From 021054e428566fa0a81c0ebada457b8e50511151 Mon Sep 17 00:00:00 2001
From: gmantele <gmantele@ari.uni-heidelberg.de>
Date: Fri, 23 Jan 2015 15:54:23 +0100
Subject: [PATCH] [UWS,TAP] Fix UPLOAD bug (the last line of the table to
upload was ignored). Fix an improbable NullPointerException in the
MultipartParser.
---
src/tap/data/VOTableIterator.java | 129 ++++++++++---------
src/tap/parameters/DALIUpload.java | 2 +-
src/uws/service/request/MultipartParser.java | 2 +
3 files changed, 72 insertions(+), 61 deletions(-)
diff --git a/src/tap/data/VOTableIterator.java b/src/tap/data/VOTableIterator.java
index c7bd03b..e60d5a8 100644
--- a/src/tap/data/VOTableIterator.java
+++ b/src/tap/data/VOTableIterator.java
@@ -51,17 +51,17 @@ public class VOTableIterator implements TableIterator {
* <p><i>Note: this may be NULL after the metadata has been read if an error occurred while performing the conversion.
* In this case, metaError contains this error.</> */
private TAPColumn[] meta = null;
-
+
/** The error which happened while converting the StarTable metadata into TAP metadata. */
private DataReadException metaError = null;
-
+
/** The last accepted row. */
private Object[] pendingRow = null;
-
+
/** Flag meaning that the end of the stream has been reached
* OR if the VOTable reading should be stopped before reading more rows. */
private boolean endReached = false;
-
+
/**
* <p>Stop nicely reading the VOTable.</p>
*
@@ -74,17 +74,17 @@ public class VOTableIterator implements TableIterator {
endReached = true;
notifyAll();
}
-
+
@Override
- public synchronized void acceptMetadata(final StarTable metaTable) throws TableFormatException {
+ public synchronized void acceptMetadata(final StarTable metaTable) throws TableFormatException{
try{
// Convert the StartTable metadata into TAP metadata:
meta = extractColMeta(metaTable);
-
+
}catch(DataReadException dre){
// Save the error ; this error will be throw when a call to getMetadata() will be done:
metaError = dre;
-
+
}finally{
// Free all waiting threads:
notifyAll();
@@ -92,18 +92,18 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public synchronized void acceptRow(final Object[] row) throws IOException {
+ public synchronized void acceptRow(final Object[] row) throws IOException{
try{
// Wait until the last accepted row has been consumed:
while(!endReached && pendingRow != null)
wait();
-
+
/* If the end has been reached, this is not normal
* (because endRows() is always called after acceptRow()...so, it means the iteration has been aborted before the end)
* and so the stream reading should be interrupted: */
if (endReached)
throw new IOException("Streaming aborted!");
-
+
// Otherwise, keep the given row:
pendingRow = row;
@@ -113,13 +113,13 @@ public class VOTableIterator implements TableIterator {
* ...which should then mean that the end of the stream has been reached. */
if (pendingRow == null)
endReached = true;
-
+
}catch(InterruptedException ie){
/* If the thread has been interrupted, set this TableSink in a state similar to
* when the end of the stream has been reached: */
pendingRow = null;
endReached = true;
-
+
}finally{
// In all cases, all waiting threads must be freed:
notifyAll();
@@ -127,15 +127,23 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public synchronized void endRows() throws IOException {
- // No more rows are available:
- pendingRow = null;
- // Set the END flag:
- endReached = true;
- // Notify all waiting threads that the end has been reached:
- notifyAll();
+ public synchronized void endRows() throws IOException{
+ try{
+ // Wait until the last accepted row has been consumed:
+ while(!endReached && pendingRow != null)
+ wait();
+ }catch(InterruptedException ie){
+ /* Nothing to do in particular ; the end of the stream will be set anyway. */
+ }finally{
+ // No more rows are available:
+ pendingRow = null;
+ // Set the END flag:
+ endReached = true;
+ // Notify all waiting threads that the end has been reached:
+ notifyAll();
+ }
}
-
+
/**
* <p>Get the metadata found in the VOTable.</p>
*
@@ -154,14 +162,14 @@ public class VOTableIterator implements TableIterator {
// Wait until metadata are available, or if an error has occurred while accepting them:
while(metaError == null && meta == null)
wait();
-
+
// If there was an error while interpreting the accepted metadata, throw it:
if (metaError != null)
throw metaError;
-
+
// Otherwise, just return the metadata:
return meta;
-
+
}catch(InterruptedException ie){
/* If the thread has been interrupted, set this TableSink in a state similar to
* when the end of the stream has been reached: */
@@ -169,13 +177,13 @@ public class VOTableIterator implements TableIterator {
/* Return the metadata ;
* NULL will be returned if the interruption has occurred before the real reading of the VOTable metadata: */
return meta;
-
+
}finally{
// In all cases, the waiting threads must be freed:
notifyAll();
}
}
-
+
/**
* <p>Get the last accepted row.</p>
*
@@ -186,35 +194,35 @@ public class VOTableIterator implements TableIterator {
*
* @return
*/
- public synchronized Object[] getRow() {
+ public synchronized Object[] getRow(){
try{
// Wait until a row has been accepted or the end has been reached:
while(!endReached && pendingRow == null)
wait();
-
+
// If there is no more rows, just return NULL (meaning for the called "end of stream"):
- if (endReached)
+ if (endReached && pendingRow == null)
return null;
-
+
/* Otherwise, reset pendingRow to NULL in order to enable the reading of the next row,
* and finally return the last accepted row: */
Object[] row = pendingRow;
pendingRow = null;
return row;
-
+
}catch(InterruptedException ie){
/* If the thread has been interrupted, set this TableSink in a state similar to
* when the end of the stream has been reached: */
endReached = true;
// Return NULL, meaning the end of the stream has been reached:
return null;
-
- }finally {
+
+ }finally{
// In all cases, the waiting threads must be freed:
notifyAll();
}
}
-
+
/**
* Extract an array of {@link TAPColumn} objects. Each corresponds to one of the columns listed in the given table,
* and so corresponds to the metadata of a column.
@@ -307,9 +315,9 @@ public class VOTableIterator implements TableIterator {
// Build the VOTable type:
return new VotType(votdatatype, arraysize, xtype);
}
-
+
}
-
+
/** Stream containing the VOTable on which this {@link TableIterator} is iterating. */
protected final InputStream input;
/** The StarTable consumer which is used to iterate on each row. */
@@ -319,14 +327,14 @@ public class VOTableIterator implements TableIterator {
protected boolean iterationStarted = false;
/** Indicate whether the last row has already been reached. */
protected boolean endReached = false;
-
+
/** The last read row. Column iteration is done on this array. */
protected Object[] row;
/** Index of the last read column (=0 just after {@link #nextRow()} and before {@link #nextCol()}, ={@link #nbColumns} after the last column has been read). */
protected int indCol = -1;
/** Number of columns available according to the metadata. */
protected int nbCol = 0;
-
+
/**
* Build a TableIterator able to read rows and columns inside the given VOTable input stream.
*
@@ -340,7 +348,7 @@ public class VOTableIterator implements TableIterator {
if (input == null)
throw new NullPointerException("Missing VOTable document input stream over which to iterate!");
this.input = input;
-
+
try{
// Set the VOTable builder/interpreter:
@@ -348,19 +356,20 @@ public class VOTableIterator implements TableIterator {
// Build the TableSink to use:
sink = new StreamVOTableSink();
-
+
// Initiate the stream process:
- Thread streamThread = new Thread() {
- public void run() {
- try{
- tb.streamStarTable(input, sink, null);
- }catch(IOException e) {
- if (e.getMessage() != null && !e.getMessage().equals("Reading interrupted!"))
- e.printStackTrace();
- }
- }
- };
- streamThread.start();
+ Thread streamThread = new Thread(){
+ @Override
+ public void run(){
+ try{
+ tb.streamStarTable(input, sink, null);
+ }catch(IOException e){
+ if (e.getMessage() != null && !e.getMessage().equals("Reading interrupted!"))
