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Cleanup

This commit is contained in:
jamesagnew 2022-01-16 14:40:51 -05:00 committed by James Agnew
parent f902d1d273
commit d3007ea73f
3 changed files with 4370 additions and 4378 deletions
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100
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
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@ -30,6 +30,31 @@ package org.hl7.fhir.r5.elementmodel;
*/ */
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorGson;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
@ -44,41 +69,8 @@ import java.util.Map;
import java.util.Map.Entry; import java.util.Map.Entry;
import java.util.Set; import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorGson;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
import org.slf4j.LoggerFactory;
public class JsonParser extends ParserBase { public class JsonParser extends ParserBase {
static {
// Helpful for troubleshooting why this class is being loaded
LoggerFactory.getLogger(JsonParser.class).debug("Loading JsonParser class");
}
private JsonCreator json; private JsonCreator json;
private Map<JsonElement, LocationData> map; private Map<JsonElement, LocationData> map;
private boolean allowComments; private boolean allowComments;
@ -99,7 +91,7 @@ public class JsonParser extends ParserBase {
public Element parse(String source, String type) throws Exception { public Element parse(String source, String type) throws Exception {
JsonObject obj = (JsonObject) new com.google.gson.JsonParser().parse(source); JsonObject obj = (JsonObject) new com.google.gson.JsonParser().parse(source);
String path = "/"+type; String path = "/" + type;
StructureDefinition sd = getDefinition(-1, -1, type); StructureDefinition sd = getDefinition(-1, -1, type);
if (sd == null) if (sd == null)
return null; return null;
@ -125,7 +117,7 @@ public class JsonParser extends ParserBase {
try { try {
obj = JsonTrackingParser.parse(source, map, false, allowComments); obj = JsonTrackingParser.parse(source, map, false, allowComments);
} catch (Exception e) { } catch (Exception e) {
logError(-1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL); logError(-1, -1, context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
return null; return null;
} }
assert (map.containsKey(obj)); assert (map.containsKey(obj));
@ -213,11 +205,11 @@ public class JsonParser extends ParserBase {
public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) { public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) {
if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) { if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) {
for (TypeRefComponent type : property.getDefinition().getType()) { for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode()); String eName = property.getName().substring(0, property.getName().length() - 3) + Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) { if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {
parseChildComplex(path, object, context, processed, property, eName); parseChildComplex(path, object, context, processed, property, eName);
break; break;
} else if (isPrimitive(type.getWorkingCode()) && (object.has(eName) || object.has("_"+eName))) { } else if (isPrimitive(type.getWorkingCode()) && (object.has(eName) || object.has("_" + eName))) {
parseChildPrimitive(object, context, processed, property, path, eName); parseChildPrimitive(object, context, processed, property, path, eName);
break; break;
} }
@ -231,17 +223,17 @@ public class JsonParser extends ParserBase {
private void parseChildComplex(String path, JsonObject object, Element element, Set<String> processed, Property property, String name) throws FHIRException { private void parseChildComplex(String path, JsonObject object, Element element, Set<String> processed, Property property, String name) throws FHIRException {
processed.add(name); processed.add(name);
String npath = path+"."+property.getName(); String npath = path + "." + property.getName();
String fpath = element.getPath()+"."+property.getName(); String fpath = element.getPath() + "." + property.getName();
JsonElement e = object.get(name); JsonElement e = object.get(name);
if (property.isList() && (e instanceof JsonArray)) { if (property.isList() && (e instanceof JsonArray)) {
JsonArray arr = (JsonArray) e; JsonArray arr = (JsonArray) e;
if (arr.size() == 0) { if (arr.size() == 0) {
logError(line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.ARRAY_CANNOT_BE_EMPTY), IssueSeverity.ERROR); logError(line(e), col(e), npath, IssueType.INVALID, context.formatMessage(I18nConstants.ARRAY_CANNOT_BE_EMPTY), IssueSeverity.ERROR);
} }
int c = 0; int c = 0;
for (JsonElement am : arr) { for (JsonElement am : arr) {
parseChildComplexInstance(npath+"["+c+"]", fpath+"["+c+"]", object, element, property, name, am); parseChildComplexInstance(npath + "[" + c + "]", fpath + "[" + c + "]", object, element, property, name, am);
c++; c++;
} }
} else { } else {
@ -293,12 +285,12 @@ public class JsonParser extends ParserBase {
} }
private void parseChildPrimitive(JsonObject object, Element element, Set<String> processed, Property property, String path, String name) throws FHIRException { private void parseChildPrimitive(JsonObject object, Element element, Set<String> processed, Property property, String path, String name) throws FHIRException {
String npath = path+"."+property.getName(); String npath = path + "." + property.getName();
String fpath = element.getPath()+"."+property.getName(); String fpath = element.getPath() + "." + property.getName();
processed.add(name); processed.add(name);
processed.add("_"+name); processed.add("_" + name);
JsonElement main = object.has(name) ? object.get(name) : null; JsonElement main = object.has(name) ? object.get(name) : null;
JsonElement fork = object.has("_"+name) ? object.get("_"+name) : null; JsonElement fork = object.has("_" + name) ? object.get("_" + name) : null;
if (main != null || fork != null) { if (main != null || fork != null) {
if (property.isList()) { if (property.isList()) {
boolean ok = true; boolean ok = true;
@ -336,7 +328,7 @@ public class JsonParser extends ParserBase {
