV),validationEngine);
|
||||
}
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void generateSnapshotMultipleSource() throws Exception {
|
||||
SessionCache sessionCache = mock(SessionCache.class);
|
||||
ValidationService validationService = new ValidationService(sessionCache);
|
||||
ValidationEngine validationEngine = mock(ValidationEngine.class);
|
||||
|
||||
StructureDefinition structureDefinition1 = mock(StructureDefinition.class);
|
||||
StructureDefinition structureDefinition2 = mock(StructureDefinition.class);
|
||||
StructureDefinition structureDefinition3 = mock(StructureDefinition.class);
|
||||
|
||||
when(validationEngine.snapshot(DUMMY_SOURCE1, DUMMY_SV)).thenReturn(structureDefinition1);
|
||||
when(validationEngine.snapshot(DUMMY_SOURCE2, DUMMY_SV)).thenReturn(structureDefinition2);
|
||||
when(validationEngine.snapshot(DUMMY_SOURCE3, DUMMY_SV)).thenReturn(structureDefinition3);
|
||||
|
||||
|
||||
CliContext cliContext = getCliContextMultipleSource();
|
||||
validationService.generateSnapshot(cliContext.setOutputSuffix(DUMMY_OUTPUT).setSv(DUMMY_SV),validationEngine);
|
||||
verify(validationEngine).snapshot(DUMMY_SOURCE1, DUMMY_SV);
|
||||
verify(validationEngine).handleOutput(eq(structureDefinition1), and(startsWith(DUMMY_SOURCE1),endsWith(DUMMY_OUTPUT)), eq(DUMMY_SV));
|
||||
verify(validationEngine).snapshot(DUMMY_SOURCE2, DUMMY_SV);
|
||||
verify(validationEngine).handleOutput(eq(structureDefinition2), and(startsWith(DUMMY_SOURCE2), endsWith(DUMMY_OUTPUT)), eq(DUMMY_SV));
|
||||
verify(validationEngine).snapshot(DUMMY_SOURCE3, DUMMY_SV);
|
||||
verify(validationEngine).handleOutput(eq(structureDefinition3), and(startsWith(DUMMY_SOURCE3), endsWith(DUMMY_OUTPUT)), eq(DUMMY_SV));
|
||||
|
||||
}
|
||||
|
||||
private CliContext getCliContextSingleSource() {
|
||||
CliContext cliContext;
|
||||
cliContext = new CliContext().setSources(Arrays.asList(DUMMY_SOURCE));
|
||||
return cliContext;
|
||||
}
|
||||
private CliContext getCliContextMultipleSource() {
|
||||
CliContext cliContext;
|
||||
cliContext = new CliContext().setSources(Arrays.asList(DUMMY_SOURCE1, DUMMY_SOURCE2, DUMMY_SOURCE3));
|
||||
return cliContext;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue