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Workaround for maxrec=0 issue & char fields
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@stvoutsin
stvoutsin committed Jan 15, 2025
1 parent df38753 commit 1ff1568
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Showing 2 changed files with 243 additions and 34 deletions.
243 changes: 212 additions & 31 deletions src/main/java/org/opencadc/tap/impl/ResultSetWriter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ public class ResultSetWriter implements TableWriter<ResultSet> {
public static final String CONTENT_TYPE_ALT = "text/xml";

// VOTable Version number.
public static final String VOTABLE_VERSION = "1.4";
public static final String VOTABLE_VERSION = "1.3";

// Uri to the XML schema.
public static final String XSI_SCHEMA = "http://www.w3.org/2001/XMLSchema-instance";
Expand Down Expand Up @@ -91,7 +91,7 @@ public long getRowCount() {
* Default constructor.
*/
public ResultSetWriter() {
this(null, uk.ac.starlink.votable.DataFormat.BINARY2, VOTableVersion.V14, -1);
this(null, uk.ac.starlink.votable.DataFormat.BINARY2, VOTableVersion.V13, -1);
}


Expand Down Expand Up @@ -325,6 +325,12 @@ protected void writeImpl(ResultSet resultSet, Writer writer, Long maxrec)
? (BufferedWriter) writer
: new BufferedWriter(writer)) {


if (maxrec != null && maxrec == 0 || resultSet == null) {
writeEmptyResult(out);
return;
}

LimitedResultSetStarTable table;
try {
table = new LimitedResultSetStarTable(this.getColumns(), resultSet, maxrec);
Expand All @@ -344,7 +350,7 @@ protected void writeImpl(ResultSet resultSet, Writer writer, Long maxrec)
version_.getXmlNamespace() )
+ ">" );
out.newLine();
out.write( "<RESOURCE>" );
out.write( "<RESOURCE type='results'>" );
out.newLine();

XMLOutputter outputter = new XMLOutputter();
Expand Down Expand Up @@ -384,6 +390,136 @@ protected void writeImpl(ResultSet resultSet, Writer writer, Long maxrec)

}
}

/**
* Write out an empty result (Used when maxrec=0)
*
* @param out
*/
void writeEmptyResult(BufferedWriter out) {
try {
/* Write header. */
out.write("<VOTABLE"
+ VOSerializer.formatAttribute("version", version_.getVersionNumber())
+ VOSerializer.formatAttribute("xmlns", version_.getXmlNamespace())
+ ">");
out.newLine();
out.write("<RESOURCE type='results'>");
out.newLine();

XMLOutputter outputter = new XMLOutputter();
outputter.setFormat(org.jdom2.output.Format.getPrettyFormat());

// Write all info elements
for (VOTableInfo info : infos) {
Element infoElement = new Element("INFO");
infoElement.setAttribute("name", info.getName());
infoElement.setAttribute("value", info.getValue());
outputter.output(infoElement, out);
out.newLine();
}

// Add TABLE element and column metadata
out.write("<TABLE>\n");

// Write all column metadata
for (ColumnInfo colInfo : columns) {
Element field = new Element("FIELD");
field.setAttribute("name", colInfo.getName());

// Set datatype
if (colInfo.getContentClass() != null) {
String datatype = getVOTableDatatype(colInfo.getContentClass());
if (datatype != null) {
field.setAttribute("datatype", datatype);

// Handle array types
if (colInfo.getContentClass().isArray()) {
if (colInfo.getContentClass().getComponentType() == String.class) {
field.setAttribute("arraysize", "*");
} else if (colInfo.getShape() != null && colInfo.getShape().length > 0) {
field.setAttribute("arraysize", String.valueOf(colInfo.getShape()[0]));
}
}
}
}

// Add standard metadata
if (colInfo.getUnitString() != null) {
field.setAttribute("unit", colInfo.getUnitString());
}
if (colInfo.getUCD() != null) {
field.setAttribute("ucd", colInfo.getUCD());
}
if (colInfo.getUtype() != null) {
field.setAttribute("utype", colInfo.getUtype());
}

// Add ID if present
DescribedValue idValue = colInfo.getAuxDatumByName("ID_INFO");
if (idValue != null && idValue.getValue() != null) {
field.setAttribute("ID", idValue.getValue().toString());
}

