public void load() throws IOException {
File file = getFile();
if (file.exists()) {
JsonObject rootObject = JSON_PARSER.parse(new FileReader(file)).getAsJsonObject();
for (JsonElement element : rootObject.getAsJsonArray("players")) {
Player player = new Player(element.getAsJsonObject());
playerDB.put(player.getName(), player);
}
for (JsonElement element : rootObject.getAsJsonArray("groups")) {
Group group = new Group(element.getAsJsonObject());
groupDB.put(group.getName(), group);
}
} else {
//noinspection ResultOfMethodCallIgnored
file.createNewFile();
JsonObject rootObject = new JsonObject();
rootObject.add("players", new JsonArray());
rootObject.add("groups", new JsonArray());
BufferedWriter bw = new BufferedWriter(new FileWriter(file));
bw.write(GSON.toJson(rootObject));
bw.close();
}
}
public void parseGroup(Group g) throws Hdf5Exception, EndOfSequenceException {
startGroup(g);
java.util.List members = g.getMemberList();
// NOTE: parsing contents twice to ensure subgroups are handled before datasets
// This is mainly because synapse_props groups will need to be parsed before dataset of
// connections
for (int j = 0; j < members.size(); j++) {
HObject obj = (HObject) members.get(j);
if (obj instanceof Group) {
Group subGroup = (Group) obj;
logger.logComment("--------- Found a sub group: " + subGroup.getName());
parseGroup(subGroup);
}
}
for (int j = 0; j < members.size(); j++) {
HObject obj = (HObject) members.get(j);
if (obj instanceof Dataset) {
Dataset ds = (Dataset) obj;
logger.logComment("Found a dataset: " + ds.getName());
dataSet(ds);
}
}
endGroup(g);
}
protected void addPropertiesWithPrefix(Properties properties, Group group) {
if (properties != null) {
if (group != null) {
String prefix = group.getName() + ".";
Properties suffixProperties = group.getProperties();
addPropertiesWithPrefix(properties, prefix, suffixProperties);
}
}
}
/*
* Loads a concept group from XML element
*/
private Group loadGroup(Element element) {
Group group = new Group();
group.name = element.getAttributeValue("name");
List children = element.getChildren("concept");
for (Iterator it = children.iterator(); it.hasNext(); ) {
Concept concept = new Concept();
Element e = (Element) it.next();
concept.id = (e.getAttributeValue("id"));
concept.rubric = (e.getAttributeValue("rubric"));
group.addConcept(concept);
}
return group;
}
GroupInvite(User sender, User receiver, Group group) {
this.sender = sender;
this.receiver = receiver;
this.group = group;
this.text =
"<a href = profile.jsp?ID="
+ sender.getID()
+ ">"
+ sender.getDisplayName()
+ "</a>"
+ " has invited you to join "
+ "<a href profile.jsp?ID="
+ group.getID()
+ ">"
+ group.getDisplayName()
+ "</a>";
type = "GroupInvite";
}
/**
* Creates a notification to a Group coordinator signaling that a user wants to join their group
*
* <p>- Requires a groupId request parameter for the GET
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void inviteAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
int groupId = Integer.parseInt(req.getParameter("groupId"));
try {
// Get the session user
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User user = userSession.getUser();
// Get the coordinator for the group
GroupManager groupMan = new GroupManager();
Group group = groupMan.get(groupId);
User coordinator = groupMan.getCoordinator(groupId);
// Send a notification to the coordinator for them to permit access to the group
NotificationManager notificationMan = new NotificationManager();
Notification notification =
new Notification(
coordinator.getId(),
coordinator,
groupId,
group,
user.getFullName() + " wants to join your group " + group.getGroupName(),
"/home/notifications?addUserId=" + user.getId() + "&groupId=" + group.getId());
