private void loadProfile(String n, Map<String, ProfileDefn> profiles) throws Exception {
File spreadsheet = new CSFile(rootDir + ini.getStringProperty("profiles", n));
if (TextFile.fileToString(spreadsheet.getAbsolutePath())
.contains("urn:schemas-microsoft-com:office:spreadsheet")) {
SpreadsheetParser sparser =
new SpreadsheetParser(
new CSFileInputStream(spreadsheet),
spreadsheet.getName(),
definitions,
srcDir,
logger,
registry);
try {
ProfileDefn profile = sparser.parseProfile(definitions);
definitions.getProfiles().put(n, profile);
} catch (Exception e) {
throw new Exception("Error Parsing Profile: '" + n + "': " + e.getMessage(), e);
}
} else {
ProfileDefn profile = new ProfileDefn();
try {
profile.setSource((Profile) new XmlParser().parse(new FileInputStream(spreadsheet)));
definitions.getProfiles().put(n, profile);
} catch (Exception e) {
throw new Exception("Error Parsing Profile: '" + n + "': " + e.getMessage(), e);
}
}
}
private void loadValueSet(String n) throws FileNotFoundException, Exception {
XmlParser xml = new XmlParser();
ValueSet vs =
(ValueSet)
xml.parse(
new CSFileInputStream(
srcDir
+ ini.getStringProperty("valuesets", n).replace('\\', File.separatorChar)));
vs.setIdentifierSimple("http://hl7.org/fhir/vs/" + n);
definitions.getExtraValuesets().put(n, vs);
}
public void checkConditions(List<String> errors, Map<String, Long> dates) throws Exception {
Utilities.checkFolder(srcDir, errors);
Utilities.checkFolder(termDir, errors);
Utilities.checkFolder(imgDir, errors);
this.dates = dates;
checkFile("required", termDir, "bindings.xml", errors, "all");
checkFile("required", dtDir, "primitives.xml", errors, "all");
for (String n : ini.getPropertyNames("types"))
if (ini.getStringProperty("types", n).equals("")) {
TypeRef t = new TypeParser().parse(n).get(0);
checkFile("type definition", dtDir, t.getName().toLowerCase() + ".xml", errors, "all");
}
for (String n : ini.getPropertyNames("structures"))
checkFile("structure definition", dtDir, n.toLowerCase() + ".xml", errors, "all");
String[] shared = ini.getPropertyNames("shared");
if (shared != null)
for (String n : shared)
checkFile("shared structure definition", dtDir, n.toLowerCase() + ".xml", errors, "all");
for (String n : ini.getPropertyNames("infrastructure"))
checkFile("infrastructure definition", dtDir, n.toLowerCase() + ".xml", errors, "all");
for (String n : ini.getPropertyNames("resources")) {
if (!new File(srcDir + n).exists()) errors.add("unable to find folder for resource " + n);
else {
if (new CSFile(srcDir + n + File.separatorChar + n + "-spreadsheet.xml").exists()) {
checkFile(
"definition", srcDir + n + File.separatorChar, n + "-spreadsheet.xml", errors, n);
} else checkFile("definition", srcDir + n + File.separatorChar, n + "-def.xml", errors, n);
checkFile("example xml", srcDir + n + File.separatorChar, n + "-example.xml", errors, n);
// now iterate all the files in the directory checking data
for (String fn : new File(srcDir + n + File.separatorChar).list())
checkFile("source", srcDir + n + File.separatorChar, fn, errors, n);
