au.csiro.ontology.importer.rf2.RF2Importer Maven / Gradle / Ivy
/**
* Copyright CSIRO Australian e-Health Research Centre (http://aehrc.com).
* All rights reserved. Use is subject to license terms and conditions.
*/
package au.csiro.ontology.importer.rf2;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.math.BigDecimal;
import java.net.URISyntaxException;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Queue;
import java.util.Set;
import java.util.TreeSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import au.csiro.ontology.Ontology;
import au.csiro.ontology.importer.BaseImporter;
import au.csiro.ontology.importer.ImportException;
import au.csiro.ontology.input.Input;
import au.csiro.ontology.input.Input.InputType;
import au.csiro.ontology.input.Inputs;
import au.csiro.ontology.input.ModuleInfo;
import au.csiro.ontology.input.RF2Input;
import au.csiro.ontology.input.Version;
import au.csiro.ontology.model.Axiom;
import au.csiro.ontology.model.Concept;
import au.csiro.ontology.model.ConceptInclusion;
import au.csiro.ontology.model.Conjunction;
import au.csiro.ontology.model.Datatype;
import au.csiro.ontology.model.DecimalLiteral;
import au.csiro.ontology.model.Existential;
import au.csiro.ontology.model.IntegerLiteral;
import au.csiro.ontology.model.Literal;
import au.csiro.ontology.model.NamedConcept;
import au.csiro.ontology.model.NamedFeature;
import au.csiro.ontology.model.NamedRole;
import au.csiro.ontology.model.Operator;
import au.csiro.ontology.model.Role;
import au.csiro.ontology.model.RoleInclusion;
import au.csiro.ontology.snomed.refset.rf2.IModuleDependencyRefset;
import au.csiro.ontology.snomed.refset.rf2.ModuleDependency;
import au.csiro.ontology.snomed.refset.rf2.RefsetRow;
import au.csiro.ontology.util.IProgressMonitor;
/**
* Imports ontologies specified in RF2 format into the internal representation.
*
* @author Alejandro Metke
*
*/
public class RF2Importer extends BaseImporter {
/**
* Logger.
*/
private final static Logger log = LoggerFactory.getLogger(RF2Importer.class);
/**
* List of problems found while importing.
*/
protected final List problems = new ArrayList();
/**
* Queue with the inputs to process.
*/
protected final Queue inputs = new LinkedList();
/**
* Imports an ontology using the supplied configuration object.
*
* @param input
*/
public RF2Importer(RF2Input input) {
this.inputs.add(input);
}
/**
* Imports a set of ontologies using the supplied configuration object.
*
* @param inputs
*/
public RF2Importer(Collection inputs) {
for(Input in : inputs) {
if(in instanceof RF2Input) {
this.inputs.add((RF2Input) in);
}
}
}
@Override
public Iterator getOntologyVersions(IProgressMonitor monitor) throws ImportException {
return new OntologyInterator(monitor);
}
@Override
public List getProblems() {
return problems;
}
/**
* Loads all the module dependency information from all RF2 inputs into a single {@link IModuleDependencyRefset}.
*
* @return
* @throws ImportException
*/
protected IModuleDependencyRefset loadModuleDependencies(RF2Input input) throws ImportException {
Set iss = new HashSet();
InputType inputType = input.getInputType();
for(String md : input.getModuleDependenciesRefsetFiles()) {
final String message = "Unable to load module " +
"dependencias. Please check your input configuration " +
"file. (input type = "+inputType+", file="+md+")";
try {
iss.add(input.getInputStream(md));
} catch (NullPointerException e) {
log.error(message, e);
throw new ImportException(message, e);
} catch (IOException e) {
log.error(message, e);
throw new ImportException(message, e);
}
}
IModuleDependencyRefset res = RefsetImporter.importModuleDependencyRefset(iss);
return res;
}
/**
* Determines which modules and versions should be loaded based on the {@link Inputs} object. Returns a {@link Map}
* with the module ids as keys and the set of versions to import as values.
*
* @return
*/
protected Map> getModuleVersionsToLoad(RF2Input in) {
Map> res = new HashMap>();
for(ModuleInfo mi : in.getModules()) {
String moduleId = mi.getId();
Set versionsToLoad = res.get(moduleId);
if(versionsToLoad == null) {
versionsToLoad = new HashSet();
res.put(moduleId, versionsToLoad);
}
for(Version v : mi.getVersions()) {
versionsToLoad.add(v);
}
}
return res;
}
/**
* Populates concrete domains information.
