water.parser.CsvParser Maven / Gradle / Ivy
package water.parser;
import org.apache.commons.lang.math.NumberUtils;
import org.apache.http.ParseException;
import water.fvec.Vec;
import water.fvec.FileVec;
import water.Key;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
class CsvParser extends Parser {
private static final byte GUESS_SEP = ParseSetup.GUESS_SEP;
private static final int NO_HEADER = ParseSetup.NO_HEADER;
private static final int GUESS_HEADER = ParseSetup.GUESS_HEADER;
private static final int HAS_HEADER = ParseSetup.HAS_HEADER;
CsvParser( ParseSetup ps, Key jobKey ) { super(ps, jobKey); }
// Parse this one Chunk (in parallel with other Chunks)
@SuppressWarnings("fallthrough")
@Override public ParseWriter parseChunk(int cidx, final ParseReader din, final ParseWriter dout) {
BufferedString str = new BufferedString();
byte[] bits = din.getChunkData(cidx);
if( bits == null ) return dout;
int offset = din.getChunkDataStart(cidx); // General cursor into the giant array of bytes
final byte[] bits0 = bits; // Bits for chunk0
boolean firstChunk = true; // Have not rolled into the 2nd chunk
byte[] bits1 = null; // Bits for chunk1, loaded lazily.
int state;
boolean isNa = false;
boolean isAllASCII = true;
// If handed a skipping offset, then it points just past the prior partial line.
if( offset >= 0 ) state = WHITESPACE_BEFORE_TOKEN;
else {
offset = 0; // Else start skipping at the start
// Starting state. Are we skipping the first (partial) line, or not? Skip
// a header line, or a partial line if we're in the 2nd and later chunks.
if (_setup._check_header == ParseSetup.HAS_HEADER || cidx > 0) state = SKIP_LINE;
else state = WHITESPACE_BEFORE_TOKEN;
}
// For parsing ARFF
if (_setup._parse_type == ParserType.ARFF && _setup._check_header == ParseSetup.HAS_HEADER) state = WHITESPACE_BEFORE_TOKEN;
int quotes = 0;
long number = 0;
int exp = 0;
int sgnExp = 1;
boolean decimal = false;
int fractionDigits = 0;
int tokenStart = 0; // used for numeric token to backtrace if not successful
int colIdx = 0;
byte c = bits[offset];
// skip comments for the first chunk (or if not a chunk)
if( cidx == 0 ) {
while ( c == '#'
|| isEOL(c)
|| c == '@' /*also treat as comments leading '@' from ARFF format*/
|| c == '%' /*also treat as comments leading '%' from ARFF format*/) {
while ((offset < bits.length) && (bits[offset] != CHAR_CR) && (bits[offset ] != CHAR_LF)) {
// System.out.print(String.format("%c",bits[offset]));
++offset;
}
if ((offset + 1 < bits.length) && (bits[offset] == CHAR_CR) && (bits[offset + 1] == CHAR_LF)) ++offset;
++offset;
// System.out.println();
if (offset >= bits.length)
return dout;
c = bits[offset];
}
}
dout.newLine();
final boolean forceable = dout instanceof FVecParseWriter && ((FVecParseWriter)dout)._ctypes != null && _setup._column_types != null;
MAIN_LOOP:
while (true) {
boolean forcedCategorical = forceable && colIdx < _setup._column_types.length && _setup._column_types[colIdx] == Vec.T_CAT;
boolean forcedString = forceable && colIdx < _setup._column_types.length && _setup._column_types[colIdx] == Vec.T_STR;
switch (state) {
// ---------------------------------------------------------------------
case SKIP_LINE:
if (isEOL(c)) {
state = EOL;
} else {
break;
}
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case EXPECT_COND_LF:
state = POSSIBLE_EMPTY_LINE;
if (c == CHAR_LF)
break;
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case STRING:
if (c == quotes) {
state = COND_QUOTE;
break;
}
if (!isEOL(c) && ((quotes != 0) || (c != CHAR_SEPARATOR))) {
str.addChar();
if ((c & 0x80) == 128) //value beyond std ASCII
isAllASCII = false;
break;
}
// fallthrough to STRING_END
// ---------------------------------------------------------------------
case STRING_END:
if ((c != CHAR_SEPARATOR) && (c == CHAR_SPACE))
break;
// we have parsed the string categorical correctly
if((str.getOffset() + str.length()) > str.getBuffer().length){ // crossing chunk boundary
assert str.getBuffer() != bits;
str.addBuff(bits);
}
if( _setup._na_strings != null
&& _setup._na_strings.length > colIdx
&& _setup._na_strings[colIdx] != null) {
for (String s : _setup._na_strings[colIdx]) {
if (str.equals(s)) {
isNa = true;
break;
}
}
}
if (!isNa) {
dout.addStrCol(colIdx, str);
if (!isAllASCII)
dout.setIsAllASCII(colIdx, isAllASCII);
} else {
dout.addInvalidCol(colIdx);
isNa = false;
}
str.set(null, 0, 0);
isAllASCII = true;
++colIdx;
state = SEPARATOR_OR_EOL;
// fallthrough to SEPARATOR_OR_EOL
// ---------------------------------------------------------------------
case SEPARATOR_OR_EOL:
if (c == CHAR_SEPARATOR) {
state = WHITESPACE_BEFORE_TOKEN;
break;
}
if (c==CHAR_SPACE)
break;
// fallthrough to EOL
// ---------------------------------------------------------------------
case EOL:
if(quotes != 0){
//System.err.println("Unmatched quote char " + ((char)quotes) + " " + (((str.length()+1) < offset && str.getOffset() > 0)?new String(Arrays.copyOfRange(bits,str.getOffset()-1,offset)):""));
String err = "Unmatched quote char " + ((char) quotes);
dout.invalidLine(new ParseWriter.ParseErr(err, cidx, dout.lineNum(), offset + din.getGlobalByteOffset()));
colIdx = 0;
quotes = 0;
}else if (colIdx != 0) {
dout.newLine();
colIdx = 0;
}
state = (c == CHAR_CR) ? EXPECT_COND_LF : POSSIBLE_EMPTY_LINE;
if( !firstChunk )
break MAIN_LOOP; // second chunk only does the first row
break;
// ---------------------------------------------------------------------
case POSSIBLE_CURRENCY:
if (((c >= '0') && (c <= '9')) || (c == '-') || (c == CHAR_DECIMAL_SEP) || (c == '+')) {
state = TOKEN;
} else {
str.set(bits, offset - 1, 0);
str.addChar();
if (c == quotes) {
state = COND_QUOTE;
break;
}
if ((quotes != 0) || ((!isEOL(c) && (c != CHAR_SEPARATOR)))) {
state = STRING;
} else {
state = STRING_END;
}
}
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case POSSIBLE_EMPTY_LINE:
if (isEOL(c)) {
if (c == CHAR_CR)
state = EXPECT_COND_LF;
break;
}
state = WHITESPACE_BEFORE_TOKEN;
// fallthrough to WHITESPACE_BEFORE_TOKEN
// ---------------------------------------------------------------------
case WHITESPACE_BEFORE_TOKEN:
if (c == CHAR_SPACE || (c == CHAR_TAB && CHAR_TAB!=CHAR_SEPARATOR)) {
break;
} else if (c == CHAR_SEPARATOR) {
// we have empty token, store as NaN
dout.addInvalidCol(colIdx++);
break;
} else if (isEOL(c)) {
dout.addInvalidCol(colIdx++);
state = EOL;
continue MAIN_LOOP;
}
// fallthrough to COND_QUOTED_TOKEN
// ---------------------------------------------------------------------
case COND_QUOTED_TOKEN:
state = TOKEN;
if( CHAR_SEPARATOR!=HIVE_SEP && // Only allow quoting in CSV not Hive files
((_setup._single_quotes && c == CHAR_SINGLE_QUOTE) || (c == CHAR_DOUBLE_QUOTE))) {
assert (quotes == 0);
quotes = c;
break;
}
// fallthrough to TOKEN
// ---------------------------------------------------------------------
case TOKEN:
if( dout.isString(colIdx) ) { // Forced already to a string col?
