diff --git a/CHANGELOG b/CHANGELOG
index 65feb96cf5847fa3eed9083aca002a0cca29b794..afc764e05f4afcace272e865ab2b977fe6f4db04 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -14,6 +14,8 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
uploaded (#683)
* Small improvement: warning about capslock is visible on login page when
necessary (#658)
+ * Small improvement: names of columns in data overlay are unified: no
+ whitespace, "_" used as separator (#596)
* Bug fix: progress bar of gene genome mapping upload is refreshing properly
(#728)
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 94223e27eb3e281ff83487916aa5a7d4bbb967a8..bdbd459409350dc2ecd9a60123d0489aa23fa4cf 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -584,7 +584,7 @@ public class LayoutService implements ILayoutService {
for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
if (columns.contains(column)) {
- sb.append(column.getTitle() + "\t");
+ sb.append(column.getColumnName() + "\t");
}
}
sb.append("matches<br/>\n");
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 4d54c42bc2dfffad14f17ae1198a8d3fde35a077..b2085821ea21ee251891e3e1cb978229ae6d7e22 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -152,8 +152,8 @@ public class ColorSchemaReader {
String[] columns = line.split("\t");
Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
- List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
- parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENETIC_VARIANT);
+ List<Pair<MiriamType, Integer>> customIdentifiers = parseColumns(columns, schemaColumns,
+ ColorSchemaType.GENETIC_VARIANT);
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
if (contigColumn == null) {
@@ -181,21 +181,21 @@ public class ColorSchemaReader {
throw new InvalidColorSchemaException("One of these columns is obligatory: name, identifier");
}
if (contigColumn == null) {
- throw new InvalidColorSchemaException(ColorSchemaColumn.CONTIG.getTitle() + " column is obligatory");
+ throw new InvalidColorSchemaException(ColorSchemaColumn.CONTIG.getColumnName() + " column is obligatory");
}
if (positionColumn == null) {
- throw new InvalidColorSchemaException(ColorSchemaColumn.POSITION.getTitle() + " column is obligatory");
+ throw new InvalidColorSchemaException(ColorSchemaColumn.POSITION.getColumnName() + " column is obligatory");
}
if (originalDnaColumn == null) {
- throw new InvalidColorSchemaException(ColorSchemaColumn.ORIGINAL_DNA.getTitle() + " column is obligatory");
+ throw new InvalidColorSchemaException(ColorSchemaColumn.ORIGINAL_DNA.getColumnName() + " column is obligatory");
}
if (referenceGenomeTypeColumn == null && genomeType == null) {
throw new InvalidColorSchemaException(
- ColorSchemaColumn.REFERENCE_GENOME_TYPE.getTitle() + " column is obligatory");
+ ColorSchemaColumn.REFERENCE_GENOME_TYPE.getColumnName() + " column is obligatory");
}
if (referenceGenomeVersionColumn == null && referenceGenomeVersionStr == null) {
throw new InvalidColorSchemaException(
- ColorSchemaColumn.REFERENCE_GENOME_VERSION.getTitle() + " column is obligatory");
+ ColorSchemaColumn.REFERENCE_GENOME_VERSION.getColumnName() + " column is obligatory");
}
lineIndex++;
line = br.readLine();
@@ -481,8 +481,7 @@ public class ColorSchemaReader {
String[] columns = line.split("\t");
Map<ColorSchemaColumn, Integer> schemaColumns = new HashMap<>();
- List<Pair<MiriamType, Integer>> customIdentifiers = new ArrayList<>();
- parseColumns(columns, schemaColumns, customIdentifiers, ColorSchemaType.GENERIC);
+ List<Pair<MiriamType, Integer>> customIdentifiers = parseColumns(columns, schemaColumns, ColorSchemaType.GENERIC);
Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
@@ -501,8 +500,10 @@ public class ColorSchemaReader {
if (nameColumn == null && identifierColumn == null && customIdentifiers.size() == 0
&& elementIdentifierColumn == null) {
- throw new InvalidColorSchemaException("One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle()
- + "," + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
+ throw new InvalidColorSchemaException(
+ "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getColumnName()
+ + "," + ColorSchemaColumn.IDENTIFIER.getColumnName() + ","
+ + ColorSchemaColumn.ELEMENT_IDENTIFIER.getColumnName());
}
if (valueColumn == null && colorColumn == null) {
@@ -678,29 +679,36 @@ public class ColorSchemaReader {
* @throws InvalidColorSchemaException
* thrown when the list of column headers contain invalid value
*/
- public void parseColumns(String[] columns, Map<ColorSchemaColumn, Integer> schemaColumns,
- List<Pair<MiriamType, Integer>> customIdentifiers, ColorSchemaType type) throws InvalidColorSchemaException {
- Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
+ public List<Pair<MiriamType, Integer>> parseColumns(String[] columns, Map<ColorSchemaColumn, Integer> schemaColumns,
+ ColorSchemaType type) throws InvalidColorSchemaException {
+ List<Pair<MiriamType, Integer>> result = new ArrayList<>();
+ Map<String, MiriamType> acceptableIdentifiers = new HashMap<>();
+ Map<String, MiriamType> deprecatedIdentifiers = new HashMap<>();
for (MiriamType miriamType : MiriamType.values()) {
- acceptableIdentifiers.put(miriamType.getCommonName().toLowerCase(), miriamType);
+ acceptableIdentifiers.put("identifier_" + miriamType.name().toLowerCase(), miriamType);
+ deprecatedIdentifiers.put(miriamType.getCommonName().toLowerCase(), miriamType);
}
for (int i = 0; i < columns.length; i++) {
boolean found = false;
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (columns[i].trim().equalsIgnoreCase(schemaColumn.getTitle()) && schemaColumn.getTypes().contains(type)) {
+ if ((columns[i].trim().equalsIgnoreCase(schemaColumn.getColumnName()) ||
+ columns[i].trim().equalsIgnoreCase(schemaColumn.getDepractedColumnName()))
+ && schemaColumn.getTypes().contains(type)) {
schemaColumns.put(schemaColumn, i);
found = true;
}
}
if (!found) {
if (acceptableIdentifiers.keySet().contains(columns[i].toLowerCase())) {
- customIdentifiers.add(new Pair<>(acceptableIdentifiers.get(columns[i].toLowerCase()), i));
+ result.add(new Pair<>(acceptableIdentifiers.get(columns[i].toLowerCase()), i));
+ } else if (deprecatedIdentifiers.keySet().contains(columns[i].toLowerCase())) {
+ result.add(new Pair<>(deprecatedIdentifiers.get(columns[i].toLowerCase()), i));
} else {
String columnNames = "";
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
if (schemaColumn.getTypes().contains(type)) {
- columnNames += schemaColumn.getTitle() + ", ";
+ columnNames += schemaColumn.getColumnName() + ", ";
}
}
for (String string : acceptableIdentifiers.keySet()) {
@@ -711,6 +719,7 @@ public class ColorSchemaReader {
}
}
}
+ return result;
}
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index 4948d346f2a2a595d3efb3947048a4d9bc219c64..1437bd37958dfe69f61f9d6886aae3127730de7e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -130,7 +130,7 @@ public class ColorSchemaXlsxReader {
String value = cell.getStringCellValue();
boolean found = false;
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
+ if (value.trim().equalsIgnoreCase(schemaColumn.getDepractedColumnName()) || value.trim().equalsIgnoreCase(schemaColumn.getColumnName())) {
foundSchemaColumns.put(schemaColumn, columnIndex - 1);
found = true;
break;
@@ -143,7 +143,7 @@ public class ColorSchemaXlsxReader {
} else {
String columnNames = "";
for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- columnNames += schemaColumn.getTitle() + ", ";
+ columnNames += schemaColumn.getColumnName() + ", ";
}
for (String string : acceptableIdentifiers.keySet()) {
columnNames += ", " + string;
@@ -174,8 +174,8 @@ public class ColorSchemaXlsxReader {
if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
&& elementIdentifierColumn == null) {
throw new InvalidColorSchemaException(
- "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
- + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
+ "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getColumnName() + ","
+ + ColorSchemaColumn.IDENTIFIER.getColumnName() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getColumnName());
}
if (valueColumn == null && colorColumn == null) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 838eeda5fee327c79a855b7cc0138f1e5601c9d1..8fd9276dfe5579067dca98d62c7c731ece156f82 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -19,41 +19,41 @@ public enum ColorSchemaColumn {
/**
* Name of the element.
*/
- NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
- GENE_NAME("gene_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ GENE_NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Name of the element.
*/
- MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ MODEL_NAME(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Value that will be transformed into new color.
*
* @see ColorSchemaColumn#COLOR
*/
- VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
+ VALUE(new ColorSchemaType[] { ColorSchemaType.GENERIC }),
/**
* In which compartment the element should be located.
*/
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ COMPARTMENT(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Class type of the element.
*/
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ TYPE(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* New element/reaction color.
*/
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ COLOR(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Identifier of the element.
*/
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
+ IDENTIFIER(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Element identifier.
@@ -74,69 +74,85 @@ public enum ColorSchemaColumn {
/**
* Position where gene variants starts.
*/
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ POSITION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Original DNA of the variant.
*/
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ ORIGINAL_DNA(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Alternative DNA of the variant.
*/
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ ALTERNATIVE_DNA(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Short description of the entry.
*/
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
+ DESCRIPTION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
/**
* Variant references.
*/
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ REFERENCES(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* What's the {@link ReferenceGenomeType}.
*/
- REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ REFERENCE_GENOME_TYPE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* {@link ReferenceGenome#version Version} of the reference genome.
*/
- REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ REFERENCE_GENOME_VERSION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Contig where variant was observed.
*/
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ CONTIG(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- CHROMOSOME("chromosome", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ CHROMOSOME(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
ALLEL_FREQUENCY("allele_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
+ VARIANT_IDENTIFIER(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* Should the direction of reaction be reversed.
*/
REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }),
-
+
/**
- * Optional amino acid change in the variant.
+ * Optional amino acid change in the variant.
*/
- AMINO_ACID_CHANGE("amino_acid_change", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT });
+ AMINO_ACID_CHANGE(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT });
+
+ /**
+ * Constructor that creates enum entry with deprecated column name.
+ *
+ * @param deprecatedColumnName
+ * {@link #deprecatedColumnName}
+ * @param types
+ * list of {@link ColorSchemaType types} where this column is allowed
+ * @deprecated As of release 12.3, replaced by {@link #ColorSchemaColumn(ColorSchemaType[])}
+ */
+ @Deprecated
+ ColorSchemaColumn(String deprecatedColumnName, ColorSchemaType[] types) {
+ this.deprecatedColumnName = deprecatedColumnName;
+ for (ColorSchemaType colorSchemaType : types) {
+ this.types.add(colorSchemaType);
+ }
+ }
/**
* Default constructor that creates enum entry.
*
- * @param title
- * {@link #title}
+ * @param deprecatedColumnName
+ * {@link #deprecatedColumnName}
* @param types
* list of {@link ColorSchemaType types} where this column is allowed
*/
- ColorSchemaColumn(String title, ColorSchemaType[] types) {
- this.title = title;
+ ColorSchemaColumn(ColorSchemaType[] types) {
for (ColorSchemaType colorSchemaType : types) {
this.types.add(colorSchemaType);
}
@@ -145,7 +161,7 @@ public enum ColorSchemaColumn {
/**
* Human readable title used in input file.
*/
- private String title;
+ private String deprecatedColumnName;
/**
* Set of types where column is allowed.
@@ -154,10 +170,16 @@ public enum ColorSchemaColumn {
/**
*
- * @return {@link #title}
+ * @return {@link #deprecatedColumnName}
+ * @deprecated As of release 12.3, replaced by {@link #getColumnName()}
*/
- public String getTitle() {
- return title;
+ @Deprecated
+ public String getDepractedColumnName() {
+ return deprecatedColumnName;
+ }
+
+ public String getColumnName() {
+ return this.name().toLowerCase();
}
/**
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 3a7d0ace0e306e47159b352a695b7d3731a161f5..8f38ead287c120fe84ebf7d78c168c6328a9d200 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -412,6 +412,25 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
}
}
+ @Test
+ public void testSchemasWithIdSnakeCase() throws Exception {
+ try {
+ ColorSchemaReader reader = new ColorSchemaReader();
+
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/schema_with_identifiers_in_snake_case.txt");
+ for (ColorSchema colorSchema : schemas) {
+ for (MiriamData md : colorSchema.getMiriamData()) {
+ assertNotNull(md.getResource());
+ assertFalse(md.getResource().isEmpty());
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testSchemasWithEmptyNameAndId() throws Exception {
try {
diff --git a/service/testFiles/coloring/schema_with_identifiers_in_snake_case.txt b/service/testFiles/coloring/schema_with_identifiers_in_snake_case.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc57ab28b2411e1b78a435c753acbc9f2de7f25e
--- /dev/null
+++ b/service/testFiles/coloring/schema_with_identifiers_in_snake_case.txt
@@ -0,0 +1,4 @@
+name identifier_Entrez identifier_Chebi identifier_go value
+ 120892 1
+ CHEBI:26523 1
+ GO:0036489 1