*
* @param cdMap
* @param referencedComponentId
* @param featureId
* @param operator
* @param value
* @param unit
*/
protected void populateCDs(Map> cdMap, String referencedComponentId, String featureId,
String operator, String value, String unit) {
List list;
// my ( $comp, $feature, $op, $value, $unit ) = @_;
if (!cdMap.containsKey(referencedComponentId)) {
list = new ArrayList();
cdMap.put(referencedComponentId, list);
} else {
list = cdMap.get(referencedComponentId);
}
list.add(new String[] { featureId, operator, value, unit });
}
protected void loadReferenceSet(RF2Input input, String refsetFile, Map modMap,
Map refsetMap, IRefsetFactory factory)
throws ImportException {
Set unknownModules = new HashSet();
BufferedReader br = null;
try {
br = new BufferedReader(new InputStreamReader(input.getInputStream(refsetFile), Charset.forName("UTF8")));
String line = br.readLine(); // Skip first line
while (null != (line = br.readLine())) {
if (line.trim().length() < 1) {
continue;
}
String[] fields = line.split("\t");
if (fields.length < 6) {
throw new RuntimeException("Refset: Mis-formatted line, expected >= 6 tab-separated fields, " +
"got: " + line);
}
final String id = fields[0];
final String effectiveTime = fields[1];
final String active = fields[2];
final String moduleId = fields[3];
final String refsetId = fields[4];
final String referencedComponentId = fields[5];
String tgtVer = modMap.get(moduleId);
if (null == tgtVer) {
unknownModules.add(moduleId);
continue;
}
// FIXME Use a more sophisticated (date/time aware) comparison method
int rel = effectiveTime.compareTo(tgtVer);
if (rel <= 0) {
RefsetRow currRow = refsetMap.get(id);
if (currRow == null || effectiveTime.compareTo(currRow.getEffectiveTime()) > 0) {
String[] extras = new String[fields.length - 6];
System.arraycopy(fields, 6, extras, 0, extras.length);
R rr = factory.create(id, effectiveTime, active, moduleId, refsetId, referencedComponentId,
extras);
refsetMap.put(id, rr);
}
}
}
} catch (Throwable t) {
log.error(t.getMessage());
throw new ImportException("Unable to load reference set file. Please check your input configuration file " +
"(input type = " + input.getInputType() + ", file=" + refsetFile + ")");
} finally {
for (String moduleId : unknownModules) {
log.warn("Refset: No version information known for " + moduleId + " found in " + refsetFile);
}
}
}
/**
* Returns a {@link VersionRows} object for an {@link ImportEntry}.
*
* @param entry
* @return
* @throws ImportException
*/
protected VersionRows getBundle(ImportEntry entry) throws ImportException {
// Add module information to map for easy lookup
Map modMap = new HashMap();
for (Module module : entry.getModules()) {
String modId = module.getModuleId();
String modVer = module.getModuleVersion();
modMap.put(modId, modVer);
}
for (Entry mapEntry: modMap.entrySet()) {
log.info("Modules: " + mapEntry.getKey() + "\t" + mapEntry.getValue());
}
// Map needed to find the correct version of each concept to load for this import entry
Map conceptMap = new HashMap();
// Map needed to find the correct version of each relationship to load
// for this import entry
Map relationshipMap = new HashMap();
Map cdMap = new HashMap();
RF2Input input = (RF2Input) entry.getInput();
InputType inputType = input.getInputType();
Set conceptsFiles = input.getConceptsFiles();
log.info("Reading concepts info: " + conceptsFiles.size());
for(String conceptsFile : conceptsFiles) {
final String message = "Unable to load concepts file. " +
"Please check your input configuration file. " +
"(input type = "+inputType+", file="+conceptsFile+")";
try {
loadConceptRows(modMap, conceptMap, input.getInputStream(conceptsFile));
} catch (NullPointerException e) {
log.error(message, e);
throw new ImportException(message, e);
} catch (IOException e) {
log.error(message, e);
throw new ImportException(message, e);
}
}
// Load relationships
Set relationshipsFiles = input.getStatedRelationshipsFiles();
if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
relationshipsFiles = input.getRelationshipsFiles();
log.info("Reading inferred relationships info: " + relationshipsFiles.size());
} else {
log.info("Reading stated relationships info: " + relationshipsFiles.size());
}
