private static void checkZeros(ExpDataManager expMan) {
int neverabove = 0;
int sometimes = 0;
int always = 0;
Histogram h = new Histogram(0.1);
for (String gene : HGNC.getAllSymbols()) {
if (!expMan.contains(gene)) continue;
double r = expMan.getNonZeroRatio(gene);
h.count(r);
if (r == 0) neverabove++;
else if (r == 1) always++;
else sometimes++;
}
System.out.println("neverabove = " + neverabove);
System.out.println("always = " + always);
System.out.println("sometimes = " + sometimes);
h.print();
}
/** @throws Exception */
private void loadWorkload() throws Exception {
final boolean debug = LOG.isDebugEnabled();
// Workload Trace
if (this.params.containsKey(PARAM_WORKLOAD)) {
assert (this.catalog_db != null) : "Missing catalog!";
String path = new File(this.params.get(PARAM_WORKLOAD)).getAbsolutePath();
boolean weightedTxns = this.getBooleanParam(PARAM_WORKLOAD_XACT_WEIGHTS, false);
if (debug) LOG.debug("Use Transaction Weights in Limits: " + weightedTxns);
// This will prune out duplicate trace records...
if (params.containsKey(PARAM_WORKLOAD_REMOVE_DUPES)) {
DuplicateTraceFilter filter = new DuplicateTraceFilter();
this.workload_filter =
(this.workload_filter != null ? filter.attach(this.workload_filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// TRANSACTION OFFSET
if (params.containsKey(PARAM_WORKLOAD_XACT_OFFSET)) {
this.workload_xact_offset = Long.parseLong(params.get(PARAM_WORKLOAD_XACT_OFFSET));
ProcedureLimitFilter filter =
new ProcedureLimitFilter(-1l, this.workload_xact_offset, weightedTxns);
// Important! The offset should go in the front!
this.workload_filter =
(this.workload_filter != null ? filter.attach(this.workload_filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// BASE PARTITIONS
if (params.containsKey(PARAM_WORKLOAD_RANDOM_PARTITIONS)
|| params.containsKey(PARAM_WORKLOAD_BASE_PARTITIONS)) {
BasePartitionTxnFilter filter =
new BasePartitionTxnFilter(new PartitionEstimator(catalog_db));
// FIXED LIST
if (params.containsKey(PARAM_WORKLOAD_BASE_PARTITIONS)) {
for (String p_str : this.getParam(PARAM_WORKLOAD_BASE_PARTITIONS).split(",")) {
workload_base_partitions.add(Integer.valueOf(p_str));
} // FOR
// RANDOM
} else {
double factor = this.getDoubleParam(PARAM_WORKLOAD_RANDOM_PARTITIONS);
List<Integer> all_partitions =
new ArrayList<Integer>(CatalogUtil.getAllPartitionIds(catalog_db));
Collections.shuffle(all_partitions, new Random());
workload_base_partitions.addAll(
all_partitions.subList(0, (int) (all_partitions.size() * factor)));
}
filter.addPartitions(workload_base_partitions);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// Txn Limit
this.workload_xact_limit = this.getLongParam(PARAM_WORKLOAD_XACT_LIMIT);
Histogram<String> proc_histogram = null;
// Include/exclude procedures from the traces
if (params.containsKey(PARAM_WORKLOAD_PROC_INCLUDE)
|| params.containsKey(PARAM_WORKLOAD_PROC_EXCLUDE)) {
Filter filter = new ProcedureNameFilter(weightedTxns);
// INCLUDE
String temp = params.get(PARAM_WORKLOAD_PROC_INCLUDE);
if (temp != null && !temp.equals(ProcedureNameFilter.INCLUDE_ALL)) {
// We can take the counts for PROC_INCLUDE and scale them
// with the multiplier
double multiplier = 1.0d;
if (this.hasDoubleParam(PARAM_WORKLOAD_PROC_INCLUDE_MULTIPLIER)) {
multiplier = this.getDoubleParam(PARAM_WORKLOAD_PROC_INCLUDE_MULTIPLIER);
if (debug) LOG.debug("Workload Procedure Multiplier: " + multiplier);
}
// Default Txn Frequencies
String procinclude = params.get(PARAM_WORKLOAD_PROC_INCLUDE);
if (procinclude.equalsIgnoreCase("default")) {
procinclude =
AbstractProjectBuilder.getProjectBuilder(catalog_type)
.getTransactionFrequencyString();
}
Map<String, Integer> limits = new HashMap<String, Integer>();
int total_unlimited = 0;
int total = 0;
for (String proc_name : procinclude.split(",")) {
int limit = -1;
// Check if there is a limit for this procedure
if (proc_name.contains(":")) {
String pieces[] = proc_name.split(":");
proc_name = pieces[0];
limit = (int) Math.round(Integer.parseInt(pieces[1]) * multiplier);
