List of usage examples for org.apache.commons.lang.builder ToStringBuilder reflectionToString
public static String reflectionToString(Object object, ToStringStyle style)
Forwards to ReflectionToStringBuilder.
From source file:com.healthmarketscience.jackcess.impl.office.EncryptionHeader.java
@Override public String toString() { return ToStringBuilder.reflectionToString(this, CustomToStringStyle.VALUE_INSTANCE); }
From source file:com.gemini.provision.loadbalancer.openstack.LoadBalancerProviderOpenStackImpl.java
@Override public List<GeminiLoadBalancerPool> listAllPools(GeminiTenant tenant, GeminiEnvironment env) { List<GeminiLoadBalancerPool> lbPools = Collections.synchronizedList(new ArrayList()); //authenticate the session with the OpenStack installation OSClient os = OSFactory.builder().endpoint(env.getEndPoint()) .credentials(env.getAdminUserName(), env.getAdminPassword()).tenantName(tenant.getName()) .authenticate();/*w w w.ja v a 2 s.c om*/ if (os == null) { Logger.error("Failed to authenticate Tenant: {}", ToStringBuilder.reflectionToString(tenant, ToStringStyle.MULTI_LINE_STYLE)); return null; } List<? extends LbPool> osLbPools = os.networking().loadbalancers().lbPool().list(); osLbPools.stream().filter(lbPool -> lbPool != null).forEach(lbPool -> { GeminiLoadBalancerPool loadBalancerPool = new GeminiLoadBalancerPool(); loadBalancerPool.setCloudID(lbPool.getId()); loadBalancerPool.setName(lbPool.getName()); loadBalancerPool.setDescription(lbPool.getDescription()); //TODO get the VpId from the pool loadBalancerPool.setVipID(lbPool.getVipId()); loadBalancerPool.setProtocol(Protocol.fromString(lbPool.getProtocol())); loadBalancerPool.setLoadBalancerAlgorithm(LoadBalancerAlgorithm.fromString(lbPool.getLbMethod())); //TODO set the pool member loadBalancerPool.setAdminState(lbPool.isAdminStateUp() ? AdminState.ADMIN_UP : AdminState.ADMIN_DOWN); GeminiSubnet subnet = env.getApplications().stream().map(GeminiApplication::getNetworks) .flatMap(List::stream).map(GeminiNetwork::getSubnets).flatMap(List::stream) .filter(s -> s.getCloudID().equals(lbPool.getId())).findFirst().get(); if (subnet == null) { Logger.info( "Load Balancer cloud ID {} references a subnet not available in environment {} Subnet ID: {}", lbPool.getId(), env.getName(), lbPool.getSubnetId()); } else { loadBalancerPool.setGeminiSubnet(subnet); } lbPools.add(loadBalancerPool); }); return lbPools; }
From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnRGraphServiceImpl.java
/** ************************************************************* * initialize the RServe connection and load the graph; * keep the open connection.//from w ww . j a va 2 s .c om * * @param sro a DvnRJobRequest object that contains various parameters * @return a Map that contains various information about the results */ public Map<String, String> initializeConnection(DvnRJobRequest sro) throws DvnRGraphException { // set the return object Map<String, String> result = new HashMap<String, String>(); try { if (sro != null) { dbgLog.fine( "sro dump:\n" + ToStringBuilder.reflectionToString(sro, ToStringStyle.MULTI_LINE_STYLE)); } else { throw new DvnRGraphException("init: NULL R JOB OBJECT"); } String SavedRworkSpace = null; String CachedRworkSpace = sro.getCachedRworkSpace(); Map<String, Object> SubsetParameters = sro.getParametersForGraphSubset(); if (SubsetParameters != null) { SavedRworkSpace = (String) SubsetParameters.get(SAVED_RWORK_SPACE); } if (SavedRworkSpace != null) { myConnection = RConnectionPool.securePooledConnection(SavedRworkSpace, null, true, 0); RDataFileName = SavedRworkSpace; } else if (CachedRworkSpace != null) { myConnection = RConnectionPool.securePooledConnection(RDataFileName, CachedRworkSpace, false, 0); } else { throw new DvnRGraphException("Initialize method called without either local or remote RData file"); } if (myConnection == 0) { throw new DvnRGraphException("failed to obtain an R connection"); } else { DvnRConnection drc = RConnectionPool.getConnection(myConnection); if (drc == null) { throw new DvnRGraphException("failed to obtain an R connection"); } else { // set the connection time stamp: Date now = new Date(); drc.setLastQueryTime(now.getTime()); drc.unlockConnection(); } } dbgLog.info("Initialize: obtained connection " + myConnection); result.put(SAVED_RWORK_SPACE, RDataFileName); result.put("dsbHost", RSERVE_HOST); result.put("dsbPort", DSB_HOST_PORT); result.put("IdSuffix", IdSuffix); } catch (DvnRGraphException dre) { throw dre; } return result; }
From source file:com.gemini.provision.security.openstack.SecurityProviderOpenStackImpl.java
@Override public List<GeminiSecurityGroupRule> listSecurityGroupRules(GeminiTenant tenant, GeminiEnvironment env, GeminiSecurityGroup securityGroup) { List<GeminiSecurityGroupRule> listSecGrpRules = Collections.synchronizedList(new ArrayList()); //authenticate the session with the OpenStack installation OSClient os = OSFactory.builder().endpoint(env.getEndPoint()) .credentials(env.getAdminUserName(), env.getAdminPassword()).tenantName(tenant.getName()) .authenticate();/* w ww . j a va 2s. c o m*/ if (os == null) { Logger.error("Failed to authenticate Tenant: {}", ToStringBuilder.reflectionToString(tenant, ToStringStyle.MULTI_LINE_STYLE)); return null; } List<? extends SecurityGroupRule> osSecGrpRules = null; try { osSecGrpRules = os.networking().securityrule().list(); } catch (NullPointerException | ClientResponseException ex) { Logger.error("Failed to get rules for tenant: {} env: {} and security Group {}", tenant.getName(), env.getName(), securityGroup.getName()); return null; } osSecGrpRules.stream().filter(osSecGrpRule -> osSecGrpRule != null).forEach(osSecGrpRule -> { //find the rule in the security group object and add it to list GeminiSecurityGroupRule gemSecGrpRule = null; try { gemSecGrpRule = securityGroup.getSecurityRules().stream() .filter(sr -> sr.getCloudID().equals(osSecGrpRule.getId())) //check cloud id too to ensure the mapping on Gemini is complete .findFirst().get(); } catch (NoSuchElementException ex) { //not an error or even log worthy ... just signifies that the rule //on Gemini Side needs to be created } if (gemSecGrpRule == null) { //the rule has not been mapped on the Gemini side, so create it gemSecGrpRule = new GeminiSecurityGroupRule(); gemSecGrpRule.setCloudID(osSecGrpRule.getId()); gemSecGrpRule.setProvisioned(true); gemSecGrpRule.setPortRangeMin(osSecGrpRule.getPortRangeMin()); gemSecGrpRule.setPortRangeMax(osSecGrpRule.getPortRangeMax()); gemSecGrpRule.setProtocol(Protocol.fromString(osSecGrpRule.getProtocol())); // gemSecGrpRule.setCidr(osSecGrpRule.getRange().getCidr()); gemSecGrpRule.setDirection( GeminiSecurityGroupRuleDirection.valueOf(osSecGrpRule.getDirection().toUpperCase())); gemSecGrpRule.setRemoteGroupId(osSecGrpRule.getRemoteGroupId()); gemSecGrpRule.setRemoteIpPrefix(osSecGrpRule.getRemoteIpPrefix()); gemSecGrpRule.setIpAddressType(IPAddressType.valueOf(osSecGrpRule.getEtherType())); gemSecGrpRule.setParent(securityGroup); securityGroup.addSecurityRule(gemSecGrpRule); } listSecGrpRules.add(gemSecGrpRule); }); Logger.debug("Successfully retrieved security groups rules Tenant: {} Env: {} security group {}", tenant.getName(), env.getName(), securityGroup.getName()); return listSecGrpRules; }
From source file:com.alibaba.otter.shared.common.utils.meta.DdlUtils.java
private static Table readTable(DatabaseMetaDataWrapper metaData, Map<String, Object> values) throws SQLException { String tableName = (String) values.get("TABLE_NAME"); Table table = null;//from w w w .j av a 2s. co m if ((tableName != null) && (tableName.length() > 0)) { table = new Table(); table.setName(tableName); table.setType((String) values.get("TABLE_TYPE")); table.setCatalog((String) values.get("TABLE_CAT")); table.setSchema((String) values.get("TABLE_SCHEM")); table.setDescription((String) values.get("REMARKS")); table.addColumns(readColumns(metaData, tableName)); Collection<String> primaryKeys = readPrimaryKeyNames(metaData, tableName); for (Object key : primaryKeys) { Column col = table.findColumn((String) key, true); if (col != null) { col.setPrimaryKey(true); } else { throw new NullPointerException(String.format("%s pk %s is null - %s %s", tableName, key, ToStringBuilder.reflectionToString(metaData, ToStringStyle.SIMPLE_STYLE), ToStringBuilder.reflectionToString(values, ToStringStyle.SIMPLE_STYLE))); } } } return table; }
From source file:com.gemini.provision.network.openstack.NetworkProviderOpenStackImpl.java
@Override public ProvisioningProviderResponseType createNetwork(GeminiTenant tenant, GeminiEnvironment env, GeminiNetwork newNetwork) {/* ww w . j av a 2 s .com*/ //authenticate the session with the OpenStack installation OSClient os = OSFactory.builder().endpoint(env.getEndPoint()) .credentials(env.getAdminUserName(), env.getAdminPassword()).tenantName(tenant.getName()) .authenticate(); if (os == null) { Logger.error("Failed to authenticate Tenant: {}", ToStringBuilder.reflectionToString(tenant, ToStringStyle.MULTI_LINE_STYLE)); return ProvisioningProviderResponseType.CLOUD_AUTH_FAILURE; } //check to see if this network exists List<? extends Network> networks = os.networking().network().list(); if (networks.stream().anyMatch(n -> n.getName().equals(newNetwork.getName()))) { Logger.error("Failed to create network - already exists. Tenant: {} Environment: {} Network: {}", tenant.getName(), env.getName(), ToStringBuilder.reflectionToString(newNetwork, ToStringStyle.MULTI_LINE_STYLE)); return ProvisioningProviderResponseType.OBJECT_EXISTS; } //create the network Network network; try { network = os.networking().network() .create(Builders.network().tenantId(tenant.getTenantID()).name(newNetwork.getName()).build()); } catch (ClientResponseException ex) { Logger.error("Cloud exception, failed to create network: status code {} tenant: {}, env: {} network {}", ex.getStatusCode(), tenant.getName(), env.getName(), newNetwork.getName()); return ProvisioningProviderResponseType.CLOUD_EXCEPTION; } //TODO: Need to get detailed error codes for the call above. Research the StatusCode class if (network == null) { Logger.error( "Failed to create network, failure in Cloud provider. Tenant: {} Environment: {} Network: {}", tenant.getName(), env.getName(), ToStringBuilder.reflectionToString(newNetwork, ToStringStyle.MULTI_LINE_STYLE)); return ProvisioningProviderResponseType.CLOUD_FAILURE; } //copy the cloud ID to the Gemini object as it is required later newNetwork.setCloudID(network.getId()); //now create subnets in network newNetwork.getSubnets().stream().forEach(gs -> { //create the subnet Subnet subnet = null; try { subnet = os.networking().subnet().create(Builders.subnet().tenantId(tenant.getTenantID()) .gateway(InetAddresses.toAddrString(gs.getGateway())).enableDHCP(gs.isEnableDHCP()) .ipVersion(gs.getNetworkType() == IPAddressType.IPv6 ? IPVersionType.V6 : IPVersionType.V4) .name(gs.getName()).networkId(newNetwork.getCloudID()).cidr(gs.getCidr()).build()); gs.setCloudID(subnet.getId()); } catch (ClientResponseException ex) { Logger.error( "Cloud exception, failed to create subnet. status code {} tenant: {} env: {} network: {} subnet: {}", ex.getStatusCode(), tenant.getName(), env.getName(), newNetwork.getName(), gs.getName()); } if (subnet == null) { Logger.error("Cloud failure, failed to create subnet. tenant: {} env: {} network: {} subnet: {}", tenant.getName(), env.getName(), newNetwork.getName(), gs.getName()); } }); Logger.debug("Successfully created network and it's subnets - Tenant: {} Environment: {} Network: {}", tenant.getName(), env.getName(), ToStringBuilder.reflectionToString(newNetwork, ToStringStyle.MULTI_LINE_STYLE)); return ProvisioningProviderResponseType.SUCCESS; }
