String constructDN(final T o, final String parentDN, final Map<String, Attribute> attrMap)
throws LDAPPersistException {
final String existingDN = getEntryDN(o);
if (existingDN != null) {
return existingDN;
}
final ArrayList<String> rdnNameList = new ArrayList<String>(1);
final ArrayList<byte[]> rdnValueList = new ArrayList<byte[]>(1);
for (final FieldInfo i : rdnFields) {
final Attribute a = attrMap.get(toLowerCase(i.getAttributeName()));
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_RDN_FIELD_MISSING_VALUE.get(type.getName(), i.getField().getName()));
}
rdnNameList.add(a.getName());
rdnValueList.add(a.getValueByteArray());
}
for (final GetterInfo i : rdnGetters) {
final Attribute a = attrMap.get(toLowerCase(i.getAttributeName()));
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_RDN_GETTER_MISSING_VALUE.get(
type.getName(), i.getMethod().getName()));
}
rdnNameList.add(a.getName());
rdnValueList.add(a.getValueByteArray());
}
final String[] rdnNames = new String[rdnNameList.size()];
rdnNameList.toArray(rdnNames);
final byte[][] rdnValues = new byte[rdnNames.length][];
rdnValueList.toArray(rdnValues);
final RDN rdn = new RDN(rdnNames, rdnValues);
if (parentDN == null) {
return new DN(rdn, defaultParentDN).toString();
} else {
try {
final DN parsedParentDN = new DN(parentDN);
return new DN(rdn, parsedParentDN).toString();
} catch (LDAPException le) {
debugException(le);
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_INVALID_PARENT_DN.get(type.getName(), parentDN, le.getMessage()),
le);
}
}
}
/**
* This will invoke the <code>startElement</code> callback in the <code>ContentHandler</code>.
*
* @param element <code>Element</code> used in callbacks.
* @param nsAtts <code>List</code> of namespaces to declare with the element or <code>null</code>.
*/
private void startElement(Element element, Attributes nsAtts) throws JDOMException {
String namespaceURI = element.getNamespaceURI();
String localName = element.getName();
String rawName = element.getQualifiedName();
// Allocate attribute list.
AttributesImpl atts = (nsAtts != null) ? new AttributesImpl(nsAtts) : new AttributesImpl();
List attributes = element.getAttributes();
Iterator i = attributes.iterator();
while (i.hasNext()) {
Attribute a = (Attribute) i.next();
atts.addAttribute(
a.getNamespaceURI(),
a.getName(),
a.getQualifiedName(),
getAttributeTypeName(a.getAttributeType()),
a.getValue());
}
try {
contentHandler.startElement(namespaceURI, localName, rawName, atts);
} catch (SAXException se) {
throw new JDOMException("Exception in startElement", se);
}
}
/* ------------------------------------------------------------ */
public AttributeList setAttributes(AttributeList attrs) {
log.debug("setAttributes");
AttributeList results = new AttributeList(attrs.size());
Iterator iter = attrs.iterator();
while (iter.hasNext()) {
try {
Attribute attr = (Attribute) iter.next();
setAttribute(attr);
results.add(new Attribute(attr.getName(), getAttribute(attr.getName())));
} catch (Exception e) {
log.warn(LogSupport.EXCEPTION, e);
}
}
return results;
}
private static void renderPassThruAttributesUnoptimized(
FacesContext context,
ResponseWriter writer,
UIComponent component,
Attribute[] knownAttributes,
Map<String, List<ClientBehavior>> behaviors)
throws IOException {
boolean isXhtml = XHTML_CONTENT_TYPE.equals(writer.getContentType());
Map<String, Object> attrMap = component.getAttributes();
for (Attribute attribute : knownAttributes) {
String attrName = attribute.getName();
String[] events = attribute.getEvents();
boolean hasBehavior =
((events != null) && (events.length > 0) && (behaviors.containsKey(events[0])));
Object value = attrMap.get(attrName);
if (value != null && shouldRenderAttribute(value) && !hasBehavior) {
writer.writeAttribute(prefixAttribute(attrName, isXhtml), value, attrName);
} else if (hasBehavior) {
renderHandler(context, component, null, attrName, value, events[0]);
}
}
}