if(relationshipsFiles == null || relationshipsFiles.isEmpty()) {
throw new ImportException("No relationships files was specified.");
}
for(String relationshipsFile : relationshipsFiles) {
final String message = "Unable to load relationships file. Please check your input configuration " +
"file. (input type = " + inputType+", file=" + relationshipsFile+")";
try {
loadRelationshipRows(modMap, relationshipMap, input.getInputStream(relationshipsFile));
} catch (NullPointerException e) {
log.error(message, e);
throw new ImportException(message, e);
} catch (IOException e) {
log.error(message, e);
throw new ImportException(message, e);
}
// Load concrete domains refsets
final Set concreteDomainRefsetFiles = input.getConcreteDomainRefsetFiles();
log.info("Reading concrete domains reference set info: " + concreteDomainRefsetFiles.size());
for (String filename : concreteDomainRefsetFiles) {
try {
loadReferenceSet(input, filename, modMap, cdMap, IRefsetFactory.CD);
} catch (ArrayIndexOutOfBoundsException e) {
final String msg = "Error loading concrete domains reference set: " + filename +
". Possibly has wrong number of columns.";
log.error(msg, e);
throw new ImportException(msg, e);
}
}
}
VersionRows vr = new VersionRows(conceptMap.values(), relationshipMap.values(), cdMap.values());
conceptMap = null;
relationshipMap = null;
cdMap = null;
return vr;
}
/**
*
* @param modMap The MDRS data for this version
* @param relationshipMap Map from Relationship SCTID to parsed row
* @param inputStream Stream to parse, filtering based on MDRS data
* @throws IOException
* @throws UnsupportedEncodingException
*/
protected void loadRelationshipRows(Map modMap, Map relationshipMap,
final InputStream inputStream) throws IOException {
BufferedReader br = null;
try {
br = new BufferedReader(new InputStreamReader(inputStream));
String line = br.readLine(); // Skip first line
while (null != (line = br.readLine())) {
if (line.trim().length() < 1) {
continue;
}
int idx1 = line.indexOf('\t');
int idx2 = line.indexOf('\t', idx1 + 1);
int idx3 = line.indexOf('\t', idx2 + 1);
int idx4 = line.indexOf('\t', idx3 + 1);
int idx5 = line.indexOf('\t', idx4 + 1);
int idx6 = line.indexOf('\t', idx5 + 1);
int idx7 = line.indexOf('\t', idx6 + 1);
int idx8 = line.indexOf('\t', idx7 + 1);
int idx9 = line.indexOf('\t', idx8 + 1);
// 0..idx1 == id
// idx1+1..idx2 == effectiveTime
// idx2+1..idx3 == active
// idx3+1..idx4 == moduleId
// idx4+1..idx5 == sourceId
// idx5+1..idx6 == destinationId
// idx6+1..idx7 == relationshipGroup
// idx7+1..idx8 == typeId
// idx8+1..idx9 == characteristicTypeId
// idx9+1..end == modifierId
if (idx1 < 0 || idx2 < 0 || idx3 < 0 || idx4 < 0 ||
idx5 < 0 || idx6 < 0 || idx7 < 0 || idx8 < 0 ||
idx9 < 0) {
br.close();
throw new RuntimeException("Relationships: Mis-formatted line, expected 10 " +
"tab-separated fields, got: " + line);
}
final String id = line.substring(0, idx1);
final String effectiveTime = line.substring(idx1 + 1, idx2);
final String active = line.substring(idx2 + 1, idx3);
final String moduleId = line.substring(idx3 + 1, idx4);
final String sourceId = line.substring(idx4 + 1, idx5);
final String destinationId = line.substring(idx5 + 1, idx6);
final String relationshipGroup = line.substring(idx6 + 1, idx7);
final String typeId = line.substring(idx7 + 1, idx8);
final String characteristicTypeId = line.substring(idx8 + 1, idx9);
final String modifierId = line.substring(idx9 + 1);
String tgtVer = modMap.get(moduleId);
if(tgtVer == null) continue;
int rel = effectiveTime.compareTo(tgtVer);
if(rel <= 0) {
RelationshipRow currRelationshipRow = relationshipMap.get(id);
if(currRelationshipRow == null || effectiveTime.compareTo(
currRelationshipRow.getEffectiveTime()) > 0) {
RelationshipRow rr = new RelationshipRow(id, effectiveTime, active, moduleId, sourceId,
destinationId, relationshipGroup, typeId, characteristicTypeId, modifierId);
relationshipMap.put(id, rr);
}
}
}
} finally {
if(br != null) {
try { br.close(); } catch(Exception e) {};
}
}
}
/**
*
* @param modMap The MDRS data for this version
* @param conceptMap Map from Concept SCTID to parsed row
* @param inputStream Stream to parse, filtering based on MDRS data
* @throws IOException
* @throws UnsupportedEncodingException
*/
