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Add support for NDJSON format, and fix bug where JSON parser was not checking for the end of content

This commit is contained in:
Grahame Grieve 2024-07-01 06:28:36 +09:30
parent 437687f5cd
commit a209c13c1a
8 changed files with 161 additions and 9 deletions
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10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
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@ -134,6 +134,10 @@ public class JsonParser extends ParserBase {
@Override
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
return parse(inStream, 0);
}
public List<ValidatedFragment> parse(InputStream inStream, int line) throws IOException, FHIRException {
// long start = System.currentTimeMillis();
byte[] content = TextFile.streamToBytes(inStream);
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content, false);
@ -146,12 +150,12 @@ public class JsonParser extends ParserBase {
if (policy == ValidationPolicy.EVERYTHING) {
try {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true, line);
} catch (Exception e) {
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, null, IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
}
} else {
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true, line);
}
if (obj != null) {

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Manager.java
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@ -47,7 +47,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
public class Manager {
//TODO use EnumMap
public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC, SHL, FML;
public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC, SHL, FML, NDJSON;
// SHC = smart health cards, including as text versions of QR codes
// SHL = smart health links, also a text version of the QR code
@ -69,6 +69,8 @@ public class Manager {
return "shl";
case FML:
return "fml";
case NDJSON:
return "ndjson";
}
return null;
}
@ -91,6 +93,8 @@ public class Manager {
return SHL;
case "fml":
return FML;
case "ndjson":
return NDJSON;
}
return null;
}
@ -127,6 +131,7 @@ public class Manager {
}
switch (format) {
case JSON : return new JsonParser(context);
case NDJSON : return new NDJsonParser(context);
case XML : return new XmlParser(context);
case TURTLE : return new TurtleParser(context);
case VBAR : return new VerticalBarParser(context);

120
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/NDJsonParser.java Normal file
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@ -0,0 +1,120 @@
package org.hl7.fhir.r5.elementmodel;
import java.io.ByteArrayInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
public class NDJsonParser extends ParserBase {
public NDJsonParser(IWorkerContext context, ProfileUtilities utilities) {
super(context, utilities);
}
public NDJsonParser(IWorkerContext context) {
super(context);
}
private ValidatedFragment processLine(int lineCount, String line) throws FHIRException, IOException {
List<ValidatedFragment> list = new JsonParser(context).parse(new ByteArrayInputStream(line.getBytes(StandardCharsets.UTF_8)), lineCount);
return list.get(0);
}
@Override
public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
String source = TextFile.streamToString(inStream);
int length = source.length();
int start = 0;
int cursor = start;
int lineCount = 0;
List<ValidatedFragment> res = new ArrayList<>();
while (cursor < length) {
while (cursor < length && source.charAt(cursor) != '\n') {
cursor++;
}
if (cursor < length) {
String line = source.substring(start, cursor);
if (line.endsWith("\r")) {
line = line.substring(0, line.length()-1);
}
if (Utilities.noString(line.trim())) {
ValidatedFragment vf = new ValidatedFragment(ValidatedFragment.ITEM_NAME, null, null, false);
logError(vf.getErrors(), "2024-06-30", lineCount+1, 1, null, IssueType.INFORMATIONAL, context.formatMessage(I18nConstants.NDJSON_EMPTY_LINE_WARNING), IssueSeverity.WARNING);
res.add(vf);
} else {
res.add(processLine(lineCount, line));
}
start = cursor+1;
} else if (cursor > start) {
String line = source.substring(start, cursor);
if (line.endsWith("\r")) {
line = line.substring(0, line.length()-1);
}
if (Utilities.noString(line.trim())) {
ValidatedFragment vf = new ValidatedFragment(ValidatedFragment.ITEM_NAME, null, null, false);
logError(vf.getErrors(), "2024-06-30", lineCount+1, 1, null, IssueType.INFORMATIONAL, context.formatMessage(I18nConstants.NDJSON_EMPTY_LINE_WARNING), IssueSeverity.WARNING);
res.add(vf);
} else {
res.add(processLine(lineCount, line));
}
start = cursor+1;
}
lineCount++;
cursor++;
}
return res;
}
@Override
public void compose(Element e, OutputStream stream, OutputStyle style, String identity) throws FHIRException, IOException {
throw new Error("Not done yet");
}
}

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ValidatedFragment.java
View File

@ -27,6 +27,7 @@ public class ValidatedFragment {
@Getter
private final boolean isDerivedContent;
public final static String FOCUS_NAME = "focus";
public final static String ITEM_NAME = "item";
@Getter
private List<ValidationMessage> errors = new ArrayList<>();

