diff --git a/screening/.classpath b/screening/.classpath
index 817753190aaab4caf3fa0373b0b6b5d239349076..87afe39d49ea46a449310ecc50eef545237c08ba 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -30,5 +30,6 @@
<classpathentry kind="lib" path="/libraries/hibernate-search/jms.jar"/>
<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
<classpathentry kind="lib" path="/libraries/spring/test/spring-test.jar" sourcepath="/libraries/spring/test/src.jar"/>
+ <classpathentry kind="lib" path="/libraries/csv/csv.jar" sourcepath="/libraries/csv/src.zip"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/IScreeningLibraryColumnExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/IScreeningLibraryColumnExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..a7f888c1fb811fea0fc664a86dc86461e8f6d2f7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/IScreeningLibraryColumnExtractor.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright 2010 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.plugin.screening.transformers;
+
+import java.util.List;
+
+/**
+ * Provides structured information from one row of the library.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IScreeningLibraryColumnExtractor
+{
+ public String getPlateCode(String[] row);
+
+ public String getWellCode(String[] row);
+
+ public String getRNASequence(String[] row);
+
+ public String getOligoId(String[] row);
+
+ public String getGeneId(String[] row);
+
+ public String getGeneCode(String[] row);
+
+ public String getGeneDescription(String[] row);
+
+ public List<String> getAdditionalOligoPropertyNames();
+
+ public List<String> getAdditionalOligoPropertyValues(String[] row, List<String> columnNames);
+
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/LibraryEntityRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/LibraryEntityRegistrator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c4fdfd53d948d831afbb5d09b27e4e9c0d25fa9a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/LibraryEntityRegistrator.java
@@ -0,0 +1,269 @@
+/*
+ * Copyright 2010 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.plugin.screening.transformers;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * Creates files to register genes, oligos and plate with wells.
+ * <p>
+ * This registrator works with the assumption that the entities which should be registered do not
+ * already exist in openBIS. If it is the case we should extend the implementation to fetch existing
+ * entities, LIBRARY_ID property can be used to recognize that.
+ * </p>
+ *
+ * @author Tomasz Pylak
+ */
+public class LibraryEntityRegistrator
+{
+ private static final String GENES_FILE_NAME = "genes.txt";
+
+ private static final String OLIGOS_FILE_NAME = "oligos.txt";
+
+ private static final String PLATES_FILE_NAME = "plates.txt";
+
+ private final GeneRegistrator geneRegistrator;
+
+ private final OligoRegistrator oligoRegistrator;
+
+ private final PlateRegistrator plateRegistrator;
+
+ public LibraryEntityRegistrator(IScreeningLibraryColumnExtractor extractor,
+ String experimentIdentifier, String plateGeometry, String groupCode) throws IOException
+ {
+ this.geneRegistrator = new GeneRegistrator(new File(GENES_FILE_NAME));
+ this.oligoRegistrator =
+ new OligoRegistrator(new File(OLIGOS_FILE_NAME), extractor
+ .getAdditionalOligoPropertyNames());
+ this.plateRegistrator =
+ new PlateRegistrator(new File(PLATES_FILE_NAME), experimentIdentifier,
+ plateGeometry, groupCode);
+ }
+
+ public void register(IScreeningLibraryColumnExtractor extractor, String[] row)
+ throws IOException
+ {
+ String geneId = geneRegistrator.register(extractor, row);
+ String oligoId = oligoRegistrator.register(extractor, row, geneId);
+ String plateId = plateRegistrator.registerPlate(extractor, row);
+ plateRegistrator.registerWell(extractor, row, plateId, oligoId);
+ }
+
+ abstract static protected class AbstractMetadataRegistrator
+ {
+ private static final String TAB = "\t";
+
+ private final OutputStream stream;
+
+ protected AbstractMetadataRegistrator(File file) throws FileNotFoundException
+ {
+ this.stream = new FileOutputStream(file);
+ }
+
+ protected void writeLine(String... tokens) throws IOException
+ {
+ writeLine(join(tokens));
+ }
+
+ // joins token into one line adding separators in between
+ public static String join(String... tokens)
+ {
+ return StringUtils.join(tokens, TAB);
+ }
+
+ private void writeLine(String line) throws IOException
+ {
+ IOUtils.writeLines(Arrays.asList(line), "\n", stream);
+ }
+ }
+
+ private static class PlateRegistrator extends AbstractMetadataRegistrator
+ {
+ private static final String HEADER_PLATES =
+ "[PLATE]\n" + join("identifier", "experiment", "$PLATE_GEOMETRY");
+
+ private static final String HEADER_OLIGOS =
+ "[OLIGO_WELL]\n" + join("identifier", "container", "OLIGO");
+
+ private final Set<String/* plate code */> registeredPlates;
+
+ private final String experimentIdentifier;
+
+ private final String plateGeometry;
+
+ private final String groupCode;
+