protected void loadConceptRows(Map modMap, Map conceptMap,
final InputStream inputStream) throws IOException, UnsupportedEncodingException {
BufferedReader br = null;
try {
br = new BufferedReader(new InputStreamReader(inputStream));
String line = br.readLine(); // Skip first line
while (null != (line = br.readLine())) {
line = new String(line.getBytes(), "UTF8");
if (line.trim().length() < 1) {
continue;
}
int idx1 = line.indexOf('\t');
int idx2 = line.indexOf('\t', idx1 + 1);
int idx3 = line.indexOf('\t', idx2 + 1);
int idx4 = line.indexOf('\t', idx3 + 1);
// 0..idx1 == id
// idx1+1..idx2 == effectiveTime
// idx2+1..idx3 == active
// idx3+1..idx4 == moduleId
// idx4+1..end == definitionStatusId
if (idx1 < 0 || idx2 < 0 || idx3 < 0 || idx4 < 0) {
br.close();
throw new RuntimeException("Concepts: Mis-formatted line, expected at least 5 tab-separated " +
"fields, got: " + line);
}
final String id = line.substring(0, idx1);
final String effectiveTime = line.substring(idx1 + 1, idx2);
final String active = line.substring(idx2 + 1, idx3);
final String moduleId = line.substring(idx3 + 1, idx4);
final String definitionStatusId = line.substring(idx4 + 1);
String tgtVer = modMap.get(moduleId);
if(tgtVer == null) continue;
int rel = effectiveTime.compareTo(tgtVer);
if(rel <= 0) {
ConceptRow currConceptRow = conceptMap.get(id);
if(currConceptRow == null || effectiveTime.compareTo(currConceptRow.getEffectiveTime()) > 0) {
ConceptRow cr = new ConceptRow(id, effectiveTime, active, moduleId, definitionStatusId);
conceptMap.put(id, cr);
}
}
}
} finally {
if(br != null) {
try { br.close(); } catch(Exception e) {};
}
}
}
protected Concept getConcept(String id, Map ci) {
Concept c = ci.get(id);
if (c == null) {
c = new NamedConcept(id);
ci.put(id, c);
}
return c;
}
protected NamedRole getRole(String id, Map ri) {
NamedRole r = ri.get(id);
if (r == null) {
r = new NamedRole(id);
ri.put(id, r);
}
return r;
}
protected NamedFeature getFeature(String id, Map fi) {
NamedFeature f = fi.get(id);
if (f == null) {
f = new NamedFeature(id);
fi.put(id, f);
}
return f;
}
protected void populateParent(String src, String tgt, Map> parents) {
Set prs = parents.get(src);
if (prs == null) {
prs = new TreeSet();
parents.put(src, prs);
}
prs.add(tgt);
}
protected void populateChildren(String src, String tgt, Map> children) {
Set prs = children.get(src);
if (prs == null) {
prs = new TreeSet();
children.put(src, prs);
}
prs.add(tgt);
}
protected void populateRels(String comp, String src, String role, String tgt, String group,
Map> rels) {
List val = rels.get(src);
if (val == null) {
val = new ArrayList();
rels.put(src, val);
}
val.add(new String[] { comp, role, tgt, group });
}
protected void populateRoles(Set roles, String parentSCTID, String rightIdentityIds, Map> children, Map> rolesMap) {
if(roles == null) return;
for (String role : roles) {
Set cs = children.get(role);
if (cs != null) {
populateRoles(cs, role, rightIdentityIds, children, rolesMap);
}
String[] ris = rightIdentityIds.split("[,]");
String ri = (ris[0].equals(role)) ? ris[1] : null;
if (ri != null) {
populateRoleDef(role, ri, parentSCTID, rolesMap);
} else {
populateRoleDef(role, "", parentSCTID, rolesMap);
}
}
}
protected void populateRoleDef(String code, String rightId, String parentRole, Map> roles) {
Map vals = roles.get(code);
if (vals == null) {
vals = new HashMap();
roles.put(code, vals);
}
vals.put("rightID", rightId);
vals.put("parentrole", parentRole);
}
protected Set> groupRoles(List groups) {
Map> roleGroups =
new HashMap>();
for (String[] group : groups) {
String comp = group[0];
String attr = group[1];
String val = group[2];
String roleGroup = group[3];
Set lrvp = roleGroups.get(roleGroup);
if (lrvp == null) {
lrvp = new HashSet();
roleGroups.put(roleGroup, lrvp);
}
lrvp.add(new RoleValuePair(attr, val, comp));
}
Set> res = new HashSet>();
for (String roleGroup : roleGroups.keySet()) {
Set val = roleGroups.get(roleGroup);
// 0 indicates not grouped
if ("0".equals(roleGroup)) {
for (RoleValuePair rvp : val) {
Set sin = new HashSet();
sin.add(rvp);
res.add(sin);
}
} else {
Set item = new HashSet();
for (RoleValuePair trvp : val) {
item.add(trvp);
}
res.add(item);
}
}
return res;
}
/**
* Hook method for subclasses to override.