/** Return index of attribute with same name and Namespace, or -1 if one doesn't exist */
private int indexOfDuplicate(Attribute attribute) {
int duplicate = -1;
String name = attribute.getName();
Namespace namespace = attribute.getNamespace();
duplicate = indexOf(name, namespace);
return duplicate;
}
/** Convert the attributes in the given XML Element into a Map of name/value pairs. */
protected static Map createAttributeMap(Element el) {
Log.debug("Creating attribute map for " + el);
Map attributes = new HashMap();
Iterator iter = el.getAttributes().iterator();
while (iter.hasNext()) {
Attribute att = (Attribute) iter.next();
attributes.put(att.getName(), att.getValue());
}
return attributes;
}
/* ------------------------------------------------------------ */
public void setAttribute(Attribute attr)
throws AttributeNotFoundException, InvalidAttributeValueException, MBeanException,
ReflectionException {
if (attr == null) return;
if (log.isDebugEnabled()) log.debug("setAttribute " + attr.getName() + "=" + attr.getValue());
Method setter = (Method) _setter.get(attr.getName());
if (setter == null) throw new AttributeNotFoundException(attr.getName());
try {
Object o = _object;
if (setter.getDeclaringClass().isInstance(this)) o = this;
setter.invoke(o, new Object[] {attr.getValue()});
} catch (IllegalAccessException e) {
log.warn(LogSupport.EXCEPTION, e);
throw new AttributeNotFoundException(e.toString());
} catch (InvocationTargetException e) {
log.warn(LogSupport.EXCEPTION, e);
throw new ReflectionException((Exception) e.getTargetException());
}
}
public static List<Variant> getPossibleVariants(
Product product, Variant variant, String selectedAttribute) {
List<Variant> matchingVariantList = new ArrayList<Variant>();
List<Attribute> desiredAttributes = new ArrayList<Attribute>();
for (Attribute attribute : variant.getAttributes()) {
if (!selectedAttribute.equals(attribute.getName())
&& hasMoreAttributeValues(product, attribute.getName())) {
desiredAttributes.add(attribute);
}
}
VariantList variantList = product.getVariants().byAttributes(desiredAttributes);
for (Attribute attr : product.getVariants().getAvailableAttributes(selectedAttribute)) {
if (variantList.byAttributes(attr).size() < 1) {
matchingVariantList.add((product.getVariants().byAttributes(attr).first()).orNull());
} else {
matchingVariantList.add((variantList.byAttributes(attr).first()).orNull());
}
}
matchingVariantList.removeAll(Collections.singleton(null));
return matchingVariantList;
}
private static boolean checkAttrs(String what, AttributeList attrs) {
if (attrs.size() != 1) {
System.out.println(
"TEST FAILS: list returned by " + what + " does not have size 1: " + attrs);
return false;
}
Attribute attr = (Attribute) attrs.get(0);
if (!"Exotic".equals(attr.getName())) {
System.out.println("TEST FAILS: " + what + " returned wrong " + "attribute: " + attr);
return false;
}
return true;
}
/** Return index of the <code>Attribute</code> with the given name and uri. */
int indexOf(String name, Namespace namespace) {
String uri = namespace.getURI();
if (elementData != null) {
for (int i = 0; i < size; i++) {
Attribute old = elementData[i];
String oldURI = old.getNamespaceURI();
String oldName = old.getName();
if (oldURI.equals(uri) && oldName.equals(name)) {
return i;
}
}
}
return -1;
}
private static void renderPassThruAttributesOptimized(
FacesContext context,
ResponseWriter writer,
UIComponent component,
Attribute[] knownAttributes,
List<String> setAttributes,
Map<String, List<ClientBehavior>> behaviors)
throws IOException {
String behaviorEventName = getSingleBehaviorEventName(behaviors);
boolean renderedBehavior = false;
Collections.sort(setAttributes);
boolean isXhtml = XHTML_CONTENT_TYPE.equals(writer.getContentType());
Map<String, Object> attrMap = component.getAttributes();
for (String name : setAttributes) {
int index = Arrays.binarySearch(knownAttributes, Attribute.attr(name));
if (index >= 0) {
Object value = attrMap.get(name);