// Add description if present
String description = colInfo.getDescription();
if (description != null && !description.isEmpty()) {
Element desc = new Element("DESCRIPTION");
desc.setText(description);
field.addContent(desc);
}

outputter.output(field, out);
out.newLine();
}

// Write the empty data section
out.write("<DATA>\n");
out.write("<BINARY2>\n");
out.write("<STREAM encoding='base64'>\n");
out.write("</STREAM>\n");
out.write("</BINARY2>\n");
out.write("</DATA>\n");

out.write("</TABLE>\n"); // Close the TABLE element

/* Write footer. */
out.write("</RESOURCE>");
out.newLine();
for (VOTableResource resource : resources) {
Element r = createResource(resource, null);
outputter.output(r, out);
out.newLine();
}
out.write("</VOTABLE>");
out.newLine();
out.flush();

} catch (IOException e) {
e.printStackTrace();
}

this.totalRows = 0;
}

/**
* Convert Java class to VOTable datatype
*
* @param clazz
* @return
*/
private String getVOTableDatatype(Class<?> clazz) {
if (clazz == Boolean.class || clazz == boolean.class) return "boolean";
if (clazz == Byte.class || clazz == byte.class) return "unsignedByte";
if (clazz == Short.class || clazz == short.class) return "short";
if (clazz == Integer.class || clazz == int.class) return "int";
if (clazz == Long.class || clazz == long.class) return "long";
if (clazz == Float.class || clazz == float.class) return "float";
if (clazz == Double.class || clazz == double.class) return "double";
if (clazz == Character.class || clazz == char.class) return "char";
if (clazz == String.class) return "char";
return null;
}

/**
* StarTable implementation which is based on a ResultSet, and which
Expand Down Expand Up @@ -452,10 +588,12 @@ public boolean lastSequenceOverflowed() {
*/
private static class ModifiedLimitRowSequence extends WrapperRowSequence {
private final Map<Integer, Boolean> accessUrlColumns;

private ColumnInfo[] columnInfos;

ModifiedLimitRowSequence(RowSequence baseSeq, ColumnInfo[] columnInfos) {
super(baseSeq);
this.accessUrlColumns = findAccessUrlColumns(columnInfos);
this.columnInfos = columnInfos;
}

/**
Expand All @@ -477,9 +615,6 @@ private static Map<Integer, Boolean> findAccessUrlColumns(ColumnInfo[] columnInf
if ("access_url".equals(actualColName)) {
boolean isObsCore = "ivoa.ObsCore".equals(tableName);
columns.put(i, isObsCore);
log.debug("Found access_url column at index " + i +
" for table " + tableName +
(isObsCore ? " (will modify URLs)" : " (won't modify URLs)"));
}
}
}
Expand All @@ -491,38 +626,83 @@ private static Map<Integer, Boolean> findAccessUrlColumns(ColumnInfo[] columnInf
}

/**
* Returns the value from a single cell, modifying it if it's a URL that needs to be rewritten.
* Return values from a row, applying necessary type conversions and URL modifications.
*
* @param icol the column index
* @return the cell contents
* This method handles two types of transformations:
* 1. String to Character conversion for VOTable char datatype fields
* 2. URL rewriting for access_url columns in ObsCore tables
*
* For char datatype columns:
* - If the input is a string and the column expects char, take the first character
* - Empty strings are converted to null
* - Non-string values are passed through unchanged
*
* @return array containing values for the current row, with appropriate type conversions
* @throws IOException if there is an error reading from the underlying sequence
*/
@Override
public Object getCell(int icol) throws IOException {
Object value = super.getCell(icol);
if (shouldModifyUrl(icol, value)) {
return modifyAccessUrl((String) value);
public Object[] getRow() throws IOException {
Object[] row = super.getRow();
if (row == null) {
return null;
}
return value;

for (int i = 0; i < row.length; i++) {
Object value = row[i];
ColumnInfo info = columnInfos[i];

if (value != null) {

// Handle conversion from String to Character for char columns
if (value instanceof String && info.getContentClass() == Character.class) {
String strVal = (String)value;
if (strVal.length() > 0) {
row[i] = strVal.charAt(0);
} else {
row[i] = null;
}
}
}

if (shouldModifyUrl(i, row[i])) {
row[i] = modifyAccessUrl((String)row[i]);
}
}

return row;
}

/**
* Returns values from an entire row, modifying any URLs that need to be rewritten.
* Returns the value from a single cell, applying necessary type conversions and URL modifications.
*
* @return array containing values for the current row
* @param icol the column index
* @return the cell contents after any necessary conversions
* @throws IOException if there is an error reading from the underlying sequence
*/
@Override
public Object[] getRow() throws IOException {
Object[] row = super.getRow();
for (Map.Entry<Integer, Boolean> entry : accessUrlColumns.entrySet()) {
int index = entry.getKey();
if (index >= 0 && index < row.length &&
shouldModifyUrl(index, row[index])) {
row[index] = modifyAccessUrl((String) row[index]);
public Object getCell(int icol) throws IOException {
Object value = super.getCell(icol);
ColumnInfo info = columnInfos[icol];

