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Merge pull request #833 from hapifhir/gg-202206-fhirpath 

fix bug counting children + fix issue with automatic string conversio…
This commit is contained in:
Grahame Grieve 2022-06-08 09:50:22 +10:00 committed by GitHub
parent a435beb29c b0dfc9f281
commit 2b3f7e7143
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
27 changed files with 358 additions and 176 deletions
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10
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
View File

@ -12,7 +12,7 @@ import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -132,12 +132,12 @@ public class PackageVisitor {
list.add(i.getId());
}
JsonObject json = JsonTrackingParser.fetchJson("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json");
for (JsonObject ig : JSONUtil.objects(json, "guides")) {
list.add(JSONUtil.str(ig, "npm-name"));
for (JsonObject ig : JsonUtilities.objects(json, "guides")) {
list.add(JsonUtilities.str(ig, "npm-name"));
}
json = JsonTrackingParser.fetchJson("https://raw.githubusercontent.com/FHIR/ig-registry/master/package-feeds.json");
for (JsonObject feed : JSONUtil.objects(json, "feeds")) {
processFeed(list, JSONUtil.str(feed, "url"));
for (JsonObject feed : JsonUtilities.objects(json, "feeds")) {
processFeed(list, JsonUtilities.str(feed, "url"));
}
return list;

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/NpmPackageVersionConverter.java
View File

@ -13,7 +13,7 @@ import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_50;
import org.hl7.fhir.convertors.factory.*;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.NpmPackageIndexBuilder;
@ -167,7 +167,7 @@ public class NpmPackageVersionConverter {
private byte[] convertPackage(byte[] cnt) throws IOException {
JsonObject json = JsonTrackingParser.parseJson(cnt);
currentVersion = json.getAsJsonArray("fhirVersions").get(0).getAsString();
String name = JSONUtil.str(json, "name");
String name = JsonUtilities.str(json, "name");
json.remove("name");
json.addProperty("name", name + "." + vCode);
json.remove("fhirVersions");

10
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/elementmodel/SHCParser.java
View File

@ -22,7 +22,7 @@ import org.hl7.fhir.r4b.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -73,7 +73,7 @@ public class SHCParser extends ParserBase {
int i = 0;
for (JsonElement e : arr) {
if (!(e instanceof JsonPrimitive)) {
logError(line(e), col(e), "$.verifiableCredential["+i+"]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found "+JSONUtil.type(e), IssueSeverity.ERROR);
logError(line(e), col(e), "$.verifiableCredential["+i+"]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found "+JsonUtilities.type(e), IssueSeverity.ERROR);
} else {
list.add(e.getAsString());
}
@ -117,7 +117,7 @@ public class SHCParser extends ParserBase {
int i = 0;
for (JsonElement e : type) {
if (!(e instanceof JsonPrimitive)) {
logError(line(e), col(e), path+".type["+i+"]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found "+JSONUtil.type(e), IssueSeverity.ERROR);
logError(line(e), col(e), path+".type["+i+"]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found "+JsonUtilities.type(e), IssueSeverity.ERROR);
} else {
types.add(e.getAsString());
}
@ -171,7 +171,7 @@ public class SHCParser extends ParserBase {
private boolean checkProperty(JsonObject obj, String path, String name, boolean required, String type) {
JsonElement e = obj.get(name);
if (e != null) {
String t = JSONUtil.type(e);
String t = JsonUtilities.type(e);
if (!type.equals(t)) {
logError(line(e), col(e), path+"."+name, IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : "+type+" but found "+t, IssueSeverity.ERROR);
} else {
@ -275,7 +275,7 @@ public class SHCParser extends ParserBase {
}
JWT res = new JWT();
res.header = JsonTrackingParser.parseJson(headerJson);
if ("DEF".equals(JSONUtil.str(res.header, "zip"))) {
if ("DEF".equals(JsonUtilities.str(res.header, "zip"))) {
payloadJson = inflate(payloadJson);
}
res.payload = JsonTrackingParser.parse(TextFile.bytesToString(payloadJson), res.map, true);

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -3744,7 +3744,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
} else if (Utilities.isAbsoluteUrl(u)) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, u);
if (sd != null) {
if (sd != null && pkp != null) {
String disp = sd.hasTitle() ? sd.getTitle() : sd.getName();
String ref = pkp.getLinkForProfile(null, sd.getUrl());
if (ref != null && ref.contains("|"))

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -1102,11 +1102,13 @@ public class Element extends Base {
public int countDescendents() {
if (descendentCount > 0) {
return descendentCount;
} else {
} else if (children != null) {
descendentCount = children.size();
for (Element e : children) {
descendentCount = descendentCount + e.countDescendents();
}
} else {
descendentCount = 0;
}
return descendentCount;
}

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/SHCParser.java
View File

@ -22,7 +22,7 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonTrackingParser.LocationData;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -73,7 +73,7 @@ public class SHCParser extends ParserBase {
int i = 0;
for (JsonElement e : arr) {
if (!(e instanceof JsonPrimitive)) {
logError(line(e), col(e), "$.verifiableCredential["+i+"]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found "+JSONUtil.type(e), IssueSeverity.ERROR);
logError(line(e), col(e), "$.verifiableCredential["+i+"]", IssueType.STRUCTURE, "Wrong Property verifiableCredential in JSON Payload. Expected : String but found "+JsonUtilities.type(e), IssueSeverity.ERROR);
} else {
list.add(e.getAsString());
}
@ -117,7 +117,7 @@ public class SHCParser extends ParserBase {
int i = 0;
for (JsonElement e : type) {
if (!(e instanceof JsonPrimitive)) {
logError(line(e), col(e), path+".type["+i+"]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found "+JSONUtil.type(e), IssueSeverity.ERROR);
logError(line(e), col(e), path+".type["+i+"]", IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : String but found "+JsonUtilities.type(e), IssueSeverity.ERROR);
} else {
types.add(e.getAsString());
}
@ -171,7 +171,7 @@ public class SHCParser extends ParserBase {
private boolean checkProperty(JsonObject obj, String path, String name, boolean required, String type) {
JsonElement e = obj.get(name);
if (e != null) {
String t = JSONUtil.type(e);
String t = JsonUtilities.type(e);
if (!type.equals(t)) {
logError(line(e), col(e), path+"."+name, IssueType.STRUCTURE, "Wrong Property Type in JSON Payload. Expected : "+type+" but found "+t, IssueSeverity.ERROR);
} else {
@ -275,7 +275,7 @@ public class SHCParser extends ParserBase {
}
JWT res = new JWT();
res.header = JsonTrackingParser.parseJson(headerJson);
if ("DEF".equals(JSONUtil.str(res.header, "zip"))) {
if ("DEF".equals(JsonUtilities.str(res.header, "zip"))) {
payloadJson = inflate(payloadJson);
}
res.payload = JsonTrackingParser.parse(TextFile.bytesToString(payloadJson), res.map, true);

35
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -262,6 +262,7 @@ public class FHIRPathEngine {
private ProfileUtilities profileUtilities;
private String location; // for error messages
private boolean allowPolymorphicNames;
private boolean doImplicitStringConversion;
// if the fhir path expressions are allowed to use constants beyond those defined in the specification
// the application can implement them by providing a constant resolver
@ -447,6 +448,14 @@ public class FHIRPathEngine {
}
public boolean isDoImplicitStringConversion() {
return doImplicitStringConversion;
}
public void setDoImplicitStringConversion(boolean doImplicitStringConversion) {
this.doImplicitStringConversion = doImplicitStringConversion;
}
// --- public API -------------------------------------------------------
/**
* Parse a path for later use using execute
@ -4211,6 +4220,7 @@ public class FHIRPathEngine {
List<Base> result = new ArrayList<Base>();
if (focus.size() == 1) {
if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String f = convertToString(focus.get(0));
if (Utilities.noString(f)) {
result.add(new StringType(""));
@ -4220,6 +4230,7 @@ public class FHIRPathEngine {
String n = f.replace(t, r);
result.add(new StringType(n));
}
}
} else {
throw makeException(expr, I18nConstants.FHIRPATH_NO_COLLECTION, "replace", focus.size());
}
@ -4233,7 +4244,9 @@ public class FHIRPathEngine {
String repl = convertToString(execute(context, focus, exp.getParameters().get(1), true));
if (focus.size() == 1 && !Utilities.noString(regex)) {
if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
result.add(new StringType(convertToString(focus.get(0)).replaceAll(regex, repl)).noExtensions());
}
} else {
result.add(new StringType(convertToString(focus.get(0))).noExtensions());
}
@ -4249,7 +4262,7 @@ public class FHIRPathEngine {
result.add(new BooleanType(false).noExtensions());
} else if (Utilities.noString(sw)) {
result.add(new BooleanType(true).noExtensions());
} else {
} else if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
if (focus.size() == 1 && !Utilities.noString(sw)) {
result.add(new BooleanType(convertToString(focus.get(0)).endsWith(sw)).noExtensions());
} else {
@ -4919,6 +4932,7 @@ public class FHIRPathEngine {
String sw = convertToString(execute(context, focus, exp.getParameters().get(0), true));
if (focus.size() == 1 && !Utilities.noString(sw)) {
if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String st = convertToString(focus.get(0));
if (Utilities.noString(st)) {
result.add(new BooleanType(false).noExtensions());
@ -4928,6 +4942,7 @@ public class FHIRPathEngine {
boolean ok = m.find();
result.add(new BooleanType(ok).noExtensions());
}
}
} else {
result.add(new BooleanType(false).noExtensions());
}
@ -4939,6 +4954,7 @@ public class FHIRPathEngine {
String sw = convertToString(execute(context, focus, exp.getParameters().get(0), true));
if (focus.size() == 1 && !Utilities.noString(sw)) {
if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String st = convertToString(focus.get(0));
if (Utilities.noString(st)) {
result.add(new BooleanType(false).noExtensions());
@ -4948,6 +4964,7 @@ public class FHIRPathEngine {
boolean ok = m.matches();
result.add(new BooleanType(ok).noExtensions());
}
}
} else {
result.add(new BooleanType(false).noExtensions());
}
@ -4962,7 +4979,7 @@ public class FHIRPathEngine {
result.add(new BooleanType(false).noExtensions());
} else if (Utilities.noString(sw)) {
result.add(new BooleanType(true).noExtensions());
} else {
} else if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String st = convertToString(focus.get(0));
if (Utilities.noString(st)) {
result.add(new BooleanType(false).noExtensions());
@ -4981,7 +4998,7 @@ public class FHIRPathEngine {
private List<Base> funcLength(ExecutionContext context, List<Base> focus, ExpressionNode exp) {
List<Base> result = new ArrayList<Base>();
if (focus.size() == 1) {
if (focus.size() == 1 && (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion)) {
String s = convertToString(focus.get(0));
result.add(new IntegerType(s.length()).noExtensions());
}
@ -5007,7 +5024,7 @@ public class FHIRPathEngine {
result.add(new BooleanType(false).noExtensions());
} else if (Utilities.noString(sw)) {
result.add(new BooleanType(true).noExtensions());
} else {
} else if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String s = convertToString(focus.get(0));
if (s == null) {
result.add(new BooleanType(false).noExtensions());
@ -5020,7 +5037,7 @@ public class FHIRPathEngine {
private List<Base> funcLower(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> result = new ArrayList<Base>();
if (focus.size() == 1) {
if (focus.size() == 1 && (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion)) {
String s = convertToString(focus.get(0));
if (!Utilities.noString(s)) {
result.add(new StringType(s.toLowerCase()).noExtensions());
@ -5031,7 +5048,7 @@ public class FHIRPathEngine {
private List<Base> funcUpper(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> result = new ArrayList<Base>();
if (focus.size() == 1) {
if (focus.size() == 1 && (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion)) {
String s = convertToString(focus.get(0));
if (!Utilities.noString(s)) {
result.add(new StringType(s.toUpperCase()).noExtensions());
@ -5042,7 +5059,7 @@ public class FHIRPathEngine {
private List<Base> funcToChars(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> result = new ArrayList<Base>();
if (focus.size() == 1) {
if (focus.size() == 1 && (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion)) {
String s = convertToString(focus.get(0));
for (char c : s.toCharArray()) {
result.add(new StringType(String.valueOf(c)).noExtensions());
@ -5059,7 +5076,7 @@ public class FHIRPathEngine {
result.add(new IntegerType(0).noExtensions());
} else if (Utilities.noString(sw)) {
result.add(new IntegerType(0).noExtensions());
} else {
} else if (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion) {
String s = convertToString(focus.get(0));
if (s == null) {
result.add(new IntegerType(0).noExtensions());
@ -5080,7 +5097,7 @@ public class FHIRPathEngine {
i2 = Integer.parseInt(n2.get(0).primitiveValue());
}
if (focus.size() == 1) {
if (focus.size() == 1 && (focus.get(0).hasType(FHIR_TYPES_STRING) || doImplicitStringConversion)) {
String sw = convertToString(focus.get(0));
String s;
if (i1 < 0 || i1 >= sw.length()) {