state = STRING; // Do not attempt a number parse, just do a string parse
str.set(bits, offset, 0);
continue MAIN_LOOP;
} else if (((c >= '0') && (c <= '9')) || (c == '-') || (c == CHAR_DECIMAL_SEP) || (c == '+')) {
state = NUMBER;
number = 0;
fractionDigits = 0;
decimal = false;
tokenStart = offset;
if (c == '-') {
exp = -1;
break;
} else if(c == '+'){
exp = 1;
break;
} else {
exp = 1;
}
// fallthrough
} else if (c == '$') {
state = POSSIBLE_CURRENCY;
break;
} else {
state = STRING;
str.set(bits, offset, 0);
continue MAIN_LOOP;
}
// fallthrough to NUMBER
// ---------------------------------------------------------------------
case NUMBER:
if ((c >= '0') && (c <= '9')) {
if (number >= LARGEST_DIGIT_NUMBER) state = NUMBER_SKIP;
else number = (number*10)+(c-'0');
break;
} else if (c == CHAR_DECIMAL_SEP) {
state = NUMBER_FRACTION;
fractionDigits = offset;
decimal = true;
break;
} else if ((c == 'e') || (c == 'E')) {
state = NUMBER_EXP_START;
sgnExp = 1;
break;
}
if (exp == -1) {
number = -number;
}
exp = 0;
// fallthrough to COND_QUOTED_NUMBER_END
// ---------------------------------------------------------------------
case COND_QUOTED_NUMBER_END:
if ( c == quotes) {
state = NUMBER_END;
quotes = 0;
break;
}
// fallthrough NUMBER_END
case NUMBER_END:
// forced
if (forcedString || forcedCategorical ) {
state = STRING;
offset = tokenStart - 1;
str.set(bits, tokenStart, 0);
break; // parse as String token now
}
if (c == CHAR_SEPARATOR && quotes == 0) {
exp = exp - fractionDigits;
dout.addNumCol(colIdx,number,exp);
++colIdx;
// do separator state here too
state = WHITESPACE_BEFORE_TOKEN;
break;
} else if (isEOL(c)) {
exp = exp - fractionDigits;
dout.addNumCol(colIdx,number,exp);
// do EOL here for speedup reasons
colIdx = 0;
dout.newLine();
state = (c == CHAR_CR) ? EXPECT_COND_LF : POSSIBLE_EMPTY_LINE;
if( !firstChunk )
break MAIN_LOOP; // second chunk only does the first row
break;
} else if ((c == '%')) {
state = NUMBER_END;
exp -= 2;
break;
} else if ((c != CHAR_SEPARATOR) && ((c == CHAR_SPACE) || (c == CHAR_TAB))) {
state = NUMBER_END;
break;
} else {
state = STRING;
offset = tokenStart-1;
str.set(bits, tokenStart, 0);
break; // parse as String token now
}
// ---------------------------------------------------------------------
case NUMBER_SKIP:
if ((c >= '0') && (c <= '9')) {
exp++;
break;
} else if (c == CHAR_DECIMAL_SEP) {
state = NUMBER_SKIP_NO_DOT;
break;
} else if ((c == 'e') || (c == 'E')) {
state = NUMBER_EXP_START;
sgnExp = 1;
break;
}
state = COND_QUOTED_NUMBER_END;
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case NUMBER_SKIP_NO_DOT:
if ((c >= '0') && (c <= '9')) {
break;
} else if ((c == 'e') || (c == 'E')) {
state = NUMBER_EXP_START;
sgnExp = 1;
break;
}
state = COND_QUOTED_NUMBER_END;
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case NUMBER_FRACTION:
if ((c >= '0') && (c <= '9')) {
if (number >= LARGEST_DIGIT_NUMBER) {
if (decimal)
fractionDigits = offset - 1 - fractionDigits;
if (exp == -1) number = -number;
exp = 0;
state = NUMBER_SKIP_NO_DOT;
} else {
number = (number*10)+(c-'0');
}
break;
} else if ((c == 'e') || (c == 'E')) {
if (decimal)
fractionDigits = offset - 1 - fractionDigits;
state = NUMBER_EXP_START;
sgnExp = 1;
break;
}
state = COND_QUOTED_NUMBER_END;
if (decimal)
fractionDigits = offset - fractionDigits-1;
if (exp == -1) {
number = -number;
}
exp = 0;
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case NUMBER_EXP_START:
if (exp == -1) {
number = -number;
}
exp = 0;
if (c == '-') {
sgnExp *= -1;
break;
} else if (c == '+'){
break;
}
if ((c < '0') || (c > '9')){