From source file:com.all.downloader.download.DownloadStatusImpl.java
@Override public String toString() { return ToStringBuilder.reflectionToString(this, ToStringStyle.NO_FIELD_NAMES_STYLE); }
From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnRDataAnalysisServiceImpl.java
/** ************************************************************* * Execute an R-based dvn statistical analysis request * * @param sro a DvnRJobRequest object that contains various parameters * @return a Map that contains various information about results *///from w ww.j a v a 2s .c om public Map<String, String> execute(DvnRJobRequest sro) { // Step 1. Copy of Rdata file // Step 2. Subset Rdata file // Step 3. Return the subsetted Rdata file instead of the original // set the return object Map<String, String> result = new HashMap<String, String>(); // temporary result Map<String, String> tmpResult = new HashMap<String, String>(); try { // Set up an Rserve connection dbgLog.info("sro dump:\n" + ToStringBuilder.reflectionToString(sro, ToStringStyle.MULTI_LINE_STYLE)); dbgLog.fine("RSERVE_USER=" + RSERVE_USER + "[default=rserve]"); dbgLog.fine("RSERVE_PWD=" + RSERVE_PWD + "[default=rserve]"); dbgLog.fine("RSERVE_PORT=" + RSERVE_PORT + "[default=6311]"); RConnection c = new RConnection(RSERVE_HOST, RSERVE_PORT); dbgLog.fine("hostname=" + RSERVE_HOST); c.login(RSERVE_USER, RSERVE_PWD); dbgLog.info("R Version = " + c.eval("R.version$version.string").asString() + "<"); dbgLog.info("SRO request type: " + sro.getRequestType()); // check working directories // This needs to be done *before* we try to create any files // there! setupWorkingDirectories(c); // save the data file at the Rserve side String infile = sro.getSubsetFileName(); InputStream inb = new BufferedInputStream(new FileInputStream(infile)); int bufsize; byte[] bffr = new byte[1024]; RFileOutputStream os = c.createFile(tempFileName); while ((bufsize = inb.read(bffr)) != -1) { os.write(bffr, 0, bufsize); } os.close(); inb.close(); // save the original data file on the server-side // WORKS STARTS HERE // os = c.createFile(tempOriginalFileName); // Rserve code starts here dbgLog.fine("DvnRserveComm: " + "wrkdir=" + wrkdir); //dbgLog.fine("DvnRserveComm: "+librarySetup); //historyEntry.add(librarySetup); //c.voidEval(librarySetup); Properties p = System.getProperties(); String domainRoot = p.getProperty("com.sun.aas.instanceRoot"); String rFunctionsFileName = domainRoot + "/config/" + DVN_R_DATA_FUNCTIONS; dbgLog.fine("Source code for the custom DVN R functions: " + rFunctionsFileName); File rFunctionsFile = new File(rFunctionsFileName); if (!rFunctionsFile.exists()) { throw new IOException("Could not find R source code file " + rFunctionsFileName); } /* * Send the R code file across: */ inb = new BufferedInputStream(new FileInputStream(rFunctionsFile)); os = c.createFile(tempRCodeFileName); while ((bufsize = inb.read(bffr)) != -1) { os.write(bffr, 0, bufsize); } os.close(); inb.close(); /* * And read it in: */ String newLibrarySetup = "source(\"" + tempRCodeFileName + "\");"; dbgLog.fine("DvnRserveComm: " + newLibrarySetup); historyEntry.add(newLibrarySetup); c.voidEval(newLibrarySetup); dbgLog.fine("DVN R Code library has been read."); // variable type /* vartyp <-c(1,1,1) */ // java side // int [] jvartyp = {1,1,1};// = mp.get("vartyp").toArray() // int [] jvartyp = sro.getVariableTypes(); /* StringBuilder sb = new StringBuilder(); for (int i = 0 ; i< jvartyp.length; i++){ if (i == (jvartyp.length -1)){ sb.append(String.valueOf(jvartyp[i])); } else { sb.append(String.valueOf(jvartyp[i])+", "); } } // R side historyEntry.add("vartyp<-c(" + sb.toString()+")"); */ //c.assign("vartyp", new REXPInteger(jvartyp)); if ("Download".equals(sro.getRequestType())) { /* * Note that we want to use the "getVariableTypesWithBoolean method * when the subset is being created for download/conversion; when * we create a SRO object for analysis, we'll still be using * the old getVariableTypes * method, that don't recognize Booleans as a distinct class. * So they will be treated simply as numeric categoricals * (factors) with the "TRUE" and "FALSE" labels. But for the purposes * of saving the subset in R format, we want to convert these into * R "logical" vectors. * * TODO: verify what's going to happen to these "logical" * variables when we call R package Foreign to convert the * dataset into STATA format. -- L.A. */ dbgLog.fine("raw variable type=" + sro.getVariableTypesWithBoolean()); c.assign("vartyp", new REXPInteger(sro.getVariableTypesWithBoolean())); String[] tmpt = c.eval("vartyp").asStrings(); dbgLog.fine("vartyp length=" + tmpt.length + "\t " + StringUtils.join(tmpt, ",")); } else { historyEntry.add("vartyp<-c(" + StringUtils.join(sro.getVariableTypesAsString(), ",") + ")"); dbgLog.fine("DvnRserveComm: " + "vartyp<-c(" + StringUtils.join(sro.getVariableTypesAsString(), ",") + ")"); dbgLog.fine("raw variable type=" + sro.getVariableTypes()); c.assign("vartyp", new REXPInteger(sro.getVariableTypes())); String[] tmpt = c.eval("vartyp").asStrings(); dbgLog.fine( "DvnRserveComm: " + "vartyp length=" + tmpt.length + "\t " + StringUtils.join(tmpt, ",")); } // variable format (date/time) /* varFmt<-list(); c.voidEval("varFmt<-list()"); */ Map<String, String> tmpFmt = sro.getVariableFormats(); dbgLog.fine("DvnRserveComm: " + "tmpFmt=" + tmpFmt); if (tmpFmt != null) { Set<String> vfkeys = tmpFmt.keySet(); String[] tmpfk = (String[]) vfkeys.toArray(new String[vfkeys.size()]); String[] tmpfv = getValueSet(tmpFmt, tmpfk); historyEntry.add("tmpfk<-c(" + StringUtils.join(tmpfk, ", ") + ")"); dbgLog.fine("DvnRserveComm: " + "tmpfk<-c(" + StringUtils.join(tmpfk, ", ") + ")"); c.assign("tmpfk", new REXPString(tmpfk)); historyEntry.add("tmpfv<-c(" + StringUtils.join(tmpfv, ", ") + ")"); dbgLog.fine("DvnRserveComm: " + "tmpfv<-c(" + StringUtils.join(tmpfv, ", ") + ")"); c.assign("tmpfv", new REXPString(tmpfv)); String fmtNamesLine = "names(tmpfv)<- tmpfk"; historyEntry.add(fmtNamesLine); dbgLog.fine("DvnRserveComm: " + fmtNamesLine); c.voidEval(fmtNamesLine); String fmtValuesLine = "varFmt<- as.list(tmpfv)"; historyEntry.add(fmtValuesLine); dbgLog.fine("DvnRserveComm: " + fmtValuesLine); c.voidEval(fmtValuesLine); } else { String[] varFmtN = {}; List<String> varFmtV = new ArrayList<String>(); historyEntry.add("varFmt <- list()"); dbgLog.fine("DvnRserveComm: " + "varFmt <- list()"); c.assign("varFmt", new REXPList(new RList(varFmtV, varFmtN))); } /* vnames<-c("race","age","vote") */ // variable names // String [] jvnames = {"race","age","vote"}; String[] jvnamesRaw = sro.getVariableNames(); String[] jvnames = null; //VariableNameFilterForR nf = new VariableNameFilterForR(jvnamesRaw); if (sro.hasUnsafedVariableNames) { // create list jvnames = sro.safeVarNames; dbgLog.fine("renamed=" + StringUtils.join(jvnames, ",")); } else { jvnames = jvnamesRaw; } //historyEntry.add("vnamnes<-c("+ StringUtils.join(jvnames, ", ")+")"); String vnQList = DvnDSButil.joinNelementsPerLine(jvnames, true); historyEntry.add("vnames<-c(" + vnQList + ")"); c.assign("vnames", new REXPString(jvnames)); // confirmation String[] tmpjvnames = c.eval("vnames").asStrings(); dbgLog.fine("DvnRserveComm: " + "vnames:" + StringUtils.join(tmpjvnames, ",")); /* x<-read.table141vdc(file="/tmp/VDC/t.28948.1.tab", col.names=vnames, colClassesx=vartyp, varFormat=varFmt) */ //String datafilename = "/nfs/home/A/asone/java/rcode/t.28948.1.tab"; // tab-delimited file name = tempFileName // vnames = Arrays.deepToString(new REXPString(jvnames).asStrings()) // vartyp = Arrays.deepToString(new REXPInteger(sro.getUpdatedVariableTypes()).asStrings()) // varFmt = dbgLog.fine("col names ..... " + Arrays.deepToString(jvnames)); dbgLog.fine("colClassesX ... " + Arrays.toString(sro.getVariableTypesWithBoolean())); dbgLog.fine("varFormat ..... " + tmpFmt); String readtableline = "x<-read.table141vdc(file='" + tempFileName + "', col.names=vnames, colClassesx=vartyp, varFormat=varFmt )"; historyEntry.add(readtableline); dbgLog.fine("DvnRserveComm: " + "readtable=" + readtableline); c.voidEval(readtableline); // safe-to-raw variable name /* attr(x, "Rsafe2raw")<-list(); */ //if (nf.hasRenamedVariables()){ if (sro.hasUnsafedVariableNames) { dbgLog.fine("unsafeVariableNames exist"); // create list //jvnames = nf.getFilteredVarNames(); jvnames = sro.safeVarNames; String[] rawNameSet = sro.renamedVariableArray; String[] safeNameSet = sro.renamedResultArray; historyEntry.add("tmpRN<-c(" + StringUtils.join(rawNameSet, ", ") + ")"); c.assign("tmpRN", new REXPString(rawNameSet)); historyEntry.add("tmpSN<-c(" + StringUtils.join(safeNameSet, ", ") + ")"); c.assign("tmpSN", new REXPString(safeNameSet)); String raw2safevarNameTableLine = "names(tmpRN)<- tmpSN"; historyEntry.add(raw2safevarNameTableLine); c.voidEval(raw2safevarNameTableLine); String attrRsafe2rawLine = "attr(x, 'Rsafe2raw')<- as.list(tmpRN)"; historyEntry.add(attrRsafe2rawLine); c.voidEval(attrRsafe2rawLine); } else { String attrRsafe2rawLine = "attr(x, 'Rsafe2raw')<-list();"; historyEntry.add(attrRsafe2rawLine); c.voidEval(attrRsafe2rawLine); } //Map<String, String> Rsafe2raw = sro.getRaw2SafeVarNameTable(); // asIs /* for (i in 1:dim(x)[2]){if (attr(x,"var.type")[i] == 0) { x[[i]]<-I(x[[i]]); x[[i]][ x[[i]] == '' ]<-NA }} */ /* * Commenting out the fragment below: * - this is now being done early on in the read.table141vdc * R function: String asIsline = "for (i in 1:dim(x)[2]){ "+ "if (attr(x,'var.type')[i] == 0) {" + "x[[i]]<-I(x[[i]]); x[[i]][ x[[i]] == '' ]<-NA }}"; historyEntry.add(asIsline); c.voidEval(asIsline); */ // replication: copy the data.frame String repDVN_Xdupline = "dvnData<-x"; c.voidEval(repDVN_Xdupline); tmpResult.put("dvn_dataframe", "dvnData"); // recoding line if (sro.hasRecodedVariables()) { // subsetting // For operations on time values during recoding we need // to set the following option (this is to enable millisecond // precision time): // -- L.A., v3.6 c.voidEval("saved.options <- options(digits.secs = 3)"); List<String> scLst = sro.getSubsetConditions(); if (scLst != null) { for (String sci : scLst) { dbgLog.fine("sci:" + sci); historyEntry.add(sci); c.voidEval(sci); } tmpResult.put("subset", "T"); } // recoding List<String> rcLst = sro.getRecodeConditions(); if (rcLst != null) { for (String rci : rcLst) { dbgLog.fine("rci:" + rci); historyEntry.add(rci); c.voidEval(rci); } // subsetting (mutating the data.frame strips non-default attributes // // variable type must be re-attached if (!"Download".equals(sro.getRequestType())) { String varTypeNew = "vartyp<-c(" + StringUtils.join(sro.getUpdatedVariableTypesAsString(), ",") + ")"; historyEntry.add(varTypeNew); dbgLog.fine("updated var Type =" + sro.getUpdatedVariableTypesAsString()); c.assign("vartyp", new REXPInteger(sro.getUpdatedVariableTypes())); } else { dbgLog.fine("updated var Type =" + sro.getUpdatedVariableTypesWithBooleanAsString()); c.assign("vartyp", new REXPInteger(sro.getUpdatedVariableTypesWithBoolean())); } String reattachVarTypeLine = "attr(x, 'var.type') <- vartyp"; historyEntry.add(reattachVarTypeLine); dbgLog.fine("DvnRserveComm: " + reattachVarTypeLine); c.voidEval(reattachVarTypeLine); // replication: variable type String repDVN_vt = "attr(dvnData, 'var.type') <- vartyp"; dbgLog.fine("DvnRserveComm: " + repDVN_vt); c.voidEval(repDVN_vt); // new (recoded) variable names: String varNamesRecoded = "recodedvnames<-c(" + StringUtils.join(sro.getRecodedVarNameSet(), ",") + ")"; historyEntry.add(varNamesRecoded); dbgLog.fine("recoded var names =" + StringUtils.join(sro.getRecodedVarNameSet(), ",")); c.assign("recodedvnames", sro.getRecodedVarNameSet()); tmpFmt = sro.getUpdatedVariableFormats(); dbgLog.fine("DvnRserveComm: " + "(recoded)tmpFmt=" + tmpFmt); if (tmpFmt != null) { Set<String> vfkeys = tmpFmt.keySet(); String[] tmpfk = (String[]) vfkeys.toArray(new String[vfkeys.size()]); String[] tmpfv = getValueSet(tmpFmt, tmpfk); historyEntry.add("tmpfk<-c(" + StringUtils.join(tmpfk, ", ") + ")"); dbgLog.fine("DvnRserveComm: " + "(recoded)tmpfk<-c(" + StringUtils.join(tmpfk, ", ") + ")"); c.assign("tmpfk", new REXPString(tmpfk)); historyEntry.add("tmpfv<-c(" + StringUtils.join(tmpfv, ", ") + ")"); dbgLog.fine("DvnRserveComm: " + "(recoded)tmpfv<-c(" + StringUtils.join(tmpfv, ", ") + ")"); c.assign("tmpfv", new REXPString(tmpfv)); String fmtNamesLine = "names(tmpfv)<- tmpfk"; historyEntry.add(fmtNamesLine); dbgLog.fine("DvnRserveComm: (recoded)" + fmtNamesLine); c.voidEval(fmtNamesLine); String fmtValuesLine = "varFmt<- as.list(tmpfv)"; historyEntry.add(fmtValuesLine); dbgLog.fine("DvnRserveComm: (recoded)" + fmtValuesLine); c.voidEval(fmtValuesLine); } else { String[] varFmtN = {}; List<String> varFmtV = new ArrayList<String>(); historyEntry.add("varFmt <- list()"); dbgLog.fine("DvnRserveComm: (recoded)" + "varFmt <- list()"); c.assign("varFmt", new REXPList(new RList(varFmtV, varFmtN))); } // run post-processing on the newly created recode variables: dbgLog.fine("running transformrecoded()"); historyEntry.add("transformrecoded()"); int recodedVarsStartIndex = sro.getVariableNames().length + 1; dbgLog.fine("recoded variables start at " + recodedVarsStartIndex); c.voidEval("x<-transformrecoded(x, recodedvarsindx=" + recodedVarsStartIndex + ", col.names=c(vnames,recodedvnames), colClassesx=vartyp, varFormat=varFmt)"); } // reset the milliseconds option: c.voidEval("options(saved.options)"); } // variable Id /* attr(x, "var.nmbr")<-c("v198057","v198059","v198060") */ // String[] jvarnmbr = {"v198057","v198059","v198060"}; //String[] jvarnmbr = sro.getVariableIds(); // after recoding String[] jvarnmbr = sro.getUpdatedVariableIds(); String viQList = DvnDSButil.joinNelementsPerLine(jvarnmbr, true); historyEntry.add("varnmbr <-c(" + viQList + ")"); c.assign("varnmbr", new REXPString(jvarnmbr)); String attrVarNmbrLine = "attr(x, 'var.nmbr')<-varnmbr"; historyEntry.add(attrVarNmbrLine); dbgLog.fine("DvnRserveComm: (varnmbr) " + attrVarNmbrLine); c.voidEval(attrVarNmbrLine); // confirmation String[] vno = c.eval("attr(x, 'var.nmbr')").asStrings(); dbgLog.fine("varNo=" + StringUtils.join(vno, ",")); // replication: variable number String repDVN_vn = "attr(dvnData, 'var.nmbr') <- varnmbr"; dbgLog.fine("DvnRserveComm: " + repDVN_vn); c.voidEval(repDVN_vn); // variable labels /* attr(x, "var.labels")<-c("race","age","vote") */ // String[] jvarlabels = {"race","age","vote"}; // String[] jvarlabels = sro.getVariableLabels(); // after recoding String[] jvarlabels = sro.getUpdatedVariableLabels(); String vlQList = DvnDSButil.joinNelementsPerLine(jvarlabels, true); historyEntry.add("varlabels <-c(" + vlQList + ")"); dbgLog.fine("DvnRserveComm: " + "varlabels <-c(" + vlQList + ")"); c.assign("varlabels", new REXPString(jvarlabels)); String attrVarLabelsLine = "attr(x, 'var.labels')<-varlabels"; historyEntry.add(attrVarLabelsLine); dbgLog.fine("DvnRserveComm: " + attrVarLabelsLine); c.voidEval(attrVarLabelsLine); // confirmation String[] vlbl = c.eval("attr(x, 'var.labels')").asStrings(); dbgLog.fine("varlabels=" + StringUtils.join(vlbl, ",")); // replication: String repDVN_vl = "attr(dvnData, 'var.labels') <- varlabels"; dbgLog.fine("DvnRserveComm: " + repDVN_vl); c.voidEval(repDVN_vl); // --------- start: block to be used for the production code // value-label table /* VALTABLE<-list() VALTABLE[["1"]]<-list( "2"="white", "1"="others") attr(x, 'val.table')<-VALTABLE */ // create the VALTABLE String vtFirstLine = "VALTABLE<-list()"; historyEntry.add(vtFirstLine); dbgLog.fine("DvnRserveComm: " + vtFirstLine); c.voidEval(vtFirstLine); c.voidEval("VALORDER<-list()"); // vltbl includes both base and recoded cases when it was generated Map<String, Map<String, String>> vltbl = sro.getValueTable(); Map<String, List<String>> orderedCategoryValues = sro.getCategoryValueOrders(); Map<String, String> rnm2vi = sro.getRawVarNameToVarIdTable(); String[] updatedVariableIds = sro.getUpdatedVariableIds(); //for (int j=0;j<jvnamesRaw.length;j++){ for (int j = 0; j < updatedVariableIds.length; j++) { // if this variable has its value-label table, // pass its key and value arrays to the Rserve // and finalize a value-table at the Rserve //String varId = rnm2vi.get(jvnamesRaw[j]); String varId = updatedVariableIds[j]; if (vltbl.containsKey(varId)) { Map<String, String> tmp = (HashMap<String, String>) vltbl.get(varId); Set<String> vlkeys = tmp.keySet(); String[] tmpk = (String[]) vlkeys.toArray(new String[vlkeys.size()]); String[] tmpv = getValueSet(tmp, tmpk); // debug dbgLog.fine("tmp:k=" + StringUtils.join(tmpk, ",")); dbgLog.fine("tmp:v=" + StringUtils.join(tmpv, ",")); // index number starts from 1(not 0) int indx = j + 1; dbgLog.fine("index=" + indx); if (tmpv.length > 0) { historyEntry.add("tmpk<-c(" + DvnDSButil.joinNelementsPerLine(tmpk, true) + ")"); c.assign("tmpk", new REXPString(tmpk)); historyEntry.add("tmpv<-c(" + DvnDSButil.joinNelementsPerLine(tmpv, true) + ")"); c.assign("tmpv", new REXPString(tmpv)); String namesValueLine = "names(tmpv)<- tmpk"; historyEntry.add(namesValueLine); c.voidEval(namesValueLine); String sbvl = "VALTABLE[['" + Integer.toString(indx) + "']]" + "<- as.list(tmpv)"; dbgLog.fine("frag=" + sbvl); historyEntry.add(sbvl); c.voidEval(sbvl); // confirmation test for j-th variable name REXP jl = c.parseAndEval(sbvl); dbgLog.fine("jl(" + j + ") = " + jl); } } if (orderedCategoryValues != null && orderedCategoryValues.containsKey(varId)) { int indx = j + 1; List<String> orderList = orderedCategoryValues.get(varId); if (orderList != null) { String[] ordv = (String[]) orderList.toArray(new String[orderList.size()]); dbgLog.fine("ordv=" + StringUtils.join(ordv, ",")); c.assign("ordv", new REXPString(ordv)); String sbvl = "VALORDER[['" + Integer.toString(indx) + "']]" + "<- as.list(ordv)"; dbgLog.fine("VALORDER[...]