From 23e20f55e530844c15d1d8ac32b5c89f338d0457 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 29 Jun 2011 14:54:29 +0000
Subject: [PATCH] LMS-2340 Improved scripts and fixed service.properties.
SVN: 21908
---
eu_basynthec/dist/etc/service.properties | 8 +++---
.../etc/transcriptomics/data-set-handler.py | 11 +++++---
eu_basynthec/etc/service.properties | 10 +++----
...TranscriptomicsDataSetRegistratorTest.java | 27 +++++++++++++++++++
4 files changed, 44 insertions(+), 12 deletions(-)
diff --git a/eu_basynthec/dist/etc/service.properties b/eu_basynthec/dist/etc/service.properties
index bc8f4aa8b44..5e124c543fe 100644
--- a/eu_basynthec/dist/etc/service.properties
+++ b/eu_basynthec/dist/etc/service.properties
@@ -128,7 +128,7 @@ metabolomics.delete-unidentified = true
metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
metabolomics.script-path = /local0/openbis/jython_scripts/metabolomics/data-set-handler.py
-metabolomics.validation-script-path = /local0/openbis/jython_scripts/metabolomics/data-set-validator.py
+metabolomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/metabolomics/data-set-validator.py
# ---------------------------------------------------------------------------
# growth-profiles thread configuration
@@ -139,7 +139,7 @@ growth-profiles.delete-unidentified = true
growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
growth-profiles.script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-validator.py
+growth-profiles.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/growth-profiles/data-set-validator.py
# ---------------------------------------------------------------------------
# transcriptomics thread configuration
@@ -150,7 +150,7 @@ transcriptomics.delete-unidentified = true
transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
transcriptomics.script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-validator.py
+transcriptomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/transcriptomics/data-set-validator.py
# ---------------------------------------------------------------------------
# proteomics thread configuration
@@ -161,7 +161,7 @@ proteomics.delete-unidentified = true
proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
proteomics.script-path = /local0/openbis/jython_scripts/proteomics/data-set-handler.py
-proteomics.validation-script-path = /local0/openbis/jython_scripts/proteomics/data-set-validator.py
+proteomics.validation-script-path = /local0/openbis/jython_scripts/shared/shared-classes.py,/local0/openbis/jython_scripts/proteomics/data-set-validator.py
#
diff --git a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
index fe8f9dc2d18..01507137934 100644
--- a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
+++ b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
@@ -55,9 +55,14 @@ def convert_data_to_tsv(tr, start_row, start_col, dataset, location):
tr.createNewDirectory(dataset, location)
tsvFileName = tr.createNewFile(dataset, location, incoming.getName() + ".tsv")
tsv = open(tsvFileName, 'w')
- for line in timeSeriesData.getRawDataLines():
- for i in range(start_row, len(line) - 1):
- tsv.write(line[i])
+ raw_data = timeSeriesData.getRawDataLines()
+ for i in range(start_row, len(raw_data)):
+ line = raw_data[i]
+ # write the metabolite id
+ tsv.write(line[0])
+ tsv.write("\t")
+ for j in range(start_col, len(line) - 1):
+ tsv.write(line[j])
tsv.write("\t")
tsv.write(line[len(line) - 1])
tsv.write("\n")
diff --git a/eu_basynthec/etc/service.properties b/eu_basynthec/etc/service.properties
index cbbebee853a..7b048f20cc4 100644
--- a/eu_basynthec/etc/service.properties
+++ b/eu_basynthec/etc/service.properties
@@ -56,7 +56,7 @@ notify-successful-registration = false
server-url = http://localhost:8888
# The username to use when contacting the openBIS server
-username = etlserver
+username = etlserver-basynthec
# The password to use when contacting the openBIS server
password = etlserver