state = STRING;
offset = tokenStart-1;
str.set(bits, tokenStart, 0);
break; // parse as String token now
}
state = NUMBER_EXP; // fall through to NUMBER_EXP
// ---------------------------------------------------------------------
case NUMBER_EXP:
if ((c >= '0') && (c <= '9')) {
exp = (exp*10)+(c-'0');
break;
}
exp *= sgnExp;
state = COND_QUOTED_NUMBER_END;
continue MAIN_LOOP;
// ---------------------------------------------------------------------
case COND_QUOTE:
if (c == quotes) {
str.addChar();
state = STRING;
break;
} else {
quotes = 0;
state = STRING_END;
continue MAIN_LOOP;
}
// ---------------------------------------------------------------------
default:
assert (false) : " We have wrong state "+state;
} // end NEXT_CHAR
// System.out.print(String.format("%c",bits[offset]));
++offset; // do not need to adjust for offset increase here - the offset is set to tokenStart-1!
if (offset < 0) { // Offset is negative?
assert !firstChunk; // Caused by backing up from 2nd chunk into 1st chunk
firstChunk = true;
bits = bits0;
offset += bits.length;
str.set(bits, offset, 0);
} else if (offset >= bits.length) { // Off end of 1st chunk? Parse into 2nd chunk
// Attempt to get more data.
if( firstChunk && bits1 == null )
bits1 = din.getChunkData(cidx+1);
// if we can't get further we might have been the last one and we must
// commit the latest guy if we had one.
if( !firstChunk || bits1 == null ) { // No more data available or allowed
// If we are mid-parse of something, act like we saw a LF to end the
// current token.
if ((state != EXPECT_COND_LF) && (state != POSSIBLE_EMPTY_LINE)) {
c = CHAR_LF; continue; // MAIN_LOOP;
}
break; // MAIN_LOOP; // Else we are just done
}
// Now parsing in the 2nd chunk. All offsets relative to the 2nd chunk start.
firstChunk = false;
if (state == NUMBER_FRACTION)
fractionDigits -= bits.length;
offset -= bits.length;
tokenStart -= bits.length;
bits = bits1; // Set main parsing loop bits
if( bits[0] == CHAR_LF && state == EXPECT_COND_LF )
break; // MAIN_LOOP; // when the first character we see is a line end
}
c = bits[offset];
if(isEOL(c) && state != COND_QUOTE && quotes != 0) // quoted string having newline character => fail the line!
state = EOL;
} // end MAIN_LOOP
if (colIdx == 0)
dout.rollbackLine();
// If offset is still validly within the buffer, save it so the next pass
// can start from there.
if( offset+1 < bits.length ) {
if( state == EXPECT_COND_LF && bits[offset+1] == CHAR_LF ) offset++;
if( offset+1 < bits.length ) din.setChunkDataStart(cidx+1, offset+1 );
}
return dout;
}
@Override protected int fileHasHeader(byte[] bits, ParseSetup ps) {
boolean hasHdr = true;
String[] lines = getFirstLines(bits);
if (lines != null && lines.length > 0) {
String[] firstLine = determineTokens(lines[0], _setup._separator, _setup._single_quotes);
if (_setup._column_names != null) {
for (int i = 0; hasHdr && i < firstLine.length; ++i)
hasHdr = (_setup._column_names[i] == firstLine[i]) || (_setup._column_names[i] != null && _setup._column_names[i].equalsIgnoreCase(firstLine[i]));
} else { // declared to have header, but no column names provided, assume header exist in all files
_setup._column_names = firstLine;
}
} // else FIXME Throw exception
return hasHdr ? ParseSetup.HAS_HEADER: ParseSetup.NO_HEADER;
// consider making insensitive to quotes
}
// ==========================================================================
/** Separators recognized by the CSV parser. You can add new separators to
* this list and the parser will automatically attempt to recognize them.
