TASK-5318 - Implement custom annotator to allow clients private files

biodata-formats/src/main/java/org/opencb/biodata/formats/variant/cosmic/CosmicParserCallback.java

@@ -0,0 +1,10 @@
+package org.opencb.biodata.formats.variant.cosmic;
+
+import org.opencb.biodata.models.sequence.SequenceLocation;
+import org.opencb.biodata.models.variant.avro.EvidenceEntry;
+
+import java.util.List;
+
+public interface CosmicParserCallback {
+    boolean processEvidenceEntries(SequenceLocation sequenceLocation, List<EvidenceEntry> evidenceEntries);
+}

biodata-formats/src/test/java/org/opencb/biodata/formats/variant/cosmic/CosmicParserTest.java

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+package org.opencb.biodata.formats.variant.cosmic;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.opencb.biodata.models.sequence.SequenceLocation;
+import org.opencb.biodata.models.variant.avro.EvidenceEntry;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+
+public class CosmicParserTest {
+
+    // Implementation of the LineCallback function
+    public class MyCallback implements CosmicParserCallback {
+        private String msg;
+        private int counter;
+
+        public MyCallback(String msg) {
+            this.msg = msg;
+            this.counter = 0;
+        }
+
+        @Override
+        public boolean processEvidenceEntries(SequenceLocation sequenceLocation, List<EvidenceEntry> evidenceEntries) {
+            System.out.println(msg);
+            System.out.println("Sequence location = " + sequenceLocation);
+            System.out.println("Num. evidences = " + evidenceEntries.size());
+            for (EvidenceEntry evidenceEntry : evidenceEntries) {
+                System.out.println("evidences = " + evidenceEntry);
+                counter++;
+            }
+            return true;
+        }
+
+        public int getCounter() {
+            return counter;
+        }
+    }
+
+    @Test
+    public void testCosmicParser() throws IOException {
+        Path cosmicFile = Paths.get(getClass().getResource("/cosmic.small.tsv.gz").getPath());
+        String version = "v95";
+        String name = "cosmic";
+        String assembly = "GRCh38";
+
+        MyCallback callback = new MyCallback(">>> Testing message");
+
+        CosmicParser.parse(cosmicFile, version, name, assembly, callback);
+        Assert.assertEquals(90, callback.getCounter());
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/common/DataVersion.java

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+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * 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 org.opencb.biodata.models.common;
+
+import org.opencb.commons.datastore.core.ObjectMap;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class DataVersion {
+
+    private String data;
+    private String name;
+    private String version;
+    private String date;
+    private String species;
+    private String assembly;
+    private List<String> files;
+    private List<String> urls;
+    private ObjectMap attributes;
+
+    public DataVersion() {
+        files = new ArrayList<>();
+        urls = new ArrayList<>();
+        attributes = new ObjectMap();
+    }
+
+    public DataVersion(String data, String name, String version, String date, String species, String assembly, List<String> files,
+                       List<String> urls, ObjectMap attributes) {
+        this.data = data;
+        this.name = name;
+        this.version = version;
+        this.date = date;
+        this.species = species;
+        this.assembly = assembly;
+        this.files = files;
+        this.urls = urls;
+        this.attributes = attributes;
+    }
+
+    public String getData() {
+        return data;
+    }
+
+    public DataVersion setData(String data) {
+        this.data = data;
+        return this;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public DataVersion setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public String getVersion() {
+        return version;
+    }
+
+    public DataVersion setVersion(String version) {
+        this.version = version;
+        return this;
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public DataVersion setDate(String date) {
+        this.date = date;
+        return this;
+    }
+
+    public String getSpecies() {
+        return species;
+    }
+
+    public DataVersion setSpecies(String species) {
+        this.species = species;
+        return this;
+    }
+
+    public String getAssembly() {
+        return assembly;
+    }
+
+    public DataVersion setAssembly(String assembly) {
+        this.assembly = assembly;
+        return this;
+    }
+
+    public List<String> getFiles() {
+        return files;
+    }
+
+    public DataVersion setFiles(List<String> files) {
+        this.files = files;
+        return this;
+    }
+
+    public List<String> getUrls() {
+        return urls;
+    }
+
+    public DataVersion setUrls(List<String> urls) {
+        this.urls = urls;
+        return this;
+    }
+
+    public ObjectMap getAttributes() {
+        return attributes;
+    }
+
+    public DataVersion setAttributes(ObjectMap attributes) {
+        this.attributes = attributes;
+        return this;
+    }
+}

biodata-models/src/main/java/org/opencb/biodata/models/sequence/SequenceLocation.java

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+package org.opencb.biodata.models.sequence;
+
+public class SequenceLocation {
+    private String chromosome;
+    private int start;
+    private int end;
+    private String reference;
+    private String alternate;
+    private String strand;
+
+    public SequenceLocation() {
+    }
+
+    SequenceLocation(String chromosome, int start, int end, String reference, String alternate) {
+        this(chromosome, start, end, reference, alternate, "+");
+    }
+
+    SequenceLocation(String chromosome, int start, int end, String reference, String alternate, String strand) {
+        this.chromosome = chromosome;
+        this.start = start;
+        this.end = end;
+        this.reference = reference;
+        this.alternate = alternate;
+        this.strand = strand;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("SequenceLocation{");
+        sb.append("chromosome='").append(chromosome).append('\'');
+        sb.append(", start=").append(start);
+        sb.append(", end=").append(end);
+        sb.append(", reference='").append(reference).append('\'');
+        sb.append(", alternate='").append(alternate).append('\'');
+        sb.append(", strand='").append(strand).append('\'');
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public int getStart() {
+        return start;
+    }
+
+    public int getEnd() {
+        return end;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public String getAlternate() {
+        return alternate;
+    }
+
+    public String getStrand() {
+        return strand;
+    }
+
+    public void setChromosome(String chromosome) {
+        this.chromosome = chromosome;
+    }
+
+    public void setStart(int start) {
+        this.start = start;
+    }
+
+    public void setEnd(int end) {
+        this.end = end;
+    }
+
+    public void setReference(String reference) {
+        this.reference = reference;
+    }
+
+    public void setAlternate(String alternate) {
+        this.alternate = alternate;
+    }
+
+    public void setStrand(String strand) {
+        this.strand = strand;
+    }
+}