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hapi-fhir
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Fix a number of problems reported by ErrorProne

This commit is contained in:
James 2017-10-16 10:00:27 -04:00
parent 22cd9d8641
commit a782bd7630
21 changed files with 11648 additions and 11423 deletions
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1
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/IgPackUploader.java
View File

@ -73,6 +73,7 @@ public class IgPackUploader extends BaseCommand {
.and(StructureDefinition.URL.matches().value(nextResourceUrl))
.execute();
}
break;
default:
throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
}

20
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_40.java
View File

@ -1,5 +1,25 @@
package org.hl7.fhir.convertors;
/*-
* #%L
* HAPI FHIR - Converter
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.ArrayList;
import java.util.List;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/ConnectionWrapper.java
View File

@ -97,7 +97,7 @@ public class ConnectionWrapper implements Connection {
@Override
public String getClientInfo(String theName) throws SQLException {
return getClientInfo(theName);
return myWrap.getClientInfo(theName);
}
@Override

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -118,8 +118,13 @@ public abstract class BaseJpaTest {
protected List<String> toUnqualifiedVersionlessIdValues(IBundleProvider theFound) {
List<String> retVal = new ArrayList<String>();
int size = theFound.size();
Integer size = theFound.size();
ourLog.info("Found {} results", size);
if (size == null) {
size = 99999;
}
List<IBaseResource> resources = theFound.getResources(0, size);
for (IBaseResource next : resources) {
retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java
View File

@ -102,6 +102,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
@ -110,6 +111,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
}
throw new IllegalStateException(); // shouldn't get here

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -133,6 +133,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
@ -141,6 +142,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
}
throw new IllegalStateException(); // shouldn't get here

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -133,6 +133,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
try {
@ -141,6 +142,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
} catch (PreconditionFailedException e) {
return (OperationOutcome) e.getOperationOutcome();
}
break;
}
throw new IllegalStateException(); // shouldn't get here

5
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/conformance/ProfileUtilities.java
View File

@ -1772,8 +1772,9 @@ public class ProfileUtilities extends TranslatingUtilities {
case BUNDLED : return "b";
case CONTAINED : return "c";
case REFERENCED: return "r";
default: return "?";
}
return "?";
}
@ -2232,7 +2233,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (definition != null && definition.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(definition.getShortElement(), gen.new Piece(null, gt(definition.getShortElement()), null)));
} else if (fallback != null && fallback != null && fallback.hasShort()) {
} else if (fallback != null && fallback.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(fallback.getShortElement(), gen.new Piece(null, gt(fallback.getShortElement()), null)));
}

5649
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/utils/FHIRPathEngine.java
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File diff suppressed because it is too large Load Diff

995
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/utils/JsonTrackingParser.java
View File