@@ -137,7 +137,7 @@ metabolomics.delete-unidentified = true
metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
metabolomics.script-path = dist/etc/metabolomics/data-set-handler.py
-metabolomics.validation-script-path = dist/etc/metabolomics/data-set-validator.py
+metabolomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/metabolomics/data-set-validator.py
# ---------------------------------------------------------------------------
# growth-profiles thread configuration
@@ -148,7 +148,7 @@ growth-profiles.delete-unidentified = true
growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
growth-profiles.script-path = dist/etc/growth-profiles/data-set-handler.py
-growth-profiles.validation-script-path = dist/etc/growth-profiles/data-set-validator.py
+growth-profiles.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/growth-profiles/data-set-validator.py
# ---------------------------------------------------------------------------
# transcriptomics thread configuration
@@ -159,7 +159,7 @@ transcriptomics.delete-unidentified = true
transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
transcriptomics.script-path = dist/etc/transcriptomics/data-set-handler.py
-transcriptomics.validation-script-path = dist/etc/transcriptomics/data-set-validator.py
+transcriptomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/transcriptomics/data-set-validator.py
# ---------------------------------------------------------------------------
# proteomics thread configuration
@@ -170,7 +170,7 @@ proteomics.delete-unidentified = true
proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
proteomics.script-path = dist/etc/proteomics/data-set-handler.py
-proteomics.validation-script-path = dist/etc/proteomics/data-set-validator.py
+proteomics.validation-script-path = dist/etc/shared/shared-classes.py,dist/etc/proteomics/data-set-validator.py
#
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
index c7871185a5e..8c26bae1286 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
+++ b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
@@ -16,10 +16,12 @@
package eu.basynthec.cisd.dss.transcriptomics;
+import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Properties;
+import org.apache.commons.io.FileUtils;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.test.RecordingMatcher;
@@ -64,6 +66,12 @@ public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecData
assertNotNull(strainProperty);
assert null != strainProperty;
assertEquals("MGP253,MGP776", strainProperty.getValue());
+
+ String location = dataSet.getLocation();
+ File tsvFile =
+ new File(new File(workingDirectory, "/1/" + location),
+ "tsv/Transcriptomics-Example.xlsx.tsv");
+ checkTsvContent(tsvFile);
context.assertIsSatisfied();
}
@@ -72,4 +80,23 @@ public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecData
{
return "dist/etc/transcriptomics/";
}
+
+ private void checkTsvContent(File tsvFile) throws IOException
+ {
+ String content = FileUtils.readFileToString(tsvFile);
+ assertEquals("Locustag\tMGP253-1 66687802\tMGP776-2 66730002\n"
+ + "BSU00010\t13.7953\t13.5517\n" + "BSU00020\t13.5907\t13.3277\n"
+ + "BSU00030\t13.8489\t13.6306\n" + "BSU00040\t14.3564\t14.1073\n"
+ + "BSU00050\t14.5239\t14.1992\n" + "BSU00060\t14.3293\t13.933\n"
+ + "BSU00070\t14.481\t14.1348\n" + "BSU00090\t15.474\t15.2813\n"
+ + "BSU00100\t14.4332\t14.1945\n" + "BSU00110\t15.2669\t14.9582\n"
+ + "BSU00120\t15.3344\t15.112\n" + "BSU_misc_RNA_1\t15.4497\t15.2485\n"
+ + "BSU00130\t13.6604\t13.5385\n" + "BSU00180\t9.8208\t9.971\n"
+ + "BSU_misc_RNA_2\t13.6614\t14.0933\n" + "BSU00190\t13.464\t13.1213\n"
+ + "BSU00200\t14.6102\t14.4169\n" + "BSU00210\t13.5285\t13.2043\n"
+ + "BSU00220\t13.1007\t12.8862\n" + "BSU00230\t11.8547\t11.6761\n"
+ + "BSU00240\t10.8623\t11.1397\n" + "BSU00250\t11.6694\t11.429\n"
+ + "BSU00260\t11.7669\t11.4658\n" + "BSU00270\t12.2675\t11.8745\n"
+ + "BSU00280\t12.5574\t12.1608\n", content);
+ }
}
--
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