* In case of doubt the separators are listed in descending order of
* probability, with space being the last one - space must always be the
* last one as it is used if all other fails because multiple spaces can be
* used as a single separator.
*/
static final byte HIVE_SEP = 0x1; // '^A', Hive table column separator
private static byte[] separators = new byte[] { HIVE_SEP, ',', ';', '|', '\t', ' '/*space is last in this list, because we allow multiple spaces*/ };
/** Dermines the number of separators in given line. Correctly handles quoted tokens. */
private static int[] determineSeparatorCounts(String from, byte singleQuote) {
int[] result = new int[separators.length];
byte[] bits = from.getBytes();
boolean inQuote = false;
for( byte c : bits ) {
if( (c == singleQuote) || (c == CsvParser.CHAR_DOUBLE_QUOTE) )
inQuote ^= true;
if( !inQuote || c == HIVE_SEP )
for( int i = 0; i < separators.length; ++i )
if( c == separators[i] )
++result[i];
}
return result;
}
/** Determines the tokens that are inside a line and returns them as strings
* in an array. Assumes the given separator.
*/
public static String[] determineTokens(String from, byte separator, boolean singleQuotes) {
final byte singleQuote = singleQuotes ? CsvParser.CHAR_SINGLE_QUOTE : -1;
return determineTokens(from, separator, singleQuote);
}
public static String[] determineTokens(String from, byte separator, byte singleQuote) {
ArrayList tokens = new ArrayList<>();
byte[] bits = from.getBytes();
int offset = 0;
int quotes = 0;
while (offset < bits.length) {
while ((offset < bits.length) && (bits[offset] == CsvParser.CHAR_SPACE)) ++offset; // skip first whitespace
if(offset == bits.length)break;
StringBuilder t = new StringBuilder();
byte c = bits[offset];
if ((c == CsvParser.CHAR_DOUBLE_QUOTE) || (c == singleQuote)) {
quotes = c;
++offset;
}
while (offset < bits.length) {
c = bits[offset];
if ((c == quotes)) {
++offset;
if ((offset < bits.length) && (bits[offset] == c)) {
t.append((char)c);
++offset;
continue;
}
quotes = 0;
} else if( quotes == 0 && ((c == separator) || CsvParser.isEOL(c)) ) {
break;
} else {
t.append((char)c);
++offset;
}
}
c = (offset == bits.length) ? CsvParser.CHAR_LF : bits[offset];
tokens.add(t.toString());
if( CsvParser.isEOL(c) || (offset == bits.length) )
break;
if (c != separator)
return new String[0]; // an error
++offset; // Skip separator
}
// If we have trailing empty columns (split by separators) such as ",,\n"
// then we did not add the final (empty) column, so the column count will
// be down by 1. Add an extra empty column here
if( bits.length > 0 && bits[bits.length-1] == separator && bits[bits.length-1] != CsvParser.CHAR_SPACE)
tokens.add("");
return tokens.toArray(new String[tokens.size()]);
}
public static byte guessSeparator(String l1, String l2, boolean singleQuotes) {
final byte singleQuote = singleQuotes ? CsvParser.CHAR_SINGLE_QUOTE : -1;
int[] s1 = determineSeparatorCounts(l1, singleQuote);
int[] s2 = determineSeparatorCounts(l2, singleQuote);
// Now we have the counts - if both lines have the same number of
// separators the we assume it is the separator. Separators are ordered by
// their likelyhoods.