notificationMan.createNotification(notification);
redirectToLocal(req, res, "/home/dashboard");
return;
} catch (Exception e) {
redirectToLocal(req, res, "/home/dashboard");
}
}
/**
* Converts the contents of the GroupInvite to a {@link java.lang.String} in order to save it to
* file. The toString method will save the invite as follows: Sender: senderID Receiver:
* receiverID Text: text ID : groupID
*/
public String toString() {
return ("Type:"
+ type
+ "\nSender:"
+ sender.getID()
+ "\nReceiver:"
+ receiver.getID()
+ "\nGroup:"
+ group.getID()
+ "\nText:"
+ text
+ "\n"); // Just for compile
}
/** @param args */
public static String Parsecsv(String data) {
try {
// CSVReader reader = new CSVReader(new FileReader(filename));
StringReader str = new StringReader(data);
CSVReader reader = new CSVReader(str);
java.util.List<String[]> content = reader.readAll();
HashMap<String, Group> groups = new HashMap<String, Group>();
for (String[] row : content) {
String Name = row[0];
String Events = row[1];
// System.out.printf("%S has attended %S events %n",Name, Events);
if (groups.containsKey(Name)) {
groups.get(Name).Add(Double.valueOf(Events));
} else {
Group g = new Group();
g.Add(Double.valueOf(Events));
groups.put(Name, g);
}
}
reader.close();
StringBuilder result = new StringBuilder();
for (String name : groups.keySet()) {
// System.out.printf("%S has attended %S events with average of %S
// %n",name,groups.get(name).Gettotal(),groups.get(name).GetAverage());
String val =
String.format(
"%S has attended %S events with average of %S %n",
name, groups.get(name).Gettotal(), groups.get(name).GetAverage());
result.append(val);
}
return result.toString();
} catch (Exception e) {
return e.toString();
}
}
public void save() {
try {
File file = getFile();
if (!file.exists()) // noinspection ResultOfMethodCallIgnored
file.createNewFile();
JsonObject rootObject = new JsonObject();
JsonArray players = new JsonArray();
for (Player player : playerDB.values()) players.add(player.toJson());
rootObject.add("players", players);
JsonArray groups = new JsonArray();
for (Group group : groupDB.values()) groups.add(group.toJson());
rootObject.add("groups", groups);
BufferedWriter bw = new BufferedWriter(new FileWriter(file));
bw.write(GSON.toJson(rootObject));
bw.close();
} catch (IOException e) {
e.printStackTrace();
}
}
private void update() {
try {
group.subscribeTo(receiver);
receiver.addGroup(group);
Date date = new Date();
receiver.post(
"<a href = profile.jsp?ID="
+ receiver.getID()
+ ">"
+ receiver.getDisplayName()
+ "</a>"
+ " joined "
+ "<a href = profile.jsp?ID="
+ group.getID()
+ ">"
+ group.getDisplayName()
+ "</a>",
receiver,
date);
} catch (Exception e) { // Fix to later return some sort of bs
e.printStackTrace();
}
}
public void endGroup(Group g) throws Hdf5Exception {
logger.logComment("----- Going out of a group: " + g.getFullName());
if (g.getName().equals(NetworkMLConstants.POPULATIONS_ELEMENT)) {
inPopulations = false;
} else if (g.getName().equals(NetworkMLConstants.PROJECTIONS_ELEMENT)) {
inProjections = false;
} else if (g.getName().equals(NetworkMLConstants.INPUTS_ELEMENT)) {
inInputs = false;
} else if (g.getName().equals(NetworkMLConstants.INPUT_ELEMENT) && inInputs) {
currentInput = null;
} else if (g.getName().startsWith(NetworkMLConstants.POPULATION_ELEMENT) && inPopulations) {
currentCellGroup = null;
} else if (g.getName().startsWith(NetworkMLConstants.PROJECTION_ELEMENT) && inProjections) {
currentNetConn = null;
globConnProps = new ArrayList<ConnSpecificProps>();
} else if (g.getName().startsWith(NetworkMLConstants.CONNECTION_ELEMENT)) {
localConnProps = new ArrayList<ConnSpecificProps>();
localAPDelay = 0;
}
}
/**
* Drives the application.