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SimpleHTTPClient.java
View File

@ -71,7 +71,7 @@ public class SimpleHTTPClient {
public void checkThrowException() throws IOException {
if (code >= 300) {
String filename = Utilities.path("[tmp]", "fhir-http-"+(++counter)+".log");
if (content.length == 0) {
if (content == null || content.length == 0) {
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (no content)");
} else {
TextFile.bytesToFile(content, filename);

24
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
View File

@ -1333,6 +1333,30 @@ public class Utilities {
return false;
}
public static boolean endsWithInList(String s, String... list) {
if (s == null) {
return false;
}
for (String l : list) {
if (s.endsWith(l)) {
return true;
}
}
return false;
}
public static boolean endsWithInList(String s, Collection<String> list) {
if (s == null) {
return false;
}
for (String l : list) {
if (s.endsWith(l)) {
return true;
}
}
return false;
}
public static final int ONE_MB = 1024;
public static final String GB = "Gb";
public static final String MB = "Mb";

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JSONUtil.java → org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JsonUtilities.java
View File

@ -45,7 +45,7 @@ import com.google.gson.JsonNull;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
public class JSONUtil {
public class JsonUtilities {
public static JsonObject parse(String json) throws IOException {
return JsonTrackingParser.parseJson(json);
@ -155,4 +155,15 @@ public class JSONUtil {
return "String";
}
public static List<String> strings(JsonArray arr) {
List<String> res = new ArrayList<String>();
for (int i = 0; i < arr.size(); i++) {
JsonElement n = arr.get(i);
if (n.isJsonPrimitive()) {
res.add(n.getAsString());
}
}
return res;
}
}

52
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
View File

@ -42,7 +42,7 @@ import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.NpmPackage.NpmPackageFolder;
import org.slf4j.Logger;
@ -414,14 +414,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
log(" done.");
}
pck = loadPackageInfo(packRoot);
if (!id.equals(JSONUtil.str(npm.getNpm(), "name")) || !v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
if (!id.equals(JSONUtil.str(npm.getNpm(), "name"))) {
npm.getNpm().addProperty("original-name", JSONUtil.str(npm.getNpm(), "name"));
if (!id.equals(JsonUtilities.str(npm.getNpm(), "name")) || !v.equals(JsonUtilities.str(npm.getNpm(), "version"))) {
if (!id.equals(JsonUtilities.str(npm.getNpm(), "name"))) {
npm.getNpm().addProperty("original-name", JsonUtilities.str(npm.getNpm(), "name"));
npm.getNpm().remove("name");
npm.getNpm().addProperty("name", id);
}
if (!v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
npm.getNpm().addProperty("original-version", JSONUtil.str(npm.getNpm(), "version"));
if (!v.equals(JsonUtilities.str(npm.getNpm(), "version"))) {
npm.getNpm().addProperty("original-version", JsonUtilities.str(npm.getNpm(), "version"));
npm.getNpm().remove("version");
npm.getNpm().addProperty("version", v);
}
@ -566,8 +566,8 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
checkBuildLoaded();
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (packageId.equals(JSONUtil.str(o, "package-id"))) {
return JSONUtil.str(o, "url");
if (packageId.equals(JsonUtilities.str(o, "package-id"))) {
return JsonUtilities.str(o, "url");
}
}
return null;
@ -577,8 +577,8 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
checkBuildLoaded();
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (!specList.containsKey(JSONUtil.str(o, "package-id"))) {
specList.put(JSONUtil.str(o, "package-id"), JSONUtil.str(o, "url"));
if (!specList.containsKey(JsonUtilities.str(o, "package-id"))) {
specList.put(JsonUtilities.str(o, "package-id"), JsonUtilities.str(o, "url"));
}
}
}
@ -604,8 +604,8 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
for (String pf : listPackages()) {
if (new File(Utilities.path(cacheFolder, pf, "package", "package.json")).exists()) {
JsonObject npm = JsonTrackingParser.parseJsonFile(Utilities.path(cacheFolder, pf, "package", "package.json"));
if (canonicalUrl.equals(JSONUtil.str(npm, "canonical"))) {
return JSONUtil.str(npm, "name");
if (canonicalUrl.equals(JsonUtilities.str(npm, "canonical"))) {
return JsonUtilities.str(npm, "name");
}
}
}
@ -624,14 +624,14 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
if (buildInfo != null) {
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (canonical.equals(JSONUtil.str(o, "url"))) {
return JSONUtil.str(o, "package-id");
if (canonical.equals(JsonUtilities.str(o, "url"))) {
return JsonUtilities.str(o, "package-id");
}
}
for (JsonElement n : buildInfo) {
JsonObject o = (JsonObject) n;
if (JSONUtil.str(o, "url").startsWith(canonical + "/ImplementationGuide/")) {
return JSONUtil.str(o, "package-id");
if (JsonUtilities.str(o, "url").startsWith(canonical + "/ImplementationGuide/")) {
return JsonUtilities.str(o, "package-id");
}
}
}
@ -644,7 +644,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
try {
String url = ciList.get(id);
JsonObject json = JsonTrackingParser.fetchJson(Utilities.pathURL(url, "package.manifest.json"));
String currDate = JSONUtil.str(json, "date");
String currDate = JsonUtilities.str(json, "date");
String packDate = p.date();
if (!currDate.equals(packDate)) {
return null; // nup, we need a new copy
@ -740,13 +740,13 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
throw new FHIRException("Error fetching package directly (" + pv + "), or fetching package list for " + id + " from " + pu + ": " + e1.getMessage(), e1);
}
}
if (!id.equals(JSONUtil.str(json, "package-id")))
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JSONUtil.str(json, "package-id"));
if (!id.equals(JsonUtilities.str(json, "package-id")))
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JsonUtilities.str(json, "package-id"));
for (JsonElement e : json.getAsJsonArray("list")) {
JsonObject vo = (JsonObject) e;
if (v.equals(JSONUtil.str(vo, "version"))) {
aurl = Utilities.pathURL(JSONUtil.str(vo, "path"), "package.tgz");
String u = Utilities.pathURL(JSONUtil.str(vo, "path"), "package.tgz");
if (v.equals(JsonUtilities.str(vo, "version"))) {
aurl = Utilities.pathURL(JsonUtilities.str(vo, "path"), "package.tgz");
String u = Utilities.pathURL(JsonUtilities.str(vo, "path"), "package.tgz");
return new InputStreamWithSrc(fetchFromUrlSpecific(u, true), u, v);
}
}
@ -771,12 +771,12 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
}
String pu = Utilities.pathURL(url, "package-list.json");
JsonObject json = JsonTrackingParser.fetchJson(pu);
if (!id.equals(JSONUtil.str(json, "package-id")))
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JSONUtil.str(json, "package-id"));
if (!id.equals(JsonUtilities.str(json, "package-id")))
throw new FHIRException("Package ids do not match in " + pu + ": " + id + " vs " + JsonUtilities.str(json, "package-id"));
for (JsonElement e : json.getAsJsonArray("list")) {
JsonObject vo = (JsonObject) e;
if (JSONUtil.bool(vo, "current")) {
return JSONUtil.str(vo, "version");
if (JsonUtilities.bool(vo, "current")) {
return JsonUtilities.str(vo, "version");
}
}