if (value != null && shouldRenderAttribute(value)) {
Attribute attr = knownAttributes[index];
if (isBehaviorEventAttribute(attr, behaviorEventName)) {
renderHandler(context, component, null, name, value, behaviorEventName);
renderedBehavior = true;
} else {
writer.writeAttribute(prefixAttribute(name, isXhtml), value, name);
}
}
}
}
if ((behaviorEventName != null) && !renderedBehavior) {
for (int i = 0; i < knownAttributes.length; i++) {
Attribute attr = knownAttributes[i];
String[] events = attr.getEvents();
if ((events != null) && (events.length > 0) && (behaviorEventName.equals(events[0]))) {
renderHandler(context, component, null, attr.getName(), null, behaviorEventName);
}
}
}
}
private synchronized NameValueMap getCachedAttributes(ObjectName objName, Set<String> attrNames)
throws InstanceNotFoundException, ReflectionException, IOException {
NameValueMap values = cachedValues.get(objName);
if (values != null && values.keySet().containsAll(attrNames)) {
return values;
}
attrNames = new TreeSet<String>(attrNames);
Set<String> oldNames = cachedNames.get(objName);
if (oldNames != null) {
attrNames.addAll(oldNames);
}
values = new NameValueMap();
final AttributeList attrs =
conn.getAttributes(objName, attrNames.toArray(new String[attrNames.size()]));
for (Attribute attr : attrs.asList()) {
values.put(attr.getName(), attr.getValue());
}
cachedValues.put(objName, values);
cachedNames.put(objName, attrNames);
return values;
}
/**
* Convert RichUsers to Identity objects with obfuscated email address and limited set of ext
* sources. Service users are removed from the list.
*
* @param list RichUsers to convert
* @return list of Identities without service ones
* @throws PerunException
*/
private List<Identity> convertToIdentities(List<RichUser> list) throws PerunException {
List<Identity> result = new ArrayList<Identity>();
if (list != null && !list.isEmpty()) {
for (RichUser u : list) {
// skip service users
if (u.isServiceUser()) continue;
Identity identity = new Identity();
identity.setName(u.getDisplayName());
identity.setId(u.getId());
for (Attribute a : u.getUserAttributes()) {
if (MailManagerImpl.URN_USER_PREFERRED_MAIL.equals(a.getName())) {
if (a.getValue() != null && !((String) a.getValue()).isEmpty()) {
String safeMail = ((String) a.getValue()).split("@")[0];
if (safeMail.length() > 2) {
safeMail =
safeMail.substring(0, 1)
+ "****"
+ safeMail.substring(safeMail.length() - 1, safeMail.length());
}
safeMail += "@" + ((String) a.getValue()).split("@")[1];
identity.setEmail(safeMail);
}
} else if ("urn:perun:user:attribute-def:def:organization".equals(a.getName())) {
if (a.getValue() != null) {
identity.setOrganization((String) a.getValue());
}
}
}
List<ExtSource> es = new ArrayList<ExtSource>();
for (UserExtSource ues : u.getUserExtSources()) {
if (ues.getExtSource().getType().equals(ExtSourcesManagerEntry.EXTSOURCE_X509)) {
es.add(ues.getExtSource());
} else if (ues.getExtSource().getType().equals(ExtSourcesManagerEntry.EXTSOURCE_IDP)) {
if (ues.getExtSource().getName().equals("https://extidp.cesnet.cz/idp/shibboleth")) {
// FIXME - hack Social IdP to let us know proper identity source
String type = ues.getLogin().split("@")[1].split("\\.")[0];
ues.getExtSource()
.setName(
"https://extidp.cesnet.cz/idp/shibboleth&authnContextClassRef=urn:cesnet:extidp:authn:"
+ type);
} else if (ues.getExtSource().getName().equals("https://login.elixir-czech.org/idp/")) {
// FIXME - hack Elixir proxy IdP to let us know proper identity source
String type = ues.getLogin().split("@")[1];
ues.getExtSource().setName("https://login.elixir-czech.org/idp/@" + type);
}
es.add(ues.getExtSource());
} else if (ues.getExtSource()
.getType()
.equals(ExtSourcesManagerEntry.EXTSOURCE_KERBEROS)) {
es.add(ues.getExtSource());
}
}
identity.setIdentities(es);
result.add(identity);
}
}
return result;
}
private Filter createFilter(final T o, final AtomicBoolean addedRequiredOrAllowed)
throws LDAPPersistException {