*
* @param args first element would be the svn access configuration file
* @throws Exception if it fails to generate a report
*/
public void drive(String[] args) throws Exception {
// We need an access config file in order to generate a report.
if (args == null || args.length < 1) {
System.out.println("=== SVN Access Auditor v1.0 ===");
System.out.println("Outputs mapping information (HTML) between SVN repos and users. ");
System.out.println("Usage:");
System.out.println(" java -jar svnaccessauditor.jar <svnaccess.conf>");
System.out.println();
System.out.println("Output: repos.html");
return;
}
File accessConfigFile = new File(args[0]);
if (!accessConfigFile.exists() || accessConfigFile.isDirectory()) {
System.out.println("File not exists at: " + args[0]);
return;
}
System.out.println("Processing the records...");
BufferedReader reader = new BufferedReader(new FileReader(accessConfigFile));
String line;
// Let the states handle the records.
currentState = new InitialState(this);
while ((line = reader.readLine()) != null) {
currentState.process(line);
}
reader.close();
// Add all users to EVERYONE group.
for (User u : users.values()) {
EVERYONE.addUser(u);
}
groups.put("EVERYONE", EVERYONE);
reportGenerator = new HtmlReportGenerator(users, groups, repos);
reportGenerator.generateReport();
}
// read all records in all files,
// divide into groups based on GDS hash
// each group has an arraylist of all records that belong to it.
// for each group, run rectlizer to derive the coordinates and variables
public List<Group> makeAggregatedGroups(
List<String> filenames, CollectionManager.Force force, Formatter f) throws IOException {
Map<Integer, Group> gdsMap = new HashMap<Integer, Group>();
boolean intvMerge = mergeIntvDefault;
f.format("GribCollection %s: makeAggregatedGroups%n", gc.getName());
int total = 0;
int fileno = 0;
for (CollectionManager dcm : collections) {
f.format(" dcm= %s%n", dcm);
FeatureCollectionConfig.GribConfig config =
(FeatureCollectionConfig.GribConfig)
dcm.getAuxInfo(FeatureCollectionConfig.AUX_GRIB_CONFIG);
Map<Integer, Integer> gdsConvert = (config != null) ? config.gdsHash : null;
FeatureCollectionConfig.GribIntvFilter intvMap = (config != null) ? config.intvFilter : null;
intvMerge =
(config == null) || (config.intvMerge == null) ? mergeIntvDefault : config.intvMerge;
for (MFile mfile : dcm.getFiles()) {
// f.format("%3d: %s%n", fileno, mfile.getPath());
filenames.add(mfile.getPath());
Grib2Index index = null;
try {
index =
(Grib2Index)
GribIndex.readOrCreateIndexFromSingleFile(
false, !isSingleFile, mfile, config, force, f);
} catch (IOException ioe) {
logger.warn(
"GribCollectionBuilder {}: reading/Creating gbx9 index failed err={}",
gc.getName(),
ioe.getMessage());
f.format(
"GribCollectionBuilder: reading/Creating gbx9 index failed err=%s%n skipping %s%n",
ioe.getMessage(), mfile.getPath() + GribIndex.IDX_EXT);
continue;
}
for (Grib2Record gr : index.getRecords()) {
if (this.tables == null) {
Grib2SectionIdentification ids =
gr.getId(); // so all records must use the same table (!)
this.tables =
Grib2Customizer.factory(
ids.getCenter_id(),
ids.getSubcenter_id(),
ids.getMaster_table_version(),
ids.getLocal_table_version());
if (config != null)
tables.setTimeUnitConverter(
config
.getTimeUnitConverter()); // LOOK doesnt really work with multiple collections
}
if (intvMap != null && filterTinv(gr, intvMap, f)) continue; // skip
gr.setFile(fileno); // each record tracks which file it belongs to
int gdsHash =
gr.getGDSsection().getGDS().hashCode(); // use GDS hash code to group records
if (gdsConvert != null
&& gdsConvert.get(gdsHash)
!= null) // allow external config to muck with gdsHash. Why? because of error in
// encoding
gdsHash = (Integer) gdsConvert.get(gdsHash); // and we need exact hash matching
Group g = gdsMap.get(gdsHash);
if (g == null) {
g = new Group(gr.getGDSsection(), gdsHash);