@ -1,494 +1,501 @@
package org.hl7.fhir.dstu3.utils;
import java.math.BigDecimal;
import java.util.Map;
import java.util.Stack;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import com.google.gson.*;
/**
* This is created to get a json parser that can track line numbers... grr...
*
* @author Grahame Grieve
*
*/
public class JsonTrackingParser {
public enum TokenType {
Open, Close, String, Number, Colon, Comma, OpenArray, CloseArray, Eof, Null, Boolean;
}
public class LocationData {
private int line;
private int col;
protected LocationData(int line, int col) {
super();
this.line = line;
this.col = col;
}
public int getLine() {
return line;
}
public int getCol() {
return col;
}
public void newLine() {
line++;
col = 1;
}
public LocationData copy() {
return new LocationData(line, col);
}
}
private class State {
private String name;
private boolean isProp;
protected State(String name, boolean isProp) {
super();
this.name = name;
this.isProp = isProp;
}
public String getName() {
return name;
}
public boolean isProp() {
return isProp;
}
}
private class Lexer {
private String source;
private int cursor;
private String peek;
private String value;
private TokenType type;
private Stack<State> states = new Stack<State>();
private LocationData lastLocationBWS;
private LocationData lastLocationAWS;
private LocationData location;
private StringBuilder b = new StringBuilder();
public Lexer(String source) throws FHIRException {
this.source = source;
cursor = -1;
location = new LocationData(1, 1);
start();
}
private boolean more() {
return peek != null || cursor < source.length();
}
private String getNext(int length) throws FHIRException {
String result = "";
if (peek != null) {
if (peek.length() > length) {
result = peek.substring(0, length);
peek = peek.substring(length);
} else {
result = peek;
peek = null;
}
}
if (result.length() < length) {
int len = length - result.length();
if (cursor > source.length() - len)
throw error("Attempt to read past end of source");
result = result + source.substring(cursor+1, cursor+len+1);
cursor = cursor + len;
}
for (char ch : result.toCharArray())
if (ch == '\n')
location.newLine();
else
location.col++;
return result;
}
private char getNextChar() throws FHIRException {
if (peek != null) {
char ch = peek.charAt(0);
peek = peek.length() == 1 ? null : peek.substring(1);
return ch;
} else {
cursor++;
if (cursor >= source.length())
return (char) 0;
char ch = source.charAt(cursor);
if (ch == '\n') {
location.newLine();
} else {
location.col++;
}
return ch;
}
}
private void push(char ch){
peek = peek == null ? String.valueOf(ch) : String.valueOf(ch)+peek;
}
private void parseWord(String word, char ch, TokenType type) throws FHIRException {
this.type = type;
value = ""+ch+getNext(word.length()-1);
if (!value.equals(word))
throw error("Syntax error in json reading special word "+word);
}
private FHIRException error(String msg) {
return new FHIRException("Error parsing JSON source: "+msg+" at Line "+Integer.toString(location.line)+" (path=["+path()+"])");
}
private String path() {
if (states.empty())
return value;
else {
String result = "";
for (State s : states)
result = result + '/'+ s.getName();
result = result + value;
return result;
}
}
public void start() throws FHIRException {
// char ch = getNextChar();
// if (ch = '\.uEF')
// begin
// // skip BOM
// getNextChar();
// getNextChar();
// end
// else
// push(ch);
next();
}
public TokenType getType() {
return type;
}
public String getValue() {
return value;
}
public LocationData getLastLocationBWS() {
return lastLocationBWS;
}
public LocationData getLastLocationAWS() {
return lastLocationAWS;
}
public void next() throws FHIRException {
lastLocationBWS = location.copy();
char ch;
do {
ch = getNextChar();
} while (more() && Utilities.charInSet(ch, ' ', '\r', '\n', '\t'));
lastLocationAWS = location.copy();
if (!more()) {
type = TokenType.Eof;
} else {
switch (ch) {
case '{' :
type = TokenType.Open;
break;
case '}' :
type = TokenType.Close;
break;
case '"' :
type = TokenType.String;
b.setLength(0);
do {
ch = getNextChar();
if (ch == '\\') {
ch = getNextChar();
switch (ch) {
case '"': b.append('"'); break;
case '\\': b.append('\\'); break;
case '/': b.append('/'); break;
case 'n': b.append('\n'); break;
case 'r': b.append('\r'); break;
case 't': b.append('\t'); break;
case 'u': b.append((char) Integer.parseInt(getNext(4), 16)); break;
default :
throw error("unknown escape sequence: \\"+ch);
}
ch = ' ';
} else if (ch != '"')
b.append(ch);
} while (more() && (ch != '"'));
if (!more())
throw error("premature termination of json stream during a string");
value = b.toString();
break;
case ':' :
type = TokenType.Colon;
break;
case ',' :
type = TokenType.Comma;
break;
case '[' :
type = TokenType.OpenArray;
break;
case ']' :
type = TokenType.CloseArray;
break;
case 't' :
parseWord("true", ch, TokenType.Boolean);
break;
case 'f' :
parseWord("false", ch, TokenType.Boolean);
break;
case 'n' :
parseWord("null", ch, TokenType.Null);
break;
default:
if ((ch >= '0' && ch <= '9') || ch == '-') {
type = TokenType.Number;
b.setLength(0);
while (more() && ((ch >= '0' && ch <= '9') || ch == '-' || ch == '.')) {
b.append(ch);
ch = getNextChar();
}
value = b.toString();
push(ch);
} else