*
* @param vr
* @param rootModuleId
* @param rootModuleVersion
* @param includeInactiveAxioms
* @return
*/
protected OntologyBuilder getOntologyBuilder(VersionRows vr, String rootModuleId, String rootModuleVersion,
Map metadata) {
return new OntologyBuilder(vr, rootModuleId, rootModuleVersion, metadata);
}
/**
* Represents a role-value pair.
*
* @author Alejandro Metke
*
*/
protected class RoleValuePair {
final String role;
final String value;
final String id;
RoleValuePair(String role, String value, String id) {
this.role = role;
this.value = value;
this.id = id;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + getOuterType().hashCode();
result = prime * result + ((role == null) ? 0 : role.hashCode());
result = prime * result + ((value == null) ? 0 : value.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
RoleValuePair other = (RoleValuePair) obj;
if (!getOuterType().equals(other.getOuterType()))
return false;
if (role == null && other.role != null)
return false;
else if (!role.equals(other.role))
return false;
if (value == null && other.value != null)
return false;
else if (!value.equals(other.value))
return false;
return true;
}
private RF2Importer getOuterType() {
return RF2Importer.this;
}
}
class OntologyInterator implements Iterator {
private final Queue entries = new LinkedList();
@SuppressWarnings("unused")
private final IProgressMonitor monitor;
private void processNext() throws ImportException {
RF2Input in = inputs.remove();
// 1. Load module dependencies
log.info("Loading module dependencies");
IModuleDependencyRefset mdr = loadModuleDependencies(in);
if(mdr == null) {
throw new ImportException("Couldn't load module dependency reference set for RF2 input files.");
}
// Each map entry contains a map of modules indexed by version
Map> deps =
mdr.getModuleDependencies();
// 2. Determine which modules and versions must be loaded
log.info("Determining which root modules and versions to load");
Map> toLoad = getModuleVersionsToLoad(in);
// 3. Create import entries
log.info("Creating import entries");
for(String rootModuleId : toLoad.keySet()) {
Set versions = toLoad.get(rootModuleId);
for(Version version : versions) {
String ver = version.getId();
Map metadata = version.getMetadata();
Map versionMap = deps.get(rootModuleId);
if (null == versionMap) {
throw new ImportException("Root module not found in MDRS: " + rootModuleId);
}
ModuleDependency md = versionMap.get(ver);
if(md == null) {
throw new ImportException("Version " + ver + " of module " + rootModuleId +
" was not found in MDRS.");
}
Set modules = new HashSet();
Queue depends = new LinkedList();
depends.add(md);
while (!depends.isEmpty()) {
ModuleDependency d = depends.poll();
modules.add(new Module(d.getId(), d.getVersion()));
depends.addAll(d.getDependencies());
}
entries.add(new ImportEntry(rootModuleId, ver, metadata, modules, in));
}
}
log.info("Found "+entries.size()+" entries to import");
}
public OntologyInterator(IProgressMonitor monitor) throws ImportException {
this.monitor = monitor;
processNext();
}
@Override
public boolean hasNext() {
return !entries.isEmpty() || !inputs.isEmpty();
}
/**
* @throws RuntimeException in case an {@code ImportException} has occurred.
*/
@Override
public Ontology next() throws RuntimeException {
try {
if(entries.isEmpty()) processNext();
ImportEntry entry = entries.remove();
VersionRows bundle = getBundle(entry);
String ontologyId = entry.getRootModuleId();
String ontologyVersion = entry.getRootModuleVersion();
log.info("Building ontology " + ontologyId + " (" + ontologyVersion + ")");
OntologyBuilder builder = getOntologyBuilder(bundle, ontologyId, ontologyVersion, entry.getMetadata());
return builder.build();
} catch (ImportException e) {
log.error(e.getMessage());
throw new RuntimeException(e);
} catch (URISyntaxException e) {
log.error(e.getMessage());
throw new RuntimeException(e);
}
}
@Override
public void remove() {
throw new UnsupportedOperationException();
}
}
/**
* Class that knows how to build an {@link Ontology} from a set of RF2 files.
