honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

fixes for errors generating IGs

This commit is contained in:
Grahame Grieve 2019-03-14 17:18:15 +11:00
parent 89c95c70ca
commit 5ce917a34c
3 changed files with 112 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -145,7 +145,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
private ValidationResult validateCode(Coding code, CodeSystem cs) {
ConceptDefinitionComponent cc = findCodeInConcept(cs.getConcept(), code.getCode());
if (cc == null)
return new ValidationResult(IssueSeverity.ERROR, "Unknown Code "+code+" in "+cs.getUrl());
return new ValidationResult(IssueSeverity.ERROR, "Unknown Code "+gen(code)+" in "+cs.getUrl());
if (code.getDisplay() == null)
return new ValidationResult(cc);
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
@ -162,6 +162,13 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
return new ValidationResult(IssueSeverity.WARNING, "Display Name for "+code.getSystem()+"#"+code.getCode()+" must be one of '"+b.toString()+"'", cc);
}
private String gen(Coding code) {
if (code.hasSystem())
return code.getSystem()+"#"+code.getCode();
else
return null;
}
private String getValueSetSystem() throws FHIRException {
if (valueset == null)
throw new FHIRException("Unable to resolve system - no value set");

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
View File

@ -1978,6 +1978,9 @@ public class NarrativeGenerator implements INarrativeGenerator {
StructureDefinition sd = context.fetchTypeDefinition(path.substring(0, path.length()-4));
if (sd == null)
return false;
if (Utilities.existsInList(path.substring(0, path.length()-4), "CapabilityStatement", "StructureDefinition", "ImplementationGuide", "SearchParameter", "MessageDefinition", "OperationDefinition", "CompartmentDefinition", "StructureMap", "GraphDefinition",
"ExampleScenario", "CodeSystem", "ValueSet", "ConceptMap", "NamingSystem", "TerminologyCapabilities"))
return true;
return sd.getBaseDefinitionElement().hasExtension("http://hl7.org/fhir/StructureDefinition/structuredefinition-codegen-super");
}

109
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/cache/PackageCacheManager.java vendored
View File