final ArrayList<Attribute> attrs = new ArrayList<Attribute>(5);
attrs.add(objectClassAttribute);
for (final FieldInfo i : requiredFilterFields) {
final Attribute a = i.encode(o, true);
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_FILTER_MISSING_REQUIRED_FIELD.get(i.getField().getName()));
} else {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final GetterInfo i : requiredFilterGetters) {
final Attribute a = i.encode(o);
if (a == null) {
throw new LDAPPersistException(
ERR_OBJECT_HANDLER_FILTER_MISSING_REQUIRED_GETTER.get(i.getMethod().getName()));
} else {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final FieldInfo i : alwaysAllowedFilterFields) {
final Attribute a = i.encode(o, true);
if (a != null) {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final GetterInfo i : alwaysAllowedFilterGetters) {
final Attribute a = i.encode(o);
if (a != null) {
attrs.add(a);
addedRequiredOrAllowed.set(true);
}
}
for (final FieldInfo i : conditionallyAllowedFilterFields) {
final Attribute a = i.encode(o, true);
if (a != null) {
attrs.add(a);
}
}
for (final GetterInfo i : conditionallyAllowedFilterGetters) {
final Attribute a = i.encode(o);
if (a != null) {
attrs.add(a);
}
}
final ArrayList<Filter> comps = new ArrayList<Filter>(attrs.size());
for (final Attribute a : attrs) {
for (final ASN1OctetString v : a.getRawValues()) {
comps.add(Filter.createEqualityFilter(a.getName(), v.getValue()));
}
}
if (superclassHandler != null) {
final Filter f = superclassHandler.createFilter(o, addedRequiredOrAllowed);
if (f.getFilterType() == Filter.FILTER_TYPE_AND) {
comps.addAll(Arrays.asList(f.getComponents()));
} else {
comps.add(f);
}
}
return Filter.createANDFilter(comps);
}
public void startGroup(Group g) throws Hdf5Exception {
logger.logComment("----- Going into a group: " + g.getFullName());
ArrayList<Attribute> attrs = Hdf5Utils.parseGroupForAttributes(g);
for (Attribute attribute : attrs) {
// attribute.
logger.logComment(
"Group: "
+ g.getName()
+ " has attribute: "
+ attribute.getName()
+ " = "
+ Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName()));
}
if (g.getName().equals(NetworkMLConstants.ROOT_ELEMENT)) {
logger.logComment("Found the main group");
String simConfigName =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.NC_SIM_CONFIG);
if (simConfigName != null) this.foundSimConfig = simConfigName;
String randomSeed =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.NC_NETWORK_GEN_RAND_SEED);
if (randomSeed != null) this.foundRandomSeed = Long.parseLong(randomSeed);
} else if (g.getName().equals(NetworkMLConstants.POPULATIONS_ELEMENT)) {
logger.logComment("Found the pops group");
inPopulations = true;
} else if (g.getName().startsWith(NetworkMLConstants.POPULATION_ELEMENT) && inPopulations) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.POP_NAME_ATTR);
logger.logComment("Found a population: " + name);
currentCellGroup = name;
} else if (g.getName().equals(NetworkMLConstants.PROJECTIONS_ELEMENT)) {
logger.logComment("Found the projections group");
inProjections = true;
String units = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.UNITS_ATTR);
projUnitSystem = UnitConverter.getUnitSystemIndex(units);
} else if (g.getName().startsWith(NetworkMLConstants.PROJECTION_ELEMENT) && inProjections) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PROJ_NAME_ATTR);
String source = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.SOURCE_ATTR);
String target = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.TARGET_ATTR);
logger.logComment("Found a projection: " + name + " from " + source + " to " + target);
if (!project.morphNetworkConnectionsInfo.isValidSimpleNetConn(name)
&& !project.volBasedConnsInfo.isValidVolBasedConn(name)) {
throw new Hdf5Exception(
"Error: there is a network connection with name: "
+ name
+ " specified in "
+ "that file, but no such NetConn exists in the project. Add one to allow import of this file");
}
/* TODO: Add checks on source & target!!
