diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..056ff984756c00995a56a88e59915e7fe5c7853c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,19 @@
+# Building openBIS
+
+## Requirements
+JDK8
+
+## Step By Step:
+```
+git clone https://sissource.ethz.ch/sispub/openbis.git
+cd installation/
+./gradlew clean
+./gradlew build -x test
+```
+## Where the build is found?
+```
+./installation/targets/gradle/distributions/openBIS-installation-standard-technologies-SNAPSHOT-rXXXXXXXXXX.tar.gz
+```
+
+## Why we disable tests to make the build?
+They slowdown the time to obtain a build plus some tests could have additional environment requirements.
\ No newline at end of file
diff --git a/openbis_benchmark/conf/config.json b/openbis_benchmark/conf/config.json
index dbaa6b6fcb0a33b7eaa6e1889a75397ed988401b..69b16fd12d65f81d7966b4953ead0461e7d0c628 100644
--- a/openbis_benchmark/conf/config.json
+++ b/openbis_benchmark/conf/config.json
@@ -6,9 +6,10 @@
"openbisTimeout" : "3600000",
"datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
"datastoreTimeout" : "3600000",
+ "threads" : 2,
"parameters" : {
- "SPACES_TO_CREATE" : 5,
- "SAMPLES_TO_CREATE" : 50000
+ "SPACES_TO_CREATE" : 1,
+ "SAMPLES_TO_CREATE" : 5000
}
}, {
"className" : "ch.ethz.sis.benchmark.impl.GlobalSearchBenchmark",
@@ -18,9 +19,9 @@
"openbisTimeout" : "3600000",
"datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
"datastoreTimeout" : "3600000",
+ "threads" : 10,
"parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
+ "ITERATIONS" : 10
}
}, {
"className" : "ch.ethz.sis.benchmark.impl.ListBenchmark",
@@ -30,152 +31,8 @@
"openbisTimeout" : "3600000",
"datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
"datastoreTimeout" : "3600000",
+ "threads" : 10,
"parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.LoadBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "SPACES_TO_CREATE" : 50,
- "SAMPLES_TO_CREATE" : 50000
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.GlobalSearchBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.ListBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.LoadBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "SPACES_TO_CREATE" : 500,
- "SAMPLES_TO_CREATE" : 50000
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.GlobalSearchBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.ListBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.LoadBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "SPACES_TO_CREATE" : 5000,
- "SAMPLES_TO_CREATE" : 50000
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.GlobalSearchBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.ListBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.LoadBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "SPACES_TO_CREATE" : 500,
- "SAMPLES_TO_CREATE" : 500000
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.GlobalSearchBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
- }
-}, {
- "className" : "ch.ethz.sis.benchmark.impl.ListBenchmark",
- "user" : "test",
- "password" : "test",
- "openbisURL" : "https://openbis-polyhub.ethz.ch/openbis/openbis/rmi-application-server-v3",
- "openbisTimeout" : "3600000",
- "datastoreURL" : "https://openbis-polyhub.ethz.ch/datastore_server/rmi-data-store-server-v3",
- "datastoreTimeout" : "3600000",
- "parameters" : {
- "ITERATIONS" : 10,
- "THREADS" : 10
+ "ITERATIONS" : 10
}
}]
\ No newline at end of file
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/Benchmark.java b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/Benchmark.java
index ace60e48c7a257a3e744fd56230d7376e2abb04c..cf23b4bb5d6e9e9ccb1cac8f7fc663de2d994b66 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/Benchmark.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/Benchmark.java
@@ -2,12 +2,16 @@ package ch.ethz.sis.benchmark;
import ch.ethz.sis.logging.LogManager;
import ch.ethz.sis.logging.Logger;
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.ssl.SslCertificateHelper;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
public abstract class Benchmark
{
protected BenchmarkConfig configuration;
protected Logger logger;
+ protected IApplicationServerApi v3;
+ protected String sessionToken;
public void start() {
logger = LogManager.getLogger(this.getClass());
@@ -22,8 +26,23 @@ public abstract class Benchmark
long end = System.currentTimeMillis();
logger.info("Benchmark took: " + (end-start) + " millis");
}
+
public abstract void startInternal() throws Exception;
+ public IApplicationServerApi login() {
+ if(v3 == null) {
+ v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, getConfiguration().getOpenbisURL(), getConfiguration().getOpenbisTimeout());
+ sessionToken = v3.login(getConfiguration().getUser(), getConfiguration().getPassword());
+ }
+ return v3;
+ }
+
+ public void logout() {
+ v3.logout(sessionToken);
+ v3 = null;
+ sessionToken = null;
+ }
+
public BenchmarkConfig getConfiguration()
{
return configuration;
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/BenchmarkConfig.java b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/BenchmarkConfig.java
index b7f37fe7fbf093271ea674970a95660e5f2eda05..32b590a5bb036ffff907f3cdeb11015e1b25e74d 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/BenchmarkConfig.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/BenchmarkConfig.java
@@ -19,4 +19,5 @@ public class BenchmarkConfig
private String datastoreURL;
private int datastoreTimeout;
private HashMap<String, String> parameters;
+ private int threads;
}
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/GlobalSearchBenchmark.java b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/GlobalSearchBenchmark.java
index a374947c7da3bbe9de49796cab847810cc04fdf0..2fc9152b5cb5e035a945ac04d3778c81e951261a 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/GlobalSearchBenchmark.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/GlobalSearchBenchmark.java
@@ -1,11 +1,7 @@
package ch.ethz.sis.benchmark.impl;
-import java.util.ArrayList;
-import java.util.List;
-
import ch.ethz.sis.benchmark.Benchmark;
import ch.ethz.sis.benchmark.util.RandomWord;
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
@@ -13,7 +9,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.GlobalSearchObject;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.fetchoptions.GlobalSearchObjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.global.search.GlobalSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
public class GlobalSearchBenchmark extends Benchmark {
@@ -21,62 +16,48 @@ public class GlobalSearchBenchmark extends Benchmark {
@Override
public void startInternal() throws Exception {
- long start = System.currentTimeMillis();
- IApplicationServerApi v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, getConfiguration().getOpenbisURL(), getConfiguration().getOpenbisTimeout());
- String sessionToken = v3.login(getConfiguration().getUser(), getConfiguration().getPassword());
-
int iterations = Integer.parseInt(this.getConfiguration().getParameters().get(Parameters.ITERATIONS.name()));
- int threads = Integer.parseInt(this.getConfiguration().getParameters().get(Parameters.THREADS.name()));
-
- List<Thread> threadsToJoin = new ArrayList<>();
- for(int t = 0; t < threads; t++) {
- Thread thread = new Thread() {
- public void run() {
- for(int i = 0; i < iterations; i++) {
- String word = RandomWord.getRandomWord();
- GlobalSearchCriteria criteria = new GlobalSearchCriteria();
- criteria.withText().thatContains(word);
-
- GlobalSearchObjectFetchOptions options = new GlobalSearchObjectFetchOptions();
- options.from(0);
- options.count(25);
-
- SampleFetchOptions sampleFetchOptions = options.withSample();
- sampleFetchOptions.withSpace();
- sampleFetchOptions.withType();
- sampleFetchOptions.withRegistrator();
- sampleFetchOptions.withModifier();
- sampleFetchOptions.withExperiment();
- sampleFetchOptions.withProperties();
-
- ExperimentFetchOptions experimentFetchOptions = options.withExperiment();
- experimentFetchOptions.withType();
- experimentFetchOptions.withRegistrator();
- experimentFetchOptions.withModifier();
- experimentFetchOptions.withProperties();
-
- DataSetFetchOptions dataSetFetchOptions = options.withDataSet();
- dataSetFetchOptions.withType();
- dataSetFetchOptions.withRegistrator();
- dataSetFetchOptions.withModifier();
- dataSetFetchOptions.withProperties();
-
- long start = System.currentTimeMillis();
- SearchResult<GlobalSearchObject> objects = v3.searchGlobally(sessionToken, criteria, options);
- long end = System.currentTimeMillis();
- logger.info("Found " + objects.getTotalCount() + " objects containting '" + word+ "' in " + (end-start) + " millis.");
- }
- }
- };
- threadsToJoin.add(thread);
- thread.start();
+ long laps = 0;
+ for(int i = 0; i < iterations; i++) {
+ String word = RandomWord.getRandomWord();
+ GlobalSearchCriteria criteria = new GlobalSearchCriteria();
+ criteria.withText().thatContains(word);
+
+ GlobalSearchObjectFetchOptions options = new GlobalSearchObjectFetchOptions();
+ options.from(0);
+ options.count(25);
+
+ SampleFetchOptions sampleFetchOptions = options.withSample();
+ sampleFetchOptions.withSpace();
+ sampleFetchOptions.withType();
+ sampleFetchOptions.withRegistrator();
+ sampleFetchOptions.withModifier();
+ sampleFetchOptions.withExperiment();
+ sampleFetchOptions.withProperties();
+
+ ExperimentFetchOptions experimentFetchOptions = options.withExperiment();
+ experimentFetchOptions.withType();
+ experimentFetchOptions.withRegistrator();
+ experimentFetchOptions.withModifier();
+ experimentFetchOptions.withProperties();
+
+ DataSetFetchOptions dataSetFetchOptions = options.withDataSet();
+ dataSetFetchOptions.withType();
+ dataSetFetchOptions.withRegistrator();
+ dataSetFetchOptions.withModifier();
+ dataSetFetchOptions.withProperties();
+
+ login();
+ long start = System.currentTimeMillis();
+ SearchResult<GlobalSearchObject> objects = v3.searchGlobally(sessionToken, criteria, options);
+ long end = System.currentTimeMillis();
+ long lap = end - start;
+ laps += lap;
+ logout();
+ logger.info("Found " + objects.getTotalCount() + " objects containting '" + word+ "' in " + lap + " millis.");
}
- for(Thread thread:threadsToJoin) {
- thread.join();
- }
- long end = System.currentTimeMillis();
- logger.info("Done " + (iterations * threads) + " objects searches in " + (end-start) + " millis, " + ((end-start)/(iterations * threads)) + " millis/search");
+ logger.info("Done " + iterations + " global searches in " + laps + " millis, " + (laps/iterations) + " millis/search avg");
}
}
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/ListBenchmark.java b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/ListBenchmark.java
index 73ba11b03a2c585f640a80712195c454b13552af..2f8ef38846ed4c6130f783c01adc892da08ae0a8 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/ListBenchmark.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/ListBenchmark.java
@@ -1,11 +1,10 @@
package ch.ethz.sis.benchmark.impl;
-import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import ch.ethz.sis.benchmark.Benchmark;
import ch.ethz.sis.benchmark.util.RandomValueGenerator;
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
@@ -16,7 +15,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriter
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
public class ListBenchmark extends Benchmark {
@@ -24,67 +22,57 @@ public class ListBenchmark extends Benchmark {
@Override
public void startInternal() throws Exception {
- long start1 = System.currentTimeMillis();
- IApplicationServerApi v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, getConfiguration().getOpenbisURL(), getConfiguration().getOpenbisTimeout());
- String sessionToken = v3.login(getConfiguration().getUser(), getConfiguration().getPassword());
-
+ login();
int iterations = Integer.parseInt(this.getConfiguration().getParameters().get(Parameters.ITERATIONS.name()));
- int threads = Integer.parseInt(this.getConfiguration().getParameters().get(Parameters.THREADS.name()));
-
- long start2 = System.currentTimeMillis();
+ long start = System.currentTimeMillis();
List<Space> spaces = v3.searchSpaces(sessionToken, new SpaceSearchCriteria(), new SpaceFetchOptions()).getObjects();
- long end2 = System.currentTimeMillis();