91
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
View File

@ -67,7 +67,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.NpmPackage.ITransformingLoader;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformationSorter;
@ -113,12 +113,12 @@ public class NpmPackage {
public PackageResourceInformation(String root, JsonObject fi) throws IOException {
super();
id = JSONUtil.str(fi, "id");
type = JSONUtil.str(fi, "resourceType");
url = JSONUtil.str(fi, "url");
version = JSONUtil.str(fi, "version");
filename = Utilities.path(root, JSONUtil.str(fi, "filename"));
supplements = JSONUtil.str(fi, "supplements");
id = JsonUtilities.str(fi, "id");
type = JsonUtilities.str(fi, "resourceType");
url = JsonUtilities.str(fi, "url");
version = JsonUtilities.str(fi, "version");
filename = Utilities.path(root, JsonUtilities.str(fi, "filename"));
supplements = JsonUtilities.str(fi, "supplements");
}
public String getId() {
return id;
@ -144,8 +144,8 @@ public class NpmPackage {
@Override
public int compare(JsonObject o0, JsonObject o1) {
String v0 = JSONUtil.str(o0, "version");
String v1 = JSONUtil.str(o1, "version");
String v0 = JsonUtilities.str(o0, "version");
String v1 = JsonUtilities.str(o1, "version");
return v0.compareTo(v1);
}
}
@ -185,8 +185,8 @@ public class NpmPackage {
this.index = index;
for (JsonElement e : index.getAsJsonArray("files")) {
JsonObject file = (JsonObject) e;
String type = JSONUtil.str(file, "resourceType");
String name = JSONUtil.str(file, "filename");
String type = JsonUtilities.str(file, "resourceType");
String name = JsonUtilities.str(file, "filename");
if (!types.containsKey(type))
types.put(type, new ArrayList<>());
types.get(type).add(name);
@ -326,7 +326,8 @@ public class NpmPackage {
}
public static boolean isInternalExemptFile(File f) {
return Utilities.existsInList(f.getName(), ".git", ".svn") || Utilities.existsInList(f.getName(), "package-list.json");
return Utilities.existsInList(f.getName(), ".git", ".svn", ".DS_Store") || Utilities.existsInList(f.getName(), "package-list.json") ||
Utilities.endsWithInList(f.getName(), ".tgz");
}
private void loadSubFolders(String rootPath, File dir) throws IOException {
@ -552,7 +553,7 @@ public class NpmPackage {
if (folder.index != null) {
for (JsonElement e : folder.index.getAsJsonArray("files")) {
JsonObject fi = e.getAsJsonObject();
if (Utilities.existsInList(JSONUtil.str(fi, "resourceType"), types)) {
if (Utilities.existsInList(JsonUtilities.str(fi, "resourceType"), types)) {
res.add(new PackageResourceInformation(folder.folder.getAbsolutePath(), fi));
}
}
@ -625,19 +626,19 @@ public class NpmPackage {
List<JsonObject> matches = new ArrayList<>();
for (JsonElement e : f.index.getAsJsonArray("files")) {
JsonObject file = (JsonObject) e;
if (canonical.equals(JSONUtil.str(file, "url"))) {
if (version != null && version.equals(JSONUtil.str(file, "version"))) {
return load("package", JSONUtil.str(file, "filename"));
if (canonical.equals(JsonUtilities.str(file, "url"))) {
if (version != null && version.equals(JsonUtilities.str(file, "version"))) {
return load("package", JsonUtilities.str(file, "filename"));
} else if (version == null) {
matches.add(file);
}
}
if (matches.size() > 0) {
if (matches.size() == 1) {
return load("package", JSONUtil.str(matches.get(0), "filename"));
return load("package", JsonUtilities.str(matches.get(0), "filename"));
} else {
Collections.sort(matches, new IndexVersionSorter());
return load("package", JSONUtil.str(matches.get(matches.size()-1), "filename"));
return load("package", JsonUtilities.str(matches.get(matches.size()-1), "filename"));
}
}
}
@ -697,7 +698,7 @@ public class NpmPackage {
* @return
*/
public String name() {
return JSONUtil.str(npm, "name");
return JsonUtilities.str(npm, "name");
}
/**
@ -705,15 +706,15 @@ public class NpmPackage {
* @return
*/
public String id() {
return JSONUtil.str(npm, "name");
return JsonUtilities.str(npm, "name");
}
public String date() {
return JSONUtil.str(npm, "date");
return JsonUtilities.str(npm, "date");
}
public String canonical() {
return JSONUtil.str(npm, "canonical");
return JsonUtilities.str(npm, "canonical");
}
/**
@ -721,7 +722,7 @@ public class NpmPackage {
* @return
*/
public String version() {
return JSONUtil.str(npm, "version");
return JsonUtilities.str(npm, "version");
}
/**
@ -729,11 +730,11 @@ public class NpmPackage {
* @return
*/
public String fhirVersion() {
if ("hl7.fhir.core".equals(JSONUtil.str(npm, "name")))
