Added handling for non-normalized (no URI) and erroneous identifiers

Instead of being excluded from the output RDF they are now cataloged as
either NonNormalizedIdentifierRecords or ErroneousIdentifierRecords.

datasource-identifiers/src/main/java/edu/ucdenver/ccp/datasource/identifiers/ProbableErrorDataSourceIdentifier.java

@@ -1,5 +1,39 @@
 package edu.ucdenver.ccp.datasource.identifiers;
 
+/*
+ * #%L
+ * Colorado Computational Pharmacology's datasource
+ * 							project
+ * %%
+ * Copyright (C) 2012 - 2016 Regents of the University of Colorado
+ * %%
+ * Redistribution and use in source and binary forms, with or without modification,
+ * are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * 3. Neither the name of the Regents of the University of Colorado nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software without
+ *    specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
 public class ProbableErrorDataSourceIdentifier extends DataSourceIdentifier<String> {
 
 	private final String dataSourceStr;

datasource-identifiers/src/main/java/edu/ucdenver/ccp/datasource/identifiers/UnknownDataSourceIdentifier.java

@@ -1,5 +1,39 @@
 package edu.ucdenver.ccp.datasource.identifiers;
 
+/*
+ * #%L
+ * Colorado Computational Pharmacology's datasource
+ * 							project
+ * %%
+ * Copyright (C) 2012 - 2016 Regents of the University of Colorado
+ * %%
+ * Redistribution and use in source and binary forms, with or without modification,
+ * are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * 3. Neither the name of the Regents of the University of Colorado nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software without
+ *    specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
 public class UnknownDataSourceIdentifier extends DataSourceIdentifier<String> {
 
 	private final String dataSourceStr;

datasource-rdfizer/src/main/java/edu/ucdenver/ccp/datasource/rdfizer/rdf/ice/ErroneousIdentifierRecord.java

@@ -0,0 +1,72 @@
+package edu.ucdenver.ccp.datasource.rdfizer.rdf.ice;
+
+/*
+ * #%L
+ * Colorado Computational Pharmacology's datasource
+ * 							project
+ * %%
+ * Copyright (C) 2012 - 2016 Regents of the University of Colorado
+ * %%
+ * Redistribution and use in source and binary forms, with or without modification,
+ * are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * 3. Neither the name of the Regents of the University of Colorado nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software without
+ *    specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+import edu.ucdenver.ccp.datasource.fileparsers.Record;
+import edu.ucdenver.ccp.datasource.fileparsers.RecordField;
+import edu.ucdenver.ccp.datasource.identifiers.DataSource;
+
+@Record(dataSource = DataSource.KABOB)
+public class ErroneousIdentifierRecord {
+
+	@RecordField
+	private final String identifier;
+
+	@RecordField
+	private final String datasource;
+
+	@RecordField
+	private final String comment;
+
+	public ErroneousIdentifierRecord(String identifier, String datasource, String comment) {
+		super();
+		this.identifier = identifier;
+		this.datasource = datasource;
+		this.comment = comment;
+	}
+
+	public String getIdentifier() {
+		return identifier;
+	}
+
+	public String getDatasource() {
+		return datasource;
+	}
+
+	public String getComment() {
+		return comment;
+	}
+
+}

datasource-rdfizer/src/main/java/edu/ucdenver/ccp/datasource/rdfizer/rdf/ice/NonNormalizedIdentifierRecord.java

@@ -0,0 +1,64 @@
+package edu.ucdenver.ccp.datasource.rdfizer.rdf.ice;
+
+/*
+ * #%L
+ * Colorado Computational Pharmacology's datasource
+ * 							project
+ * %%
+ * Copyright (C) 2012 - 2016 Regents of the University of Colorado
+ * %%
+ * Redistribution and use in source and binary forms, with or without modification,
+ * are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * 3. Neither the name of the Regents of the University of Colorado nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software without
+ *    specific prior written permission.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ * IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ * OF THE POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+import edu.ucdenver.ccp.datasource.fileparsers.Record;
+import edu.ucdenver.ccp.datasource.fileparsers.RecordField;
+import edu.ucdenver.ccp.datasource.identifiers.DataSource;
+
+@Record(dataSource = DataSource.KABOB)
+public class NonNormalizedIdentifierRecord {
+
+	@RecordField
+	private final String identifier;
+
+	@RecordField
+	private final String datasource;
+
+	public NonNormalizedIdentifierRecord(String identifier, String datasource) {
+		super();
+		this.identifier = identifier;
+		this.datasource = datasource;
+	}
+
+	public String getIdentifier() {
+		return identifier;
+	}
+
+	public String getDatasource() {
+		return datasource;
+	}
+
+}