- logger.info("Found " + spaces.size() + " spaces in " + (end2-start2) + " millis.");
+ long end = System.currentTimeMillis();
+ logger.info("Found " + spaces.size() + " spaces in " + (end-start) + " millis.");
final RandomValueGenerator<Space> random = new RandomValueGenerator<>();
random.addAll(spaces);
+ logout();
- List<Thread> threadsToJoin = new ArrayList<>();
- for(int t = 0; t < threads; t++) {
- Thread thread = new Thread() {
- public void run() {
- for(int i = 0; i < iterations; i++) {
- Space space = random.getRandom();
-
- ExperimentSearchCriteria experimentSearchCriteria = new ExperimentSearchCriteria();
- experimentSearchCriteria.withProject().withSpace().withCode().thatEquals(space.getCode());
-
- ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
-
- long start1 = System.currentTimeMillis();
- Experiment experiment = v3.searchExperiments(sessionToken, experimentSearchCriteria, experimentFetchOptions).getObjects().get(0);
- long end1 = System.currentTimeMillis();
- logger.info("Found experiment '" + experiment.getPermId().getPermId()+ "' from space " + space.getCode() + " in " + (end1-start1) + " millis.");
-
- SampleSearchCriteria criteria = new SampleSearchCriteria();
- criteria.withExperiment().withPermId().thatEquals(experiment.getPermId().getPermId());
-
- SampleFetchOptions options = new SampleFetchOptions();
- options.from(0);
- options.count(25);
- options.withType();
- options.withSpace();
- options.withRegistrator();
- options.withModifier();
- options.withProperties();
- options.withParents();
- options.withChildren();
-
- long start2 = System.currentTimeMillis();
- SearchResult<Sample> samples = v3.searchSamples(sessionToken, criteria, options);
- long end2 = System.currentTimeMillis();
- logger.info("Found " + samples.getTotalCount() + " objects in experiment '" + experiment.getPermId().getPermId()+ "' from space " + space.getCode() + " in " + (end2-start2) + " millis.");
- }
- }
- };
- threadsToJoin.add(thread);
- thread.start();
- }
-
- for(Thread thread:threadsToJoin) {
- thread.join();
+ long laps = 0;
+ for(int i = 0; i < iterations; i++) {
+ login();
+
+ List<Experiment> experiments = Collections.emptyList();
+ Space space = null;
+ long lapStart1 = System.currentTimeMillis();
+ while(experiments.isEmpty()) {
+ space = random.getRandom();
+ ExperimentSearchCriteria experimentSearchCriteria = new ExperimentSearchCriteria();
+ experimentSearchCriteria.withProject().withSpace().withCode().thatEquals(space.getCode());
+ ExperimentFetchOptions experimentFetchOptions = new ExperimentFetchOptions();
+ experiments = v3.searchExperiments(sessionToken, experimentSearchCriteria, experimentFetchOptions).getObjects();
+ }
+ long lapEnd1 = System.currentTimeMillis();
+ Experiment experiment = experiments.get(0);
+ logger.info("Found experiment '" + experiment.getPermId().getPermId()+ "' from space " + space.getCode() + " in " + (lapEnd1-lapStart1) + " millis.");
+
+ SampleSearchCriteria criteria = new SampleSearchCriteria();
+ criteria.withExperiment().withPermId().thatEquals(experiment.getPermId().getPermId());
+
+ SampleFetchOptions options = new SampleFetchOptions();
+ options.from(0);
+ options.count(25);
+ options.withType();
+ options.withSpace();
+ options.withRegistrator();
+ options.withModifier();
+ options.withProperties();
+ options.withParents();
+ options.withChildren();
+
+ long lapStart2 = System.currentTimeMillis();
+ SearchResult<Sample> samples = v3.searchSamples(sessionToken, criteria, options);
+ long lapEnd2 = System.currentTimeMillis();
+ long lap = lapEnd2 - lapStart2;
+ laps += lap;
+ logger.info("Found " + samples.getTotalCount() + " objects in experiment '" + experiment.getPermId().getPermId()+ "' from space " + space.getCode() + " in " + lap + " millis.");
+ logout();
}
- long end1 = System.currentTimeMillis();
- logger.info("Done " + (iterations * threads) + " sample searches in " + (end1-start1) + " millis, " + ((end1-start1)/(iterations * threads)) + " millis/search");
+ logger.info("Done " + (iterations) + " experiment object lists in " + laps + " millis, " + ((laps)/(iterations)) + " millis/search avg");