return JSONUtil.str(npm, "version");
else if (JSONUtil.str(npm, "name").startsWith("hl7.fhir.r2.") || JSONUtil.str(npm, "name").startsWith("hl7.fhir.r2b.") || JSONUtil.str(npm, "name").startsWith("hl7.fhir.r3.") ||
JSONUtil.str(npm, "name").startsWith("hl7.fhir.r4.") || JSONUtil.str(npm, "name").startsWith("hl7.fhir.r4b.") || JSONUtil.str(npm, "name").startsWith("hl7.fhir.r5."))
return JSONUtil.str(npm, "version");
if ("hl7.fhir.core".equals(JsonUtilities.str(npm, "name")))
return JsonUtilities.str(npm, "version");
else if (JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r2.") || JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r2b.") || JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r3.") ||
JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r4.") || JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r4b.") || JsonUtilities.str(npm, "name").startsWith("hl7.fhir.r5."))
return JsonUtilities.str(npm, "version");
else {
JsonObject dep = null;
if (npm.has("dependencies") && npm.get("dependencies").isJsonObject()) {
@ -778,11 +779,11 @@ public class NpmPackage {
}
public String type() {
return JSONUtil.str(npm, "type");
return JsonUtilities.str(npm, "type");
}
public String description() {
return JSONUtil.str(npm, "description");
return JsonUtilities.str(npm, "description");
}
public String getPath() {
@ -800,24 +801,24 @@ public class NpmPackage {
}
public String homepage() {
return JSONUtil.str(npm, "homepage");
return JsonUtilities.str(npm, "homepage");
}
public String url() {
return JSONUtil.str(npm, "url");
return JsonUtilities.str(npm, "url");
}
public String title() {
return JSONUtil.str(npm, "title");
return JsonUtilities.str(npm, "title");
}
public String toolsVersion() {
return JSONUtil.str(npm, "tools-version");
return JsonUtilities.str(npm, "tools-version");
}
public String license() {
return JSONUtil.str(npm, "license");
return JsonUtilities.str(npm, "license");
}
// /**
@ -833,7 +834,7 @@ public class NpmPackage {
if (npm.has("url") && npm.get("url").isJsonPrimitive()) {
return PackageHacker.fixPackageUrl(npm.get("url").getAsString());
} else {
return JSONUtil.str(npm, "canonical");
return JsonUtilities.str(npm, "canonical");
}
}
@ -842,8 +843,8 @@ public class NpmPackage {
JsonArray files = f.index.getAsJsonArray("files");
for (JsonElement e : files) {
JsonObject i = (JsonObject) e;
if (type.equals(JSONUtil.str(i, "resourceType")) && id.equals(JSONUtil.str(i, "id"))) {
return load("package", JSONUtil.str(i, "filename"));
if (type.equals(JsonUtilities.str(i, "resourceType")) && id.equals(JsonUtilities.str(i, "id"))) {
return load("package", JsonUtilities.str(i, "filename"));
}
}
return null;
@ -858,8 +859,8 @@ public class NpmPackage {
JsonArray files = f.index.getAsJsonArray("files");
for (JsonElement e : files) {
JsonObject i = (JsonObject) e;
if (type.equals(JSONUtil.str(i, "resourceType")) && id.equals(JSONUtil.str(i, "id"))) {
return load("example", JSONUtil.str(i, "filename"));
if (type.equals(JsonUtilities.str(i, "resourceType")) && id.equals(JsonUtilities.str(i, "id"))) {
return load("example", JsonUtilities.str(i, "filename"));
}
}
}
@ -1094,7 +1095,7 @@ public class NpmPackage {
}
public boolean isCore() {
return Utilities.existsInList(JSONUtil.str(npm, "type"), "fhir.core", "Core");
return Utilities.existsInList(JsonUtilities.str(npm, "type"), "fhir.core", "Core");
}
public boolean hasCanonical(String url) {
@ -1107,8 +1108,8 @@ public class NpmPackage {
if (folder != null) {
for (JsonElement e : folder.index.getAsJsonArray("files")) {
JsonObject o = (JsonObject) e;
if (u.equals(JSONUtil.str(o, "url"))) {
if (v == null || v.equals(JSONUtil.str(o, "version"))) {
if (u.equals(JsonUtilities.str(o, "url"))) {
if (v == null || v.equals(JsonUtilities.str(o, "version"))) {
return true;
}
}
@ -1126,7 +1127,7 @@ public class NpmPackage {
if (Utilities.existsInList(name(), "fhir.test.data.r2", "fhir.test.data.r3", "fhir.test.data.r4", "fhir.tx.support.r2", "fhir.tx.support.r3", "fhir.tx.support.r4", "us.nlm.vsac")) {
return true;
}
if (JSONUtil.bool(npm, "lazy-load")) {
if (JsonUtilities.bool(npm, "lazy-load")) {
return true;
}
if (!hasFile("other", "spec.internals")) {
@ -1136,7 +1137,7 @@ public class NpmPackage {
}
public boolean isNotForPublication() {
return JSONUtil.bool(npm, "notForPublication");
return JsonUtilities.bool(npm, "notForPublication");
}
public InputStream load(PackageResourceInformation p) throws FileNotFoundException {