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -1091,4 +1091,5 @@ public class I18nConstants {
public static final String IG_DEPENDENCY_VERSION_WARNING = "IG_DEPENDENCY_VERSION_WARNING";
public static final String IG_DEPENDENCY_EXCEPTION = "IG_DEPENDENCY_EXCEPTION";
public static final String IG_DEPENDENCY_PACKAGE_UNKNOWN = "IG_DEPENDENCY_PACKAGE_UNKNOWN";
public static final String NDJSON_EMPTY_LINE_WARNING = "NDJSON_EMPTY_LINE_WARNING";
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/parser/JsonLexer.java
View File

@ -51,12 +51,12 @@ public class JsonLexer {
private boolean isUnquoted;
private String sourceName;
public JsonLexer(String source, boolean allowComments, boolean allowUnquotedStrings) throws IOException {
public JsonLexer(String source, boolean allowComments, boolean allowUnquotedStrings, int line) throws IOException {
this.source = source;
this.allowComments = allowComments;
this.allowUnquotedStrings = allowUnquotedStrings;
cursor = -1;
location = new JsonLocationData(1, 1);
location = new JsonLocationData(line+1, 1);
start();
}

26
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/parser/JsonParser.java
View File

@ -52,6 +52,15 @@ import org.hl7.fhir.utilities.json.parser.JsonLexer.TokenType;
*/
public class JsonParser {
protected JsonParser() {
super();
}
protected JsonParser(int line) {
super();
this.line = line;
}
public static JsonObject parseObject(InputStream stream) throws IOException, JsonException {
return new JsonParser().parseJsonObject(TextFile.streamToString(stream), false, false);
}
@ -107,6 +116,10 @@ public class JsonParser {
return new JsonParser().parseJsonObject(source, isJson5, allowDuplicates);
}
public static JsonObject parseObject(String source, boolean isJson5, boolean allowDuplicates, int line) throws IOException, JsonException {
return new JsonParser(line).parseJsonObject(source, isJson5, allowDuplicates);
}
// ================================================================
public static JsonElement parse(InputStream stream) throws IOException, JsonException {
@ -221,6 +234,7 @@ public class JsonParser {
private boolean itemUnquoted;
private boolean valueUnquoted;
private String sourceName;
private int line = 0;
private JsonObject parseJsonObject(String source, boolean isJson5, boolean allowDuplicates) throws IOException, JsonException {
this.allowDuplicates = allowDuplicates;
@ -231,7 +245,7 @@ public class JsonParser {
}
private JsonObject parseSource(String source) throws IOException, JsonException {
lexer = new JsonLexer(source, allowComments, allowUnquotedStrings);
lexer = new JsonLexer(source, allowComments, allowUnquotedStrings, line);
lexer.setSourceName(sourceName);
JsonObject result = new JsonObject();
lexer.takeComments(result);
@ -249,8 +263,14 @@ public class JsonParser {
if (lexer.getType() != TokenType.Close) {
parseProperty();
readObject("$", result, true);
result.setEnd(endProperty != null ? endProperty.copy() : lexer.getLocation().copy());
} else {
result.setEnd(endProperty != null ? endProperty.copy() : lexer.getLocation().copy());
lexer.next();
}
if (lexer.getType() != TokenType.Eof) {
throw lexer.error("Unexpected content at end of JSON: "+lexer.getType().toString());
}
result.setEnd(endProperty != null ? endProperty.copy() : lexer.getLocation().copy());
return result;
}
@ -263,7 +283,7 @@ public class JsonParser {
}
private JsonElement parseSourceElement(String source) throws IOException, JsonException {
lexer = new JsonLexer(source, allowComments, allowUnquotedStrings);
lexer = new JsonLexer(source, allowComments, allowUnquotedStrings, line);
switch (lexer.getType()) {
case Boolean:
JsonBoolean bool = new JsonBoolean(lexer.getValue().equals("true"));

1
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -1119,3 +1119,4 @@ IG_DEPENDENCY_PACKAGE_UNKNOWN = The package {0} could not be found so the versio
IG_DEPENDENCY_VERSION_ERROR = The ImplementationGuide is based on FHIR version {0} but package {1} is based on FHIR version {2}. Use the package {3} instead
IG_DEPENDENCY_VERSION_WARNING = The ImplementationGuide is based on FHIR version {0} but package {1} is based on FHIR version {2}. In general, this version mismatch should be avoided - some tools will try to make this work with variable degrees of success, but others will not even try
IG_DEPENDENCY_EXCEPTION = Exception checking package version consistency: {0}
NDJSON_EMPTY_LINE_WARNING = The NDJSON source contains an empty line. This may not be accepted by some processors