}
}
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/LoadBenchmark.java b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/LoadBenchmark.java
index 5582ea27b0b447e9553278f3b84b17509f7b3a79..32acb8df0ce42dc4c245de1f928b3c0a4d5e9cdb 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/LoadBenchmark.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/benchmark/impl/LoadBenchmark.java
@@ -9,7 +9,6 @@ import java.util.Set;
import ch.ethz.sis.benchmark.Benchmark;
import ch.ethz.sis.benchmark.util.RandomValueGenerator;
import ch.ethz.sis.benchmark.util.RandomWord;
-import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentTypeCreation;
@@ -27,7 +26,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.DataType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create.PropertyAssignmentCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.create.PropertyTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.id.PropertyTypePermId;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
public class LoadBenchmark extends Benchmark {
@@ -36,8 +34,7 @@ public class LoadBenchmark extends Benchmark {
@Override
public void startInternal() throws Exception {
- IApplicationServerApi v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi.class, getConfiguration().getOpenbisURL(), getConfiguration().getOpenbisTimeout());
- String sessionToken = v3.login(getConfiguration().getUser(), getConfiguration().getPassword());
+ login();
String propertyTypeCode1 = "BENCHMARK_STRING_1";
String propertyTypeCode2 = "BENCHMARK_STRING_2";
@@ -157,6 +154,7 @@ public class LoadBenchmark extends Benchmark {
long end3 = System.currentTimeMillis();
logger.info("Create " + spacesToCreate + " Collections took: " + (end3-start3) + " millis - " + ((end3-start3)/spacesToCreate) + " millis/collection");
+ logout();
//
// Part 4 - Creating Samples
//
@@ -181,10 +179,12 @@ public class LoadBenchmark extends Benchmark {
sampleCreation.setSpaceId(new SpacePermId(Prefix.SPACE_ + code)); // Spaces are distributed randomly
sampleCreation.setExperimentId(new ExperimentIdentifier("/" + Prefix.SPACE_ + code + "/" + Prefix.PROJECT_ + code + "/" + Prefix.COLLECTION_ + code));
sampleCreations.add(sampleCreation);
- if(i % sampleBatchSize == 0) { // Every 5000, send to openBIS
+ if((i+1) % sampleBatchSize == 0) { // Every 5000, send to openBIS
+ login();
long lapStart4 = System.currentTimeMillis();
v3.createSamples(sessionToken, sampleCreations);
long lapEnd4 = System.currentTimeMillis();
+ logout();
logger.info("Create " + sampleCreations.size() + " Samples took: " + (lapEnd4 - lapStart4) + " millis - " + ((lapEnd4-lapStart4)/sampleCreations.size()) + " millis/sample");
sampleCreations.clear();
}
diff --git a/openbis_benchmark/src/main/java/ch/ethz/sis/startup/Main.java b/openbis_benchmark/src/main/java/ch/ethz/sis/startup/Main.java
index cdfe2279f14a4b3c7e0d6deddd3b85816a4e7d04..45f4b314683ace0243e69dd7c100469fba1e9073 100644
--- a/openbis_benchmark/src/main/java/ch/ethz/sis/startup/Main.java
+++ b/openbis_benchmark/src/main/java/ch/ethz/sis/startup/Main.java
@@ -2,6 +2,9 @@ package ch.ethz.sis.startup;
import java.io.File;
import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.List;
+
import ch.ethz.sis.benchmark.Benchmark;
import ch.ethz.sis.benchmark.BenchmarkConfig;
import ch.ethz.sis.json.jackson.JacksonObjectMapper;
@@ -42,9 +45,36 @@ public class Main
BenchmarkConfig[] benchmarkConfigs = JacksonObjectMapper.getInstance().readValue(new FileInputStream(configFile), BenchmarkConfig[].class);
for(BenchmarkConfig benchmarkConfig:benchmarkConfigs) {
- Benchmark benchmark = (Benchmark) Class.forName(benchmarkConfig.getClassName()).newInstance();
- benchmark.setConfiguration(benchmarkConfig);
- benchmark.start();
+ List<BenchmarkThread> threadsToJoin = new ArrayList<>();
+ for(int t = 0; t < benchmarkConfig.getThreads(); t++) {
+ BenchmarkThread thread = new BenchmarkThread(benchmarkConfig) {
+ public void run() {
+ Benchmark benchmark = null;
+ try {