48
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageClient.java
View File

@ -9,7 +9,7 @@ import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import java.io.ByteArrayInputStream;
@ -81,12 +81,12 @@ public class PackageClient {
if (versions != null) {
for (String v : sorted(versions.keySet())) {
JsonObject obj = versions.getAsJsonObject(v);
res.add(new PackageInfo(JSONUtil.str(obj, "Name", "name"),
JSONUtil.str(obj, "Version", "version"),
JSONUtil.str(obj, "FhirVersion", "fhirVersion"),
JSONUtil.str(obj, "Description", "description"),
JSONUtil.str(obj, "url"),
JSONUtil.str(obj, "canonical"),
res.add(new PackageInfo(JsonUtilities.str(obj, "Name", "name"),
JsonUtilities.str(obj, "Version", "version"),
JsonUtilities.str(obj, "FhirVersion", "fhirVersion"),
JsonUtilities.str(obj, "Description", "description"),
JsonUtilities.str(obj, "url"),
JsonUtilities.str(obj, "canonical"),
address));
}
}
@ -121,12 +121,12 @@ public class PackageClient {
JsonArray json = fetchJsonArray(Utilities.pathURL(address, "catalog?")+params.toString());
for (JsonElement e : json) {
JsonObject obj = (JsonObject) e;
res.add(new PackageInfo(JSONUtil.str(obj, "Name", "name"),
JSONUtil.str(obj, "Version", "version"),
JSONUtil.str(obj, "FhirVersion", "fhirVersion"),
JSONUtil.str(obj, "Description", "description"),
JSONUtil.str(obj, "url"),
JSONUtil.str(obj, "canonical"),
res.add(new PackageInfo(JsonUtilities.str(obj, "Name", "name"),
JsonUtilities.str(obj, "Version", "version"),
JsonUtilities.str(obj, "FhirVersion", "fhirVersion"),
JsonUtilities.str(obj, "Description", "description"),
JsonUtilities.str(obj, "url"),
JsonUtilities.str(obj, "canonical"),
address));
}
} catch (IOException e1) {
@ -192,10 +192,10 @@ public class PackageClient {
}
protected PackageInfo getPackageInfoFromJSON(JsonObject o, String name, String canonical, String fhirVersion) {
String id = JSONUtil.str(o, "npm-name");
String pname = JSONUtil.str(o, "name");
String pcanonical = JSONUtil.str(o, "canonical");
String description = JSONUtil.str(o, "description");
String id = JsonUtilities.str(o, "npm-name");
String pname = JsonUtilities.str(o, "name");
String pcanonical = JsonUtilities.str(o, "canonical");
String description = JsonUtilities.str(o, "description");
boolean ok = true;
if (ok && !Utilities.noString(name)) {
ok = (pname != null && pname.contains(name)) || (description != null && description.contains(name)) || (id != null && id.contains(name));
@ -209,15 +209,15 @@ public class PackageClient {
if (ok) {
// if we can find something...
for (JsonObject e : JSONUtil.objects(o, "editions")) {
if (fhirVersion == null || fhirVersion.equals(JSONUtil.str(e, "fhir-version"))) {
String v = JSONUtil.str(e, "ig-version");
for (JsonObject e : JsonUtilities.objects(o, "editions")) {
if (fhirVersion == null || fhirVersion.equals(JsonUtilities.str(e, "fhir-version"))) {
String v = JsonUtilities.str(e, "ig-version");
if (version == null || VersionUtilities.isThisOrLater(version, v)) {
version = v;
fVersion = e.getAsJsonArray("fhir-version").get(0).getAsString();
url = JSONUtil.str(e, "url");
url = JsonUtilities.str(e, "url");
String npmPackage = JSONUtil.str(e, "package");
String npmPackage = JsonUtilities.str(e, "package");
if (npmPackage != null && id == null) {
id = npmPackage.substring(0, npmPackage.indexOf("#"));
}
@ -231,7 +231,7 @@ public class PackageClient {
public List<PackageInfo> listFromRegistry(String name, String canonical, String fhirVersion) throws IOException {
List<PackageInfo> result = new ArrayList<>();
JsonObject packages = JsonTrackingParser.fetchJson("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json?nocache=" + System.currentTimeMillis());
for (JsonObject o : JSONUtil.objects(packages, "guides")) {
for (JsonObject o : JsonUtilities.objects(packages, "guides")) {
if (o.has("canonical")) {
final PackageInfo packageInfo = getPackageInfoFromJSON(o, name, canonical, fhirVersion);
if (packageInfo.getVersion() != null) {
@ -249,7 +249,7 @@ public class PackageClient {
JsonArray json = fetchJsonArray(Utilities.pathURL(address, "catalog?")+params.toString());
for (JsonElement e : json) {
JsonObject obj = (JsonObject) e;
list.add(JSONUtil.str(obj, "Name", "name"));
list.add(JsonUtilities.str(obj, "Name", "name"));
}
} catch (IOException e1) {
}

52
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageHacker.java
View File

@ -5,6 +5,7 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@ -27,7 +28,7 @@ public class PackageHacker {
private static boolean useSecureReferences = false;
public static void main(String[] args) throws FileNotFoundException, IOException {
new PackageHacker().edit("/Users/grahamegrieve/work/test-cases/validator/swiss.mednet.fhir#0.5.0.tgz");
new PackageHacker().edit(args[0]);
}
private void edit(String name) throws FileNotFoundException, IOException {
@ -39,7 +40,14 @@ public class PackageHacker {
System.out.println("Altering Package "+f.getAbsolutePath());
System.out.println(nice(pck.getNpm()));
change(pck.getNpm(), pck.getFolders().get("package").getContent());
change(pck.getNpm());
fixContent(pck.getFolders().get("package").getContent());
if (pck.getFolders().containsKey("openapi")) {
fixContent(pck.getFolders().get("openapi").getContent());
}
if (pck.getFolders().containsKey("xml")) {
fixContent(pck.getFolders().get("xml").getContent());
}
System.out.println("Revised Package");
System.out.println("=======================");
@ -53,11 +61,16 @@ public class PackageHacker {
}
}
private void fixContent(Map<String, byte[]> content) {
fixVersionInContent(content);
}
private String nice(JsonObject json) {
return new GsonBuilder().setPrettyPrinting().create().toJson(json);
}
private void change(JsonObject npm, Map<String, byte[]> content) throws FileNotFoundException, IOException {
private void change(JsonObject npm) throws FileNotFoundException, IOException {
fixVersions(npm);
// npm.remove("notForPublication");
// npm.addProperty("url", "http://hl7.org/fhir/us/carin-rtpbc/STU1");
@ -67,21 +80,36 @@ public class PackageHacker {
// npm.addProperty("canonical", "http://hl7.org/fhir/us/davinci-drug-formulary");
//// npm.remove("description");
//// npm.addProperty("description", "Group Wrapper that includes all the R4 packages");
// npm.remove("url");
// npm.addProperty("url", "https://terminology.hl7.org/1.0.0/");
npm.remove("dependencies");
JsonObject dep = new JsonObject();
npm.add("dependencies", dep);
dep.addProperty("hl7.fhir.r4.core", "4.0.1");
dep.addProperty("ch.fhir.ig.ch-core", "2.0.0");
dep.addProperty("ch.fhir.ig.ch-epr-term", "2.0.4");
dep.addProperty("ch.fhir.ig.ch-emed","current");
npm.remove("url");
npm.addProperty("url", "http://hl7.org/fhir/R4B");
npm.remove("homepage");
npm.addProperty("homepage", "http://hl7.org/fhir/R4B");
// npm.remove("dependencies");
// JsonObject dep = new JsonObject();
// npm.add("dependencies", dep);
// dep.addProperty("hl7.fhir.r4.core", "4.0.1");
// dep.addProperty("ch.fhir.ig.ch-core", "2.0.0");
// dep.addProperty("ch.fhir.ig.ch-epr-term", "2.0.4");
// dep.addProperty("ch.fhir.ig.ch-emed","current");
// dep.addProperty("hl7.fhir.r4.examples", "4.0.1");
// dep.addProperty("hl7.fhir.r4.expansions", "4.0.1");
// dep.addProperty("hl7.fhir.r4.elements", "4.0.1");
}
private void fixVersionInContent(Map<String, byte[]> content) {
for (String n : content.keySet()) {
if (n.endsWith(".json") || n.endsWith(".xml") || n.endsWith(".xsd")) {
String json = new String(content.get(n));
if (json.contains("4.3.0-cibuild") && !json.contains("4.3.0-snapshot1")) {
json = json.replace("4.3.0-cibuild", "4.3.0");
content.put(n, json.getBytes(StandardCharsets.UTF_8));
}
}
}
}
private void fixVersions(JsonObject npm) {
npm.remove("fhirVersions");
JsonArray a = new JsonArray();