}
}
for (String n : ini.getPropertyNames("special-resources")) {
if (new CSFile(srcDir + n + File.separatorChar + n + "-spreadsheet.xml").exists())
checkFile("definition", srcDir + n + File.separatorChar, n + "-spreadsheet.xml", errors, n);
else checkFile("definition", srcDir + n + File.separatorChar, n + "-def.xml", errors, n);
// now iterate all the files in the directory checking data
for (String fn : new File(srcDir + n + File.separatorChar).list())
checkFile("source", srcDir + n + File.separatorChar, fn, errors, n);
}
}
private String loadCompositeType(String n, Map<String, ElementDefn> map) throws Exception {
TypeParser tp = new TypeParser();
List<TypeRef> ts = tp.parse(n);
definitions.getKnownTypes().addAll(ts);
try {
TypeRef t = ts.get(0);
File csv = new CSFile(dtDir + t.getName().toLowerCase() + ".xml");
if (csv.exists()) {
SpreadsheetParser p =
new SpreadsheetParser(
new CSFileInputStream(csv), csv.getName(), definitions, srcDir, logger, registry);
ElementDefn el = p.parseCompositeType();
map.put(t.getName(), el);
el.getAcceptableGenericTypes().addAll(ts.get(0).getParams());
return el.getName();
} else {
String p = ini.getStringProperty("types", n);
csv = new CSFile(dtDir + p.toLowerCase() + ".xml");
if (!csv.exists()) throw new Exception("unable to find a definition for " + n + " in " + p);
XLSXmlParser xls = new XLSXmlParser(new CSFileInputStream(csv), csv.getAbsolutePath());
Sheet sheet = xls.getSheets().get("Restrictions");
boolean found = false;
for (int i = 0; i < sheet.rows.size(); i++) {
if (sheet.getColumn(i, "Name").equals(n)) {
found = true;
Invariant inv = new Invariant();
inv.setId(n);
inv.setEnglish(sheet.getColumn(i, "Rules"));
inv.setOcl(sheet.getColumn(i, "OCL"));
inv.setXpath(sheet.getColumn(i, "XPath"));
definitions.getConstraints().put(n, new DefinedCode(n, sheet.getColumn(i, "Rules"), p));
definitions.getConstraintInvariants().put(n, inv);
}
}
if (!found) throw new Exception("Unable to find definition for " + n);
return n;
}
} catch (Exception e) {
throw new Exception("Unable to load " + n + ": " + e.getMessage(), e);
}
}
private ResourceDefn loadResource(String n, Map<String, ResourceDefn> map, boolean sandbox)
throws Exception {
String src = sandbox ? sndBoxDir : srcDir;
File spreadsheet =
new CSFile(
(sandbox ? sndBoxDir : srcDir) + n + File.separatorChar + n + "-spreadsheet.xml");
if (!spreadsheet.exists())
spreadsheet =
new CSFile((sandbox ? sndBoxDir : srcDir) + n + File.separatorChar + n + "-def.xml");
SpreadsheetParser sparser =
new SpreadsheetParser(
new CSFileInputStream(spreadsheet),
spreadsheet.getName(),
definitions,
src,
logger,
registry);
ResourceDefn root;
try {
root = sparser.parseResource();
} catch (Exception e) {
throw new Exception("Error Parsing Resource " + n + ": " + e.getMessage(), e);
}
root.setSandbox(sandbox);
for (EventDefn e : sparser.getEvents()) processEvent(e, root.getRoot());
// EK: Commented this out, seems double with next statement, since
// loadResource()
// is always called with definitions.getResources in its map argument.