*/
if (project.morphNetworkConnectionsInfo.isValidSimpleNetConn(name)) {
// if (project.morphNetworkConnectionsInfo)
}
currentNetConn = name;
} else if (g.getName().startsWith(NetworkMLConstants.SYN_PROPS_ELEMENT + "_")
&& inProjections) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.SYN_TYPE_ATTR);
ConnSpecificProps cp = new ConnSpecificProps(name);
String internalDelay =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INTERNAL_DELAY_ATTR);
if (internalDelay != null)
cp.internalDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(internalDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
// Lump them in to the internal delay...
String preDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PRE_DELAY_ATTR);
if (preDelay != null)
cp.internalDelay =
cp.internalDelay
+ (float)
UnitConverter.getTime(
Float.parseFloat(preDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
String postDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.POST_DELAY_ATTR);
if (postDelay != null)
cp.internalDelay =
cp.internalDelay
+ (float)
UnitConverter.getTime(
Float.parseFloat(postDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
cp.weight =
Float.parseFloat(Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.WEIGHT_ATTR));
String propDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PROP_DELAY_ATTR);
if (propDelay != null)
globAPDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(propDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
logger.logComment("Found: " + cp);
globConnProps.add(cp);
} else if (g.getName().equals(NetworkMLConstants.INPUTS_ELEMENT)) {
logger.logComment("Found the Inputs group");
inInputs = true;
String units = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.UNITS_ATTR);
inputUnitSystem = UnitConverter.getUnitSystemIndex(units);
} else if (g.getName().startsWith(NetworkMLConstants.INPUT_ELEMENT) && inInputs) {
// The table of input sites is within the input group so get sites from here
String inputName = g.getName().substring(6);
// String inputName = Hdf5Utils.getFirstStringValAttr(attrs,
// NetworkMLConstants.INPUT_ELEMENT);
logger.logComment("Found an Input: " + inputName);
// inInput = true;
if (project.elecInputInfo.getStim(inputName) == null) {
throw new Hdf5Exception(
"Error: there is an electrical input with name: "
+ inputName
+ " specified in "
+ "that file, but no such electrical input exists in the project. Add one to allow import of this file");
}
// Get the atributes of the Input and compare them with the attributes within the project
// Test to find out what type of input this is
} else if (g.getName().startsWith("IClamp") && inInputs) {
String inputName = g.getParent().getName().substring(6);
// Get the input sites from the table
String cellGroup =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR);
if (cellGroup == null) {
cellGroup =
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.INPUT_TARGET_CELLGROUP_OLD_ATTR); // check old name
}
float readDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_DELAY_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
float readDuration =
(float)
UnitConverter.getTime(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_DUR_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
float readAmp =
(float)
UnitConverter.getCurrent(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_AMP_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
StimulationSettings nextStim = project.elecInputInfo.getStim(inputName);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
IClamp ic = (IClamp) myElectricalInput;
logger.logComment("Found an IClamp Input");
float currDelay = -1, currDur = -1, currAmp = -1;
/*
try
{
ic.getDelay().reset();
currDelay = ic.getDelay().getNumber();
ic.getDuration().reset();
currDur = ic.getDuration().getNumber();
ic.getAmplitude().reset();
currAmp = ic.getAmplitude().getNumber();
}
catch (Exception ex)
{
logger.logError("Legacy error getting iclamp params!!");
}*/
currDelay = ic.getDel().getNominalNumber();
currDur = ic.getDur().getNominalNumber();
currAmp = ic.getAmp().getNominalNumber();
if ((!project.elecInputInfo.getStim(inputName).getCellGroup().equals(cellGroup))
|| (readDelay != currDelay)
|| (readDuration != currDur)
|| (readAmp != currAmp)) {
throw new Hdf5Exception(
"Error: the input properties of the file do not match those in the project for input "
+ inputName
+ ""
+ "\nreadDelay: "
+ readDelay
+ ", currDelay: "
+ currDelay
+ "\nreadDuration: "
+ readDuration
+ ", currDur: "
+ currDur
+ "\nreadAmp: "
+ readAmp
+ ", currAmp: "
+ currAmp
+ ", str: "
+ Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_AMP_ATTR));
}
currentInput = inputName;
} else if (g.getName().startsWith("RandomSpikeTrain") && inInputs) {
String inputName = g.getParent().getName().substring(6);
// Get the input sites from the table
String cellGroup =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR);
if (cellGroup == null) {
cellGroup =
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.INPUT_TARGET_CELLGROUP_OLD_ATTR); // check old name
}
float frequency =
(float)
UnitConverter.getRate(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.RND_STIM_FREQ_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
String mechanism =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.RND_STIM_MECH_ATTR);
StimulationSettings nextStim = project.elecInputInfo.getStim(inputName);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
RandomSpikeTrain rs = (RandomSpikeTrain) myElectricalInput;
logger.logComment("Found an Random Spike Train Input");
if ((!project.elecInputInfo.getStim(inputName).getCellGroup().equals(cellGroup))
|| frequency != rs.getRate().getFixedNum()
|| !rs.getSynapseType().equals(mechanism)) {
throw new Hdf5Exception(
"Error: the input properties of the file do not match those in the project for input "
+ inputName);
}
currentInput = inputName;
}
}
public void dataSet(Dataset d) throws Hdf5Exception {
logger.logComment("----- Looking through dataset: " + d);
ArrayList<Attribute> attrs = Hdf5Utils.parseDatasetForAttributes(d);
for (Attribute attribute : attrs) {
logger.logComment(
"Dataset: "
+ d.getName()
+ " has attribute: "
+ attribute.getName()
+ " = "
+ Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName()));
}
float[][] data = Hdf5Utils.parse2Ddataset(d);
logger.logComment("Data has size: (" + data.length + ", " + data[0].length + ")");
if (inPopulations && currentCellGroup != null) {
for (int i = 0; i < data.length; i++) {
int id = (int) data[i][0];
float x = data[i][1];
float y = data[i][2];
float z = data[i][3];
PositionRecord posRec = new PositionRecord(id, x, y, z);
if (data[0].length == 5) {
posRec.setNodeId((int) data[i][4]);
}
this.project.generatedCellPositions.addPosition(currentCellGroup, posRec);
}
}
if (inProjections && currentNetConn != null) {
logger.logComment("Adding info for NetConn: " + currentNetConn);
int id_col = -1;
int pre_cell_id_col = -1;
int pre_segment_id_col = -1;
int pre_fraction_along_col = -1;
int post_cell_id_col = -1;
int post_segment_id_col = -1;
int post_fraction_along_col = -1;
int prop_delay_col = -1;
for (Attribute attribute : attrs) {
String storedInColumn = Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName());
if (storedInColumn.equals(NetworkMLConstants.CONNECTION_ID_ATTR)) {
id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("id col: " + id_col);
} else if (storedInColumn.equals(NetworkMLConstants.PRE_CELL_ID_ATTR)) {
pre_cell_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.PRE_SEGMENT_ID_ATTR)) {
pre_segment_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("pre_segment_id_col: " + pre_segment_id_col);
} else if (storedInColumn.equals(NetworkMLConstants.PRE_FRACT_ALONG_ATTR)) {
pre_fraction_along_col =
Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("pre_fraction_along_col: " + pre_fraction_along_col);
} else if (storedInColumn.equals(NetworkMLConstants.POST_CELL_ID_ATTR)) {
post_cell_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.POST_SEGMENT_ID_ATTR)) {
post_segment_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.POST_FRACT_ALONG_ATTR)) {
post_fraction_along_col =
Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.startsWith(NetworkMLConstants.PROP_DELAY_ATTR)) {
prop_delay_col = Integer.parseInt(attribute.getName().substring("column_".length()));
}
for (String synType : getConnectionSynTypes()) {
if (storedInColumn.endsWith(synType)) {
ConnSpecificProps cp = null;
for (ConnSpecificProps currCp : localConnProps) {
if (currCp.synapseType.equals(synType)) cp = currCp;
}
if (cp == null) {
cp = new ConnSpecificProps(synType);
cp.internalDelay = -1;
cp.weight = -1;
localConnProps.add(cp);
}
if (storedInColumn.startsWith(NetworkMLConstants.INTERNAL_DELAY_ATTR)) {
cp.internalDelay =
Integer.parseInt(
attribute
.getName()
.substring("column_".length())); // store the col num temporarily..