*
* @author Alejandro Metke
*
*/
protected class OntologyBuilder {
protected final VersionRows vr;
protected final String rootModuleId;
protected final String rootModuleVersion;
protected final Map primitive = new HashMap();
protected final Map> parents = new HashMap>();
protected final Map> children = new HashMap>();
protected final Map> rels = new HashMap>();
protected final Map> roles = new HashMap>();
protected final List lateralizableConcepts = new LinkedList();
protected final String conceptDefinedId;
protected final String someId;
protected final String isAId;
protected String lateralityId;
protected final String conceptModelAttId;
protected final String neverGroupedIdsString;
protected final String fsnId;
protected final String synonymId;
protected final String definitionId;
protected final String rightIdentityIds;
protected final String roleGroupId;
protected final String measurementTypeInt;
protected final String measurementTypeFloat;
protected final String equalsOperatorId;
protected final String unitRoleId;
protected final Set neverGroupedIds = new HashSet();
protected final Map ci = new HashMap();
protected final Map ri = new HashMap();
protected final Map fi = new HashMap();
protected final Collection statedAxioms = new ArrayList();
protected final Map featureType = new HashMap();
protected final Map> cdsMap = new HashMap>();
public OntologyBuilder(VersionRows vr, String rootModuleId, String rootModuleVersion,
Map metadata) {
this.vr = vr;
this.rootModuleId = rootModuleId;
this.rootModuleVersion = rootModuleVersion;
conceptDefinedId = metadata.get("conceptDefinedId");
someId = metadata.get("someId");
isAId = metadata.get("isAId");
lateralityId = metadata.get("lateralityId");
conceptModelAttId = metadata.get("conceptModelAttId");
neverGroupedIdsString = metadata.get("neverGroupedIds");
fsnId = metadata.get("fsnId");
synonymId = metadata.get("synonymId");
definitionId = metadata.get("definitionId");
rightIdentityIds = metadata.get("rightIdentityIds");
roleGroupId = metadata.get("roleGroupId");
measurementTypeInt = metadata.get("intTypeId");
measurementTypeFloat = metadata.get("floatTypeId");
equalsOperatorId = metadata.get("equalsOperatorId");
unitRoleId = metadata.get("unitRoleId");
if (conceptDefinedId == null) {
log.warn("Metadata value for conceptDefinedId was not found. "
+ "Import process might produce unexpected results.");
}
if (someId == null) {
log.warn("Metadata value for someId was not found. "
+ "Import process might produce unexpected results.");
}
if (isAId == null) {
log.warn("Metadata value for isAId was not found. "
+ "Import process might produce unexpected results.");
}
if (lateralityId == null) {
lateralityId = "";
log.warn("Metadata value for lateralityId was not found. "
+ "Import process might produce unexpected results.");
}
if (conceptModelAttId == null) {
log.warn("Metadata value for conceptModelAttId was not found. "
+ "Import process might produce unexpected results.");
}
if (neverGroupedIdsString == null) {
log.warn("Metadata value for neverGroupedIds was not found. "
+ "Import process might produce unexpected results.");
} else {
String[] parts = neverGroupedIdsString.split("[,]");
for (String part : parts)
neverGroupedIds.add(part);
}
if (fsnId == null) {
log.warn("Metadata value for fsnId was not found. "
+ "Import process might produce unexpected results.");
}
if (synonymId == null) {
log.warn("Metadata value for synonymId was not found. "
+ "Import process might produce unexpected results.");
}
if (definitionId == null) {
log.warn("Metadata value for definitionId was not found. "
+ "Import process might produce unexpected results.");
}
if (rightIdentityIds == null) {
log.warn("Metadata value for rightIdentityIds was not found. "
+ "Import process might produce unexpected results.");
}
if (roleGroupId == null) {
log.warn("Metadata value for roleGroupId was not found. "
+ "Import process might produce unexpected results.");
}
if (measurementTypeFloat == null) {
log.warn("Metadata value for floatTypeId was not found. "
+ "Import process might produce unexpected results.");
}
if (measurementTypeInt == null) {
log.warn("Metadata value for intTypeId was not found. "
+ "Import process might produce unexpected results.");
}
if (equalsOperatorId == null) {