+ benchmark = (Benchmark) Class.forName(benchmarkConfig.getClassName()).newInstance();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ benchmark.setConfiguration(benchmarkConfig);
+ benchmark.start();
+ }
+ };
+ threadsToJoin.add(thread);
+ thread.start();
+ }
+
+ for(BenchmarkThread thread:threadsToJoin) {
+ thread.join();
+ }
}
}
+
+ static private abstract class BenchmarkThread extends Thread {
+ private final BenchmarkConfig benchmarkConfig;
+
+ public BenchmarkThread(BenchmarkConfig benchmarkConfig) {
+ super();
+ this.benchmarkConfig = benchmarkConfig;
+ }
+ }
}
diff --git a/openbis_standard_technologies/build.gradle b/openbis_standard_technologies/build.gradle
index d0ba4842f03ed959fb24fc80ff4e78bc9207cf16..259f97a04f4770f66d1795c6320598f98d43b0de 100644
--- a/openbis_standard_technologies/build.gradle
+++ b/openbis_standard_technologies/build.gradle
@@ -1,3 +1,27 @@
+buildscript {
+ apply from: '../gradle/repository.gradle'
+
+ repositories repositoryConfig
+
+ dependencies {
+ classpath 'apache:commons-codec:+',
+ 'owasp:dependency-check-gradle:+'
+ }
+}
+
+apply plugin: org.owasp.dependencycheck.gradle.DependencyCheckPlugin
+
+dependencyCheck {
+ failBuildOnCVSS = 7 // 0 - 4 = low, 4 - 7 = medium, 7 - 9 = high, 9-10 = critical
+ analyzers{
+ assemblyEnabled = false
+ }
+ proxy {
+ server = 'proxy.ethz.ch'
+ port = 3128
+ }
+}
+
evaluationDependsOn(':commonbase')
evaluationDependsOn(':common')
evaluationDependsOn(':openbis_api')
@@ -12,6 +36,7 @@ evaluationDependsOn(':rtd_yeastx')
evaluationDependsOn(':deep_sequencing_unit')
evaluationDependsOn(':plasmid')
+
apply from: '../gradle/javaproject.gradle'
apply from: 'query-api.gradle'
apply from: 'screening-api.gradle'
@@ -80,16 +105,6 @@ dependencies {
project(path:':screening')
}
-buildscript {
- apply from: '../gradle/repository.gradle'
-
- repositories repositoryConfig
-
- dependencies {
- classpath 'apache:commons-codec:+'
- }
-}
-
task compileGwt (dependsOn: classes, type: JavaExec) {
ext.buildDir = "${project.buildDir}/gwt"
@@ -431,4 +446,4 @@ build.dependsOn zipDss
build.dependsOn clientsAndApis
build.dependsOn dssUploadGuiStandaloneZip
build.dependsOn dssUploadGuiStandaloneJar
-build.dependsOn generateJavadoc
\ No newline at end of file
+build.dependsOn generateJavadoc
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/ELNDictionary.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/ELNDictionary.js
index d9431aae0189e7706e45c89e135ede80b1ac97dd..504ac9540998433362983aa6c261cf98cd0b582d 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/ELNDictionary.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/config/ELNDictionary.js
@@ -50,11 +50,11 @@ ELNDictionary.settingsView = {
},
dataSetTypeForFileName : {
title : "Dataset types for filenames",
- info : "When listing a combination of file extension / " + ELNDictionary.Sample + " Type on this section the Dataset uploader will select a Dataset Type by default. This decision can be overridden by users afterwards but provides a nice default to avoid mistakes.",
+ info : "When listing a combination of file extension / Dataset Type on this section the Dataset uploader will select a Dataset Type by default. This decision can be overridden by users afterwards but provides a nice default to avoid mistakes.",
},
sampleTypeDefinitionsExtension : {
title : ELNDictionary.Sample +" Type definitions Extension",
- info : "This section is used to extend the common openBIS definitions to: 1. Enable the storage. 2. Specify if the object type is a protocol. 3. Add intended parent/children hints. 4. Support annotations for these links using properties. 5. Show in dropdowns.",
+ info : "This section is used to extend the common openBIS definitions to: 1. Enable the storage. 2. Specify if the " + ELNDictionary.sample + " type is a protocol. 3. Add intended parent/children hints. 4. Support annotations for these links using properties. 5. Show in dropdowns.",
},
}
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
index b8c0bf524d96e6f3b8f236010081622396fea61d..92bfae40a748a260d468ac531fc96fb3431d6705 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataGrid/SampleDataGridUtil.js
