From 617ccb48320d1a7eff90542e8f960f64f70258e8 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Mon, 17 Aug 2015 09:27:43 +0000
Subject: [PATCH] added extra fields, like SAMPLE_TYPE and SAMPLE_CODE
SVN: 34463
---
.../cisd/dsu/metadata/create_metadata.java | 41 ++++++++++++++++++-
1 file changed, 40 insertions(+), 1 deletion(-)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/metadata/create_metadata.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/metadata/create_metadata.java
index f719077766f..3bc3b617219 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/metadata/create_metadata.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/metadata/create_metadata.java
@@ -57,14 +57,26 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
public class create_metadata
{
+ private static final String SEQUENCER = "SEQUENCER";
+
+ private static final String SEQUENCER_MODEL = "SEQUENCER_MODEL";
+
+ private static final String ILLUMINA_FLOW_LANE = "ILLUMINA_FLOW_LANE";
+
+ private static final String LANE_NUMBER = "LANE_NUMBER";
+
private static final String TSV_ENDING = ".tsv";
private static final String FLOW_CELL_PROPERTIES_NAME = "FLOW_CELL_PROPERTIES";
private static final String EXPERIMENT_NAME = "EXPERIMENT";
+ private static final String SAMPLE_CODE = "SAMPLE_CODE";
+
private static final String SAMPLE_TYPE_ILLUMINA_SEQUENCING = "ILLUMINA_SEQUENCING";
+ private static final String SAMPLE_TYPE = "SAMPLE_TYPE";
+
private static final String INDEX1_NOINDEX_VALUE = "NOINDEX";
private static final String DATASET_TYPE_CODE_FASTQ_GZ = "FASTQ_GZ";
@@ -84,6 +96,16 @@ public class create_metadata
private static final char[] HEX_CHARACTERS =
{ '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'a', 'b', 'c', 'd', 'e', 'f', };
+ private static final Map<String, String> SEQUENCER_NAMING;
+ static
+ {
+ SEQUENCER_NAMING = new HashMap<String, String>();
+ SEQUENCER_NAMING.put("D00535", "Illumina HiSeq 2500");
+ SEQUENCER_NAMING.put("J00121", "Illumina HiSeq 3000");
+ SEQUENCER_NAMING.put("M01761", "Illumina MiSeq");
+ SEQUENCER_NAMING.put("NS500318", "Illumina NextSeq 500");
+ }
+
public static void main(String[] args)
{
try
@@ -131,6 +153,11 @@ public class create_metadata
for (String sampleCode : sampleCodeList)
{
List<Sample> sampleList = searchSample(infoService, sessionToken, sampleCode, fetchOptions);
+ if (sampleList.size() < 1)
+ {
+ System.out.println(sampleCode + " Not found!");
+ }
+
SortedMap<String, SortedMap<String, String>> sampleMap = getProperties(sampleList);
SortedMap<String, SortedMap<String, String>> flowcellMap = null;
String flowcellCode = "";
@@ -142,9 +169,14 @@ public class create_metadata
HashMap<String, Integer> dbResult = DbAccess.doQuery(connection, permId);
for (Sample child : children)
{
- if (child.getSampleTypeCode().equals("ILLUMINA_FLOW_LANE"))
+ if (child.getSampleTypeCode().equals(ILLUMINA_FLOW_LANE))
{
flowcellCode = child.getCode().split(":")[0];
+ String flowlaneCode = child.getCode().split(":")[1];
+ SortedMap<String, String> sampleProps = sampleMap.get(sampleCode);
+ sampleProps.put(LANE_NUMBER, flowlaneCode);
+ sampleMap.put(sampleCode, sampleProps);
+
List<Sample> flowcellList = searchSample(infoService, sessionToken, flowcellCode, flowcellFetchOptions);
flowcellMap = getProperties(flowcellList);
}
@@ -169,11 +201,18 @@ public class create_metadata
{
sortedProperties.put(key, cleanString(sampleProperties.get(key).toString()));
}
+ if (key.equals(SEQUENCER))
+ {
+ sortedProperties.put(SEQUENCER_MODEL, SEQUENCER_NAMING.get(sampleProperties.get(key)));
+ }
}
if (sample.getSampleTypeCode().equals(SAMPLE_TYPE_ILLUMINA_SEQUENCING))
{
sortedProperties.put(EXPERIMENT_NAME, sample.getExperimentIdentifierOrNull());
}
+ sortedProperties.put(SAMPLE_CODE, sample.getCode());
+ sortedProperties.put(SAMPLE_TYPE, sample.getSampleTypeCode());
+
sampleMap.put(sample.getCode(), sortedProperties);
}
return sampleMap;
--
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