+ // we register wells and plates in the same file. This flag tells us in which section we
+ // are, the one for plates or one for wells
+ private boolean lastRegisteredWasWell;
+
+ public PlateRegistrator(File outputFile, String experimentIdentifier, String plateGeometry,
+ String groupCode) throws IOException
+ {
+ super(outputFile);
+ this.experimentIdentifier = experimentIdentifier;
+ this.plateGeometry = plateGeometry;
+ this.groupCode = groupCode;
+ this.registeredPlates = new HashSet<String>();
+ lastRegisteredWasWell = false;
+ writeLine(HEADER_PLATES);
+ }
+
+ /** @return sampleIdentifier */
+ public String registerPlate(IScreeningLibraryColumnExtractor extractor, String[] row)
+ throws IOException
+ {
+ String plateCode = extractor.getPlateCode(row);
+ String sampleIdentifier = getSampleIdentifier(plateCode);
+ if (registeredPlates.contains(plateCode) == false)
+ {
+ if (lastRegisteredWasWell)
+ {
+ lastRegisteredWasWell = false;
+ writeLine(HEADER_PLATES);
+ }
+ writeLine(sampleIdentifier, experimentIdentifier, plateGeometry);
+ registeredPlates.add(plateCode);
+ }
+ return sampleIdentifier;
+ }
+
+ private String getSampleIdentifier(String plateCode)
+ {
+ return "/" + groupCode + "/" + plateCode;
+ }
+
+ public void registerWell(IScreeningLibraryColumnExtractor extractor, String[] row,
+ String plateId, String oligoId) throws IOException
+ {
+ if (lastRegisteredWasWell == false)
+ {
+ lastRegisteredWasWell = true;
+ writeLine(HEADER_OLIGOS);
+ }
+ String wellCode = extractor.getWellCode(row);
+ String wellIdentifier = plateId + ":" + wellCode;
+ String oligoMaterialProperty = oligoId + " (OLIGO)";
+ writeLine(wellIdentifier, plateId, oligoMaterialProperty);
+ }
+
+ }
+
+ private static class GeneRegistrator extends AbstractMetadataRegistrator
+ {
+ private static final String HEADER = join("CODE", "DESCRIPTION", "LIBRARY_ID");
+
+ private final Set<String/* gene code */> registeredGenes;
+
+ public GeneRegistrator(File genesFile) throws IOException
+ {
+ super(genesFile);
+ this.registeredGenes = new HashSet<String>();
+ writeLine(HEADER);
+ }
+
+ // / returns gene id
+ public String register(IScreeningLibraryColumnExtractor extractor, String[] row)
+ throws IOException
+ {
+ String geneSymbol = extractor.getGeneCode(row);
+ if (registeredGenes.contains(geneSymbol) == false)
+ {
+ String desc = extractor.getGeneDescription(row);
+ String libraryId = extractor.getGeneId(row);
+ writeLine(geneSymbol, desc, libraryId);
+ registeredGenes.add(geneSymbol);
+ }
+ return geneSymbol;
+ }
+ }
+
+ private static class OligoRegistrator extends AbstractMetadataRegistrator
+ {
+ private static final String HEADER =
+ join("CODE", "NUCLEOTIDE_SEQUENCE", "INHIBITOR_OF", "LIBRARY_ID");
+
+ private final Set<String/* code */> registeredOligos;
+
+ private final List<String> additionalPropertyNames;
+
+ public OligoRegistrator(File file, List<String> additionalPropertyNames) throws IOException
+ {
+ super(file);
+ this.registeredOligos = new HashSet<String>();
+ this.additionalPropertyNames = additionalPropertyNames;
+ writeLine(createHeader(additionalPropertyNames));
+ }
+
+ private static String createHeader(List<String> additionalPropertyNames)
+ {
+ String header = HEADER;
+ for (String propertyName : additionalPropertyNames)
+ {
+ header = join(header, propertyName);
+ }
+ return header;
+ }
+
+ // / returns openbis id
+ public String register(IScreeningLibraryColumnExtractor extractor, String[] row,
+ String inhibitedGeneCode) throws IOException
+ {
+ String geneSymbol = extractor.getGeneCode(row);
+ String oligoId = extractor.getOligoId(row);
+ String openbisOligoId = geneSymbol + "_" + oligoId;
+ if (containsCaseInsensitive(registeredOligos, openbisOligoId) == false)
+ {
+ String seq = extractor.getRNASequence(row);
+ String geneMaterialProperty = inhibitedGeneCode + " (GENE)";
+ String line = join(openbisOligoId, seq, geneMaterialProperty, oligoId);
+ // add additional properties
+ List<String> propertyValues =
+ extractor.getAdditionalOligoPropertyValues(row, additionalPropertyNames);
+ for (int i = 0; i < propertyValues.size(); i++)
+ {
+ line = join(line, propertyValues.get(i));
+ }
+
+ writeLine(line);
+ addCaseInsensitive(registeredOligos, openbisOligoId);
+ }
+ return openbisOligoId;
+ }
+
+ private void addCaseInsensitive(Set<String> set, String value)
+ {
+ set.add(value.toLowerCase());
+ }
+
+ private boolean containsCaseInsensitive(Set<String> set, String value)
+ {
+ return set.contains(value.toLowerCase());
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/QiagenScreeningLibraryColumnExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/QiagenScreeningLibraryColumnExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..461b93b0823630bc48fb68db5ae71fd02a910dd1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/QiagenScreeningLibraryColumnExtractor.java
@@ -0,0 +1,216 @@
+/*
+ * Copyright 2010 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.plugin.screening.transformers;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Provides structured information from one row of the QIAGEN library.