}
if (storedInColumn.startsWith(NetworkMLConstants.WEIGHT_ATTR)) {
cp.weight =
Integer.parseInt(
attribute
.getName()
.substring("column_".length())); // store the col num temporarily..
}
}
}
}
for (int i = 0; i < data.length; i++) {
int pre_seg_id = 0;
float pre_fract_along = 0.5f;
int post_seg_id = 0;
float post_fract_along = 0.5f;
int id = (int) data[i][id_col];
int pre_cell_id = (int) data[i][pre_cell_id_col];
int post_cell_id = (int) data[i][post_cell_id_col];
float prop_delay = 0;
if (pre_segment_id_col >= 0) pre_seg_id = (int) data[i][pre_segment_id_col];
if (pre_fraction_along_col >= 0) pre_fract_along = data[i][pre_fraction_along_col];
if (post_segment_id_col >= 0) post_seg_id = (int) data[i][post_segment_id_col];
if (post_fraction_along_col >= 0) post_fract_along = data[i][post_fraction_along_col];
// (float)UnitConverter.getTime(XXXXXXXXX, UnitConverter.NEUROCONSTRUCT_UNITS,
// unitSystem)+"";
if (prop_delay_col >= 0)
prop_delay =
(float)
UnitConverter.getTime(
data[i][prop_delay_col], projUnitSystem, UnitConverter.NEUROCONSTRUCT_UNITS);
ArrayList<ConnSpecificProps> props = new ArrayList<ConnSpecificProps>();
if (localConnProps.size() > 0) {
for (ConnSpecificProps currCp : localConnProps) {
logger.logComment("Pre cp: " + currCp);
ConnSpecificProps cp2 = new ConnSpecificProps(currCp.synapseType);
if (currCp.internalDelay > 0) // index was stored in this val...
cp2.internalDelay =
(float)
UnitConverter.getTime(
data[i][(int) currCp.internalDelay],
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
if (currCp.weight > 0) // index was stored in this val...
cp2.weight = data[i][(int) currCp.weight];
logger.logComment("Filled cp: " + cp2);
props.add(cp2);
}
}
this.project.generatedNetworkConnections.addSynapticConnection(
currentNetConn,
GeneratedNetworkConnections.MORPH_NETWORK_CONNECTION,
pre_cell_id,
pre_seg_id,
pre_fract_along,
post_cell_id,
post_seg_id,
post_fract_along,
prop_delay,
props);
}
}
if (inInputs && currentInput != null) {
logger.logComment("Adding info for: " + currentInput);
StimulationSettings nextStim = project.elecInputInfo.getStim(currentInput);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
String electricalInputType = myElectricalInput.getType();
String cellGroup = nextStim.getCellGroup();
for (int i = 0; i < data.length; i++) {
Float fileCellId = data[i][0];
Float fileSegmentId = data[i][1];
Float fractionAlong = data[i][2];
int cellId = fileCellId.intValue();
int segmentId = fileSegmentId.intValue();
SingleElectricalInput singleElectricalInputFromFile =
new SingleElectricalInput(
electricalInputType, cellGroup, cellId, segmentId, fractionAlong, null);
this.project.generatedElecInputs.addSingleInput(
currentInput, singleElectricalInputFromFile);
}
}
}
public String getName() {
return att.getName();
}