log.warn("Metadata value for equalsOperatorId was not found. "
+ "Import process might produce unexpected results.");
}
if (unitRoleId == null) {
log.warn("Metadata value for unitRoleId was not found. "
+ "Import process might produce unexpected results.");
}
}
protected Ontology build() throws URISyntaxException {
// Process concept rows
log.info("Processing " + vr.getConceptRows().size() + " concept rows");
for (ConceptRow cr : vr.getConceptRows()) {
String id = cr.getId();
if (isActive(cr.getActive())) {
if (!conceptDefinedId.equals(cr.getDefinitionStatusId())) {
primitive.put(id, "1");
} else {
primitive.put(id, "0");
}
}
}
// Process relationship rows
log.info("Processing " + vr.getRelationshipRows().size() + " relationship rows");
for (RelationshipRow rr : vr.getRelationshipRows()) {
if (!someId.equals(rr.getModifierId())) {
throw new RuntimeException("Only existentials are supported.");
}
// only process active concepts and defining relationships
if (isActive(rr.getActive())) {
String type = rr.getTypeId();
String src = rr.getSourceId();
String dest = rr.getDestinationId();
if (isAId.equals(type)) {
populateParent(src, dest, parents);
populateChildren(dest, src, children);
} else {
if (lateralityId.equals(type)) {
lateralizableConcepts.add(src);
}
// Populate relationships
populateRels(rr.getId(), src, type, dest, rr.getRelationshipGroup(), rels);
}
}
}
log.info("Processing " + vr.getConcreteDomainRows().size() + " concrete domain rows");
Set untypedFeatures = new HashSet();
for (RefsetRow rr : vr.getConcreteDomainRows()) {
if (isActive(rr.getActive())) {
// 0id 1effectiveTime 2active 3moduleId 4refSetId
// 5referencedComponentId 6unitId 7operatorId 8value
// &populateCDs( $values[5], $values[4], $values[7],
// $values[8], $values[6] );
final String[] extras = rr.getExtras();
populateCDs(cdsMap, rr.getReferencedComponentId(), rr.getRefsetId(), extras[1], extras[2],
extras[0]);
Set allParents = parents.get(rr.getRefsetId());
if(allParents == null) {
log.error("Could not find refset id " + rr.getRefsetId() + " in meta-data hierarchy. There "
+ "might be a problem with the concrete domains definitions.");
continue;
}
if (allParents.contains(measurementTypeFloat)) {
featureType.put(rr.getRefsetId(), "float");
} else if (allParents.contains(measurementTypeInt)) {
featureType.put(rr.getRefsetId(), "int");
} else {
untypedFeatures.add(rr.getRefsetId());
}
}
}
for (String refsetId : untypedFeatures) {
log.error("ERROR: Could not determine the type (int/float) of " + refsetId);
}
log.info("Creating role axioms");
populateRoles(children.get(conceptModelAttId), "", rightIdentityIds, children, roles);
// Add role axioms
for (String r1 : roles.keySet()) {
String parentRole = roles.get(r1).get("parentrole");
if (!"".equals(parentRole)) {
Role lhs = getRole(r1, ri);
Role rhs = getRole(parentRole, ri);
statedAxioms.add(new RoleInclusion(new Role[] { lhs }, rhs));
}
String rightId = roles.get(r1).get("rightID");
if (!"".equals(rightId)) {
Role lhs1 = getRole(r1, ri);
Role lhs2 = getRole(rightId, ri);
statedAxioms.add(new RoleInclusion(new Role[] { lhs1, lhs2 }, lhs1));
}
}
// Add concept axioms
log.info("Creating axioms for " + primitive.size() + " active concepts");
for (String c1 : primitive.keySet()) {
Set prs = parents.get(c1);
int numParents = (prs != null) ? prs.size() : 0;
List relsVal = rels.get(c1);
int numRels = (relsVal != null) ? 1 : 0;
List cdsVal = cdsMap.get(c1);
int numCds = (cdsVal != null) ? 1 : 0;
int numElems = numParents + numRels + numCds;
if (numParents == 0 && numElems > 0) {
log.warn("Root concept " + c1 + " has non-ISA relationships but no ISA relationships.");
}
if (numElems == 0) {
// do nothing
} else if (numElems == 1 && numParents == 1) {
Concept lhs = getConcept(c1, ci);
Concept rhs = getConcept(prs.iterator().next(), ci);
statedAxioms.add(new ConceptInclusion(lhs, rhs));
} else {
List conjs = new ArrayList();
// Add parents
if (prs != null) {
for (String pr : prs) {
conjs.add(getConcept(pr, ci));
}
}
// Process concrete domains
if (cdsVal != null) {
for (String[] datatype : cdsVal) {
mapDatatype(conjs, datatype);
}
}
// Process relationships
if (relsVal != null) {
for (Set rvs : groupRoles(relsVal)) {
mapRoles(conjs, rvs);
}
}
final ConceptInclusion axiom = new ConceptInclusion(