// definitions.getResources().put(root.getName(), root);
if (map != null) {
map.put(root.getName(), root);
definitions
.getKnownResources()
.put(root.getName(), new DefinedCode(root.getName(), root.getRoot().getDefinition(), n));
}
root.setStatus(ini.getStringProperty("status", n));
return root;
}
public void parse(Calendar genDate, String version) throws Exception {
logger.log("Loading", LogMessageType.Process);
eCoreParseResults = DefinitionsImpl.build(genDate.getTime(), version);
loadGlobalConceptDomains();
eCoreParseResults
.getBinding()
.addAll(
sortBindings(
BindingConverter.buildBindingsFromFhirModel(
definitions.getBindings().values(), null)));
loadPrimitives();
eCoreParseResults
.getPrimitive()
.addAll(
PrimitiveConverter.buildPrimitiveTypesFromFhirModel(
definitions.getPrimitives().values()));
for (String n : ini.getPropertyNames("removed-resources"))
definitions.getDeletedResources().add(n);
for (String n : ini.getPropertyNames("types")) loadCompositeType(n, definitions.getTypes());
for (String n : ini.getPropertyNames("structures"))
loadCompositeType(n, definitions.getStructures());
String[] shared = ini.getPropertyNames("shared");
if (shared != null)
for (String n : shared)
definitions.getShared().add(loadCompositeType(n, definitions.getStructures()));
for (String n : ini.getPropertyNames("infrastructure"))
loadCompositeType(n, definitions.getInfrastructure());
List<TypeDefn> allFhirComposites = new ArrayList<TypeDefn>();
allFhirComposites.add(CompositeTypeConverter.buildElementBaseType());
allFhirComposites.addAll(
PrimitiveConverter.buildCompositeTypesForPrimitives(eCoreParseResults.getPrimitive()));
allFhirComposites.addAll(
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getTypes().values(), null));
allFhirComposites.addAll(
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getStructures().values(), null));
List<CompositeTypeDefn> infra =
CompositeTypeConverter.buildCompositeTypesFromFhirModel(
definitions.getInfrastructure().values(), null);
for (CompositeTypeDefn composite : infra) composite.setInfrastructure(true);
allFhirComposites.addAll(infra);
allFhirComposites.addAll(
ConstrainedTypeConverter.buildConstrainedTypesFromFhirModel(
definitions.getConstraints().values(), definitions.getConstraintInvariants()));
eCoreParseResults.getType().addAll(sortTypes(allFhirComposites));
for (String n : ini.getPropertyNames("resources"))
loadResource(n, definitions.getResources(), false);
ResourceDefn baseResource = loadResource("resource", null, false);
baseResource.setAbstract(true);
definitions.setBaseResource(baseResource);
loadCompartments();
loadStatusCodes();
org.hl7.fhir.definitions.ecore.fhir.ResourceDefn eCoreBaseResource =
CompositeTypeConverter.buildResourceFromFhirModel(baseResource, null);
eCoreBaseResource.getElement().add(CompositeTypeConverter.buildInternalIdElement());
eCoreParseResults.getType().add(eCoreBaseResource);
eCoreParseResults
.getType()
.addAll(
sortTypes(
CompositeTypeConverter.buildResourcesFromFhirModel(
definitions.getResources().values())));
eCoreParseResults.getType().add(CompositeTypeConverter.buildBinaryResourceDefn());
for (String n : ini.getPropertyNames("svg"))
definitions.getDiagrams().put(n, ini.getStringProperty("svg", n));
if (ini.getPropertyNames("future-resources") != null)
for (String n : ini.getPropertyNames("future-resources")) {
DefinedCode cd =
new DefinedCode(ini.getStringProperty("future-resources", n), "Yet to be defined", n);
definitions.getKnownResources().put(n, cd);
ResourceDefn futureResource = new ResourceDefn();
futureResource.setName(cd.getCode());
futureResource.setDefinition("Future resource " + cd.getCode() + ". As yet undefined.");
futureResource.setForFutureUse(true);
definitions.getFutureResources().put(cd.getCode(), futureResource);
}
eCoreParseResults
.getType()
.addAll(
CompositeTypeConverter.buildResourcesFromFhirModel(
definitions.getFutureResources().values()));
eCoreParseResults
.getEvent()
.addAll(EventConverter.buildEventsFromFhirModel(definitions.getEvents().values()));
// As a second pass, resolve typerefs to the types
fixTypeRefs(eCoreParseResults);
eCoreParseResults
.getBinding()
.add(BindingConverter.buildResourceTypeBinding(eCoreParseResults));
for (String n : ini.getPropertyNames("special-resources"))
definitions.getAggregationEndpoints().add(n);
String[] pn = ini.getPropertyNames("valuesets");
if (pn != null)
for (String n : pn) {
loadValueSet(n);
}
for (String n : ini.getPropertyNames("profiles")) {
loadProfile(n, definitions.getProfiles());
}
for (ResourceDefn r : definitions.getResources().values()) {
for (RegisteredProfile p : r.getProfiles()) {
SpreadsheetParser sparser =
new SpreadsheetParser(
new CSFileInputStream(p.getFilepath()),
p.getName(),
definitions,
srcDir,
logger,
registry);
sparser.setFolder(Utilities.getDirectoryForFile(p.getFilepath()));
p.setProfile(sparser.parseProfile(definitions));
}
}
}