/**
* Combines a list of clusters and a list of interfaces, taking the union.
*
* @param requestedIfacesStr
* @param requestedClusterStr
* @param ifaceList
* @return
*/
public static IntervalSet parseInterfaceListWithClusters(
String ifaceStr, String clusterStr, List<Interface> ifaceList) {
// If one of interfaces and clusters is specified, return it
// If either are '*', return null (all)
// If both are specified, return their union
if (ifaceStr == null) {
if (clusterStr == null) {
// If neither are specified, return all
return new IntervalSet(Interval.INFINITE_INTERVAL);
}
// Only clusters specified
if (clusterStr.equals('*')) return new IntervalSet(Interval.INFINITE_INTERVAL);
IntervalSet clusterSet = new IntervalSet(clusterStr);
return mapClusters(clusterSet, ifaceList);
} else {
if (clusterStr == null) {
// Only interfaces specified
return new IntervalSet(ifaceStr);
}
// Both specified
if (ifaceStr.equals('*') || clusterStr.equals('*'))
return new IntervalSet(Interval.INFINITE_INTERVAL);
IntervalSet clusterSet = new IntervalSet(clusterStr);
IntervalSet interfaces = mapClusters(clusterSet, ifaceList);
interfaces.addAll(new IntervalSet(ifaceStr));
return interfaces.getMergedIntervalSet();
}
}
/**
* Expand a list of interface cluster numbers to a full list of interfaces
*
* @param clusters
* @param ifaceList
* @return
*/
private static IntervalSet mapClusters(IntervalSet clusters, Collection<Interface> ifaceList) {
SortedSet<Integer> interfaces = new TreeSet<>();
for (Interface iface : ifaceList) {
if (clusters.contains(iface.getClusterId())) {
// Only interfaces specified
interfaces.add(iface.getInterfaceId());
}
}
return new IntervalSet(interfaces);
}
@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// TODO add type=interface/assembly as parameter, so that assemblies can also be supported
String jobId = request.getParameter(FileDownloadServlet.PARAM_ID);
String requestedIfacesStr = request.getParameter(PARAM_INTERFACES);
String requestedClusterStr = request.getParameter(PARAM_CLUSTERS);
String size = request.getParameter(JmolViewerServlet.PARAM_SIZE);
String format = request.getParameter(PARAM_FORMAT);
logger.info(
"Requested Lattice Graph page for jobId={},interfaces={},clusters={},format={}",
jobId,
requestedIfacesStr,
requestedClusterStr,
format);
PrintWriter outputStream = null;
try {
LatticeGraphServletInputValidator.validateLatticeGraphInput(
jobId, requestedIfacesStr, requestedClusterStr, format);
PdbInfo pdbInfo = getPdbInfo(jobId);
String input = pdbInfo.getInputName();
// String inputPrefix = pdbInfo.getTruncatedInputName();
// job directory on local filesystem
File dir = DirLocatorUtil.getJobDir(new File(destination_path), jobId);
// Construct filename for AU cif file
File auFile = getAuFileName(dir, input, atomCachePath);
String inputFileNameNoGz = auFile.getName();
if (auFile.getName().endsWith(".gz")) {
inputFileNameNoGz = auFile.getName().substring(0, auFile.getName().lastIndexOf(".gz"));
} else if (auFile.getName().endsWith(".GZ")) {
inputFileNameNoGz = auFile.getName().substring(0, auFile.getName().lastIndexOf(".GZ"));
}
// the URL has no gz at the end because it's served as plain text via content-encoding: gzip
String auURI = DirLocatorUtil.getJobUrlPath(resultsLocation, jobId) + "/" + inputFileNameNoGz;
List<Interface> ifaceList = getInterfaceList(pdbInfo);
// TODO better to filter interfaces here before construction, or afterwards?
IntervalSet requestedIntervals =
parseInterfaceListWithClusters(requestedIfacesStr, requestedClusterStr, ifaceList);
Collection<Integer> requestedIfaces = requestedIntervals.getIntegerSet();
String title = jobId + " - Lattice Graph";
if (requestedIfaces != null && !requestedIfaces.isEmpty()) {
title += " for interfaces " + requestedIfacesStr;
}
outputStream = new PrintWriter(response.getOutputStream());
// String molviewerurl = properties.getProperty("urlNglJs");
if (format != null && format.equalsIgnoreCase("json")) {
LatticeGraphPageGenerator.generateJSONPage(
dir, input, auFile, ifaceList, requestedIfaces, outputStream);
} else {
String nglJsUrl = properties.getProperty("urlNglJs");
if (nglJsUrl == null || nglJsUrl.equals("")) {
logger.info(
"The URL for NGL js is not set in config file. Will use the js file inside the ewui war");
nglJsUrl =
JmolViewerServlet
.DEFAULT_NGL_URL; // we set it to the js file within the war, the leading '/' is
// important to point to the right path here
}
// Request URL, with format=json
StringBuffer jsonURL = request.getRequestURL();
Map<String, String[]> query = new LinkedHashMap<>(request.getParameterMap());
query.put("format", new String[] {"json"});
jsonURL
.append('?')
.append(
query
.entrySet()
.stream()
.<String>flatMap(
entry -> Arrays.stream(entry.getValue()).map(s -> entry.getKey() + "=" + s))
.collect(Collectors.joining("&")));
LatticeGraphPageGenerator.generateHTMLPage(
dir,
input,
auFile,
auURI,
title,
size,
jsonURL.toString(),
ifaceList,
requestedIfaces,
outputStream,
nglJsUrl);
// TODO start generating JSON now, since we know that request is coming
}
} catch (ValidationException e) {
response.sendError(
HttpServletResponse.SC_PRECONDITION_FAILED,
"Input values are incorrect: " + e.getMessage());
} catch (IOException e) {
response.sendError(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error during preparation of Lattice Graph page.");
logger.error("Error during preparation of Lattice Graph page.", e);
} catch (DaoException e) {
response.sendError(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error during preparation of Lattice Graph page.");
logger.error("Error during preparation of Lattice Graph page.", e);
} catch (StructureException e) {
response.sendError(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error during preparation of Lattice Graph page.");
logger.error("Error during preparation of Lattice Graph page.", e);
} catch (Exception e) {
response.sendError(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
"Error during preparation of Lattice Graph page.");
logger.error("Error during preparation of Lattice Graph page.", e);
} finally {
if (outputStream != null) {
try {
outputStream.close();
} catch (Throwable t) {
}
}
}
}