int max = 0;
for( int i = 0; i < s1.length; ++i ) {
if( s1[i] == 0 ) continue; // Separator does not appear; ignore it
if( s1[max] < s1[i] ) max=i; // Largest count sep on 1st line
if( s1[i] == s2[i] ) { // Sep counts are equal?
try {
String[] t1 = determineTokens(l1, separators[i], singleQuote);
String[] t2 = determineTokens(l2, separators[i], singleQuote);
if( t1.length != s1[i]+1 || t2.length != s2[i]+1 )
continue; // Token parsing fails
return separators[i];
} catch( Exception ignore ) { /*pass; try another parse attempt*/ }
}
}
// No sep's appeared, or no sep's had equal counts on lines 1 & 2. If no
// separators have same counts, the largest one will be used as the default
// one. If there's no largest one, space will be used.
if( s1[max]==0 ) max=separators.length-1; // Try last separator (space)
if( s1[max]!=0 ) {
String[] t1 = determineTokens(l1, separators[max], singleQuote);
String[] t2 = determineTokens(l2, separators[max], singleQuote);
if( t1.length == s1[max]+1 && t2.length == s2[max]+1 )
return separators[max];
}
return GUESS_SEP;
}
// Guess number of columns
public static int guessNcols( String[] columnNames, String[][] data ) {
if( columnNames != null ) return data[0].length;
int longest = 0; // Longest line
for( String[] s : data ) if( s.length > longest ) longest = s.length;
if( longest == data[0].length )
return longest; // 1st line is longer than all the rest; take it
// we don't have lines of same length, pick the most common length
int lengths[] = new int[longest+1];
for( String[] s : data ) lengths[s.length]++;
int maxCnt = 0; // Most common line length
for( int i=0; i<=longest; i++ ) if( lengths[i] > lengths[maxCnt] ) maxCnt = i;
return maxCnt;
}
/** Determines the CSV parser setup from the first few lines. Also parses
* the next few lines, tossing out comments and blank lines.
*
* If the separator is GUESS_SEP, then it is guessed by looking at tokenization
* and column count of the first few lines.
*
* If ncols is -1, then it is guessed similarly to the separator.
*
* singleQuotes is honored in all cases (and not guessed).
*
*/
static ParseSetup guessSetup(byte[] bits, byte sep, int ncols, boolean singleQuotes, int checkHeader, String[] columnNames, byte[] columnTypes, String[][] naStrings) {
String[] lines = getFirstLines(bits);
if(lines.length==0 )
throw new ParseDataset.H2OParseException("No data!");
// Guess the separator, columns, & header
String[] labels;
final String[][] data = new String[lines.length][];
if( lines.length == 1 ) { // Ummm??? Only 1 line?
if( sep == GUESS_SEP) {
if (lines[0].split(",").length > 1) sep = (byte) ',';
else if (lines[0].split(" ").length > 1) sep = ' ';
else { //one item, guess type
data[0] = new String[]{lines[0]};
byte[] ctypes = new byte[1];
String[][] domains = new String[1][];
if (NumberUtils.isNumber(data[0][0])) {
ctypes[0] = Vec.T_NUM;
} else { // non-numeric
BufferedString str = new BufferedString(data[0][0]);
if (ParseTime.isTime(str))
ctypes[0] = Vec.T_TIME;
else if (ParseUUID.isUUID(str))
ctypes[0] = Vec.T_UUID;
else { // give up and guess categorical
ctypes[0] = Vec.T_CAT;
domains[0] = new String[]{data[0][0]};
}
}
//FIXME should set warning message and let fall through
return new ParseSetup(ParserType.CSV, GUESS_SEP, singleQuotes, checkHeader, 1, null, ctypes, domains, naStrings, data, new ParseWriter.ParseErr[0],FileVec.DFLT_CHUNK_SIZE);
}
}
data[0] = determineTokens(lines[0], sep, singleQuotes);
ncols = (ncols > 0) ? ncols : data[0].length;
if( checkHeader == GUESS_HEADER) {