throw error("Unexpected char '"+ch+"' in json stream");
}
}
}
public String consume(TokenType type) throws FHIRException {
if (this.type != type)
throw error("JSON syntax error - found "+type.toString()+" expecting "+type.toString());
String result = value;
next();
return result;
}
}
enum ItemType {
Object, String, Number, Boolean, Array, End, Eof, Null;
}
private Map<JsonElement, LocationData> map;
private Lexer lexer;
private ItemType itemType = ItemType.Object;
private String itemName;
private String itemValue;
public static JsonObject parse(String source, Map<JsonElement, LocationData> map) throws FHIRException {
JsonTrackingParser self = new JsonTrackingParser();
self.map = map;
return self.parse(source);
}
private JsonObject parse(String source) throws FHIRException {
lexer = new Lexer(source);
JsonObject result = new JsonObject();
LocationData loc = lexer.location.copy();
if (lexer.getType() == TokenType.Open) {
lexer.next();
lexer.states.push(new State("", false));
}
else
throw lexer.error("Unexpected content at start of JSON: "+lexer.getType().toString());
parseProperty();
readObject(result, true);
map.put(result, loc);
return result;
}
private void readObject(JsonObject obj, boolean root) throws FHIRException {
map.put(obj, lexer.location.copy());
while (!(itemType == ItemType.End) || (root && (itemType == ItemType.Eof))) {
if (obj.has(itemName))
throw lexer.error("Duplicated property name: "+itemName);
switch (itemType) {
case Object:
JsonObject child = new JsonObject(); //(obj.path+'.'+ItemName);
LocationData loc = lexer.location.copy();
obj.add(itemName, child);
next();
readObject(child, false);
map.put(obj, loc);
break;
case Boolean :
JsonPrimitive v = new JsonPrimitive(Boolean.valueOf(itemValue));
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case String:
v = new JsonPrimitive(itemValue);
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case Number:
v = new JsonPrimitive(new BigDecimal(itemValue));
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case Null:
JsonNull n = new JsonNull();
obj.add(itemName, n);
map.put(n, lexer.location.copy());
break;
case Array:
JsonArray arr = new JsonArray(); // (obj.path+'.'+ItemName);
loc = lexer.location.copy();
obj.add(itemName, arr);
next();
readArray(arr, false);
map.put(arr, loc);
break;
case Eof :
throw lexer.error("Unexpected End of File");
}
next();
}
}
private void readArray(JsonArray arr, boolean root) throws FHIRException {
while (!((itemType == ItemType.End) || (root && (itemType == ItemType.Eof)))) {
switch (itemType) {
case Object:
JsonObject obj = new JsonObject(); // (arr.path+'['+inttostr(i)+']');
LocationData loc = lexer.location.copy();
arr.add(obj);
next();
readObject(obj, false);
map.put(obj, loc);
break;
case String:
JsonPrimitive v = new JsonPrimitive(itemValue);
arr.add(v);
map.put(v, lexer.location.copy());
break;
case Number:
v = new JsonPrimitive(new BigDecimal(itemValue));
arr.add(v);
map.put(v, lexer.location.copy());
break;
case Null :
JsonNull n = new JsonNull();
arr.add(n);
map.put(n, lexer.location.copy());
break;
case Array:
JsonArray child = new JsonArray(); // (arr.path+'['+inttostr(i)+']');
loc = lexer.location.copy();
arr.add(child);
next();
readArray(child, false);
map.put(arr, loc);
break;
case Eof :
throw lexer.error("Unexpected End of File");
}
next();
}
}
private void next() throws FHIRException {
switch (itemType) {
case Object :
lexer.consume(TokenType.Open);
lexer.states.push(new State(itemName, false));
if (lexer.getType() == TokenType.Close) {
itemType = ItemType.End;
lexer.next();
} else
parseProperty();
break;
case Null:
case String:
case Number:
case End:
case Boolean :
if (itemType == ItemType.End)
lexer.states.pop();
if (lexer.getType() == TokenType.Comma) {
lexer.next();
parseProperty();
} else if (lexer.getType() == TokenType.Close) {
itemType = ItemType.End;
lexer.next();
} else if (lexer.getType() == TokenType.CloseArray) {
itemType = ItemType.End;
lexer.next();
} else if (lexer.getType() == TokenType.Eof) {
itemType = ItemType.Eof;
} else
throw lexer.error("Unexpected JSON syntax");
break;
case Array :
lexer.next();
lexer.states.push(new State(itemName+"[]", true));
parseProperty();
break;
case Eof :
throw lexer.error("JSON Syntax Error - attempt to read past end of json stream");
default:
throw lexer.error("not done yet (a): "+itemType.toString());
}
}
private void parseProperty() throws FHIRException {
if (!lexer.states.peek().isProp) {
itemName = lexer.consume(TokenType.String);
itemValue = null;
lexer.consume(TokenType.Colon);
}
switch (lexer.getType()) {
case Null :
itemType = ItemType.Null;
itemValue = lexer.value;
lexer.next();
break;
case String :
itemType = ItemType.String;
itemValue = lexer.value;
lexer.next();
break;
case Boolean :
itemType = ItemType.Boolean;
itemValue = lexer.value;
lexer.next();
break;
case Number :
itemType = ItemType.Number;
itemValue = lexer.value;
lexer.next();
break;
case Open :
itemType = ItemType.Object;
break;
case OpenArray :
itemType = ItemType.Array;
break;
case CloseArray :
itemType = ItemType.End;
break;
// case Close, , case Colon, case Comma, case OpenArray, !
default:
throw lexer.error("not done yet (b): "+lexer.getType().toString());
}
}
}
package org.hl7.fhir.dstu3.utils;
