diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index f1f74069f..bc7d5c6ca 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -90,19 +90,12 @@ public class GATKRunReport { protected static Logger logger = Logger.getLogger(GATKRunReport.class); - // the listing of the fields is somewhat important; this is the order that the simple XML will output them - @ElementList(required = true, name = "gatk_header_Information") - private List mGATKHeader; - @Element(required = false, name = "id") private final String id; @Element(required = false, name = "exception") private final ExceptionToXML mException; - @Element(required = true, name = "working_directory") - private String currentPath; - @Element(required = true, name = "start_time") private String startTime = "ND"; @@ -112,9 +105,6 @@ public class GATKRunReport { @Element(required = true, name = "run_time") private long runTime = 0; - @Element(required = true, name = "command_line") - private String cmdLine = "COULD NOT BE DETERMINED"; - @Element(required = true, name = "walker_name") private String walkerName; @@ -127,9 +117,6 @@ public class GATKRunReport { @Element(required = true, name = "max_memory") private long maxMemory; - @Element(required = true, name = "java_tmp_directory") - private String tmpDir; - @Element(required = true, name = "user_name") private String userName; @@ -145,9 +132,6 @@ public class GATKRunReport { @Element(required = true, name = "iterations") private long nIterations; - @Element(required = true, name = "reads") - private long nReads; - public enum PhoneHomeOption { /** Disable phone home */ NO_ET, @@ -172,15 +156,8 @@ public class GATKRunReport { logger.debug("Aggregating data for run report"); - mGATKHeader = CommandLineGATK.createApplicationHeader(); - currentPath = System.getProperty("user.dir"); - // what did we run? id = org.apache.commons.lang.RandomStringUtils.randomAlphanumeric(32); - try { - cmdLine = engine.createApproximateCommandLineArgumentString(engine, walker); - } catch (Exception ignore) { } - walkerName = engine.getWalkerName(walker.getClass()); svnVersion = CommandLineGATK.getVersionNumber(); @@ -191,7 +168,6 @@ public class GATKRunReport { startTime = dateFormat.format(engine.getStartTime()); runTime = (end.getTime() - engine.getStartTime().getTime()) / 1000L; // difference in seconds } - tmpDir = System.getProperty("java.io.tmpdir"); // deal with memory usage Runtime.getRuntime().gc(); // call GC so totalMemory is ~ used memory @@ -202,12 +178,11 @@ public class GATKRunReport { if ( engine.getCumulativeMetrics() != null ) { // it's possible we aborted so early that these data structures arent initialized nIterations = engine.getCumulativeMetrics().getNumIterations(); - nReads = engine.getCumulativeMetrics().getNumReadsSeen(); } // user and hostname -- information about the runner of the GATK userName = System.getProperty("user.name"); - hostName = "unknown"; // resolveHostname(); + hostName = Utils.resolveHostname(); // basic java information java = Utils.join("-", Arrays.asList(System.getProperty("java.vendor"), System.getProperty("java.version")));