+ *
+ * @author Tomasz Pylak
+ */
+public class QiagenScreeningLibraryColumnExtractor implements IScreeningLibraryColumnExtractor
+{
+ // ----- column names
+
+ private final static String PLATE_NAME = "barcode";
+
+ private final static String WELL_ROW = "row";
+
+ private final static String WELL_COL = "col";
+
+ // gene
+
+ private final static String GENE_ID = "geneId";
+
+ private final static String GENE_SYMBOL = "symbol";
+
+ private final static String GENE_DESC = "description";
+
+ // oligo
+
+ private final static String RNA_SEQUENCE = "sirna";
+
+ private final static String OLIGO_ID = "productId";
+
+ private final static String[] ALL_COLUMNS = new String[]
+ { PLATE_NAME, WELL_ROW, WELL_COL, RNA_SEQUENCE, GENE_ID, GENE_SYMBOL, GENE_DESC, OLIGO_ID };
+
+ // -------------
+
+ private final Map<String/* column name */, Integer/* index in the header table */> columnIndices;
+
+ private final Map<String/* column name */, Integer/* index in the header table */> unknownColumnIndices;
+
+ public QiagenScreeningLibraryColumnExtractor(String[] headerTokens)
+ {
+ this.columnIndices = createColumnIndex(headerTokens);
+ this.unknownColumnIndices = getOmittedIndices(columnIndices, headerTokens);
+ }
+
+ public List<String> getAdditionalOligoPropertyNames()
+ {
+ return new ArrayList<String>(unknownColumnIndices.keySet());
+ }
+
+ // ------------
+
+ private static Map<String, Integer> getOmittedIndices(Map<String, Integer> columnIndex,
+ String[] headers)
+ {
+ Map<String, Integer> omittedIndices = new HashMap<String, Integer>();
+ Set<Integer> knownIndices = new HashSet<Integer>(columnIndex.values());
+ for (int i = 0; i < headers.length; i++)
+ {
+ if (knownIndices.contains(i) == false)
+ {
+ omittedIndices.put(headers[i], i);
+ }
+ }
+ return omittedIndices;
+ }
+
+ private static Map<String, Integer> createColumnIndex(String[] headers)
+ {
+ Map<String, Integer> map = new HashMap<String, Integer>();
+ for (String columnName : ALL_COLUMNS)
+ {
+ findAndPut(map, headers, columnName);
+ }
+ return map;
+ }
+
+ private static void findAndPut(Map<String, Integer> map, String[] headers, String columnName)
+ {
+ int ix = findIndexOrDie(headers, columnName);
+ map.put(columnName, ix);
+ }
+
+ private static int findIndexOrDie(String[] headers, String columnName)
+ {
+ for (int i = 0; i < headers.length; i++)
+ {
+ if (headers[i].equalsIgnoreCase(columnName))
+ {
+ return i;
+ }
+ }
+ throw new UserFailureException("Column " + columnName + " does not exist in "
+ + CollectionUtils.abbreviate(headers, -1));
+ }
+
+ private String getValue(String[] row, String columnName)
+ {
+ Integer ix = columnIndices.get(columnName);
+ return valueAt(row, ix);
+ }
+
+ private static String valueAt(String[] row, Integer ix)
+ {
+ if (ix >= row.length)
+ {
+ return "";
+ } else
+ {
+ return row[ix];
+ }
+ }
+
+ private String asCode(String value)
+ {
+ String code = "";
+ for (int i = 0; i < value.length(); i++)
+ {
+ char ch = value.charAt(i);
+ if (isValidCodeCharacter(ch) == false)
+ {
+ ch = '_';
+ }
+ code += ch;
+ }
+ return code;
+ }
+
+ private boolean isValidCodeCharacter(char ch)
+ {
+ return Character.isLetterOrDigit(ch) || ch == '.' || ch == '-' || ch == '_';
+ }
+
+ private String getCodeValue(String[] row, String columnName)
+ {
+ return asCode(getValue(row, columnName));
+ }
+
+ // ------------
+
+ public String getPlateCode(String[] row)
+ {
+ return getCodeValue(row, PLATE_NAME);
+ }
+
+ public String getWellCode(String[] row)
+ {
+ String wellRow = getValue(row, WELL_ROW);
+ String wellCol = getValue(row, WELL_COL);