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageScanner.java
View File

@ -9,7 +9,7 @@ import java.util.Set;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import com.google.gson.JsonObject;
@ -63,7 +63,7 @@ public class PackageScanner {
} catch (Exception e) {
fv = "--";
}
output.add(pck.name()+"\t"+pck.version()+"\t"+pck.canonical()+"\t"+fv+'\t'+pck.fhirVersionList()+'\t'+JSONUtil.str(json, "kind")+'\t'+JSONUtil.str(json, "type")+'\t'+JsonTrackingParser.writeDense(json)); } catch (Exception e) {
output.add(pck.name()+"\t"+pck.version()+"\t"+pck.canonical()+"\t"+fv+'\t'+pck.fhirVersionList()+'\t'+JsonUtilities.str(json, "kind")+'\t'+JsonUtilities.str(json, "type")+'\t'+JsonTrackingParser.writeDense(json)); } catch (Exception e) {
System.out.println("Error acessing "+pi.getId()+"#"+piv.getVersion()+": "+e.getMessage());
e.printStackTrace();
}

59
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/ResourceRenamer.java Normal file
View File

@ -0,0 +1,59 @@
package org.hl7.fhir.utilities.npm;
import java.io.File;
import java.io.IOException;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import com.google.gson.JsonObject;
public class ResourceRenamer {
public static void main(String[] args) throws IOException {
new ResourceRenamer().processArg(new File(args[0]));
}
private void processArg(File file) throws IOException {
if (file.isDirectory()) {
process(file);
} else {
unbundle(file);
}
}
private void unbundle(File f) throws IOException {
JsonObject j = JsonTrackingParser.parseJson(f);
for (JsonObject e : JsonUtilities.objects(j, "entry")) {
JsonObject r = e.getAsJsonObject("resource");
String rt = r.get("resourceType").getAsString();
String id = r.get("id").getAsString();
String nn = Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), rt+"-"+id+".json");
JsonTrackingParser.write(r, new File(nn), true);
}
}
private void process(File dir) {
for (File f : dir.listFiles()) {
if (f.getName().endsWith(".json")) {
try {
JsonObject j = JsonTrackingParser.parseJson(f);
String rt = j.get("resourceType").getAsString();
String id = j.get("id").getAsString();
String nn = Utilities.path(Utilities.getDirectoryForFile(f.getAbsolutePath()), rt+"-"+id+".json");
File nf = new File(nn);
if (!nn.equals(f.getAbsolutePath())) {
System.out.println("Rename "+f.getName()+" to "+nf.getName());
f.renameTo(nf);
}
} catch (Exception e) {
System.out.println("Error Processing "+f.getName()+" : "+e.getMessage());
}
}
}
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/IgLoader.java
View File

@ -24,7 +24,7 @@ import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ResourceChecker.java
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@ -8,7 +8,7 @@ import org.hl7.fhir.r5.elementmodel.SHCParser.JWT;
import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import com.google.gson.JsonObject;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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@ -158,6 +158,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
@Getter @Setter private boolean crumbTrails;
@Getter @Setter private boolean allowExampleUrls;
@Getter @Setter private boolean showMessagesFromReferences;
@Getter @Setter private boolean doImplicitFHIRPathStringConversion;
@Getter @Setter private Locale locale;
@Getter @Setter private List<ImplementationGuide> igs = new ArrayList<>();
@Getter @Setter private List<String> extensionDomains = new ArrayList<>();
@ -623,6 +624,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
validator.setQuestionnaireMode(questionnaireMode);
validator.setLevel(level);
validator.setNoUnicodeBiDiControlChars(noUnicodeBiDiControlChars);
validator.setDoImplicitFHIRPathStringConversion(doImplicitFHIRPathStringConversion);
if (format == FhirFormat.SHC) {
igLoader.loadIg(getIgs(), getBinaries(), SHCParser.CURRENT_PACKAGE, true);
}

12
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
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@ -46,6 +46,8 @@ public class CliContext {
private boolean noInvariants = false;
@JsonProperty("wantInvariantsInMessages")
private boolean wantInvariantsInMessages = false;
@JsonProperty("doImplicitFHIRPathStringConversion")
private boolean doImplicitFHIRPathStringConversion = false;
@JsonProperty("map")
private String map = null;
@ -233,6 +235,16 @@ public class CliContext {
return this;
}
@JsonProperty("doImplicitFHIRPathStringConversion")
public boolean isDoImplicitFHIRPathStringConversion() {
return doImplicitFHIRPathStringConversion;
}
@JsonProperty("doImplicitFHIRPathStringConversion")
public void setDoImplicitFHIRPathStringConversion(boolean doImplicitFHIRPathStringConversion) {
this.doImplicitFHIRPathStringConversion = doImplicitFHIRPathStringConversion;
}
@JsonProperty("locale")
public String getLanguageCode() {
return locale;