import java.math.BigDecimal;
import java.util.Map;
import java.util.Stack;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.Utilities;
import com.google.gson.*;
/**
* This is created to get a json parser that can track line numbers... grr...
*
* @author Grahame Grieve
*
*/
public class JsonTrackingParser {
public enum TokenType {
Open, Close, String, Number, Colon, Comma, OpenArray, CloseArray, Eof, Null, Boolean;
}
public class LocationData {
private int line;
private int col;
protected LocationData(int line, int col) {
super();
this.line = line;
this.col = col;
}
public int getLine() {
return line;
}
public int getCol() {
return col;
}
public void newLine() {
line++;
col = 1;
}
public LocationData copy() {
return new LocationData(line, col);
}
}
private class State {
private String name;
private boolean isProp;
protected State(String name, boolean isProp) {
super();
this.name = name;
this.isProp = isProp;
}
public String getName() {
return name;
}
public boolean isProp() {
return isProp;
}
}
private class Lexer {
private String source;
private int cursor;
private String peek;
private String value;
private TokenType type;
private Stack<State> states = new Stack<State>();
private LocationData lastLocationBWS;
private LocationData lastLocationAWS;
private LocationData location;
private StringBuilder b = new StringBuilder();
public Lexer(String source) throws FHIRException {
this.source = source;
cursor = -1;
location = new LocationData(1, 1);
start();
}
private boolean more() {
return peek != null || cursor < source.length();
}
private String getNext(int length) throws FHIRException {
String result = "";
if (peek != null) {
if (peek.length() > length) {
result = peek.substring(0, length);
peek = peek.substring(length);
} else {
result = peek;
peek = null;
}
}
if (result.length() < length) {
int len = length - result.length();
if (cursor > source.length() - len)
throw error("Attempt to read past end of source");
result = result + source.substring(cursor+1, cursor+len+1);
cursor = cursor + len;
}
for (char ch : result.toCharArray())
if (ch == '\n')
location.newLine();
else
location.col++;
return result;
}
private char getNextChar() throws FHIRException {
if (peek != null) {
char ch = peek.charAt(0);
peek = peek.length() == 1 ? null : peek.substring(1);
return ch;
} else {
cursor++;
if (cursor >= source.length())
return (char) 0;
char ch = source.charAt(cursor);
if (ch == '\n') {
location.newLine();
} else {
location.col++;
}
return ch;
}
}
private void push(char ch){
peek = peek == null ? String.valueOf(ch) : String.valueOf(ch)+peek;
}
private void parseWord(String word, char ch, TokenType type) throws FHIRException {
this.type = type;
value = ""+ch+getNext(word.length()-1);
if (!value.equals(word))
throw error("Syntax error in json reading special word "+word);
}
private FHIRException error(String msg) {
return new FHIRException("Error parsing JSON source: "+msg+" at Line "+Integer.toString(location.line)+" (path=["+path()+"])");
}
private String path() {
if (states.empty())
return value;
else {
String result = "";
for (State s : states)
result = result + '/'+ s.getName();
result = result + value;
return result;
}
}
public void start() throws FHIRException {
// char ch = getNextChar();
// if (ch = '\.uEF')
// begin
// // skip BOM
// getNextChar();
// getNextChar();
// end
// else
// push(ch);
next();
}
public TokenType getType() {
return type;
}
public String getValue() {
return value;
}
public LocationData getLastLocationBWS() {
return lastLocationBWS;
}
public LocationData getLastLocationAWS() {
return lastLocationAWS;
}
public void next() throws FHIRException {
lastLocationBWS = location.copy();
char ch;
do {
ch = getNextChar();
} while (more() && Utilities.charInSet(ch, ' ', '\r', '\n', '\t'));
lastLocationAWS = location.copy();
if (!more()) {
type = TokenType.Eof;
} else {
switch (ch) {
case '{' :
type = TokenType.Open;
break;
case '}' :
type = TokenType.Close;
break;
case '"' :
type = TokenType.String;
b.setLength(0);
do {
ch = getNextChar();
if (ch == '\\') {
ch = getNextChar();
switch (ch) {
case '"': b.append('"'); break;
case '\\': b.append('\\'); break;
case '/': b.append('/'); break;
case 'n': b.append('\n'); break;
case 'r': b.append('\r'); break;
case 't': b.append('\t'); break;
case 'u': b.append((char) Integer.parseInt(getNext(4), 16)); break;
default :
throw error("unknown escape sequence: \\"+ch);
}
ch = ' ';
} else if (ch != '"')
b.append(ch);
} while (more() && (ch != '"'));
if (!more())
throw error("premature termination of json stream during a string");
value = b.toString();
break;
case ':' :
type = TokenType.Colon;
break;
case ',' :
type = TokenType.Comma;
break;
case '[' :
type = TokenType.OpenArray;
break;
case ']' :
type = TokenType.CloseArray;
break;
case 't' :
parseWord("true", ch, TokenType.Boolean);
break;
case 'f' :
parseWord("false", ch, TokenType.Boolean);
break;
case 'n' :
parseWord("null", ch, TokenType.Null);
break;
default:
if ((ch >= '0' && ch <= '9') || ch == '-') {
type = TokenType.Number;
b.setLength(0);
while (more() && ((ch >= '0' && ch <= '9') || ch == '-' || ch == '.')) {
b.append(ch);
ch = getNextChar();
}
value = b.toString();
push(ch);
} else
throw error("Unexpected char '"+ch+"' in json stream");
}
}
}
public String consume(TokenType type) throws FHIRException {
if (this.type != type)
throw error("JSON syntax error - found "+type.toString()+" expecting "+type.toString());
String result = value;
next();
return result;
}
}
enum ItemType {
Object, String, Number, Boolean, Array, End, Eof, Null;
}
private Map<JsonElement, LocationData> map;
private Lexer lexer;
private ItemType itemType = ItemType.Object;
private String itemName;
private String itemValue;
public static JsonObject parse(String source, Map<JsonElement, LocationData> map) throws FHIRException {
JsonTrackingParser self = new JsonTrackingParser();
self.map = map;
return self.parse(source);
}
private JsonObject parse(String source) throws FHIRException {
lexer = new Lexer(source);
JsonObject result = new JsonObject();
LocationData loc = lexer.location.copy();
if (lexer.getType() == TokenType.Open) {
lexer.next();
lexer.states.push(new State("", false));
}
else
throw lexer.error("Unexpected content at start of JSON: "+lexer.getType().toString());
parseProperty();
readObject(result, true);
map.put(result, loc);
return result;
}
private void readObject(JsonObject obj, boolean root) throws FHIRException {
map.put(obj, lexer.location.copy());
while (!(itemType == ItemType.End) || (root && (itemType == ItemType.Eof))) {
if (obj.has(itemName))
throw lexer.error("Duplicated property name: "+itemName);
switch (itemType) {
case Object:
JsonObject child = new JsonObject(); //(obj.path+'.'+ItemName);
LocationData loc = lexer.location.copy();
obj.add(itemName, child);
next();
readObject(child, false);
map.put(obj, loc);
break;
case Boolean :
JsonPrimitive v = new JsonPrimitive(Boolean.valueOf(itemValue));
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case String:
v = new JsonPrimitive(itemValue);
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case Number:
v = new JsonPrimitive(new BigDecimal(itemValue));
obj.add(itemName, v);
map.put(v, lexer.location.copy());
break;
case Null:
JsonNull n = new JsonNull();
obj.add(itemName, n);
map.put(n, lexer.location.copy());
break;
case Array:
JsonArray arr = new JsonArray(); // (obj.path+'.'+ItemName);
loc = lexer.location.copy();
obj.add(itemName, arr);
next();
readArray(arr, false);
map.put(arr, loc);
break;
case Eof :
throw lexer.error("Unexpected End of File");
case End:
// TODO: anything?\
break;
}
next();
}
}
private void readArray(JsonArray arr, boolean root) throws FHIRException {
while (!((itemType == ItemType.End) || (root && (itemType == ItemType.Eof)))) {
switch (itemType) {
case Object:
JsonObject obj = new JsonObject(); // (arr.path+'['+inttostr(i)+']');
LocationData loc = lexer.location.copy();
arr.add(obj);
next();
readObject(obj, false);
map.put(obj, loc);
break;
case String:
JsonPrimitive v = new JsonPrimitive(itemValue);
arr.add(v);
map.put(v, lexer.location.copy());
break;
case Number:
v = new JsonPrimitive(new BigDecimal(itemValue));
arr.add(v);
map.put(v, lexer.location.copy());
break;
case Null :
JsonNull n = new JsonNull();
arr.add(n);
map.put(n, lexer.location.copy());
break;
case Array:
JsonArray child = new JsonArray(); // (arr.path+'['+inttostr(i)+']');
loc = lexer.location.copy();
arr.add(child);
next();
readArray(child, false);
map.put(arr, loc);
break;
case Eof :
throw lexer.error("Unexpected End of File");
case End:
case Boolean:
// TODO: anything?
break;
}
next();
}
}
private void next() throws FHIRException {
switch (itemType) {
case Object :
lexer.consume(TokenType.Open);
lexer.states.push(new State(itemName, false));
if (lexer.getType() == TokenType.Close) {
itemType = ItemType.End;
lexer.next();
} else
parseProperty();
break;
case Null:
case String:
case Number:
case End:
case Boolean :
if (itemType == ItemType.End)
lexer.states.pop();
if (lexer.getType() == TokenType.Comma) {
lexer.next();
parseProperty();
} else if (lexer.getType() == TokenType.Close) {
itemType = ItemType.End;
lexer.next();
} else if (lexer.getType() == TokenType.CloseArray) {
itemType = ItemType.End;
lexer.next();
} else if (lexer.getType() == TokenType.Eof) {
itemType = ItemType.Eof;
} else
throw lexer.error("Unexpected JSON syntax");
break;
case Array :
lexer.next();
lexer.states.push(new State(itemName+"[]", true));
parseProperty();
break;
case Eof :
throw lexer.error("JSON Syntax Error - attempt to read past end of json stream");
default:
throw lexer.error("not done yet (a): "+itemType.toString());
}
}
private void parseProperty() throws FHIRException {
if (!lexer.states.peek().isProp) {
itemName = lexer.consume(TokenType.String);
itemValue = null;
lexer.consume(TokenType.Colon);
}
switch (lexer.getType()) {
case Null :
itemType = ItemType.Null;
itemValue = lexer.value;
lexer.next();
break;
case String :
itemType = ItemType.String;
itemValue = lexer.value;
lexer.next();
break;
case Boolean :
itemType = ItemType.Boolean;
itemValue = lexer.value;
lexer.next();
break;
case Number :
itemType = ItemType.Number;
itemValue = lexer.value;
lexer.next();
break;
case Open :
itemType = ItemType.Object;
break;
case OpenArray :
itemType = ItemType.Array;
break;
case CloseArray :
itemType = ItemType.End;
break;
// case Close, , case Colon, case Comma, case OpenArray, !
default:
throw lexer.error("not done yet (b): "+lexer.getType().toString());
}
}
}

5450
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/utils/StructureMapUtilities.java
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1003
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/utils/formats/JsonTrackingParser.java
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5341
hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/utils/FHIRPathEngine.java
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2
hapi-fhir-structures-hl7org-dstu2/src/main/java/org/hl7/fhir/instance/utils/ProfileUtilities.java
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@ -1628,7 +1628,7 @@ public class ProfileUtilities {
if (definition != null && definition.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(definition.getShortElement(), gen.new Piece(null, definition.getShort(), null)));
} else if (fallback != null && fallback != null && fallback.hasShort()) {
} else if (fallback != null && fallback.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(fallback.getShortElement(), gen.new Piece(null, fallback.getShort(), null)));
}

4340
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java
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2
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/OperationOutcomeUtilities.java
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@ -35,6 +35,7 @@ public class OperationOutcomeUtilities {
case ERROR : return IssueSeverity.ERROR;
case WARNING : return IssueSeverity.WARNING;
case INFORMATION : return IssueSeverity.INFORMATION;
case NULL : return IssueSeverity.NULL;
}
return IssueSeverity.NULL;
}
@ -70,6 +71,7 @@ public class OperationOutcomeUtilities {
case TIMEOUT: return IssueType.TIMEOUT;
case THROTTLED: return IssueType.THROTTLED;
case INFORMATIONAL: return IssueType.INFORMATIONAL;
case NULL: return IssueType.NULL;
}
return IssueType.NULL;
}