+ return wellRow + wellCol;
+ }
+
+ public String getRNASequence(String[] row)
+ {
+ return getValue(row, RNA_SEQUENCE);
+ }
+
+ public String getOligoId(String[] row)
+ {
+ return getValue(row, OLIGO_ID);
+ }
+
+ public String getGeneId(String[] row)
+ {
+ return getValue(row, GENE_ID);
+ }
+
+ public String getGeneCode(String[] row)
+ {
+ return getCodeValue(row, GENE_SYMBOL);
+ }
+
+ public String getGeneDescription(String[] row)
+ {
+ return getValue(row, GENE_DESC);
+ }
+
+ public List<String> getAdditionalOligoPropertyValues(String[] row, List<String> columnNames)
+ {
+ List<String> values = new ArrayList<String>();
+ for (String columnName : columnNames)
+ {
+ Integer ix = unknownColumnIndices.get(columnName);
+ String value = valueAt(row, ix);
+ values.add(value);
+ }
+ return values;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/ScreeningLibraryTransformer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/ScreeningLibraryTransformer.java
new file mode 100644
index 0000000000000000000000000000000000000000..1a22475d429af1a4557fdb144b1899c606c39bd3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/ScreeningLibraryTransformer.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2010 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.plugin.screening.transformers;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.charset.Charset;
+
+import com.csvreader.CsvReader;
+
+/**
+ * Transforms a screening library file and produces files which can be uploaded to openBIS: genes,
+ * oligos and plates with wells.
+ *
+ * @author Tomasz Pylak
+ */
+public class ScreeningLibraryTransformer
+{
+ private final static char SEPARATOR = ',';
+
+ public static void main(String[] args) throws FileNotFoundException, IOException
+ {
+ if (args.length != 4)
+ {
+ error("Invalid parameters. Expected: "
+ + "<master-plate-file-path> <experiment-identifier> <plate-geometry> <group>");
+ }
+ CsvReader csvReader = readFile(args[0]);
+ String experimentIdentifier = args[1];
+ String plateGeometry = args[2];
+ String groupCode = args[3];
+ readLibrary(csvReader, experimentIdentifier, plateGeometry, groupCode);
+ csvReader.close();
+ }
+
+ private static void readLibrary(CsvReader csvReader, String experimentIdentifier,
+ String plateGeometry, String groupCode) throws IOException
+ {
+ System.out.println("Processing...");
+ boolean headerPresent = csvReader.readRecord();
+ if (headerPresent == false)
+ {
+ error("header not found");
+ return;
+ }
+ String[] headers = csvReader.getValues();
+ IScreeningLibraryColumnExtractor extractor = new QiagenScreeningLibraryColumnExtractor(headers);
+ LibraryEntityRegistrator registrator =
+ new LibraryEntityRegistrator(extractor, experimentIdentifier, plateGeometry, groupCode);
+ while (csvReader.readRecord())
+ {
+ String[] row = csvReader.getValues();
+ registrator.register(extractor, row);
+ }
+ System.out.println("Done, look for results in " + new File(".").getAbsolutePath());
+ }
+
+ private static CsvReader readFile(String path) throws FileNotFoundException, IOException
+ {
+ File masterPlatesFile = new File(path);
+ if (masterPlatesFile.isFile() == false)
+ {
+ error(masterPlatesFile + " does not exist or is not a file.");
+ }
+ FileInputStream fileInputStream = new FileInputStream(masterPlatesFile);
+
+ CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
+ csvReader.setDelimiter(SEPARATOR);
+ csvReader.setSafetySwitch(false);
+ return csvReader;
+ }
+
+ private static void error(String msg)
+ {
+ System.err.println(msg);
+ System.exit(1);
+ }
+}