From fcc28ee865ca9b7074027ea914e5e88f3aff386f Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 5 Oct 2012 13:47:59 +0000
Subject: [PATCH] SP-299 BIS-211 add simple feature vectors test
SVN: 27065
---
.../FeatureVectorsDropboxTest/features.csv | 97 +++++++++++++
.../feature-vector-data-set-handler.py | 65 +++++++++
.../plugin.properties | 8 ++
.../FeatureVectorsDropboxTest.java | 129 ++++++++++++++++++
4 files changed, 299 insertions(+)
create mode 100644 screening/resource/test-data/FeatureVectorsDropboxTest/features.csv
create mode 100644 screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/feature-vector-data-set-handler.py
create mode 100644 screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/plugin.properties
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/FeatureVectorsDropboxTest.java
diff --git a/screening/resource/test-data/FeatureVectorsDropboxTest/features.csv b/screening/resource/test-data/FeatureVectorsDropboxTest/features.csv
new file mode 100644
index 00000000000..c82d36b5b69
--- /dev/null
+++ b/screening/resource/test-data/FeatureVectorsDropboxTest/features.csv
@@ -0,0 +1,97 @@
+barcode,Well,row number,column number,TPU,STATE
+PLATE-1,A1,1,1,0.0109905507275,UNSTABLE
+PLATE-1,A2,1,2,-0.0182003436984,UNSTABLE
+PLATE-1,A3,1,3,-0.00805361743168,STABLE
+PLATE-1,A4,1,4,0.0810000328417,STABLE
+PLATE-1,A5,1,5,0.0259230435927,STABLE
+PLATE-1,A6,1,6,-0.036430571554,UNSTABLE
+PLATE-1,A7,1,7,-0.0101872401882,UNSTABLE
+PLATE-1,A8,1,8,-0.00727317718048,STABLE
+PLATE-1,A9,1,9,0.0315700979161,STABLE
+PLATE-1,A10,1,10,0.168559091956,STABLE
+PLATE-1,A11,1,11,-0.0250794227724,STABLE
+PLATE-1,A12,1,12,0.257636061574,STABLE
+PLATE-1,B1,2,1,0.100434155899,STABLE
+PLATE-1,B2,2,2,0.0976115450765,UNSTABLE
+PLATE-1,B3,2,3,0.0864925097496,UNSTABLE
+PLATE-1,B4,2,4,0.0878168382557,STABLE
+PLATE-1,B5,2,5,0.00728303315339,STABLE
+PLATE-1,B6,2,6,0.00135844915617,UNSTABLE
+PLATE-1,B7,2,7,0.071667990849,UNSTABLE
+PLATE-1,B8,2,8,0.134576738033,STABLE
+PLATE-1,B9,2,9,0.062517688301,STABLE
+PLATE-1,B10,2,10,-0.0559872246124,STABLE
+PLATE-1,B11,2,11,-0.0619564845848,STABLE
+PLATE-1,B12,2,12,0.0324420596004,UNSTABLE
+PLATE-1,C1,3,1,0.206954055141,UNSTABLE
+PLATE-1,C2,3,2,0.19680434536,UNSTABLE
+PLATE-1,C3,3,3,0.229279401419,UNSTABLE
+PLATE-1,C4,3,4,0.193351284437,STABLE
+PLATE-1,C5,3,5,0.129062893555,STABLE
+PLATE-1,C6,3,6,0.126673623384,STABLE
+PLATE-1,C7,3,7,0.229037975734,STABLE
+PLATE-1,C8,3,8,0.223431359979,STABLE
+PLATE-1,C9,3,9,0.190028172309,STABLE
+PLATE-1,C10,3,10,-0.0674441033456,UNSTABLE
+PLATE-1,C11,3,11,0.0339637772352,STABLE
+PLATE-1,C12,3,12,0.164178194792,STABLE
+PLATE-1,D1,4,1,0.297974218656,UNSTABLE
+PLATE-1,D2,4,2,0.298059135512,STABLE
+PLATE-1,D3,4,3,0.350772745466,UNSTABLE
+PLATE-1,D4,4,4,0.313919901769,UNSTABLE
+PLATE-1,D5,4,5,0.252290578613,STABLE
+PLATE-1,D6,4,6,0.324830425263,UNSTABLE
+PLATE-1,D7,4,7,0.162928227992,STABLE
+PLATE-1,D8,4,8,0.265496427715,UNSTABLE
+PLATE-1,D9,4,9,0.123242462625,STABLE
+PLATE-1,D10,4,10,0.0156365936527,STABLE
+PLATE-1,D11,4,11,0.318001502397,STABLE
+PLATE-1,D12,4,12,0.20854731993,STABLE
+PLATE-1,E1,5,1,0.393536251276,UNSTABLE
+PLATE-1,E2,5,2,0.399605077357,STABLE
+PLATE-1,E3,5,3,0.433901537831,STABLE
+PLATE-1,E4,5,4,0.378871120619,UNSTABLE
+PLATE-1,E5,5,5,0.453098222167,STABLE
+PLATE-1,E6,5,6,0.308155666544,UNSTABLE
+PLATE-1,E7,5,7,0.45538138854,STABLE
+PLATE-1,E8,5,8,0.372161727461,STABLE
+PLATE-1,E9,5,9,0.308752403413,STABLE
+PLATE-1,E10,5,10,0.357322858215,UNSTABLE
+PLATE-1,E11,5,11,0.408261827863,UNSTABLE
+PLATE-1,E12,5,12,0.276512650311,UNSTABLE
+PLATE-1,F1,6,1,0.518565455665,UNSTABLE
+PLATE-1,F2,6,2,0.501353504253,UNSTABLE
+PLATE-1,F3,6,3,0.486441514218,UNSTABLE
+PLATE-1,F4,6,4,0.530701442681,STABLE
+PLATE-1,F5,6,5,0.526764248567,UNSTABLE
