Merge branch '508-correct-headers-of-the-genomic-dataset-format' into 'devel_12.1.x'

Resolve "Correct headers of the genomic dataset format"

See merge request !395

persist/src/main/java/lcsb/mapviewer/persist/CustomDatabasePopulator.java

@@ -28,6 +28,7 @@ public class CustomDatabasePopulator implements DatabasePopulator {
     flyway.setBaselineVersionAsString("12.1.0");
     flyway.setOutOfOrder(true);
     flyway.setBaselineOnMigrate(true);
+    flyway.setValidateOnMigrate(false);
     flyway.migrate();
 
   }

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java

@@ -151,12 +151,18 @@ public class ColorSchemaReader {
       }
       String[] columns = line.split("\t");
 
-      Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<ColorSchemaColumn, Integer>();
-      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
+      Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
+      List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
       parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENETIC_VARIANT);
       Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
       Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
+      if (contigColumn == null) {
+        contigColumn = schemaColumns.get(ColorSchemaColumn.CHROMOSOME);
+      }
       Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+      if (nameColumn == null) {
+        nameColumn = schemaColumns.get(ColorSchemaColumn.GENE_NAME);
+      }
       Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
       Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
       Integer variantIdentifierColumn = schemaColumns.get(ColorSchemaColumn.VARIANT_IDENTIFIER);

service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java

@@ -3,6 +3,8 @@ package lcsb.mapviewer.services.utils.data;
 import java.util.HashSet;
 import java.util.Set;
 
+import org.primefaces.component.export.Exporter.ColumnType;
+
 import lcsb.mapviewer.model.map.layout.ReferenceGenome;
 import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
 
@@ -20,6 +22,8 @@ public enum ColorSchemaColumn {
    */
   NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
 
+  GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
   /**
    * Name of the element.
    */
@@ -56,7 +60,7 @@ public enum ColorSchemaColumn {
    * Element identifier.
    */
   ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-  
+
   /**
    * Element identifier.
    */
@@ -108,6 +112,8 @@ public enum ColorSchemaColumn {
    */
   CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
 
+  CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
   ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
 
   VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //

service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java

@@ -102,6 +102,40 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     }
   }
 
+  @Test
+  public void testReadGeneVariantsWithNewNamingSchema() throws Exception {
+    try {
+      File f = new File("testFiles/coloring/gene_variants_new_naming.txt");
+      InputStream in = new FileInputStream(f);
+
+      byte[] buff = new byte[8000];
+
+      int bytesRead = 0;
+
+      ByteArrayOutputStream bao = new ByteArrayOutputStream();
+
+      while ((bytesRead = in.read(buff)) != -1) {
+        bao.write(buff, 0, bytesRead);
+      }
+      in.close();
+      bao.close();
+
+      byte[] data = bao.toByteArray();
+
+      ByteArrayInputStream bin = new ByteArrayInputStream(data);
+
+      ColorSchemaReader reader = new ColorSchemaReader();
+
+      Collection<ColorSchema> schemas = reader.readColorSchema(bin,
+          TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
+      assertNotNull(schemas);
+      assertEquals(3, schemas.size());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testReadGeneVariantsSchemaWithAF() throws Exception {
     try {