private void parseChildPrimitiveInstance(Element element, Property property, String name, String npath, String fpath, JsonElement main, JsonElement fork) throws FHIRException { private void parseChildPrimitiveInstance(Element element, Property property, String name, String npath, String fpath, JsonElement main, JsonElement fork) throws FHIRException {
if (main != null && !(main instanceof JsonPrimitive)) if (main != null && !(main instanceof JsonPrimitive))
logError(line(main), col(main), npath, IssueType.INVALID, context.formatMessage( logError(line(main), col(main), npath, IssueType.INVALID, context.formatMessage(
I18nConstants.THIS_PROPERTY_MUST_BE_AN_SIMPLE_VALUE_NOT_, describe(main), name, npath), IssueSeverity.ERROR); I18nConstants.THIS_PROPERTY_MUST_BE_AN_SIMPLE_VALUE_NOT_, describe(main), name, npath), IssueSeverity.ERROR);
else if (fork != null && !(fork instanceof JsonObject)) else if (fork != null && !(fork instanceof JsonObject))
logError(line(fork), col(fork), npath, IssueType.INVALID, context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_OBJECT_NOT_, describe(fork), name, npath), IssueSeverity.ERROR); logError(line(fork), col(fork), npath, IssueType.INVALID, context.formatMessage(I18nConstants.THIS_PROPERTY_MUST_BE_AN_OBJECT_NOT_, describe(fork), name, npath), IssueSeverity.ERROR);
else { else {
@ -387,7 +379,7 @@ public class JsonParser extends ParserBase {
String name = rt.getAsString(); String name = rt.getAsString();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, context.getOverrideVersionNs())); StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, context.getOverrideVersionNs()));
if (sd == null) { if (sd == null) {
logError(line(res), col(res), npath, IssueType.INVALID, context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, name), IssueSeverity.FATAL); logError(line(res), col(res), npath, IssueType.INVALID, context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, name), IssueSeverity.FATAL);
} else { } else {
parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities), SpecialElement.fromProperty(parent.getProperty()), elementProperty); parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
parent.setType(name); parent.setType(name);
@ -406,14 +398,14 @@ public class JsonParser extends ParserBase {
} }
private int line(JsonElement e) { private int line(JsonElement e) {
if (map == null|| !map.containsKey(e)) if (map == null || !map.containsKey(e))
return -1; return -1;
else else
return map.get(e).getLine(); return map.get(e).getLine();
} }
private int col(JsonElement e) { private int col(JsonElement e) {
if (map == null|| !map.containsKey(e)) if (map == null || !map.containsKey(e))
return -1; return -1;
else else
return map.get(e).getCol(); return map.get(e).getCol();
@ -516,19 +508,19 @@ public class JsonParser extends ParserBase {
} }
closeArray(); closeArray();
} }
name = "_"+name; name = "_" + name;
} }
if (complex) { if (complex) {
openArray(name, linkResolver == null ? null : linkResolver.resolveProperty(list.get(0).getProperty())); openArray(name, linkResolver == null ? null : linkResolver.resolveProperty(list.get(0).getProperty()));
for (Element item : list) { for (Element item : list) {
if (item.hasChildren()) { if (item.hasChildren()) {
open(null,null); open(null, null);
if (item.getProperty().isResource()) { if (item.getProperty().isResource()) {
prop("resourceType", item.getType(), linkResolver == null ? null : linkResolver.resolveType(item.getType())); prop("resourceType", item.getType(), linkResolver == null ? null : linkResolver.resolveType(item.getType()));
} }
Set<String> done = new HashSet<String>(); Set<String> done = new HashSet<String>();
for (Element child : item.getChildren()) { for (Element child : item.getChildren()) {
compose(path+"."+name+"[]", item, done, child); compose(path + "." + name + "[]", item, done, child);
} }
close(); close();
} else } else
@ -564,7 +556,7 @@ public class JsonParser extends ParserBase {
if (element.isPrimitive() || isPrimitive(element.getType())) { if (element.isPrimitive() || isPrimitive(element.getType())) {
if (element.hasValue()) if (element.hasValue())
primitiveValue(name, element); primitiveValue(name, element);
name = "_"+name; name = "_" + name;
if (element.getType().equals("xhtml")) if (element.getType().equals("xhtml"))
json.anchor("end-xhtml"); json.anchor("end-xhtml");
} }
@ -575,7 +567,7 @@ public class JsonParser extends ParserBase {
} }
Set<String> done = new HashSet<String>(); Set<String> done = new HashSet<String>();
for (Element child : element.getChildren()) { for (Element child : element.getChildren()) {
compose(path+"."+element.getName(), element, done, child); compose(path + "." + element.getName(), element, done, child);
} }
close(); close();
} }

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
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@ -53,7 +53,6 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities; import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement; import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.FormatUtilities; import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.DateTimeType; import org.hl7.fhir.r5.model.DateTimeType;
@ -75,7 +74,6 @@ import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import org.hl7.fhir.utilities.xml.IXMLWriter; import org.hl7.fhir.utilities.xml.IXMLWriter;
import org.hl7.fhir.utilities.xml.XMLUtil; import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.utilities.xml.XMLWriter; import org.hl7.fhir.utilities.xml.XMLWriter;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document; import org.w3c.dom.Document;
import org.w3c.dom.Node; import org.w3c.dom.Node;
import org.xml.sax.InputSource; import org.xml.sax.InputSource;
@ -83,11 +81,6 @@ import org.xml.sax.XMLReader;
public class XmlParser extends ParserBase { public class XmlParser extends ParserBase {
static {
// Helpful for troubleshooting why this class is being loaded
LoggerFactory.getLogger(XmlParser.class).debug("Loading JsonParser class");
}
private boolean allowXsiLocation; private boolean allowXsiLocation;
private String version; private String version;

8641
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/XmlParser.java
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