gdsMap.put(gdsHash, g);
}
g.records.add(gr);
total++;
}
fileno++;
}
}
f.format(" total grib records= %d%n", total);
Grib2Rectilyser.Counter c = new Grib2Rectilyser.Counter(); // debugging
List<Group> result = new ArrayList<Group>(gdsMap.values());
for (Group g : result) {
g.rect = new Grib2Rectilyser(tables, g.records, g.gdsHash, intvMerge);
f.format(" GDS hash %d == ", g.gdsHash);
g.rect.make(f, c, filenames);
}
f.format(
" Rectilyser: nvars=%d records unique=%d total=%d dups=%d (%f) %n",
c.vars, c.recordsUnique, c.records, c.dups, ((float) c.dups) / c.records);
return result;
}
/**
* Displays a given Research Group page for a HTTP Get, or creates a new Group for a HTTP Post
*
* <p>- Requires a cookie for the session user - Requires a groupId request parameter for a GET -
* Requires a groupName, description, createdByUserId request parameters for a POST
*
* @param req The HTTP Request
* @param res The HTTP Response
*/
public void researchgroupAction(HttpServletRequest req, HttpServletResponse res) {
// Ensure there is a cookie for the session user
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
viewData.put("title", "Research Group");
if (req.getMethod() == HttpMethod.Get) {
// Load group data into Map
GroupManager gm = new GroupManager();
int groupId = Integer.parseInt(req.getParameter("groupId"));
Group group = gm.get(groupId);
if (group != null) {
// Load Group into map
viewData.put("group", group);
// Load group members into Map
List<String> groupMembers = gm.getGroupMembers(groupId);
viewData.put("groupMembers", groupMembers);
// Load meetings into map
MeetingManager meetMan = new MeetingManager();
List<Meeting> groupMeetings = meetMan.getGroupMeetings(groupId);
viewData.put("groupMeetings", groupMeetings);
// Load Document Data into Map
DocumentManager docMan = new DocumentManager();
List<Document> groupDocuments = docMan.getGroupDocuments(groupId);
viewData.put("groupDocuments", groupDocuments);
// Load discussion threads
DiscussionManager dm = new DiscussionManager();
viewData.put("groupDiscussions", dm.getThreads(groupId));
// Check if the user is a member
boolean isMember = false;
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User user = userSession.getUser();
for (Group g : gm.getAllGroups(user.getId())) {
if (g.getId() == group.getId()) {
isMember = true;
break;
}
}
viewData.put("notMember", !isMember);
// View group page.
view(req, res, "/views/group/ResearchGroup.jsp", viewData);
} else {
httpNotFound(req, res);
}
} else if (req.getMethod() == HttpMethod.Post) {
// Create Group
// Get data from parameters
String groupName = req.getParameter("groupName");
String description = req.getParameter("description");
int adminId = Integer.parseInt(req.getParameter("createdByUserId"));
// Create the Group
GroupManager groupMan = new GroupManager();
Group group = new Group();
group.setGroupName(groupName);
group.setDescription(description);
group.setCoordinatorId(adminId);
// Create the mapping
groupMan.createGroup(group);
int groupId = groupMan.getIdFor(group);
groupMan.createMapping(groupId, adminId);
group.setId(groupId);
// Update the User Session to show new group
HttpSession session = req.getSession();
Session userSession = (Session) session.getAttribute("userSession");
User admin = userSession.getUser();
admin.getGroups().add(group);
// Show the Group Page
viewData.put("groupName", group.getGroupName());
List<String> groupMembers = groupMan.getGroupMembers(groupId);
viewData.put("groupMembers", groupMembers);
view(req, res, "/views/group/ResearchGroup.jsp", viewData);
}
}
protected Group getJoinedGroup(String userRole, Group group1, Group group2) {
Group res = null;
{
Principal principal = null;
String id = null;
String name = null;
// Set 'principal':
{
principal = new SimplePrincipal(userRole);
}
// Set 'id':
{
id = userRole;
}
// Set 'name':
{
name = ApplicationUserRoles.getDisplayName(userRole);
}
if (group1 == null) {
if (group2 == null) {
res = null;
} else {
// Set result from 'group2':
{
AbstractUserAuthorizor.DefaultGroup g = new AbstractUserAuthorizor.DefaultGroup(group2);
g.setName(name);
g.setPrincipal(principal);
res = g;
}
}
} else {
if (group2 == null) {
// Set result from 'group1':
{
AbstractUserAuthorizor.DefaultGroup g = new AbstractUserAuthorizor.DefaultGroup(group1);
g.setName(name);
g.setPrincipal(principal);
res = g;
}
} else {
Properties properties = null;
Map<String, List<String>> attributes = null;
List<Principal> userPrincipals = null;
List<Principal> superGroupPrincipals = null;
List<Principal> groupPrincipals = null;
// Set 'properties':
{
properties = new Properties();
// Add properties from 'group1':
{
addPropertiesWithPrefix(properties, group1);
}
// Add properties from 'group2':
{
addPropertiesWithPrefix(properties, group2);
}
}
// Set 'attributes':
{
Map<String, List<String>> attributes1 = group1.getAttributes();
Map<String, List<String>> attributes2 = group2.getAttributes();
attributes = joinAttributes(attributes1, attributes2);
}
// Set 'userPrincipals':
{
userPrincipals = new ArrayList<Principal>();
// Add user principals from 'group1':
{
List<Principal> l = group1.getUserPrincipals();
if (l != null) {
userPrincipals.addAll(l);
}
}
// Add user principals from 'group2':
{
List<Principal> l = group2.getUserPrincipals();
if (l != null) {
userPrincipals.addAll(l);
}
}
}
// Set 'superGroupPrincipals':
{
superGroupPrincipals = new ArrayList<Principal>();
// Add super-group principals from 'group1':
{
List<Principal> l = group1.getSuperGroupPrincipals();
if (l != null) {
superGroupPrincipals.addAll(l);
}
}
// Add super-group principals from 'group2':
{
List<Principal> l = group2.getSuperGroupPrincipals();
if (l != null) {
superGroupPrincipals.addAll(l);
}
}
}
// Set 'groupPrincipals':
{
groupPrincipals = new ArrayList<Principal>();
// Add group principals from 'group1':
{
List<Principal> l = group1.getGroupPrincipals();
if (l != null) {
groupPrincipals.addAll(l);
}
}
// Add group principals from 'group2':
{
List<Principal> l = group2.getGroupPrincipals();
if (l != null) {
groupPrincipals.addAll(l);
}
}
}
res =
new AbstractUserAuthorizor.DefaultGroup(
principal,
id,
name,
properties,
attributes,
userPrincipals,
superGroupPrincipals,
groupPrincipals);
}
}
}
return res;
}
// read all records in all files,
// divide into groups based on GDS hash
// each group has an arraylist of all records that belong to it.
// for each group, run rectlizer to derive the coordinates and variables
public List<Group> makeAggregatedGroups(
ArrayList<String> filenames, CollectionManager.Force force, Formatter f) throws IOException {
Map<Integer, Group> gdsMap = new HashMap<Integer, Group>();
f.format("GribCollection %s: makeAggregatedGroups%n", gc.getName());
int total = 0;
int fileno = 0;
for (CollectionManager dcm : collections) {
// dcm.scanIfNeeded(); // LOOK ??
f.format(" dcm= %s%n", dcm);
Map<Integer, Integer> gdsConvert = (Map<Integer, Integer>) dcm.getAuxInfo("gdsHash");
for (MFile mfile : dcm.getFiles()) {
// f.format("%3d: %s%n", fileno, mfile.getPath());
filenames.add(mfile.getPath());
Grib2Index index = new Grib2Index();
try {
if (!index.readIndex(
mfile.getPath(),
mfile.getLastModified(),
force)) { // heres where the index date is checked against the data file
index.makeIndex(mfile.getPath(), f);
f.format(
" Index written: %s == %d records %n",
mfile.getName() + Grib2Index.IDX_EXT, index.getRecords().size());
} else if (debug) {
f.format(
" Index read: %s == %d records %n",
mfile.getName() + Grib2Index.IDX_EXT, index.getRecords().size());
}
} catch (IOException ioe) {
f.format(
"GribCollectionBuilder: reading/Creating gbx9 index failed err=%s%n skipping %s%n",
ioe.getMessage(), mfile.getPath() + Grib2Index.IDX_EXT);
continue;
}
for (Grib2Record gr : index.getRecords()) {