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
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@ -21,7 +21,7 @@ import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
@ -165,8 +165,8 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
JsonObject json;
try {
json = JsonTrackingParser.fetchJson("http://hl7.org/fhir/mappingspaces.json");
for (JsonObject ms : JSONUtil.objects(json, "spaces")) {
mappingsUris.add(JSONUtil.str(ms, "url"));
for (JsonObject ms : JsonUtilities.objects(json, "spaces")) {
mappingsUris.add(JsonUtilities.str(ms, "url"));
}
} catch (IOException e) {
// frozen R4 list

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -354,6 +354,7 @@ public class ValidationService {
validator.setSnomedExtension(cliContext.getSnomedCTCode());
validator.setAssumeValidRestReferences(cliContext.isAssumeValidRestReferences());
validator.setShowMessagesFromReferences(cliContext.isShowMessagesFromReferences());
validator.setDoImplicitFHIRPathStringConversion(cliContext.isDoImplicitFHIRPathStringConversion());
validator.setNoExtensibleBindingMessages(cliContext.isNoExtensibleBindingMessages());
validator.setNoUnicodeBiDiControlChars(cliContext.isNoUnicodeBiDiControlChars());
validator.setNoInvariantChecks(cliContext.isNoInvariants());

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -68,6 +68,7 @@ public class Params {
public static final String SHOW_TIMES = "-show-times";
public static final String ALLOW_EXAMPLE_URLS = "-allow-example-urls";
public static final String OUTPUT_STYLE = "-output-style";
public static final String DO_IMPLICIT_FHIRPATH_STRING_CONVERSION = "-implicit-fhirpath-string-conversions";
private static final Object JURISDICTION = "-jurisdiction";
/**
@ -167,6 +168,8 @@ public class Params {
cliContext.setRecursive(true);
} else if (args[i].equals(SHOW_MESSAGES_FROM_REFERENCES)) {
cliContext.setShowMessagesFromReferences(true);
} else if (args[i].equals(DO_IMPLICIT_FHIRPATH_STRING_CONVERSION)) {
cliContext.setDoImplicitFHIRPathStringConversion(true);
} else if (args[i].equals(LOCALE)) {
if (i + 1 == args.length) {
throw new Error("Specified -locale without indicating locale");

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -544,6 +544,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
this.crumbTrails = crumbTrails;
}
public boolean isDoImplicitFHIRPathStringConversion() {
return fpe.isDoImplicitStringConversion();
}
public void setDoImplicitFHIRPathStringConversion(boolean doImplicitFHIRPathStringConversion) {
fpe.setDoImplicitStringConversion(doImplicitFHIRPathStringConversion);
}
private boolean allowUnknownExtension(String url) {
if ((allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression"))
// Added structuredefinition-expression explicitly because it wasn't defined in the version of the spec it needs to be used with

12
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
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@ -56,7 +56,7 @@ import org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -91,7 +91,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
manifest = (JsonObject) new com.google.gson.JsonParser().parse(contents);
for (JsonElement e : manifest.getAsJsonArray("test-cases")) {
JsonObject o = (JsonObject) e;
examples.put(JSONUtil.str(o, "name"), o);
examples.put(JsonUtilities.str(o, "name"), o);
}
List<String> names = new ArrayList<String>(examples.size());
@ -168,7 +168,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
if (content.has("use-test") && !content.get("use-test").getAsBoolean())
return;
byte[] testCaseContent = TestingUtilities.loadTestResource("validator", JSONUtil.str(content, "file")).getBytes(StandardCharsets.UTF_8);
byte[] testCaseContent = TestingUtilities.loadTestResource("validator", JsonUtilities.str(content, "file")).getBytes(StandardCharsets.UTF_8);
// load and process content
FhirFormat fmt = determineFormat(content, testCaseContent);
@ -177,7 +177,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
val.getContext().setClientRetryCount(4);
val.setDebug(false);
if (content.has("fetcher") && "standalone".equals(JSONUtil.str(content, "fetcher"))) {
if (content.has("fetcher") && "standalone".equals(JsonUtilities.str(content, "fetcher"))) {
val.setFetcher(vCurr);
vCurr.setFetcher(new StandAloneValidatorFetcher(vCurr.getPcm(), vCurr.getContext(), vCurr));
} else {
@ -337,8 +337,8 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
private FhirFormat determineFormat(JsonObject config, byte[] cnt) throws IOException {
String name = JSONUtil.str(config, "file");
return org.hl7.fhir.validation.ResourceChecker.checkIsResource(vCurr.getContext(), true, cnt, name, !JSONUtil.bool(config, "guess-format"));
String name = JsonUtilities.str(config, "file");
return org.hl7.fhir.validation.ResourceChecker.checkIsResource(vCurr.getContext(), true, cnt, name, !JsonUtilities.bool(config, "guess-format"));
}
private List<StructureDefinition> asSdList(StructureDefinition sd) {

14
org.hl7.fhir.validation/src/test/resources/txCache/4.5.0/snomed.cache
View File

@ -203,3 +203,17 @@ v: {
"system" : "http://snomed.info/sct"
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"version" : "http://snomed.info/sct/11000172109/version/20210915",
"code" : "132037003",
"display" : "Pineywoods pig breed. Not."
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"display" : "Pineywoods pig",
"code" : "132037003",
"system" : "http://snomed.info/sct",
"severity" : "warning",
"error" : "The display \"Pineywoods pig breed. Not.\" is not a valid display for the code {http://snomed.info/sct}132037003 - should be one of ['Pineywoods pig', 'Pineywoods pig breed (organism)', 'Pineywoods pig breed'] (from http://tx.fhir.org/r4)"
}
-------------------------------------------------------------------------------------

2
pom.xml
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@ -19,7 +19,7 @@
<properties>
<hapi_fhir_version>5.4.0</hapi_fhir_version>
<validator_test_case_version>1.1.100</validator_test_case_version>
<validator_test_case_version>1.1.101-SNAPSHOT</validator_test_case_version>
<junit_jupiter_version>5.7.1</junit_jupiter_version>
<junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>
<maven_surefire_version>3.0.0-M5</maven_surefire_version>