}
if (limit < 0) {
if (proc_histogram == null) {
if (debug) LOG.debug("Generating procedure histogram from workload file");
proc_histogram = WorkloadUtil.getProcedureHistogram(new File(path));
}
limit = (int) proc_histogram.get(proc_name, 0);
total_unlimited += limit;
} else {
total += limit;
}
limits.put(proc_name, limit);
} // FOR
// If we have a workload limit and some txns that we want
// to get unlimited
// records from, then we want to modify the other txns so
// that we fill in the "gap"
if (this.workload_xact_limit != null && total_unlimited > 0) {
int remaining = this.workload_xact_limit.intValue() - total - total_unlimited;
if (remaining > 0) {
for (Entry<String, Integer> e : limits.entrySet()) {
double ratio = e.getValue() / (double) total;
e.setValue((int) Math.ceil(e.getValue() + (ratio * remaining)));
} // FOR
}
}
Histogram<String> proc_multiplier_histogram = null;
if (debug) {
if (proc_histogram != null) LOG.debug("Full Workload Histogram:\n" + proc_histogram);
proc_multiplier_histogram = new Histogram<String>();
}
total = 0;
for (Entry<String, Integer> e : limits.entrySet()) {
if (debug) proc_multiplier_histogram.put(e.getKey(), e.getValue());
((ProcedureNameFilter) filter).include(e.getKey(), e.getValue());
total += e.getValue();
} // FOR
if (debug)
LOG.debug("Multiplier Histogram [total=" + total + "]:\n" + proc_multiplier_histogram);
}
// EXCLUDE
temp = params.get(PARAM_WORKLOAD_PROC_EXCLUDE);
if (temp != null) {
for (String proc_name : params.get(PARAM_WORKLOAD_PROC_EXCLUDE).split(",")) {
((ProcedureNameFilter) filter).exclude(proc_name);
} // FOR
}
// Sampling!!
if (this.getBooleanParam(PARAM_WORKLOAD_PROC_SAMPLE, false)) {
if (debug) LOG.debug("Attaching sampling filter");
if (proc_histogram == null)
proc_histogram = WorkloadUtil.getProcedureHistogram(new File(path));
Map<String, Integer> proc_includes = ((ProcedureNameFilter) filter).getProcIncludes();
SamplingFilter sampling_filter = new SamplingFilter(proc_includes, proc_histogram);
filter = sampling_filter;
if (debug) LOG.debug("Workload Procedure Histogram:\n" + proc_histogram);
}
// Attach our new filter to the chain (or make it the head if
// it's the first one)
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// TRANSACTION LIMIT
if (this.workload_xact_limit != null) {
ProcedureLimitFilter filter =
new ProcedureLimitFilter(this.workload_xact_limit, weightedTxns);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
if (debug) LOG.debug("Attached " + filter.debugImpl());
}
// QUERY LIMIT
if (params.containsKey(PARAM_WORKLOAD_QUERY_LIMIT)) {
this.workload_query_limit = Long.parseLong(params.get(PARAM_WORKLOAD_QUERY_LIMIT));
QueryLimitFilter filter = new QueryLimitFilter(this.workload_query_limit);
this.workload_filter =
(this.workload_filter != null ? this.workload_filter.attach(filter) : filter);
}
if (this.workload_filter != null && debug)
LOG.debug("Workload Filters: " + this.workload_filter.toString());
this.workload = new Workload(this.catalog);
this.workload.load(path, this.catalog_db, this.workload_filter);
this.workload_path = new File(path).getAbsolutePath();
if (this.workload_filter != null) this.workload_filter.reset();
}
// Workload Statistics
if (this.catalog_db != null) {
this.stats = new WorkloadStatistics(this.catalog_db);
if (this.params.containsKey(PARAM_STATS)) {
String path = this.params.get(PARAM_STATS);
if (debug) LOG.debug("Loading in workload statistics from '" + path + "'");
this.stats_path = new File(path).getAbsolutePath();
try {
this.stats.load(path, this.catalog_db);
} catch (Throwable ex) {
throw new RuntimeException("Failed to load stats file '" + this.stats_path + "'", ex);
}
}
// Scaling
if (this.params.containsKey(PARAM_STATS_SCALE_FACTOR)) {
double scale_factor = this.getDoubleParam(PARAM_STATS_SCALE_FACTOR);
LOG.info("Scaling TableStatistics: " + scale_factor);
AbstractTableStatisticsGenerator generator =
AbstractTableStatisticsGenerator.factory(
this.catalog_db, this.catalog_type, scale_factor);
generator.apply(this.stats);
}
}
}