gr.setFile(fileno); // each record tracks which file it belongs to
int gdsHash =
gr.getGDSsection().getGDS().hashCode(); // use GDS hash code to group records
if (gdsConvert != null
&& gdsConvert.get(gdsHash)
!= null) { // allow external config to muck with gdsHash. Why? because of error in
// encoding
gdsHash = (Integer) gdsConvert.get(gdsHash); // and we need exact hash matching
}
Group g = gdsMap.get(gdsHash);
if (g == null) {
g = new Group(gr.getGDSsection(), gdsHash);
gdsMap.put(gdsHash, g);
}
g.records.add(gr);
total++;
}
fileno++;
}
}
f.format(" total grib records= %d%n", total);
Grib2Rectilyser.Counter c = new Grib2Rectilyser.Counter();
List<Group> result = new ArrayList<Group>(gdsMap.values());
for (Group g : result) {
g.rect = new Grib2Rectilyser(g.records, g.gdsHash);
f.format(" GDS hash %d == ", g.gdsHash);
g.rect.make(f, c);
}
f.format(
" Rectilyser: nvars=%d records unique=%d total=%d dups=%d (%f) %n",
c.vars, c.recordsUnique, c.records, c.dups, ((float) c.dups) / c.records);
return result;
}
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;
}
}
private void createIndex(
File indexFile, List<Group> groups, ArrayList<String> filenames, Formatter f)
throws IOException {
Grib2Record first = null; // take global metadata from here
if (indexFile.exists()) indexFile.delete(); // replace it
f.format(" createIndex for %s%n", indexFile.getPath());
RandomAccessFile raf = new RandomAccessFile(indexFile.getPath(), "rw");
raf.order(RandomAccessFile.BIG_ENDIAN);
try {
//// header message
raf.write(MAGIC_START.getBytes("UTF-8"));
raf.writeInt(version);
long lenPos = raf.getFilePointer();
raf.writeLong(0); // save space to write the length of the record section
long countBytes = 0;
int countRecords = 0;
for (Group g : groups) {
g.fileSet = new HashSet<Integer>();
for (Grib2Rectilyser.VariableBag vb : g.rect.getGribvars()) {
if (first == null) first = vb.first;
GribCollectionProto.VariableRecords vr = writeRecordsProto(vb, g.fileSet);
byte[] b = vr.toByteArray();
vb.pos = raf.getFilePointer();
vb.length = b.length;
raf.write(b);
countBytes += b.length;
countRecords += vb.recordMap.length;
}
}
long bytesPerRecord = countBytes / ((countRecords == 0) ? 1 : countRecords);
f.format(
" write RecordMaps: bytes = %d record = %d bytesPerRecord=%d%n",
countBytes, countRecords, bytesPerRecord);
if (first == null) {
logger.error("GribCollection {}: has no files\n{}", gc.getName(), f.toString());
throw new IllegalArgumentException("GribCollection " + gc.getName() + " has no files");
}
long pos = raf.getFilePointer();
raf.seek(lenPos);
raf.writeLong(countBytes);
raf.seek(pos); // back to the output.
GribCollectionProto.GribCollectionIndex.Builder indexBuilder =
GribCollectionProto.GribCollectionIndex.newBuilder();
indexBuilder.setName(gc.getName());
for (String fn : filenames) indexBuilder.addFiles(fn);
for (Group g : groups) indexBuilder.addGroups(writeGroupProto(g));
/* int count = 0;
for (DatasetCollectionManager dcm : collections) {
indexBuilder.addParams(makeParamProto(new Parameter("spec" + count, dcm.())));
count++;
} */
// what about just storing first ??
Grib2SectionIdentification ids = first.getId();
indexBuilder.setCenter(ids.getCenter_id());
indexBuilder.setSubcenter(ids.getSubcenter_id());
indexBuilder.setMaster(ids.getMaster_table_version());
indexBuilder.setLocal(ids.getLocal_table_version());
Grib2Pds pds = first.getPDS();
indexBuilder.setGenProcessType(pds.getGenProcessType());
indexBuilder.setGenProcessId(pds.getGenProcessId());
indexBuilder.setBackProcessId(pds.getBackProcessId());
GribCollectionProto.GribCollectionIndex index = indexBuilder.build();
byte[] b = index.toByteArray();
NcStream.writeVInt(raf, b.length); // message size
raf.write(b); // message - all in one gulp
f.format(" write GribCollectionIndex= %d bytes%n", b.length);
} finally {
f.format(" file size = %d bytes%n", raf.length());
raf.close();
if (raf != null) raf.close();
}
}