=" + sbvl); historyEntry.add(sbvl); c.voidEval(sbvl); } else { dbgLog.fine("NULL orderedCategoryValues list."); } } } // debug: confirmation test for value-table dbgLog.fine("length of vl=" + c.eval("length(VALTABLE)").asInteger()); String attrValTableLine = "attr(x, 'val.table')<-VALTABLE"; historyEntry.add(attrValTableLine); c.voidEval(attrValTableLine); // replication: value-label table String repDVN_vlt = "attr(dvnData, 'val.table') <- VALTABLE"; c.voidEval(repDVN_vlt); // --------- end: block to be used for the production code // missing-value list: TO DO /* MSVLTBL<-list(); attr(x, 'missval.table')<-MSVLTBL */ String msvStartLine = "MSVLTBL<-list();"; historyEntry.add(msvStartLine); c.voidEval(msvStartLine); // data structure String attrMissvalLine = "attr(x, 'missval.table')<-MSVLTBL"; historyEntry.add(attrMissvalLine); c.voidEval(attrMissvalLine); // replication: missing value table String repDVN_mvlt = "attr(dvnData, 'missval.table') <- MSVLTBL"; c.voidEval(repDVN_mvlt); // attach attributes(tables) to the data.frame /* x<-createvalindex(dtfrm=x, attrname='val.index') x<-createvalindex(dtfrm=x, attrname='missval.index') */ String createVIndexLine = "x<-createvalindex(dtfrm=x, attrname='val.index');"; historyEntry.add(createVIndexLine); c.voidEval(createVIndexLine); String createMVIndexLine = "x<-createvalindex(dtfrm=x, attrname='missval.index');"; historyEntry.add(createMVIndexLine); c.voidEval(createMVIndexLine); // reflection block: start ------------------------------------------> String requestTypeToken = sro.getRequestType();// (Download|EDA|Xtab|Zelig) dbgLog.fine("requestTypeToken=" + requestTypeToken); historyEntry.add("#### The Request is " + requestTypeToken + " ####"); // get a test method Method mthd = runMethods.get(requestTypeToken); dbgLog.fine("method=" + mthd); try { // invoke this method result = (Map<String, String>) mthd.invoke(this, sro, c); } catch (InvocationTargetException e) { //Throwable cause = e.getCause(); //err.format(cause.getMessage()); e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } // add the variable list result.put("variableList", joinNelementsPerLine(jvnamesRaw, 5, null, false, null, null)); //result.put("variableList",StringUtils.join(jvnamesRaw, ", ")); // replication: var-level unf String repDVN_varUNF = "attr(dvnData, 'variableUNF') <- paste(unf(dvnData,version=3))"; c.voidEval(repDVN_varUNF); // calculate the file-leve UNF String fileUNFline = "fileUNF <- paste(summary(unf(dvnData, version=3)))"; c.voidEval(fileUNFline); String fileUNF = c.eval("fileUNF").asString(); if (fileUNF == null) { fileUNF = "NA"; } // replication: file-level unf String repDVN_fileUNF = "attr(dvnData, 'fileUNF') <- fileUNF"; c.voidEval(repDVN_fileUNF); String RversionLine = "R.Version()$version.string"; String Rversion = c.eval(RversionLine).asString(); dbgLog.fine(String.format("R-version String = %s", Rversion)); // replication: R version String repDVN_Rversion = "attr(dvnData, 'R.version') <- R.Version()$version.string"; c.voidEval(repDVN_Rversion); String zeligVersionLine = "packageDescription('Zelig')$Version"; String zeligVersion = c.eval(zeligVersionLine).asString(); //String RexecDate = c.eval("date()").asString(); String RexecDate = c.eval("as.character(as.POSIXct(Sys.time()))").asString(); // replication: date String repDVN_date = "attr(dvnData, 'date') <- as.character(as.POSIXct(Sys.time()))"; c.voidEval(repDVN_date); String repDVN_dfOrigin = "attr(dvnData, 'data.frame.origin')<- " + "list('provider'='Dataverse Network Project'," + "'format' = list('name' = 'DVN data.frame', 'version'='1.3'))"; c.voidEval(repDVN_dfOrigin); /* if (result.containsKey("option")){ result.put("R_run_status", "T"); } else { result.put("option", requestTypeToken.toLowerCase()); //download zelig eda xtab result.put("R_run_status", "F"); } */ if (sro.hasRecodedVariables()) { if (sro.getSubsetConditions() != null) { result.put("subsettingCriteria", StringUtils.join(sro.getSubsetConditions(), "\n")); // replication: subset lines String[] sbst = null; sbst = (String[]) sro.getSubsetConditions() .toArray(new String[sro.getSubsetConditions().size()]); c.assign("sbstLines", new REXPString(sbst)); String repDVN_sbst = "attr(dvnData, 'subsetLines') <- sbstLines"; c.voidEval(repDVN_sbst); } /* to be used in the future? */ if (sro.getRecodeConditions() != null) { result.put("recodingCriteria", StringUtils.join(sro.getRecodeConditions(), "\n")); String[] rcd = null; rcd = (String[]) sro.getRecodeConditions() .toArray(new String[sro.getRecodeConditions().size()]); c.assign("rcdtLines", new REXPString(rcd)); String repDVN_rcd = "attr(dvnData, 'recodeLines') <- rcdtLines"; c.voidEval(repDVN_rcd); } } // save workspace as a replication data set String RdataFileName = "DVNdataFrame." + PID + ".RData"; result.put("Rdata", "/" + requestdir + "/" + RdataFileName); String saveWS = "save('dvnData', file='" + wrkdir + "/" + RdataFileName + "')"; dbgLog.fine("save the workspace=" + saveWS); c.voidEval(saveWS); // write back the R workspace to the dvn String wrkspFileName = wrkdir + "/" + RdataFileName; dbgLog.fine("wrkspFileName=" + wrkspFileName); int wrkspflSize = getFileSize(c, wrkspFileName); File wsfl = writeBackFileToDvn(c, wrkspFileName, RWRKSP_FILE_PREFIX, "RData", wrkspflSize); result.put("dvn_RData_FileName", wsfl.getName()); if (wsfl != null) { result.put("wrkspFileName", wsfl.getAbsolutePath()); dbgLog.fine("wrkspFileName=" + wsfl.getAbsolutePath()); } else { dbgLog.fine("wrkspFileName is