@@ -48,7 +48,38 @@ var SampleDataGridUtil = new function() {
label : 'Code',
property : 'code',
isExportable: false,
- sortable : true
+ sortable : true,
+ render : function(data, grid) {
+ var paginationInfo = null;
+ if(isDynamic) {
+ var indexFound = null;
+ for(var idx = 0; idx < grid.lastReceivedData.objects.length; idx++) {
+ if(grid.lastReceivedData.objects[idx].permId === data.permId) {
+ indexFound = idx + (grid.lastUsedOptions.pageIndex * grid.lastUsedOptions.pageSize);
+ break;
+ }
+ }
+
+ if(indexFound !== null) {
+ paginationInfo = {
+ pagFunction : _this.getDataListDynamic(samplesOrCriteria, false),
+ pagOptions : grid.lastUsedOptions,
+ currentIndex : indexFound,
+ totalCount : grid.lastReceivedData.totalCount
+ }
+ }
+ }
+ return (isLinksDisabled)?data.code:FormUtil.getFormLink(data.code, "Sample", data.permId, paginationInfo);
+ },
+ filter : function(data, filter) {
+ return data.identifier.toLowerCase().indexOf(filter) !== -1;
+ },
+ sort : function(data1, data2, asc) {
+ var value1 = data1.identifier;
+ var value2 = data2.identifier;
+ var sortDirection = (asc)? 1 : -1;
+ return sortDirection * naturalSort(value1, value2);
+ }
});
columnsFirst.push({
@@ -87,14 +118,44 @@ var SampleDataGridUtil = new function() {
label : 'Parents',
property : 'parents',
isExportable: true,
- sortable : false
+ sortable : false,
+ render : function(data, grid) {
+ var output = $("<span>");
+ if(data.parents) {
+ var elements = data.parents.split(", ");
+ for (var eIdx = 0; eIdx < elements.length; eIdx++) {
+ var eIdentifier = elements[eIdx];
+ var eComponent = (isLinksDisabled)?eIdentifier:FormUtil.getFormLink(eIdentifier, "Sample", eIdentifier, null);
+ if(eIdx != 0) {
+ output.append(", ");
+ }
+ output.append(eComponent);
+ }
+ }
+ return output;
+ }
});
columnsFirst.push({
label : 'Children',
property : 'children',
isExportable: false,
- sortable : false
+ sortable : false,
+ render : function(data, grid) {
+ var output = $("<span>");
+ if(data.children) {
+ var elements = data.children.split(", ");
+ for (var eIdx = 0; eIdx < elements.length; eIdx++) {
+ var eIdentifier = elements[eIdx];
+ var eComponent = (isLinksDisabled)?eIdentifier:FormUtil.getFormLink(eIdentifier, "Sample", eIdentifier, null);
+ if(eIdx != 0) {
+ output.append(", ");
+ }
+ output.append(eComponent);
+ }
+ }
+ return output;
+ }
});
columnsFirst.push({
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerModel.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerModel.js
index 2395ca44039df68dc43143cbfe50762195af4518..c42346b5d68dc08921b4c1288f2ecf6e8759518a 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerModel.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/DatasetViewerModel.js
@@ -83,9 +83,10 @@ function DataSetViewerModel(containerId, profile, entity, serverFacade, datastor
}
this._isIconableImage = function(pathInDataSet) {
- return this._hasExtension(pathInDataSet, ["jpg", "jpeg", "png", "gif"]);
+ var filename = pathInDataSet.split('/').slice(-1)[0];
+ return !filename.startsWith('.') && this._hasExtension(pathInDataSet, ["jpg", "jpeg", "png", "gif"]);
}
-
+
this._isJupyterNotebook = function(pathInDataSet) {
return this._hasExtension(pathInDataSet, ["ipynb"]);
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/ImagePreviewIconLoader.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/ImagePreviewIconLoader.js
index c0830e100b97e70c685846127639c5d3b7afbd5d..569b03ae2909feaaf1f3868e092db743fb64df67 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/ImagePreviewIconLoader.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/DataSetForm/widgets/ImagePreviewIconLoader.js
@@ -34,7 +34,7 @@ function ImagePreviewIconLoader() {
}
this._shouldLoadPreview = function(node) {
- return ! node.data.previewLoaded && node.data.fileSize <= profile.datasetViewerMaxFilesizeForImagePreview;
+ return ! node.data.previewLoading && ! node.data.previewLoaded && node.data.fileSize <= profile.datasetViewerMaxFilesizeForImagePreview;
}
this._addToQueue = function(node) {
@@ -58,6 +58,9 @@ function ImagePreviewIconLoader() {