+PLATE-1,F6,6,6,0.535393254659,STABLE
+PLATE-1,F7,6,7,0.485971393901,STABLE
+PLATE-1,F8,6,8,0.446866206382,STABLE
+PLATE-1,F9,6,9,0.500105016099,STABLE
+PLATE-1,F10,6,10,0.572554837409,UNSTABLE
+PLATE-1,F11,6,11,0.421581223622,UNSTABLE
+PLATE-1,F12,6,12,0.566179719687,STABLE
+PLATE-1,G1,7,1,0.597014347164,STABLE
+PLATE-1,G2,7,2,0.595574322803,STABLE
+PLATE-1,G3,7,3,0.573275879833,UNSTABLE
+PLATE-1,G4,7,4,0.565598774935,UNSTABLE
+PLATE-1,G5,7,5,0.580255468506,UNSTABLE
+PLATE-1,G6,7,6,0.731126618477,UNSTABLE
+PLATE-1,G7,7,7,0.586449329876,STABLE
+PLATE-1,G8,7,8,0.504383391301,UNSTABLE
+PLATE-1,G9,7,9,0.57029228861,UNSTABLE
+PLATE-1,G10,7,10,0.571055758388,UNSTABLE
+PLATE-1,G11,7,11,0.729508274912,STABLE
+PLATE-1,G12,7,12,0.651282199669,UNSTABLE
+PLATE-1,H1,8,1,0.708336042851,UNSTABLE
+PLATE-1,H2,8,2,0.693510468853,STABLE
+PLATE-1,H3,8,3,0.680500191339,UNSTABLE
+PLATE-1,H4,8,4,0.682631399189,UNSTABLE
+PLATE-1,H5,8,5,0.771686970996,UNSTABLE
+PLATE-1,H6,8,6,0.592031721228,STABLE
+PLATE-1,H7,8,7,0.683612608169,STABLE
+PLATE-1,H8,8,8,0.632227578807,UNSTABLE
+PLATE-1,H9,8,9,0.90031946922,UNSTABLE
+PLATE-1,H10,8,10,0.750539227015,STABLE
+PLATE-1,H11,8,11,0.826335733676,UNSTABLE
+PLATE-1,H12,8,12,0.467946755513,UNSTABLE
diff --git a/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/feature-vector-data-set-handler.py b/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/feature-vector-data-set-handler.py
new file mode 100644
index 00000000000..d6059bd49ad
--- /dev/null
+++ b/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/feature-vector-data-set-handler.py
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+PLATE_GEOMETRY = "384_WELLS_16X24"
+
+"""
+An Jython dropbox for importing HCS image datasets for use by the FeatureVectorsDropboxTest
+"""
+
+import os
+from java.util import Properties
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v2 import SimpleFeatureVectorDataConfig
+from java.io import File
+
+def create_experiment(tr):
+ space = tr.getSpace("TEST")
+ if space == None:
+ space = tr.createNewSpace("TEST", "etlserver")
+ project = tr.getProject("/TEST/TEST-PROJECT")
+ if project == None:
+ project = tr.createNewProject("/TEST/TEST-PROJECT")
+ expid = "/TEST/TEST-PROJECT/TRANSFORMED_THUMBNAILS_EXP"
+
+ exp = tr.createNewExperiment(expid, 'SIRNA_HCS')
+ exp.setPropertyValue("DESCRIPTION", "Test experiment")
+
+ return exp
+
+def create_plate(tr, experiment, plateCode):
+ plateId = "/TEST/" + plateCode
+ plate = tr.createNewSample(plateId, 'PLATE')
+ plate.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
+ plate.setExperiment(experiment)
+
+ wellA1 = tr.createNewSample(plate.getSampleIdentifier() + ":A1", "SIRNA_WELL")
+ wellA1.setContainer(plate)
+
+ wellA2 = tr.createNewSample(plate.getSampleIdentifier() + ":A2", "SIRNA_WELL")
+ wellA2.setContainer(plate)
+
+ return plate
+
+def config_props():
+ config = Properties()
+ config.setProperty("separator", ",")
+ config.setProperty("well-name-row", "Well")
+ config.setProperty("well-name-col", "Well")
+ config.setProperty("well-name-col-is-alphanum", "true")
+ return config
+
+def process(transaction):
+ experiment = create_experiment(transaction)
+ plate = create_plate(transaction, experiment, 'PLATE-FEATURE-VECTOR-TEST')
+
+ configProps = config_props()
+ config = SimpleFeatureVectorDataConfig(configProps)
+
+ featuresPath = os.path.join(transaction.getIncoming().getAbsolutePath(), "features.csv")
+ featureDataSet = transaction.createNewFeatureVectorDataSet(config, File(featuresPath))
+ featureDataSet.setFileFormatType('CSV')
+
+ featureDataSet.setSample(plate)
+ transaction.moveFile(featuresPath, featureDataSet)
+
+ print featureDataSet
\ No newline at end of file