if (ParseSetup.allStrings(data[0]) && !data[0][0].isEmpty()) {
labels = data[0];
checkHeader = HAS_HEADER;
} else {
labels = null;
checkHeader = NO_HEADER;
}
}
else if( checkHeader == HAS_HEADER ) labels = data[0];
else labels = null;
} else { // 2 or more lines
// First guess the field separator by counting occurrences in first few lines
if( sep == GUESS_SEP) { // first guess the separator
sep = guessSeparator(lines[0], lines[1], singleQuotes);
if( sep == GUESS_SEP && lines.length > 2 ) {
sep = guessSeparator(lines[1], lines[2], singleQuotes);
if( sep == GUESS_SEP) sep = guessSeparator(lines[0], lines[2], singleQuotes);
}
if( sep == GUESS_SEP) sep = (byte)' '; // Bail out, go for space
}
// Tokenize the first few lines using the separator
for( int i = 0; i < lines.length; ++i )
data[i] = determineTokens(lines[i], sep, singleQuotes );
// guess columns from tokenization
ncols = guessNcols(columnNames,data);
// Asked to check for a header, so see if 1st line looks header-ish
if( checkHeader == HAS_HEADER
|| ( checkHeader == GUESS_HEADER && ParseSetup.hasHeader(data[0], data[1]))) {
checkHeader = HAS_HEADER;
labels = data[0];
} else {
checkHeader = NO_HEADER;
labels = columnNames;
}
// See if compatible headers
if( columnNames != null && labels != null ) {
if( labels.length != columnNames.length )
throw new ParseDataset.H2OParseException("Already have "+columnNames.length+" column labels, but found "+labels.length+" in this file");
else {
for( int i = 0; i < labels.length; ++i )
if( !labels[i].equalsIgnoreCase(columnNames[i]) ) {
throw new ParseDataset.H2OParseException("Column "+(i+1)+" label '"+labels[i]+"' does not match '"+columnNames[i]+"'");
}
labels = columnNames; // Keep prior case & count in any case
}
}
}
// Assemble the setup understood so far
ParseSetup resSetup = new ParseSetup(ParserType.CSV, sep, singleQuotes, checkHeader, ncols, labels, null, null /*domains*/, naStrings, data);
// now guess the types
if (columnTypes == null || ncols != columnTypes.length) {
InputStream is = new ByteArrayInputStream(bits);
CsvParser p = new CsvParser(resSetup, null);
PreviewParseWriter dout = new PreviewParseWriter(resSetup._number_columns);
try {
p.streamParse(is, dout);
resSetup._column_previews = dout;
resSetup._errs = dout._errs;
} catch (Throwable e) {
throw new RuntimeException(e);
}
} else {
// If user sets column type as unknown/bad, guess numeric.
for(int i=0; i < columnTypes.length; i++) if (columnTypes[i] == Vec.T_BAD) columnTypes[i] = Vec.T_NUM;
resSetup._column_types = columnTypes;
resSetup._na_strings = null;
}
// Return the final setup
return resSetup;
}
private static String[] getFirstLines(byte[] bits) {
// Parse up to 10 lines (skipping hash-comments & ARFF comments)
String[] lines = new String[10]; // Parse 10 lines
int nlines = 0;
int offset = 0;
while( offset < bits.length && nlines < lines.length ) {
int lineStart = offset;
while( offset < bits.length && !CsvParser.isEOL(bits[offset]) ) ++offset;
int lineEnd = offset;
++offset;
// For Windoze, skip a trailing LF after CR
if( (offset < bits.length) && (bits[offset] == CsvParser.CHAR_LF)) ++offset;
if( bits[lineStart] == '#') continue; // Ignore comment lines
if( bits[lineStart] == '%') continue; // Ignore ARFF comment lines
if( bits[lineStart] == '@') continue; // Ignore ARFF lines
if( lineEnd > lineStart ) {
String str = new String(bits, lineStart,lineEnd-lineStart).trim();
if( !str.isEmpty() ) lines[nlines++] = str;
}
}
return Arrays.copyOf(lines, nlines);
}
}
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