}
this._initLoading = function(node) {
+
+ node.data.previewLoading = true;
+
var $span = $(node.span);
var $imageContainer = $("<span>", { id : "image-container" }).css({
@@ -122,6 +125,7 @@ function ImagePreviewIconLoader() {
$imageContainer.append($iconImg);
params.node.data.previewLoaded = true;
+ params.node.data.previewLoading = false;
params.done();
});
}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
index fce3682ddc92eb14801cfcc3ae62cae7b95df31d..c4f73efa7a0060aade880d266e20797cb4bc9ec6 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormController.js
@@ -21,11 +21,6 @@ function SettingsFormController(mainController, settingsSample, mode) {
this._settingsManager = new SettingsManager(this._mainController.serverFacade);
this.init = function(views) {
-
- if (!profile.isAdmin) {
- return;
- }
-
// apply settings to copy of profile, even if invalid, for editing
var profileToEdit = jQuery.extend(true, {}, profile);
this._settingsManager.loadSettingsAndApplyToProfile((function() {
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
index 4a3e99695161a57a696c7f8bce1035f695df6ec4..9e1c5b6bbe7bdd7db389dc7076796bc5f19ee97c 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/as/webapps/eln-lims/html/js/views/SettingsForm/SettingsFormView.js
@@ -427,29 +427,28 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
{ label : "Settings for" },
{ label : "Section name" },
{ label : "Disable section" },
- { label : "Disable addition of any object type" }
+ { label : "Disable addition of any " + ELNDictionary.sample + " type" }
];
- tableModel.rowBuilders = {
- "Settings for" : function(rowData) {
+ tableModel.rowBuilders = {}
+ tableModel.rowBuilders["Settings for"] = function(rowData) {
return $("<span>").text(rowData.parentsOrChildren);
- },
- "Section name" : function(rowData) {
- return $("<input>", { type : "text", class : "form-control" }).val(rowData.title);
- },
- "Disable section" : function(rowData) {
- var $checkbox = $("<input>", { type : "checkbox" });
- if (rowData.disabled) {
- $checkbox.attr("checked", true);
- }
- return $checkbox;
- },
- "Disable addition of any object type" : function(rowData) {
- var $checkbox = $("<input>", { type : "checkbox" });
- if (rowData.anyTypeDisabled) {
- $checkbox.attr("checked", true);
- }
- return $checkbox;
- },
+ };
+ tableModel.rowBuilders["Section name"] = function(rowData) {
+ return $("<input>", { type : "text", class : "form-control" }).val(rowData.title);
+ };
+ tableModel.rowBuilders["Disable section"] = function(rowData) {
+ var $checkbox = $("<input>", { type : "checkbox" });
+ if (rowData.disabled) {
+ $checkbox.attr("checked", true);
+ }
+ return $checkbox;
+ };
+ tableModel.rowBuilders["Disable addition of any " + ELNDictionary.sample + " type"] = function(rowData) {
+ var $checkbox = $("<input>", { type : "checkbox" });
+ if (rowData.anyTypeDisabled) {
+ $checkbox.attr("checked", true);
+ }
+ return $checkbox;
};
// add data
if (sampleTypeSettings) { // values from profile
@@ -490,7 +489,7 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
if (rowValues["Disable section"]) {
settings["SAMPLE_PARENTS_DISABLED"] = true;
}
- if (rowValues["Disable addition of any object type"]) {
+ if (rowValues["Disable addition of any " + ELNDictionary.sample + " type"]) {
settings["SAMPLE_PARENTS_ANY_TYPE_DISABLED"] = true;
}
} else if (rowValues["Settings for"] === "Children") {
@@ -500,7 +499,7 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
if (rowValues["Disable section"]) {
settings["SAMPLE_CHILDREN_DISABLED"] = true;
}
- if (rowValues["Disable addition of any object type"]) {
+ if (rowValues["Disable addition of any " + ELNDictionary.sample + " type"]) {
settings["SAMPLE_CHILDREN_ANY_TYPE_DISABLED"] = true;
}
}
@@ -646,7 +645,7 @@ function SettingsFormView(settingsFormController, settingsFormModel) {
tableModel.rowBuilders[params.columnName] = function(rowData) {
return FormUtil.getDropdown(params.options.map(function(option) {
return {
- label : option,
+ label : Util.getDisplayNameFromCode(option),
value : option,
selected : option === rowData,
};