22
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/QuestionnaireBuilder.java
View File

@ -589,20 +589,20 @@ public class QuestionnaireBuilder {
private Type convertType(Base value, QuestionnaireItemType af, ValueSet vs, String path) throws FHIRException {
switch (af) {
// simple cases
case BOOLEAN: if (value instanceof BooleanType) return (Type) value;
case DECIMAL: if (value instanceof DecimalType) return (Type) value;
case INTEGER: if (value instanceof IntegerType) return (Type) value;
case DATE: if (value instanceof DateType) return (Type) value;
case DATETIME: if (value instanceof DateTimeType) return (Type) value;
case TIME: if (value instanceof TimeType) return (Type) value;
case BOOLEAN: if (value instanceof BooleanType) return (Type) value; break;
case DECIMAL: if (value instanceof DecimalType) return (Type) value; break;
case INTEGER: if (value instanceof IntegerType) return (Type) value; break;
case DATE: if (value instanceof DateType) return (Type) value; break;
case DATETIME: if (value instanceof DateTimeType) return (Type) value; break;
case TIME: if (value instanceof TimeType) return (Type) value; break;
case STRING:
if (value instanceof StringType)
return (Type) value;
else if (value instanceof UriType)
return new StringType(((UriType) value).asStringValue());
case TEXT: if (value instanceof StringType) return (Type) value;
case QUANTITY: if (value instanceof Quantity) return (Type) value;
break;
case TEXT: if (value instanceof StringType) return (Type) value; break;
case QUANTITY: if (value instanceof Quantity) return (Type) value; break;
// complex cases:
// ? QuestionnaireItemTypeAttachment: ...?
@ -621,6 +621,7 @@ public class QuestionnaireBuilder {
cc.setSystem(getSystemForCode(vs, cc.getCode(), path));
return cc;
}
break;
case REFERENCE:
if (value instanceof Reference)
@ -629,6 +630,9 @@ public class QuestionnaireBuilder {
Reference r = new Reference();
r.setReference(((StringType) value).asStringValue());
}
break;
default:
break;
}
throw new FHIRException("Unable to convert from '"+value.getClass().toString()+"' for Answer Format "+af.toCode()+", path = "+path);

9
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java
View File

@ -365,11 +365,14 @@ public class StructureMapUtilities {
private static void renderGroup(StringBuilder b, StructureMapGroupComponent g) {
b.append("group ");
switch (g.getTypeMode()) {
case TYPES: b.append("for types");
case TYPEANDTYPES: b.append("for type+types ");
case TYPES:
b.append("for types");
break;
case TYPEANDTYPES:
b.append("for type+types ");
break;
default: // NONE, NULL
}
b.append("for types ");
b.append(g.getName());
if (g.hasExtends()) {
b.append(" extends ");

7
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/formats/JsonTrackingParser.java
View File

@ -364,6 +364,9 @@ public class JsonTrackingParser {
break;
case Eof :
throw lexer.error("Unexpected End of File");
case End:
// TODO GG: This isn't handled. Should it be?
break;
}
next();
}
@ -405,6 +408,10 @@ public class JsonTrackingParser {
break;
case Eof :
throw lexer.error("Unexpected End of File");
case End:
case Boolean:
// TODO GG: These aren't handled. SHould they be?
break;
}
next();
}