datasource-rdfizer/src/main/java/edu/ucdenver/ccp/datasource/rdfizer/rdf/ice/RdfRecordUriFactory.java

@@ -44,15 +44,19 @@
 import java.util.Map.Entry;
 import java.util.Set;
 
+import org.openrdf.model.Statement;
 import org.openrdf.model.Value;
 import org.openrdf.model.impl.URIImpl;
 import org.openrdf.rio.ntriples.NTriplesUtil;
 
+import edu.ucdenver.ccp.common.collections.CollectionsUtil;
 import edu.ucdenver.ccp.common.digest.DigestUtil;
 import edu.ucdenver.ccp.common.reflection.PrivateAccessor;
 import edu.ucdenver.ccp.datasource.fileparsers.RecordField;
 import edu.ucdenver.ccp.datasource.fileparsers.RecordUtil;
 import edu.ucdenver.ccp.datasource.identifiers.DataSource;
+import edu.ucdenver.ccp.datasource.identifiers.ProbableErrorDataSourceIdentifier;
+import edu.ucdenver.ccp.datasource.identifiers.UnknownDataSourceIdentifier;
 import edu.ucdenver.ccp.datasource.rdfizer.rdf.vocabulary.KIAO;
 
 /**
@@ -178,6 +182,30 @@ private static List<String> getSortedFieldValueUriStrs(Collection<Object> fieldV
 	 *            could be a collection, if so we return one string per value
 	 */
 	private static String getFieldValueUri(Object fieldValue) {
+		/* address unknown and probable error data source identifiers here? */
+		if (fieldValue instanceof UnknownDataSourceIdentifier) {
+			UnknownDataSourceIdentifier id = (UnknownDataSourceIdentifier) fieldValue;
+			NonNormalizedIdentifierRecord record = new NonNormalizedIdentifierRecord(id.getDataElement(), id.getDataSourceStr());
+			URIImpl recordUri = RdfRecordUriFactory.createRecordUri(record);
+			List<Statement> recordInstanceStatements = RdfRecordUtil.getRecordInstanceStatements(record, System.currentTimeMillis(),
+					recordUri, null, null, null);
+			recordInstanceStatements.remove(0);
+			/* this is used to generate sha1 hashes, so it doesn't need to be a true uri */
+			return CollectionsUtil.createDelimitedString(recordInstanceStatements, " ");
+		} else if (fieldValue instanceof ProbableErrorDataSourceIdentifier) {
+			ProbableErrorDataSourceIdentifier id = (ProbableErrorDataSourceIdentifier) fieldValue;
+			ErroneousIdentifierRecord record = new ErroneousIdentifierRecord(id.getDataElement(),
+					id.getDataSourceStr(), id.getErrorMessage());
+			URIImpl recordUri = RdfRecordUriFactory.createRecordUri(record);
+			List<Statement> recordInstanceStatements = RdfRecordUtil.getRecordInstanceStatements(record, System.currentTimeMillis(),
+					recordUri, null, null, null);
+			/*
+			 * the first statement returned is a dataset has_part record triple
+			 * which we do not need
+			 */
+			recordInstanceStatements.remove(0);
+			return CollectionsUtil.createDelimitedString(recordInstanceStatements, " ");
+		}
 		Value value = RdfUtil.getValue(fieldValue);
 		return NTriplesUtil.toNTriplesString(value);
 	}
@@ -224,7 +252,6 @@ private static Collection<Object> getFieldValues(Object record, Field field) {
 			return null;
 		}
 
-		int fieldCount = 0;
 		Collection<Object> fieldValues = new ArrayList<Object>();
 
 		if (!(fieldValue instanceof Collection)) {