diff --git a/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/plugin.properties b/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/plugin.properties
new file mode 100644
index 00000000000..900b82a6dbb
--- /dev/null
+++ b/screening/sourceTest/core-plugins/FeatureVectorsDropboxTest/1/dss/drop-boxes/FeatureVectorsDropboxTest-drop-box/plugin.properties
@@ -0,0 +1,8 @@
+incoming-dir = ${root-dir}/incoming-FeatureVectorsDropboxTest
+incoming-dir-create = true
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
+script-path = feature-vector-data-set-handler.py
+storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+storage-processor.data-source = imaging-db
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/FeatureVectorsDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/FeatureVectorsDropboxTest.java
new file mode 100644
index 00000000000..f7cc1a1bba2
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/FeatureVectorsDropboxTest.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.screening.systemtests;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.springframework.mock.web.MockHttpServletRequest;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.servlet.SpringRequestContextProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+@Test(groups =
+ { "slow", "systemtest" })
+public class FeatureVectorsDropboxTest extends AbstractScreeningSystemTestCase
+{
+ private MockHttpServletRequest request;
+
+ private String sessionToken;
+
+ private IScreeningClientService screeningClientService;
+
+ private IScreeningApiServer screeningServer;
+
+ private IScreeningOpenbisServiceFacade screeningFacade;
+
+ @BeforeTest
+ public void dropAnExampleDataSet() throws IOException, Exception
+ {
+ File exampleDataSet = createTestDataContents();
+ moveFileToIncoming(exampleDataSet);
+ waitUntilDataSetImported();
+ }
+
+ @BeforeMethod
+ public void setUp() throws Exception
+ {
+ screeningClientService =
+ (IScreeningClientService) applicationContext
+ .getBean(ResourceNames.SCREENING_PLUGIN_SERVICE);
+ request = new MockHttpServletRequest();
+ ((SpringRequestContextProvider) applicationContext.getBean("request-context-provider"))
+ .setRequest(request);
+ Object bean = applicationContext.getBean(ResourceNames.SCREENING_PLUGIN_SERVER);
+ screeningServer = (IScreeningApiServer) bean;
+ sessionToken = screeningClientService.tryToLogin("admin", "a").getSessionID();
+ screeningFacade = ScreeningOpenbisServiceFacade.tryCreateForTest(sessionToken, "http://localhost:" + SYSTEM_TEST_CASE_SERVER_PORT, screeningServer);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ File[] files = getIncomingDirectory().listFiles();
+ for (File file : files)
+ {
+ FileUtilities.deleteRecursively(file);
+ }
+ }
+
+ @Test
+ public void testFeatureVectors() throws Exception
+ {
+ List<Plate> plates = screeningFacade.listPlates();
+
+ List<FeatureVectorDatasetReference> features =
+ screeningFacade.listFeatureVectorDatasets(plates);
+
+ // exactly one feature vector data set should be created in this test
+ assertEquals(1, features.size());
+
+ FeatureVectorDatasetReference feature = features.get(0);
+ assertEquals("HCS_ANALYSIS_CONTAINER_WELL_FEATURES", feature.getDataSetType());
+
+ }
+
+ private File createTestDataContents() throws IOException
+ {
+ File dest = new File(workingDirectory, "test-data");
+ dest.mkdirs();
+
+ File featureSrc = getFeatureVectorsTestData();
+ FileUtils.copyFileToDirectory(featureSrc, dest);
+ // Copy the test data set to the location for processing
+ return dest;
+ }
+
+ private File getFeatureVectorsTestData()
+ {
+ return new File("../screening/resource/test-data/FeatureVectorsDropboxTest/",
+ "features.csv");
+ }
+
+ @Override
+ protected int dataSetImportWaitDurationInSeconds()
+ {
+ return 60;
+ }
+
+}
--
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