if (value != null) {
// Handle conversion from String to Character for char columns
if (value instanceof String && info.getContentClass() == Character.class) {
String strVal = (String)value;
if (strVal.length() > 0) {
value = strVal.charAt(0);
} else {
value = null;
}
}
}
return row;

if (shouldModifyUrl(icol, value)) {
value = modifyAccessUrl((String)value);
}

return value;
}

/**
* Determines whether a value at a given index should have its URL modified.
*
Expand Down Expand Up @@ -552,12 +732,11 @@ private String modifyAccessUrl(String url) {
URL base_url = new URL(BASE_URL);
URL rewritten = new URL(orig.getProtocol(), base_url.getHost(), orig.getFile());
log.debug( "Rewritten URL: " + rewritten.toExternalForm());

return rewritten.toExternalForm();
} catch (MalformedURLException ex) {
throw new RuntimeException("BUG: Failed to rewrite URL: " + s, ex);
}
throw new RuntimeException("BUG: Failed to rewrite URL: " + s, ex);
}
}
return url;
}
}
Expand Down Expand Up @@ -679,7 +858,7 @@ private Element createResource(VOTableResource votResource, Namespace namespace)
*/
protected Document createDocument() {
// the root VOTABLE element
Namespace vot = Namespace.getNamespace(VOTABLE_14_NS_URI);
Namespace vot = Namespace.getNamespace(VOTABLE_13_NS_URI);
Namespace xsi = Namespace.getNamespace("xsi", XSI_SCHEMA);
Element votable = new Element("VOTABLE", vot);
votable.setAttribute("version", VOTABLE_VERSION);
Expand Down Expand Up @@ -713,7 +892,9 @@ private String getThrownExceptions(Throwable thrown) {
sb.append(thrown.getMessage());
}
}
return sb.toString();
String result = sb.toString().trim();
return result.isEmpty() ? "An unknown error occurred" : result;

}


Expand Down
34 changes: 31 additions & 3 deletions src/main/java/org/opencadc/tap/impl/RubinTableWriter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -417,19 +417,26 @@ public void write(ResultSet rs, Writer out, Long maxrec) throws IOException
columnNames.add(fullColumnName.replace(".", "_"));
listIndex++;
// Generate a ColumnInfo list, to be used by ResultSetWriter for generating the field metadata
ColumnInfo colInfo = new ColumnInfo(resultCol.getName(), getDatatypeClass(resultCol.getDatatype(), newField.getArraysize()), newField.description);
String colArraySize = newField.getArraysize();
if (colArraySize == null && "CHAR".equals(newField.getDatatype().toUpperCase())) {
colArraySize = "1";
}

ColumnInfo colInfo = new ColumnInfo(resultCol.getName(), getDatatypeClass(resultCol.getDatatype(), colArraySize), newField.description);
colInfo.setUCD(resultCol.ucd);
colInfo.setUtype(resultCol.utype);
colInfo.setUnitString(resultCol.unit);
colInfo.setXtype(newField.xtype);
colInfo.setShape(getShape(colArraySize));


colInfo.setAuxDatum(new DescribedValue(VOStarTable.ID_INFO, newField.id));
colInfo.setAuxDatum(new DescribedValue(new DefaultValueInfo(TABLE_NAME_INFO, String.class),
resultCol.tableName));
colInfo.setAuxDatum(new DescribedValue(new DefaultValueInfo(ACTUAL_COLUMN_NAME_INFO, String.class),
resultCol.getColumnName()));

columnInfoList.add(colInfo);

}

ColumnInfo[] columnInfoArray = columnInfoList.toArray(new ColumnInfo[0]);
Expand Down Expand Up @@ -526,6 +533,27 @@ protected static final Class<?> getDatatypeClass(final TapDataType datatype, fin
}
}

/**
* Convert the given VOTable arraysize into a {@link ColumnInfo} shape.
*
* @param arraysize Value of the VOTable attribute "arraysize".
*
* @return The corresponding {@link ColumnInfo} shape.
*/
protected static final int[] getShape(final String arraysize) {
if (arraysize == null)
return new int[0];
else if (arraysize.charAt(arraysize.length() - 1) == '*')
return new int[]{ -1 };
else {
try {
return new int[]{ Integer.parseInt(arraysize) };
} catch(NumberFormatException nfe) {
return new int[0];
}
}
}

/**
* Generates a list of VOTable meta resources.
*
Expand Down

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