@ -67,6 +67,26 @@ import com.google.gson.JsonObject;
*/
public class PackageCacheManager {
public class VersionHistory {
private String id;
private String canonical;
private String current;
private Map<String, String> versions = new HashMap<>();
public String getCanonical() {
return canonical;
}
public String getCurrent() {
return current;
}
public Map<String, String> getVersions() {
return versions;
}
public String getId() {
return id;
}
}
public class PackageEntry {
private byte[] bytes;
@ -95,6 +115,8 @@ public class PackageCacheManager {
private boolean progress = true;
private List<NpmPackage> temporaryPackages = new ArrayList<NpmPackage>();
private Map<String, String> ciList = new HashMap<String, String>();
private List<String> allUrls;
private Map<String, VersionHistory> historyCache = new HashMap<>();
public PackageCacheManager(boolean userMode, int toolsVersion) throws IOException {
if (userMode)
@ -104,15 +126,17 @@ public class PackageCacheManager {
if (!(new File(cacheFolder).exists()))
Utilities.createDirectory(cacheFolder);
if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
TextFile.stringToFile("[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"));
TextFile.stringToFile("[cache]\r\nversion="+CACHE_VERSION+"\r\n\r\n[urls]\r\n\r\n[local]\r\n\r\n", Utilities.path(cacheFolder, "packages.ini"), false);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
boolean save = false;
if ("1".equals(ini.getStringProperty("cache", "version"))) {
String v = ini.getStringProperty("cache", "version");
if ("1".equals(v)) {
convertPackageCacheFrom1To2();
ini.setStringProperty("cache", "version", "2", null);
v = ini.getStringProperty("cache", "version");
save = true;
}
if (!CACHE_VERSION.equals(ini.getStringProperty("cache", "version"))) {
if (!CACHE_VERSION.equals(v)) {
clearCache();
ini.setStringProperty("cache", "version", CACHE_VERSION, null);
save = true;
@ -123,8 +147,8 @@ public class PackageCacheManager {
save = checkIniHasMapping("fhir.argonaut.scheduling", "http://fhir.org/guides/argonaut-scheduling", ini) || save;
save = checkIniHasMapping("fhir.hspc.acog", "http://hl7.org/fhir/fpar", ini) || save;
save = checkIniHasMapping("hl7.fhir.au.argonaut", "http://hl7.org.au/fhir/argonaut", ini) || save;
save = checkIniHasMapping("hl7.fhir.au.base", "http://hl7.org.au/fhir", ini) || save;
save = checkIniHasMapping("hl7.fhir.au.pd", "http://hl7.org.au/fhir", ini) || save;
save = checkIniHasMapping("hl7.fhir.au.base", "http://hl7.org.au/fhir/base", ini) || save;
save = checkIniHasMapping("hl7.fhir.au.pd", "http://hl7.org.au/fhir/pd", ini) || save;
save = checkIniHasMapping("hl7.fhir.smart", "http://hl7.org/fhir/smart-app-launch", ini) || save;
save = checkIniHasMapping("hl7.fhir.snomed", "http://hl7.org/fhir/ig/snomed", ini) || save;
save = checkIniHasMapping("hl7.fhir.test.v10", "http://hl7.org/fhir/test-ig-10", ini) || save;
@ -148,8 +172,12 @@ public class PackageCacheManager {
save = checkIniHasMapping("hl7.fhir.uv.vhdir", "http://hl7.org/fhir/ig/vhdir", ini) || save;
save = checkIniHasMapping("hl7.fhir.vn.base", "http://hl7.org/fhir/ig/vietnam", ini) || save;
save = checkIniHasMapping("hl7.fhir.vocabpoc", "http://hl7.org/fhir/ig/vocab-poc", ini) || save;
if (save)
ini.save();
if (save) {
if (!CACHE_VERSION.equals(ini.getStringProperty("cache", "version"))) {
throw new Error("what?");
}
ini.save();
}
checkDeleteVersion("hl7.fhir.core", "1.0.2", 2);
checkDeleteVersion("hl7.fhir.core", "1.4.0", 2);
checkDeleteVersion("hl7.fhir.core", "current", toolsVersion);
@ -217,9 +245,19 @@ public class PackageCacheManager {
public void recordMap(String url, String id) throws IOException {
if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
throw new Error("what?");
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.setStringProperty("urls", id, url, null);
if (!CACHE_VERSION.equals(ini.getStringProperty("cache", "version"))) {
throw new Error("what?");
}
if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
throw new Error("what?");
ini.save();
if (!(new File(Utilities.path(cacheFolder, "packages.ini")).exists()))
throw new Error("what?");
}
public String getPackageUrl(String id) throws IOException {
@ -318,7 +356,9 @@ public class PackageCacheManager {
System.out.print("|");
JsonObject npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.bytesToString(npmb));
if (npm.get("name") == null || id == null || !id.equals(npm.get("name").getAsString()))
throw new IOException("Attempt to import a mis-identified package "+id);
// work around for stupid core-r4 problem
if (!npm.get("name").getAsString().startsWith(id))
throw new IOException("Attempt to import a mis-identified package. Expected "+id+", got "+npm.get("name").getAsString());
if (version == null)
version = npm.get("version").getAsString();
@ -649,4 +689,57 @@ public class PackageCacheManager {
return false;
}
public List<String> getUrls() throws IOException {
if (allUrls == null)
{
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
allUrls = new ArrayList<>();
for (String s : ini.getPropertyNames("urls"))
allUrls.add(ini.getStringProperty("urls", s));
try {
System.out.println("Listing known Implementation Guides");
URL url = new URL("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json?nocache=" + System.currentTimeMillis());
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
connection.setRequestMethod("GET");
InputStream json = connection.getInputStream();
JsonObject packages = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
JsonArray guides = packages.getAsJsonArray("guides");
for (JsonElement g : guides) {
JsonObject gi = (JsonObject) g;
if (gi.has("canonical"))
if (!allUrls.contains(gi.get("canonical").getAsString()))
allUrls.add(gi.get("canonical").getAsString());
}
} catch (Exception e) {
System.out.println(" .. failed: "+e.getMessage());
}
}
return allUrls;
}
public VersionHistory listVersions(String url) throws IOException {
if (historyCache.containsKey(url))
return historyCache.get(url);
URL url1 = new URL(Utilities.pathURL(url, "package-list.json")+"?nocache=" + System.currentTimeMillis());
HttpURLConnection connection = (HttpURLConnection) url1.openConnection();
connection.setRequestMethod("GET");
InputStream json = connection.getInputStream();
JsonObject packageList = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.streamToString(json));
VersionHistory res = new VersionHistory();
res.id = packageList.get("package-id").getAsString();
res.canonical = packageList.get("canonical").getAsString();
for (JsonElement j : packageList.getAsJsonArray("list")) {
JsonObject jo = (JsonObject) j;
if ("current".equals(jo.get("version").getAsString()))
res.current = jo.get("path").getAsString();
else
res.versions.put(jo.get("version").getAsString(), jo.get("path").getAsString());
}
historyCache.put(url, res);
return res;
}
}