2
hapi-fhir-structures-r4/src/test/java/org/hl7/fhir/r4/test/support/TestingUtilities.java
View File

@ -270,7 +270,7 @@ public class TestingUtilities {
JsonArray a1 = (JsonArray) n1;
JsonArray a2 = (JsonArray) n2;
if (a1.size() != a1.size())
if (a1.size() != a2.size())
return "array properties differ at "+path+": count "+Integer.toString(a1.size())+"/"+Integer.toString(a2.size());
for (int i = 0; i < a1.size(); i++) {
String s = compareNodes(path+"["+Integer.toString(i)+"]", a1.get(i), a2.get(i));

208
hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/BaseController.java
View File

@ -1,24 +1,31 @@
package ca.uhn.fhir.to;
import static org.apache.commons.lang3.StringUtils.defaultString;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.*;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Conformance;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.client.impl.GenericClient;
import ca.uhn.fhir.to.model.HomeRequest;
import ca.uhn.fhir.util.ExtensionConstants;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.Header;
import org.apache.http.entity.ContentType;
import org.apache.http.message.BasicHeader;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CapabilityStatement;
import org.hl7.fhir.dstu3.model.CapabilityStatement.CapabilityStatementRestComponent;
import org.hl7.fhir.dstu3.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IDomainResource;
@ -26,23 +33,19 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.ui.ModelMap;
import org.thymeleaf.TemplateEngine;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Conformance;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.impl.GenericClient;
import ca.uhn.fhir.to.model.HomeRequest;
import ca.uhn.fhir.util.ExtensionConstants;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class BaseController {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseController.class);
static final String PARAM_RESOURCE = "resource";
static final String RESOURCE_COUNT_EXT_URL = "http://hl7api.sourceforge.net/hapi-fhir/res/extdefs.html#resourceCount";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseController.class);
@Autowired
protected TesterConfig myConfig;
private Map<FhirVersionEnum, FhirContext> myContexts = new HashMap<FhirVersionEnum, FhirContext>();
@ -294,13 +297,15 @@ public class BaseController {
private IBaseResource loadAndAddConf(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
switch (theRequest.getFhirVersion(myConfig)) {
case DSTU2:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
case DSTU3:
return loadAndAddConfDstu3(theServletRequest, theRequest, theModel);
case DSTU2_1:
case DSTU2_HL7ORG:
break;
case DSTU2:
return loadAndAddConfDstu2(theServletRequest, theRequest, theModel);
case DSTU3:
return loadAndAddConfDstu3(theServletRequest, theRequest, theModel);
case R4:
return loadAndAddConfR4(theServletRequest, theRequest, theModel);
case DSTU2_1:
case DSTU2_HL7ORG:
break;
}
throw new IllegalStateException("Unknown version: " + theRequest.getFhirVersion(myConfig));
}
@ -379,7 +384,7 @@ public class BaseController {
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(capabilityStatement));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
@ -427,6 +432,67 @@ public class BaseController {
return capabilityStatement;
}
private IBaseResource loadAndAddConfR4(HttpServletRequest theServletRequest, final HomeRequest theRequest, final ModelMap theModel) {
CaptureInterceptor interceptor = new CaptureInterceptor();
GenericClient client = theRequest.newClient(theServletRequest, getContext(theRequest), myConfig, interceptor);
org.hl7.fhir.r4.model.CapabilityStatement capabilityStatement = new org.hl7.fhir.r4.model.CapabilityStatement();
try {
capabilityStatement = client.fetchConformance().ofType(org.hl7.fhir.r4.model.CapabilityStatement.class).execute();
} catch (Exception ex) {
ourLog.warn("Failed to load conformance statement, error was: {}", ex.toString());
theModel.put("errorMsg", toDisplayError("Failed to load conformance statement, error was: " + ex.toString(), ex));
}
theModel.put("jsonEncodedConf", getContext(theRequest).newJsonParser().encodeResourceToString(capabilityStatement));
Map<String, Number> resourceCounts = new HashMap<String, Number>();
long total = 0;
for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent nextRest : capabilityStatement.getRest()) {
for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
List<org.hl7.fhir.r4.model.Extension> exts = nextResource.getExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (exts != null && exts.size() > 0) {
Number nextCount = ((org.hl7.fhir.r4.model.DecimalType) (exts.get(0).getValue())).getValueAsNumber();
resourceCounts.put(nextResource.getTypeElement().getValue(), nextCount);
total += nextCount.longValue();
}
}
}
theModel.put("resourceCounts", resourceCounts);
if (total > 0) {
for (org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestComponent nextRest : capabilityStatement.getRest()) {
Collections.sort(nextRest.getResource(), new Comparator<org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent>() {
@Override
public int compare(org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent theO1, org.hl7.fhir.r4.model.CapabilityStatement.CapabilityStatementRestResourceComponent theO2) {
org.hl7.fhir.r4.model.DecimalType count1 = new org.hl7.fhir.r4.model.DecimalType();
List<org.hl7.fhir.r4.model.Extension> count1exts = theO1.getExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count1exts != null && count1exts.size() > 0) {
count1 = (org.hl7.fhir.r4.model.DecimalType) count1exts.get(0).getValue();
}
org.hl7.fhir.r4.model.DecimalType count2 = new org.hl7.fhir.r4.model.DecimalType();
List<org.hl7.fhir.r4.model.Extension> count2exts = theO2.getExtensionsByUrl(RESOURCE_COUNT_EXT_URL);
if (count2exts != null && count2exts.size() > 0) {
count2 = (org.hl7.fhir.r4.model.DecimalType) count2exts.get(0).getValue();
}
int retVal = count2.compareTo(count1);
if (retVal == 0) {
retVal = theO1.getTypeElement().getValue().compareTo(theO2.getTypeElement().getValue());
}
return retVal;
}
});
}
}
theModel.put("requiredParamExtension", ExtensionConstants.PARAM_IS_REQUIRED);
theModel.put("conf", capabilityStatement);
return capabilityStatement;
}
protected String logPrefix(ModelMap theModel) {
return "[server=" + theModel.get("serverId") + "] - ";
}
@ -485,7 +551,7 @@ public class BaseController {
}
protected void processAndAddLastClientInvocation(GenericClient theClient, ResultType theResultType, ModelMap theModelMap, long theLatency, String outcomeDescription,
CaptureInterceptor theInterceptor, HomeRequest theRequest) {
CaptureInterceptor theInterceptor, HomeRequest theRequest) {
try {
// ApacheHttpRequest lastRequest = theInterceptor.getLastRequest();
// HttpResponse lastResponse = theInterceptor.getLastResponse();
@ -505,7 +571,7 @@ public class BaseController {
// ContentType ct = lastResponse != null ? ContentType.get(lastResponse.getEntity()) : null;
// String mimeType = ct != null ? ct.getMimeType() : null;
IHttpRequest lastRequest = theInterceptor.getLastRequest();
IHttpResponse lastResponse = theInterceptor.getLastResponse();
String requestBody = null;
@ -524,7 +590,7 @@ public class BaseController {
resultStatus = "HTTP " + lastResponse.getStatus() + " " + lastResponse.getStatusInfo();
lastResponse.bufferEntity();
resultBody = IOUtils.toString(lastResponse.readEntity(), Constants.CHARSET_UTF8);
List<String> ctStrings = lastResponse.getHeaders(Constants.HEADER_CONTENT_TYPE);
if (ctStrings != null && ctStrings.isEmpty() == false) {
ct = ContentType.parse(ctStrings.get(0));
@ -543,25 +609,25 @@ public class BaseController {
resultDescription.append("Non-FHIR response");
} else {
switch (ctEnum) {
case JSON:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("JSON resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("JSON bundle");
riBundle = context.newJsonParser().parseResource(resultBody);
}
break;
case XML:
default:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("XML resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("XML bundle");
riBundle = context.newXmlParser().parseResource(resultBody);
}
break;
case JSON:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("JSON resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("JSON bundle");
riBundle = context.newJsonParser().parseResource(resultBody);
}
break;
case XML:
default:
if (theResultType == ResultType.RESOURCE) {
narrativeString = parseNarrative(theRequest, ctEnum, resultBody);
resultDescription.append("XML resource");
} else if (theResultType == ResultType.BUNDLE) {
resultDescription.append("XML bundle");
riBundle = context.newXmlParser().parseResource(resultBody);
}
break;
}
}
@ -599,6 +665,22 @@ public class BaseController {
}
/**
* A hook to be overridden by subclasses. The overriding method can modify the error message
* based on its content and/or the related exception.
*
* @param theErrorMsg The original error message to be displayed to the user.
* @param theException The exception that occurred. May be null.
* @return The modified error message to be displayed to the user.
*/
protected String toDisplayError(String theErrorMsg, Exception theException) {
return theErrorMsg;
}
protected enum ResultType {
BUNDLE, NONE, RESOURCE, TAGLIST
}
public static class CaptureInterceptor implements IClientInterceptor {
private IHttpRequest myLastRequest;
@ -620,7 +702,7 @@ public class BaseController {
@Override
public void interceptRequest(IHttpRequest theRequest) {
assert myLastRequest == null;
myLastRequest = theRequest;
}
@ -667,20 +749,4 @@ public class BaseController {
}
protected enum ResultType {
BUNDLE, NONE, RESOURCE, TAGLIST
}
/**
* A hook to be overridden by subclasses. The overriding method can modify the error message
* based on its content and/or the related exception.
*
* @param theErrorMsg The original error message to be displayed to the user.
* @param theException The exception that occurred. May be null.
* @return The modified error message to be displayed to the user.
*/
protected String toDisplayError(String theErrorMsg, Exception theException) {
return theErrorMsg;
}
}