getConcept(c1, ci), new Conjunction(conjs));
statedAxioms.add(axiom);
if (primitive.get(c1).equals("0")) {
statedAxioms.add(new ConceptInclusion(new Conjunction(
conjs), getConcept(c1, ci)));
}
}
}
log.info("Finished building ontology");
return new Ontology(rootModuleId, rootModuleVersion, statedAxioms, null);
}
protected boolean isActive(final String active) {
return "1".equals(active);
}
protected void mapRoles(List conjs, Set rvs) {
if (rvs.size() > 1) {
Concept[] innerConjs = new Concept[rvs.size()];
int j = 0;
for (RoleValuePair rv : rvs) {
NamedRole role = getRole(rv.role, ri);
Concept filler = resolveFiller(getConcept(rv.value, ci), rv.id);
Existential exis = new Existential(role, filler);
innerConjs[j++] = exis;
}
// Wrap with a role group
conjs.add(new Existential(getRole(roleGroupId, ri), new Conjunction(innerConjs)));
} else {
RoleValuePair first = rvs.iterator().next();
NamedRole role = getRole(first.role, ri);
Concept filler = resolveFiller(getConcept(first.value, ci), first.id);
Existential exis = new Existential(role, filler);
if (neverGroupedIds.contains(first.role)) {
// Does not need a role group
conjs.add(exis);
} else {
// Needs a role group
conjs.add(new Existential(getRole(roleGroupId, ri), exis));
}
}
}
protected Concept resolveFiller(Concept value, String compId) {
if (cdsMap.containsKey(compId)) {
final List concepts = new ArrayList();
concepts.add(value);
for (String[] datatype : cdsMap.get(compId)) {
mapDatatype(concepts, datatype);
}
final Conjunction result = new Conjunction(concepts);
if (log.isTraceEnabled()) {
log.trace("Mapping CD info: " + result.toString());
}
return result;
} else {
return value;
}
}
protected void mapDatatype(List conjs, String[] datatype) {
NamedFeature feature = getFeature(datatype[0], fi);
String type = featureType.get(datatype[0]);
if(type == null) {
log.error("Ignoring feature " + datatype[0] + " (it has no type). There might be a problem with the "
+ "concrete domains definitions.");
return;
}
String operatorId = datatype[1];
String unitId = datatype[3];
Literal value;
if (type.equals("int")) {
value = new IntegerLiteral(Integer.parseInt(datatype[2]));
} else if (type.equals("float")) {
value = new DecimalLiteral(new BigDecimal(datatype[2]));
} else {
log.error("Unknown type: " + type);
return;
}
if (equalsOperatorId.equals(operatorId)) {
Concept[] concepts = {
new Existential(getRole(unitRoleId, ri), getConcept(unitId, ci)),
new Datatype(feature, Operator.EQUALS, value), };
conjs.add(new Existential(getRole(roleGroupId, ri), new Conjunction(concepts)));
} else {
log.error("Unknown operator: " + operatorId);
}
}
protected void populateInactiveRels(String comp, String src,
String role, String tgt, String group,
Map> inactiveRels) {
List val = inactiveRels.get(src);
if (val == null) {
val = new ArrayList();
inactiveRels.put(src, val);
}
val.add(new String[] { comp, role, tgt, group });
}
protected void populateInactiveParent(String src, String tgt,
Map> inactiveParents) {
Set prs = inactiveParents.get(src);
if (prs == null) {
prs = new TreeSet();
inactiveParents.put(src, prs);
}
prs.add(tgt);
}
protected void populateInactiveChildren(String src, String tgt,
Map> inactiveChildren) {
Set prs = inactiveChildren.get(src);
if (prs == null) {
prs = new TreeSet();
inactiveChildren.put(src, prs);
}
prs.add(tgt);
}
protected void populateInactiveRoles(Set roles,
String parentSCTID, String version, String rightIdentityIds,
Map> inactiveChildren,
Map> inactiveRoles) {
if (roles == null)
return;
for (String role : roles) {
Set cs = inactiveChildren.get(role);
if (cs != null) {
populateInactiveRoles(cs, role, version, rightIdentityIds,
inactiveChildren, inactiveRoles);
}
String[] ris = rightIdentityIds.split("[,]");
String ri = (ris[0].equals(role)) ? ris[1] : null;
if (ri != null) {
populateInactiveRoleDef(role, ri, parentSCTID,
inactiveRoles);
} else {
populateInactiveRoleDef(role, "", parentSCTID,
inactiveRoles);
}
}
}
protected void populateInactiveRoleDef(String code, String rightId,
String parentRole,
Map> inactiveRoles) {
Map vals = inactiveRoles.get(code);
if (vals == null) {
vals = new HashMap();
inactiveRoles.put(code, vals);
}
vals.put("rightID", rightId);
vals.put("parentrole", parentRole);
}
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy