From 4b63adc8035eac3e507a52dd08eee8f2ffe56ce5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 25 Jan 2018 13:42:58 +0100
Subject: [PATCH] allow user to upload overlay and filter by model_name
---
.../services/impl/LayoutService.java | 4 +
.../services/utils/ColorSchemaReader.java | 17 +
.../services/utils/ColorSchemaXlsxReader.java | 549 +++++++++---------
.../utils/data/ColorSchemaColumn.java | 268 ++++-----
4 files changed, 440 insertions(+), 398 deletions(-)
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 4104e98609..3e56dd04c2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -792,6 +792,8 @@ public class LayoutService implements ILayoutService {
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.NAME)) {
sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) {
+ sb.append(schema.getModelName() + "\t");
} else if (column.equals(ColorSchemaColumn.VALUE)) {
sb.append(schema.getValue() + "\t");
} else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
@@ -847,6 +849,8 @@ public class LayoutService implements ILayoutService {
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.NAME)) {
sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) {
+ sb.append(schema.getModelName() + "\t");
} else if (column.equals(ColorSchemaColumn.VALUE)) {
sb.append(schema.getValue() + "\t");
} else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
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 2f358661b2..0176a0da7e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -157,6 +157,7 @@ public class ColorSchemaReader {
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+ Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
Integer variantIdentifierColumn = schemaColumns.get(ColorSchemaColumn.VARIANT_IDENTIFIER);
Integer allelFrequencyColumn = schemaColumns.get(ColorSchemaColumn.ALLEL_FREQUENCY);
@@ -202,6 +203,9 @@ public class ColorSchemaReader {
if (nameColumn != null) {
processNameColumn(schema, values[nameColumn]);
}
+ if (modelNameColumn != null) {
+ processModelNameColumn(schema, values[modelNameColumn]);
+ }
if (compartmentColumn != null) {
processCompartmentColumn(schema, values[compartmentColumn]);
}
@@ -328,6 +332,12 @@ public class ColorSchemaReader {
schema.setName(content);
}
}
+ private void processModelNameColumn(ColorSchema schema, String content) {
+ if (!content.isEmpty()) {
+ schema.setModelName(content);
+ }
+ }
+
/**
* Sets proper compartment names to {@link ColorSchema} from cell content.
@@ -463,6 +473,7 @@ public class ColorSchemaReader {
Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+ Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
Integer reactionIdentifierColumn = schemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
@@ -499,6 +510,9 @@ public class ColorSchemaReader {
if (nameColumn != null) {
processNameColumn(schema, values[nameColumn]);
}
+ if (modelNameColumn != null) {
+ processModelNameColumn(schema, values[modelNameColumn]);
+ }
if (valueColumn != null) {
schema.setValue(parseValueColumn(values[valueColumn], errorPrefix));
}
@@ -729,6 +743,9 @@ public class ColorSchemaReader {
if (schema.getName() != null) {
result.add(ColorSchemaColumn.NAME);
}
+ if (schema.getModelName() != null) {
+ result.add(ColorSchemaColumn.MODEL_NAME);
+ }
if (schema.getReactionIdentifier() != null) {
result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
}
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 f852f697bc..be39f1a333 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -41,285 +41,302 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
*
*/
public class ColorSchemaXlsxReader {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
- /**
- * @param fileName
- * file name
- * @param sheetName
- * sheet name.
- * @return list of ColorSchema.
- * @throws IOException
- * exception related to opening the input stream.
- * @throws InvalidColorSchemaException
- * invalid color schema exception.
- */
- public Collection<ColorSchema> readColorSchema(String fileName, String sheetName) throws IOException, InvalidColorSchemaException {
- ColorParser colorParser = new ColorParser();
- List<ColorSchema> result = new ArrayList<>();
- FileInputStream file = null;
- Workbook workbook = null;
+ /**
+ * @param fileName
+ * file name
+ * @param sheetName
+ * sheet name.
+ * @return list of ColorSchema.
+ * @throws IOException
+ * exception related to opening the input stream.
+ * @throws InvalidColorSchemaException
+ * invalid color schema exception.
+ */
+ public Collection<ColorSchema> readColorSchema(String fileName, String sheetName)
+ throws IOException, InvalidColorSchemaException {
+ ColorParser colorParser = new ColorParser();
+ List<ColorSchema> result = new ArrayList<>();
+ FileInputStream file = null;
+ Workbook workbook = null;
- try {
- file = new FileInputStream(fileName);
- // Using XSSF for xlsx format, for xls use HSSF
- // <-Interface, accepts both HSSF and XSSF.
- if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
- workbook = new HSSFWorkbook(file);
- } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
- workbook = new XSSFWorkbook(file);
- } else {
- throw new IllegalArgumentException("Received file does not have a standard excel extension.");
- }
- Sheet sheet = null;
- if (sheetName == null) {
- sheet = workbook.getSheetAt(0);
- } else {
- sheet = workbook.getSheet(sheetName);
- }
- DataFormat fmt = workbook.createDataFormat();
- CellStyle textStyle = workbook.createCellStyle();
- textStyle.setDataFormat(fmt.getFormat("@"));
+ try {
+ file = new FileInputStream(fileName);
+ // Using XSSF for xlsx format, for xls use HSSF
+ // <-Interface, accepts both HSSF and XSSF.
+ if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
+ workbook = new HSSFWorkbook(file);
+ } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
+ workbook = new XSSFWorkbook(file);
+ } else {
+ throw new IllegalArgumentException("Received file does not have a standard excel extension.");
+ }
+ Sheet sheet = null;
+ if (sheetName == null) {
+ sheet = workbook.getSheetAt(0);
+ } else {
+ sheet = workbook.getSheet(sheetName);
+ }
+ DataFormat fmt = workbook.createDataFormat();
+ CellStyle textStyle = workbook.createCellStyle();
+ textStyle.setDataFormat(fmt.getFormat("@"));
- Iterator<Row> rowIterator = sheet.iterator();
- Integer valueColumn = null;
- Integer colorColumn = null;
- Integer nameColumn = null;
- Integer identifierColumn = null;
- Integer reactionIdentifierColumn = null;
- Integer compartmentColumn = null;
- Integer typeColumn = null;
- Integer lineWidthColumn = null;
- Integer reverseReactionColumn = null;
- List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
- int lineIndex = 0;
- Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
- while (rowIterator.hasNext()) {
- Row row = rowIterator.next();
- Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
- if (cell == null) {
- continue;
- } else {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- if (cell.getStringCellValue().startsWith("#")) {
- continue;
- }
- }
- lineIndex++;
- if (lineIndex == 1) {
+ Iterator<Row> rowIterator = sheet.iterator();
+ Integer valueColumn = null;
+ Integer colorColumn = null;
+ Integer nameColumn = null;
+ Integer modelNameColumn = null;
+ Integer identifierColumn = null;
+ Integer reactionIdentifierColumn = null;
+ Integer compartmentColumn = null;
+ Integer typeColumn = null;
+ Integer lineWidthColumn = null;
+ Integer reverseReactionColumn = null;
+ List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
+ int lineIndex = 0;
+ Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
+ while (rowIterator.hasNext()) {
+ Row row = rowIterator.next();
+ Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
+ if (cell == null) {
+ continue;
+ } else {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ if (cell.getStringCellValue().startsWith("#")) {
+ continue;
+ }
+ }
+ lineIndex++;
+ if (lineIndex == 1) {
- Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
- for (MiriamType type : MiriamType.values()) {
- acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
- }
+ Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
+ for (MiriamType type : MiriamType.values()) {
+ acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
+ }
- Iterator<Cell> cellIterator = row.cellIterator();
- int columnIndex = 0;
- while (cellIterator.hasNext()) {
- columnIndex++;
- sheet.setDefaultColumnStyle(columnIndex, textStyle);
- cell = cellIterator.next();
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- boolean found = false;
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
- foundSchemaColumns.put(schemaColumn, columnIndex - 1);
- found = true;
- break;
- }
- }
- if (!found) {
- if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
- foundCustomIdentifiers.add(new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
- } else {
- String columnNames = "";
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- columnNames += schemaColumn.getTitle() + ", ";
- }
- for (String string : acceptableIdentifiers.keySet()) {
- columnNames += ", " + string;
- }
- throw new InvalidColorSchemaException("Unknown column type: " + value + ". Acceptable column name: " + columnNames);
- }
- }
- }
- valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
- colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
- nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
- identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
- reactionIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
- compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
- typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
- lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
- reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
+ Iterator<Cell> cellIterator = row.cellIterator();
+ int columnIndex = 0;
+ while (cellIterator.hasNext()) {
+ columnIndex++;
+ sheet.setDefaultColumnStyle(columnIndex, textStyle);
+ cell = cellIterator.next();
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ boolean found = false;
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
+ foundSchemaColumns.put(schemaColumn, columnIndex - 1);
+ found = true;
+ break;
+ }
+ }
+ if (!found) {
+ if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
+ foundCustomIdentifiers.add(
+ new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
+ } else {
+ String columnNames = "";
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ columnNames += schemaColumn.getTitle() + ", ";
+ }
+ for (String string : acceptableIdentifiers.keySet()) {
+ columnNames += ", " + string;
+ }
+ throw new InvalidColorSchemaException(
+ "Unknown column type: " + value + ". Acceptable column name: " + columnNames);
+ }
+ }
+ }
+ valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
+ colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
+ nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
+ modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME);
+ identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
+ reactionIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+ compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
+ typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
+ lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
+ reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
- if (valueColumn != null && colorColumn != null) {
- throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
- }
+ if (valueColumn != null && colorColumn != null) {
+ throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
+ }
- if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0 && reactionIdentifierColumn == null) {
- throw new InvalidColorSchemaException("One of these columns is obligatory: name, identifier, reactionIdentifier");
- }
+ if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
+ && reactionIdentifierColumn == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns is obligatory: name, identifier, reactionIdentifier");
+ }
- if (valueColumn == null && colorColumn == null) {
- throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
- }
+ if (valueColumn == null && colorColumn == null) {
+ throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
+ }
- } else {
- ColorSchema schema = new GenericColorSchema();
- if (nameColumn != null) {
- schema.setName(row.getCell(nameColumn).getStringCellValue());
- }
- if (valueColumn != null) {
- try {
- cell = row.getCell(valueColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
- } catch (Exception e) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
- }
- if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Value " + schema.getValue() + " out of range. Only values between -1 and 1 are allowed.");
- }
- }
- if (compartmentColumn != null) {
- String value = row.getCell(compartmentColumn).getStringCellValue();
- if (value != null) {
- String[] compartments = value.split(",");
- schema.addCompartments(compartments);
- }
- }
- if (typeColumn != null) {
- String value = row.getCell(typeColumn).getStringCellValue();
- if (value != null) {
- String[] types = value.split(",");
- for (String string : types) {
- SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
- if (mapping != null) {
- schema.addType(mapping.getModelClazz());
- } else {
- throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
- }
- }
- }
- }
- if (colorColumn != null) {
- schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
- }
- if (reactionIdentifierColumn != null) {
- schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
- }
- if (lineWidthColumn != null) {
- cell = row.getCell(lineWidthColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- if (value != null && !value.trim().isEmpty()) {
- try {
- schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
- } catch (NumberFormatException e) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
- }
- }
- }
- if (reverseReactionColumn != null) {
- cell = row.getCell(reverseReactionColumn);
- if (cell != null) {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
- }
- }
- if (identifierColumn != null) {
- cell = row.getCell(identifierColumn);
- if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
- MiriamConnector miriamConnector = new MiriamConnector();
- String value = cell.getStringCellValue().trim();
- if (miriamConnector.isValidIdentifier(value)) {
- schema.setGeneralIdentifier(value);
- } else {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
- }
- }
- }
- for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
- cell = row.getCell(pair.getRight());
- if (cell != null) {
- schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
- }
- }
+ } else {
+ ColorSchema schema = new GenericColorSchema();
+ if (nameColumn != null) {
+ schema.setName(row.getCell(nameColumn).getStringCellValue());
+ }
+ if (modelNameColumn != null) {
+ schema.setModelName(row.getCell(modelNameColumn).getStringCellValue());
+ }
+ if (valueColumn != null) {
+ try {
+ cell = row.getCell(valueColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
+ } catch (Exception e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
+ }
+ if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "] Value " + schema.getValue()
+ + " out of range. Only values between -1 and 1 are allowed.");
+ }
+ }
+ if (compartmentColumn != null) {
+ String value = row.getCell(compartmentColumn).getStringCellValue();
+ if (value != null) {
+ String[] compartments = value.split(",");
+ schema.addCompartments(compartments);
+ }
+ }
+ if (typeColumn != null) {
+ String value = row.getCell(typeColumn).getStringCellValue();
+ if (value != null) {
+ String[] types = value.split(",");
+ for (String string : types) {
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
+ if (mapping != null) {
+ schema.addType(mapping.getModelClazz());
+ } else {
+ throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
+ }
+ }
+ }
+ }
+ if (colorColumn != null) {
+ schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
+ }
+ if (reactionIdentifierColumn != null) {
+ schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
+ }
+ if (lineWidthColumn != null) {
+ cell = row.getCell(lineWidthColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ if (value != null && !value.trim().isEmpty()) {
+ try {
+ schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
+ } catch (NumberFormatException e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
+ }
+ }
+ }
+ if (reverseReactionColumn != null) {
+ cell = row.getCell(reverseReactionColumn);
+ if (cell != null) {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
+ }
+ }
+ if (identifierColumn != null) {
+ cell = row.getCell(identifierColumn);
+ if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
+ MiriamConnector miriamConnector = new MiriamConnector();
+ String value = cell.getStringCellValue().trim();
+ if (miriamConnector.isValidIdentifier(value)) {
+ schema.setGeneralIdentifier(value);
+ } else {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
+ }
+ }
+ }
+ for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
+ cell = row.getCell(pair.getRight());
+ if (cell != null) {
+ schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
+ }
+ }
- if ((schema.getValue() != null && schema.getColor() != null) || (schema.getValue() == null && schema.getColor() == null)) {
- throw new InvalidColorSchemaException("Value or Color is needed not both");
- }
+ if ((schema.getValue() != null && schema.getColor() != null)
+ || (schema.getValue() == null && schema.getColor() == null)) {
+ throw new InvalidColorSchemaException("Value or Color is needed not both");
+ }
- if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
- && schema.getReactionIdentifier() == null) {
- throw new InvalidColorSchemaException("One of these columns values is obligatory: name, identifier, reactionIdentifier");
- }
- result.add(schema);
- }
- }
- } finally {
- try {
- if (file != null) {
- file.close();
- }
- if (workbook != null) {
- workbook.close();
- }
- } catch (Exception e) {
+ if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
+ && schema.getReactionIdentifier() == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns values is obligatory: name, identifier, reactionIdentifier");
+ }
+ result.add(schema);
+ }
+ }
+ } finally {
+ try {
+ if (file != null) {
+ file.close();
+ }
+ if (workbook != null) {
+ workbook.close();
+ }
+ } catch (Exception e) {
- }
- }
- return result;
+ }
+ }
+ return result;
- }
+ }
- /**
- * Returns list of columns that should be printed for given coloring schemas.
- *
- * @param schemas
- * list of schemas
- * @return list of columns that should be printed (were set in the coloring
- * schemas)
- */
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
- for (ColorSchema schema : schemas) {
- if (schema.getColor() != null) {
- result.add(ColorSchemaColumn.COLOR);
- }
- if (schema.getCompartments().size() > 0) {
- result.add(ColorSchemaColumn.COMPARTMENT);
- }
- if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
- result.add(ColorSchemaColumn.IDENTIFIER);
- }
- if (schema.getLineWidth() != null) {
- result.add(ColorSchemaColumn.LINE_WIDTH);
- }
- if (schema.getName() != null) {
- result.add(ColorSchemaColumn.NAME);
- }
- if (schema.getReactionIdentifier() != null) {
- result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
- }
- if (schema.getReverseReaction() != null) {
- result.add(ColorSchemaColumn.REVERSE_REACTION);
- }
- if (schema.getTypes().size() > 0) {
- result.add(ColorSchemaColumn.TYPE);
- }
- if (schema.getValue() != null) {
- result.add(ColorSchemaColumn.VALUE);
- }
- }
- return result;
- }
+ /**
+ * Returns list of columns that should be printed for given coloring schemas.
+ *
+ * @param schemas
+ * list of schemas
+ * @return list of columns that should be printed (were set in the coloring
+ * schemas)
+ */
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
+ for (ColorSchema schema : schemas) {
+ if (schema.getColor() != null) {
+ result.add(ColorSchemaColumn.COLOR);
+ }
+ if (schema.getCompartments().size() > 0) {
+ result.add(ColorSchemaColumn.COMPARTMENT);
+ }
+ if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
+ result.add(ColorSchemaColumn.IDENTIFIER);
+ }
+ if (schema.getLineWidth() != null) {
+ result.add(ColorSchemaColumn.LINE_WIDTH);
+ }
+ if (schema.getName() != null) {
+ result.add(ColorSchemaColumn.NAME);
+ }
+ if (schema.getModelName() != null) {
+ result.add(ColorSchemaColumn.MODEL_NAME);
+ }
+ if (schema.getReactionIdentifier() != null) {
+ result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
+ }
+ if (schema.getReverseReaction() != null) {
+ result.add(ColorSchemaColumn.REVERSE_REACTION);
+ }
+ if (schema.getTypes().size() > 0) {
+ result.add(ColorSchemaColumn.TYPE);
+ }
+ if (schema.getValue() != null) {
+ result.add(ColorSchemaColumn.VALUE);
+ }
+ }
+ return result;
+ }
}
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 6792e10ef5..a5a4025546 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
@@ -3,7 +3,6 @@ package lcsb.mapviewer.services.utils.data;
import java.util.HashSet;
import java.util.Set;
-
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
@@ -16,136 +15,141 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
*/
public enum ColorSchemaColumn {
- /**
- * Name of the element.
- */
- NAME("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 }), //
-
- /**
- * In which compartment the element should be located.
- */
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Class type of the element.
- */
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * New element/reaction color.
- */
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Identifier of the element.
- */
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Reaction identifier.
- */
- REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * New line width of the reaction.
- */
- LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * Position where gene variants starts.
- */
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Original DNA of the variant.
- */
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Alternative DNA of the variant.
- */
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Short description of the entry.
- */
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
-
- /**
- * Variant references.
- */
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * What's the {@link ReferenceGenomeType}.
- */
- REFERENCE_GENOME_TYPE("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 }), //
-
- /**
- * Contig where variant was observed.
- */
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Should the direction of reaction be reversed.
- */
- REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
-
- /**
- * Default constructor that creates enum entry.
- *
- * @param title
- * {@link #title}
- * @param types
- * list of {@link ColumnType types} where this column is allowed
- */
- ColorSchemaColumn(String title, ColorSchemaType[] types) {
- this.title = title;
- for (ColorSchemaType colorSchemaType : types) {
- this.types.add(colorSchemaType);
- }
- }
-
- /**
- * Human readable title used in input file.
- */
- private String title;
-
- /**
- * Set of types where column is allowed.
- */
- private Set<ColorSchemaType> types = new HashSet<>();
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public Set<ColorSchemaType> getTypes() {
- return types;
- }
+ /**
+ * Name of the element.
+ */
+ NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Name of the element.
+ */
+ MODEL_NAME("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 }), //
+
+ /**
+ * In which compartment the element should be located.
+ */
+ COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Class type of the element.
+ */
+ TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * New element/reaction color.
+ */
+ COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Identifier of the element.
+ */
+ IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Reaction identifier.
+ */
+ REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * New line width of the reaction.
+ */
+ LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * Position where gene variants starts.
+ */
+ POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Original DNA of the variant.
+ */
+ ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Alternative DNA of the variant.
+ */
+ ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Short description of the entry.
+ */
+ DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
+
+ /**
+ * Variant references.
+ */
+ REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * What's the {@link ReferenceGenomeType}.
+ */
+ REFERENCE_GENOME_TYPE("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 }), //
+
+ /**
+ * Contig where variant was observed.
+ */
+ CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Should the direction of reaction be reversed.
+ */
+ REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
+
+ /**
+ * Default constructor that creates enum entry.
+ *
+ * @param title
+ * {@link #title}
+ * @param types
+ * list of {@link ColumnType types} where this column is allowed
+ */
+ ColorSchemaColumn(String title, ColorSchemaType[] types) {
+ this.title = title;
+ for (ColorSchemaType colorSchemaType : types) {
+ this.types.add(colorSchemaType);
+ }
+ }
+
+ /**
+ * Human readable title used in input file.
+ */
+ private String title;
+
+ /**
+ * Set of types where column is allowed.
+ */
+ private Set<ColorSchemaType> types = new HashSet<>();
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public Set<ColorSchemaType> getTypes() {
+ return types;
+ }
}
--
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