service/testFiles/coloring/gene_variants_new_naming.txt

+#TYPE=GENETIC_VARIANT						
+#GENOME_TYPE=UCSC						
+#GENOME_VERSION=hg38						
+position	original_dna	alternative_dna	gene_name	description	color	chromosome
+10146	AC	A	DDX11L1	upstream	#ff0000	chr1
+10439	AC	A	DDX11L1;WASH7P	upstream;downstream	#ff0001	chr1
+10583	G	A	DDX11L1;WASH7P	upstream;downstream	#ff0002	chr1
+10611	C	G	DDX11L1;WASH7P	upstream;downstream	#ff0003	chr1
+10616	CCGCCGTTGCAAAGGCGCGCCG	C	DDX11L1;WASH7P	upstream;downstream	#ff0004	chr1
+10904	G	A	DDX11L1;WASH7P	upstream;downstream	#ff0005	chr1
+12783	G	A	DDX11L1	intronic	#ff0006	chr1
+13116	T	G	DDX11L1	intronic	#ff0007	chr1
+13118	A	G	DDX11L1	intronic	#ff0008	chr1
+13143	G	C	DDX11L1	intronic	#ff0009	chr1
+13273	G	C	DDX11L1	intronic	#ff0010	chr1
+13302	C	T	DDX11L1	intronic	#ff0011	chr1
+13417	C	CGAGA	DDX11L1	exonic	#ff0012	chr1
+13550	G	A	DDX11L1	exonic	#ff0013	chr1
+13656	CAG	C	DDX11L1	UTR3	#ff0014	chr1
+13668	G	A	DDX11L1	UTR3	#ff0015	chr1
+13813	T	G	DDX11L1	UTR3	#ff0016	chr1
+13838	C	T	DDX11L1	UTR3	#ff0017	chr1
+13868	A	G	DDX11L1	UTR3	#ff0018	chr1
+13896	C	A	DDX11L1	UTR3	#ff0019	chr1
+13957	TC	T	DDX11L1	UTR3	#ff0020	chr1
+14354	C	A	DDX11L1	UTR3	#ff0021	chr1
+14464	A	T	WASH7P	ncRNA_exonic	#ff0022	chr1
+14653	C	T	WASH7P	ncRNA_exonic	#ff0023	chr1
+14671	G	C	WASH7P	ncRNA_exonic	#ff0024	chr1
+14673	G	C	WASH7P	ncRNA_exonic	#ff0025	chr1
+14677	G	A	WASH7P	ncRNA_exonic	#ff0026	chr1
+14699	C	G	WASH7P	ncRNA_exonic	#ff0027	chr1
+14907	A	G	WASH7P	ncRNA_exonic	#ff0028	chr1
+14930	A	G	WASH7P	ncRNA_exonic	#ff0029	chr1
+14933	G	A	WASH7P	ncRNA_exonic	#ff0030	chr1
+14976	G	A	WASH7P	ncRNA_exonic	#ff0031	chr1
+15118	A	G	WASH7P	ncRNA_exonic	#ff0032	chr1
+15190	G	A	WASH7P	ncRNA_exonic	#ff0033	chr1
+15211	T	G	WASH7P	ncRNA_exonic	#ff0034	chr1
+15274	A	G,T	WASH7P	ncRNA_exonic	#ff0035	chr1
+15447	A	G	WASH7P	ncRNA_exonic	#ff0036	chr1
+15688	C	T	WASH7P	ncRNA_exonic	#ff0037	chr1
+15820	G	T	WASH7P	ncRNA_exonic	#ff0038	chr1
+15903	G	GC	WASH7P	ncRNA_exonic	#ff0039	chr1
+16014	C	T	WASH7P	ncRNA_exonic	#ff0040	chr1
+16068	T	C	WASH7P	ncRNA_exonic	#ff0041	chr1
+16103	T	G	WASH7P	ncRNA_exonic	#ff0042	chr1
+16206	T	A	WASH7P	ncRNA_exonic	#ff0043	chr1
+16226	AG	A	WASH7P	ncRNA_exonic	#ff0044	chr1
+16257	G	C	WASH7P	ncRNA_exonic	#ff0045	chr1
+16288	C	G	WASH7P	ncRNA_exonic	#ff0046	chr1
+16298	C	T	WASH7P	ncRNA_exonic	#ff0047	chr1
+16378	T	C	WASH7P	ncRNA_exonic	#ff0048	chr1
+16487	T	C	WASH7P	ncRNA_exonic	#ff0049	chr1
+16495	G	C	WASH7P	ncRNA_exonic	#ff0050	chr1
+16497	A	G	WASH7P	ncRNA_exonic	#ff0051	chr1
+16534	C	T	WASH7P	ncRNA_exonic	#ff0052	chr1
+16571	G	A	WASH7P	ncRNA_exonic	#ff0053	chr1
+16682	G	A	WASH7P	ncRNA_exonic	#ff0054	chr1
+16688	G	A	WASH7P	ncRNA_exonic	#ff0055	chr1
+16719	T	A	WASH7P	ncRNA_exonic	#ff0056	chr1
+16737	G	T	WASH7P	ncRNA_exonic	#ff0057	chr1
+16742	G	C	WASH7P	ncRNA_exonic	#ff0058	chr1
+16809	C	G	WASH7P	ncRNA_intronic	#ff0059	chr1
+16841	G	T	WASH7P	ncRNA_intronic	#ff0060	chr1
+16949	A	C	WASH7P	ncRNA_exonic	#ff0061	chr1
+16963	G	A	WASH7P	ncRNA_exonic	#ff0062	chr1
+16977	G	A	WASH7P	ncRNA_exonic	#ff0063	chr1
+17020	G	A	WASH7P	ncRNA_exonic	#ff0064	chr1
+17222	A	G	WASH7P	ncRNA_intronic	#ff0065	chr1
+17385	G	A	MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4	ncRNA_exonic	#ff0066	chr1
+17408	C	G	MIR6859-1,MIR6859-2,MIR6859-3,MIR6859-4	ncRNA_exonic	#ff0067	chr1
+17538	C	A	WASH7P	ncRNA_exonic	#ff0068	chr1
+17594	C	T	WASH7P	ncRNA_exonic	#ff0069	chr1
+17614	G	A	WASH7P	ncRNA_exonic	#ff0070	chr1
+17697	G	C	WASH7P	ncRNA_exonic	#ff0071	chr1
+17730	C	A	WASH7P	ncRNA_exonic	#ff0072	chr1
+17746	A	G	WASH7P	ncRNA_exonic;splicing	#ff0073	chr1
+17765	G	A	WASH7P	ncRNA_exonic	#ff0074	chr1
+17961	TG	T	WASH7P	ncRNA_exonic	#ff0075	chr1
+19004	A	G	WASH7P	ncRNA_exonic	#ff0076	chr1
+19322	C	T	WASH7P	ncRNA_exonic	#ff0077	chr1
+19583	A	G	WASH7P	ncRNA_exonic	#ff0078	chr1
+19592	T	C	WASH7P	ncRNA_exonic	#ff0079	chr1
+19600	A	T	WASH7P	ncRNA_exonic	#ff0080	chr1
+19604	T	C	WASH7P	ncRNA_exonic	#ff0081	chr1
+19776	A	G	WASH7P	ncRNA_intronic	#ff0082	chr1
+19788	C	T	WASH7P	ncRNA_intronic	#ff0083	chr1
+19858	C	T	WASH7P	ncRNA_intronic	#ff0084	chr1
+19942	G	C	WASH7P	ncRNA_intronic	#ff0085	chr1
+20094	TAA	T	WASH7P	ncRNA_intronic	#ff0086	chr1
+20098	CAG	C	WASH7P	ncRNA_intronic	#ff0087	chr1
+20129	C	T	WASH7P	ncRNA_intronic	#ff0088	chr1
+20136	T	C	WASH7P	ncRNA_intronic	#ff0089	chr1
+20144	G	A	WASH7P	ncRNA_intronic	#ff0090	chr1
+20191	T	G	WASH7P	ncRNA_intronic	#ff0091	chr1
+20206	C	T	WASH7P	ncRNA_intronic	#ff0092	chr1
+20207	G	A	WASH7P	ncRNA_intronic	#ff0093	chr1
+20212	A	G	WASH7P	ncRNA_intronic	#ff0094	chr1
+20227	T	A	WASH7P	ncRNA_intronic	#ff0095	chr1
+20235	G	A	WASH7P	ncRNA_intronic	#ff0096	chr1
+20245	G	A	WASH7P	ncRNA_intronic	#ff0097	chr1
+20250	T	C	WASH7P	ncRNA_intronic	#ff0098	chr1