null"); } result.put("library_1", "VDCutil"); result.put("fileUNF", fileUNF); result.put("dsbHost", RSERVE_HOST); result.put("dsbPort", DSB_HOST_PORT); result.put("dsbContextRootDir", DSB_CTXT_DIR); result.put("PID", PID); result.put("Rversion", Rversion); result.put("zeligVersion", zeligVersion); result.put("RexecDate", RexecDate); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); result.putAll(tmpResult); dbgLog.fine("result object (before closing the Rserve):\n" + result); // reflection block: end // create a zip file of the directory created: //String zipTmpDir = "system(\"(cd "+DSB_TMP_DIR+"; zip -r /tmp/"+requestdir+".zip "+requestdir+")\")"; //c.voidEval(zipTmpDir); // transfer the zip file to the application side: //RFileInputStream ris = null; //OutputStream outbr = null; //int zipSize = getFileSize(c,"/tmp/"+requestdir+".zip"); String listAnalysisFiles = "list.files('" + DSB_TMP_DIR + "/" + requestdir + "', recursive=TRUE)"; dbgLog.fine("looking up the analysis result files on the DSB/Rserve side: " + listAnalysisFiles); String[] analysisReportFiles = c.eval(listAnalysisFiles).asStrings(); RFileInputStream ris = null; OutputStream outbr = null; try { File localReportDir = new File(TEMP_DIR + "/DVN", requestdir); if (!localReportDir.exists()) { localReportDir.mkdir(); } for (int i = 0; i < analysisReportFiles.length; i++) { String reportFile = analysisReportFiles[i]; int reportFileSize = getFileSize(c, DSB_TMP_DIR + "/" + requestdir + "/" + reportFile); dbgLog.fine("DvnRData: transferring file " + reportFile); dbgLog.fine("DvnRData: file size: " + reportFileSize); if (reportFile.lastIndexOf("/") > 0) { File localReportSubDir = new File(TEMP_DIR + "/DVN/" + requestdir, reportFile.substring(0, reportFile.lastIndexOf("/"))); if (!localReportSubDir.exists()) { localReportSubDir.mkdirs(); } } ris = c.openFile(DSB_TMP_DIR + "/" + requestdir + "/" + reportFile); outbr = new BufferedOutputStream( new FileOutputStream(new File(TEMP_DIR + "/DVN/" + requestdir, reportFile))); byte[] obuf = new byte[reportFileSize]; int obufsize = 0; while ((obufsize = ris.read(obuf)) != -1) { outbr.write(obuf, 0, reportFileSize); } ris.close(); outbr.close(); } //String unZipCmd = "/usr/bin/unzip "+TEMP_DIR+"/DVN/"+requestdir+".zip -d "+TEMP_DIR+"/DVN"; //int exitValue = 1; //dbgLog.fine("attempting to execute "+unZipCmd); //try { //Runtime runtime = Runtime.getRuntime(); //Process process = runtime.exec(unZipCmd); //exitValue = process.waitFor(); //} catch (Exception e) { //e.printStackTrace(); //exitValue = 1; //} //if (exitValue == 0) { //result.put("webFolderArchived",TEMP_DIR+"/DVN/"+requestdir+".zip"); //} } catch (FileNotFoundException fe) { fe.printStackTrace(); } catch (IOException ie) { ie.printStackTrace(); } finally { if (ris != null) { ris.close(); } if (outbr != null) { outbr.close(); } } // // move the temp dir to the web-temp root dir //String mvTmpDir = "file.rename('"+wrkdir+"','"+webwrkdir+"')"; //dbgLog.fine("web-temp_dir="+mvTmpDir); //c.voidEval(mvTmpDir); // close the Rserve connection c.close(); } catch (RserveException rse) { // RserveException (Rserve is not running) rse.printStackTrace(); result.put("dsbContextRootDir", DSB_CTXT_DIR); result.put("PID", PID); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); result.put("option", sro.getRequestType().toLowerCase()); result.put("RexecError", "true"); return result; } catch (REXPMismatchException mme) { // REXP mismatch exception (what we got differs from what we expected) mme.printStackTrace(); result.put("dsbContextRootDir", DSB_CTXT_DIR); result.put("PID", PID); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); result.put("option", sro.getRequestType().toLowerCase()); result.put("RexecError", "true"); return result; } catch (IOException ie) { ie.printStackTrace(); result.put("dsbContextRootDir", DSB_CTXT_DIR); result.put("PID", PID); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); result.put("option", sro.getRequestType().toLowerCase()); result.put("RexecError", "true"); return result; } catch (Exception ex) { ex.printStackTrace(); result.put("dsbContextRootDir", DSB_CTXT_DIR); result.put("PID", PID); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); result.put("option", sro.getRequestType().toLowerCase()); result.put("RexecError", "true"); return result; } return result; }
From source file:edu.harvard.iq.dvn.ingest.dsb.impl.DvnRGraphServiceImpl.java
/** ************************************************************* * Execute an R-based dvn analysis request on a Graph object * using an open connection created during the Initialize call. * * @param sro a DvnJobRequest object that contains various parameters * @return a Map that contains various information about the results *///w ww. j av a 2 s . c om public Map<String, String> liveConnectionExecute(DvnRJobRequest sro) throws DvnRGraphException { // set the return object Map<String, String> result = new HashMap<String, String>(); if (sro != null) { dbgLog.fine( "LCE sro dump:\n" + ToStringBuilder.reflectionToString(sro, ToStringStyle.MULTI_LINE_STYLE)); } else { throw new DvnRGraphException("execute method called with a NULL job ob ject."); } String SavedRworkSpace = null; Map<String, Object> SubsetParameters = sro.getParametersForGraphSubset(); if (SubsetParameters != null) { SavedRworkSpace = (String) SubsetParameters.get(SAVED_RWORK_SPACE); } else { throw new DvnRGraphException("execute method called with a null parameters object"); } DvnRConnection drc = null; try { // let's see if we have a connection that we can use: if (myConnection == 0) { throw new DvnRGraphException("execute method called without securing a connection first"); } myConnection = RConnectionPool.securePooledConnection(SavedRworkSpace, null, true, myConnection); dbgLog.info("Execute: obtained connection " + myConnection); drc = RConnectionPool.getConnection(myConnection); String GraphSubsetType = (String) SubsetParameters.get(RSUBSETFUNCTION); if (GraphSubsetType != null) { if (GraphSubsetType.equals(MANUAL_QUERY_SUBSET)) { String manualQueryType = (String) SubsetParameters.get(MANUAL_QUERY_TYPE); String manualQuery = (String) SubsetParameters.get(MANUAL_QUERY); String subsetCommand = null; if (manualQueryType != null) { if (manualQueryType.equals(EDGE_SUBSET)) { String dropDisconnected = (String) SubsetParameters.get(ELIMINATE_DISCONNECTED); if (dropDisconnected != null) { subsetCommand = "edge_subset(g, '" + manualQuery + "', TRUE)"; } else { subsetCommand = "edge_subset(g, '" + manualQuery + "')"; } } else if (manualQueryType.equals(VERTEX_SUBSET)) { subsetCommand = "vertex_subset(g, '" + manualQuery + "')"; } else { throw new DvnRGraphException("execute: unsupported manual query subset"); } dbgLog.fine("LCE: manualQuerySubset=" + subsetCommand); historyEntry.add(subsetCommand); String cmdResponse = safeEval(drc.Rcon, subsetCommand).asString(); } } else if (GraphSubsetType.equals(NETWORK_MEASURE)) { String networkMeasureType = (String) SubsetParameters.get(NETWORK_MEASURE_TYPE); String networkMeasureCommand = null; if (networkMeasureType != null) { List<NetworkMeasureParameter> networkMeasureParameterList = (List<NetworkMeasureParameter>) SubsetParameters .get(NETWORK_MEASURE_PARAMETER); networkMeasureCommand = networkMeasureType + "(g" + buildParameterComponent(networkMeasureParameterList) + ")"; } if (networkMeasureCommand == null) { throw new DvnRGraphException("ILLEGAL OR UNSUPPORTED NETWORK MEASURE QUERY"); } historyEntry.add(networkMeasureCommand); String addedColumn = safeEval(drc.Rcon, networkMeasureCommand).asString(); if (addedColumn != null) { result.put(NETWORK_MEASURE_NEW_COLUMN, addedColumn); } else { throw new DvnRGraphException("FAILED TO READ ADDED COLUMN NAME"); } } else if (GraphSubsetType.equals(AUTOMATIC_QUERY_SUBSET)) { String automaticQueryType = (String) SubsetParameters.get(AUTOMATIC_QUERY_TYPE); String autoQueryCommand = null; if (automaticQueryType != null) { String n = (String) SubsetParameters.get(AUTOMATIC_QUERY_N_VALUE); autoQueryCommand = automaticQueryType + "(g, " + n + ")"; } if (autoQueryCommand == null) { throw new DvnRGraphException("NULL OR UNSUPPORTED AUTO QUERY"); } historyEntry.add(autoQueryCommand); String cEval = safeEval(drc.Rcon, autoQueryCommand).asString(); } else if (GraphSubsetType.equals(UNDO)) { String cEval = safeEval(drc.Rcon, "undo()").asString(); } else if (GraphSubsetType.equals(RESET)) { dbgLog.info("resetting the workspace; using reset(" + SavedRworkSpace + ")"); String cEval = safeEval(drc.Rcon, "reset('" + SavedRworkSpace + "')").asString(); } } // get the vertices and edges counts: String countCommand = "vcount(g)"; int countResponse = safeEval(drc.Rcon, countCommand).asInteger(); result.put(NUMBER_OF_VERTICES, Integer.toString(countResponse)); countCommand = "ecount(g)"; countResponse = safeEval(drc.Rcon, countCommand).asInteger(); result.put(NUMBER_OF_EDGES, Integer.toString(countResponse)); result.put(SAVED_RWORK_SPACE, RDataFileName); // we're done; let's add some potentially useful // information to the result and return: String RexecDate = drc.Rcon.eval("as.character(as.POSIXct(Sys.time()))").asString(); String RversionLine = "R.Version()$version.string"; String Rversion = drc.Rcon.eval(RversionLine).asString(); result.put("dsbHost", RSERVE_HOST); result.put("dsbPort", DSB_HOST_PORT); result.put("IdSuffix", IdSuffix); result.put("Rversion", Rversion); result.put("RexecDate", RexecDate); result.put("RCommandHistory", StringUtils.join(historyEntry, "\n")); if (!SavedRworkSpace.equals(drc.getWorkSpace())) { throw new DvnRGraphException("Could not execute query: connection lost"); } } catch (DvnRGraphException dre) { throw dre; } catch (RException re) { throw new DvnRGraphException(re.getMessage()); } catch (RserveException rse) { dbgLog.info("LCE: rserve exception message: " + rse.getMessage()); dbgLog.info("LCE: rserve exception description: " + rse.getRequestErrorDescription()); throw new DvnRGraphException("RServe failure: " + rse.getMessage()); } catch (REXPMismatchException mme) { throw new DvnRGraphException("REXPmismatchException occured"); } catch (Exception ex) { throw new DvnRGraphException("Execute: unknown exception occured: " + ex.getMessage()); } finally { if (drc != null) { // set the connection time stamp: Date now = new Date(); drc.setLastQueryTime(now.getTime()); drc.unlockConnection(); } } return result; }
From source file:com.gemini.provision.loadbalancer.openstack.LoadBalancerProviderOpenStackImpl.java
@Override public List<GeminiPoolMember> getPoolMembers(GeminiTenant tenant, GeminiEnvironment env, GeminiLoadBalancerPool pool) {/*from w w w .ja va2 s .c o m*/ List<GeminiPoolMember> lbPools = Collections.synchronizedList(new ArrayList()); //authenticate the session with the OpenStack installation OSClient os = getOSClient(tenant, env); if (os == null) { Logger.error("Failed to authenticate Tenant: {}", ToStringBuilder.reflectionToString(tenant, ToStringStyle.MULTI_LINE_STYLE)); return null; } List<? extends Member> members = os.networking().loadbalancers().member().list(); members.stream().filter(member -> member != null).forEach(member -> { GeminiPoolMember geminiPoolMember = new GeminiPoolMember(); geminiPoolMember.setCloudID(member.getId()); geminiPoolMember.setAdminState(member.isAdminStateUp() ? AdminState.ADMIN_UP : AdminState.ADMIN_DOWN); geminiPoolMember.setProvisionState(ProvisionState.fromString(member.getStatus())); geminiPoolMember.setIpAddress(member.getAddress()); geminiPoolMember.setProtocolPort(member.getProtocolPort()); geminiPoolMember.setWeight(member.getWeight()); geminiPoolMember.setPoolId(member.getPoolId()); lbPools.add(geminiPoolMember); }); return lbPools; }