+ e.printStackTrace();
+ }
+ }
+ };
+ streamThread.start();
}catch(Exception ex){
throw new DataReadException("Unable to parse/read the given VOTable input stream!", ex);
@@ -368,33 +377,33 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public TAPColumn[] getMetadata() throws DataReadException {
+ public TAPColumn[] getMetadata() throws DataReadException{
return sink.getMeta();
}
@Override
- public boolean nextRow() throws DataReadException {
+ public boolean nextRow() throws DataReadException{
// If no more rows, return false directly:
if (endReached)
return false;
-
+
// Fetch the row:
row = sink.getRow();
-
+
// Reset the column iteration:
if (!iterationStarted){
iterationStarted = true;
nbCol = sink.getMeta().length;
}
indCol = 0;
-
+
// Tells whether there is more rows or not:
endReached = (row == null);
return !endReached;
}
@Override
- public boolean hasNextCol() throws IllegalStateException, DataReadException {
+ public boolean hasNextCol() throws IllegalStateException, DataReadException{
// Check the read state:
checkReadState();
@@ -403,7 +412,7 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public Object nextCol() throws NoSuchElementException, IllegalStateException, DataReadException {
+ public Object nextCol() throws NoSuchElementException, IllegalStateException, DataReadException{
// Check the read state and ensure there is still at least one column to read:
if (!hasNextCol())
throw new NoSuchElementException("No more field to read!");
@@ -413,7 +422,7 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public DBType getColType() throws IllegalStateException, DataReadException {
+ public DBType getColType() throws IllegalStateException, DataReadException{
// Basically check the read state (for rows iteration):
checkReadState();
@@ -428,7 +437,7 @@ public class VOTableIterator implements TableIterator {
}
@Override
- public void close() throws DataReadException {
+ public void close() throws DataReadException{
endReached = true;
sink.stop();
// input.close(); // in case sink.stop() is not enough to stop the VOTable reading!
diff --git a/src/tap/parameters/DALIUpload.java b/src/tap/parameters/DALIUpload.java
index 71694b8..e55c74a 100644
--- a/src/tap/parameters/DALIUpload.java
+++ b/src/tap/parameters/DALIUpload.java
@@ -512,7 +512,7 @@ public class DALIUpload {
// Check the label:
if (!parts[0].matches("[a-zA-Z][a-zA-Z0-9_]*"))
- throw new TAPException("Wrong uploaded item name syntax: \"" + parts[0] + "\"! An uploaded item must have a label with the syntax: [a-zA-Z][a-zA-Z0-9_]*.", UWSException.BAD_REQUEST);
+ throw new TAPException("Wrong uploaded item name syntax: \"" + parts[0] + "\"! An uploaded item must have a label respecting the 'regular_identifier' production of ADQL 2.0 (regular expression: [a-zA-Z][a-zA-Z0-9_]*).", UWSException.BAD_REQUEST);
// Check the URI:
else if (!parts[1].matches("[a-zA-Z][a-zA-Z0-9\\+\\.\\-]*:.+"))
throw new TAPException("Bad URI syntax: \"" + parts[1] + "\"! A URI must start with: \"<scheme>:\", where <scheme>=\"[a-zA-Z][a-zA-Z0-9+.-]*\".", UWSException.BAD_REQUEST);
diff --git a/src/uws/service/request/MultipartParser.java b/src/uws/service/request/MultipartParser.java
index 5d4fc6a..a6760ac 100644
--- a/src/uws/service/request/MultipartParser.java
+++ b/src/uws/service/request/MultipartParser.java
@@ -166,6 +166,8 @@ public class MultipartParser implements RequestParser {
throw new UWSException(UWSException.BAD_REQUEST, "Uploads are not allowed by this service!");
while(e.hasMoreElements()){
param = e.nextElement();
+ if (multipart.getFile(param) == null)
+ continue;
/*
* TODO !!!POSSIBLE ISSUE!!!
--
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