Adding first version of parser.

SVN: 116

common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java

+package ch.systemsx.cisd.common.parser;
+
+import java.util.EnumMap;
+import java.util.Map;
+
+import org.apache.commons.lang.text.StrMatcher;
+import org.apache.commons.lang.text.StrTokenizer;
+
+/**
+ * A default <code>ILineTokenizer</code> implementation that parses a line into an array of <code>String</code>
+ * objects.
+ * <p>
+ * The default separator chars used here are <code>\t</code>. If you want to change that, use
+ * {@link #setProperty(PropertyKey, String)} with corresponding property key defined here.
+ * </p>
+ * 
+ * @author Christian Ribeaud
+ */
+public class DefaultLineTokenizer implements ILineTokenizer
+{
+    
+    /** Allowed <code>Properties</code> keys. */
+    public static enum PropertyKey {
+        /** The property key for setting some delimiter characters. */
+        SEPARATOR_CHARS,
+        /** The property key for setting some quote characters. */
+        QUOTE_CHARS,
+        /** The property key for setting some ignored characters. */
+        IGNORED_CHARS,
+        /** The property key for setting some trimmer characters. */
+        TRIMMER_CHARS,
+    }
+    
+    /** Some properties for this tab parser. */
+    private final Map<PropertyKey, String> properties;
+    
+    private StrTokenizer tokenizer;
+    
+    public DefaultLineTokenizer()
+    {
+        this.properties = new EnumMap<PropertyKey, String>(PropertyKey.class);
+    }
+
+    /**
+     * Sets a property for this <code>TabReaderParser</code>.
+     * 
+     * @throws IllegalArgumentException if given <code>key</code> could not found in {@link PropertyKey}.
+     */
+    public final void setProperty(PropertyKey key, String value)
+    {
+        properties.put(key, value);
+    }
+    
+    /** Converts a defined <code>PropertyKey</code> into <code>StrMatcher</code>. */
+    private final StrMatcher getStrMatcher(PropertyKey key, StrMatcher defaultMatcher) {
+        StrMatcher strMatcher = defaultMatcher;
+        String value = properties.get(key);
+        if (value != null)
+        {
+            strMatcher = StrMatcher.charSetMatcher(value);
+        }
+        return strMatcher;
+    }
+    
+    ///////////////////////////////////////////////////////
+    // ILineTokenizer
+    ///////////////////////////////////////////////////////
+    
+    public final void init()
+    {   
+        StrTokenizer strTokenizer = new StrTokenizer();
+        strTokenizer.setDelimiterMatcher(getStrMatcher(PropertyKey.SEPARATOR_CHARS, StrMatcher.tabMatcher()));
+        strTokenizer.setQuoteMatcher(getStrMatcher(PropertyKey.QUOTE_CHARS, StrMatcher.noneMatcher()));
+        strTokenizer.setTrimmerMatcher(getStrMatcher(PropertyKey.TRIMMER_CHARS, StrMatcher.trimMatcher()));
+        strTokenizer.setIgnoredMatcher(getStrMatcher(PropertyKey.IGNORED_CHARS, StrMatcher.noneMatcher()));
+        strTokenizer.setEmptyTokenAsNull(false);
+        strTokenizer.setIgnoreEmptyTokens(false);
+        this.tokenizer = strTokenizer;
+    }
+    
+    public final String[] tokenize(int lineNumber, String line)
+    {
+        return tokenizer.reset(line).getTokenArray();
+    }
+    
+    public final void destroy()
+    {
+        tokenizer = null;
+    }
+}
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/DefaultPropertyMapper.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * 
+ *
+ * @author Christian Ribeaud
+ */
+public class DefaultPropertyMapper implements IPropertyMapper
+{
+    private final Map<String, Property> properties;
+    
+    DefaultPropertyMapper(List<Property> properties) {
+        this.properties = listToMap(properties);
+    }
+    
+    private final static Map<String, Property> listToMap(List<Property> properties)
+    {
+        Map<String, Property> map = new HashMap<String, Property>(properties.size());
+        for (Property property : properties)
+        {
+            map.put(property.name, property);
+        }
+        return map;
+    }
+
+    ///////////////////////////////////////////////////////
+    // IPropertyMapper
+    ///////////////////////////////////////////////////////
+
+    public Property getProperty(String name)
+    {
+        return properties.get(name);
+    }
+
+}

common/source/java/ch/systemsx/cisd/common/parser/DefaultReaderParser.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
+
+/**
+ * A default <code>IReaderParser</code> implementation.
+ * <p>
+ * The object type returned by this implementation is generic. This implementation defines a <code>ILineFilter</code>
+ * that filters out comment and empty lines.
+ * </p>
+ * 
+ * @author Christian Ribeaud
+ */
+public class DefaultReaderParser<E> implements IReaderParser<E>
+{
+    /**
+     * A <code>LineFilter</code> implementation that filters out comment and empty lines (lines starting with '#').
+     */
+    private final static ILineFilter COMMENT_AND_EMPTY_LINE_FILTER = new ILineFilter()
+        {
+            ///////////////////////////////////////////////////////
+            // LineFilter
+            ///////////////////////////////////////////////////////
+
+            public boolean acceptLine(String line)
+            {
+                String trimmed = line.trim();
+                return trimmed.length() > 0 && trimmed.startsWith("#") == false;
+            }
+        };
+
+    private final ILineTokenizer lineTokenizer;
+    
+    private IParserObjectFactory<E> factory;
+    
+    private IPropertyMapperFactory mapperFactory;
+    
+    public DefaultReaderParser()
+    {
+        this(new DefaultLineTokenizer());
+    }
+    
+    public DefaultReaderParser(ILineTokenizer lineTokenizer)
+    {
+        this.lineTokenizer = lineTokenizer;
+    }
+    
+    protected E createObject(String[] tokens) {
+        return factory.createObject(tokens);
+    }
+    
+    /**
+     * Parses given <code>line</code> into an element.
+     * <p>
+     * Uses <code>ILineTokenizer</code> to do its job.
+     * </p>
+     */
+    protected String[] parseLine(int lineNumber, String line)
+    {
+        return lineTokenizer.tokenize(lineNumber, line);
+    }
+    
+    /** Inits the parsing. */
+    protected void initParsing() {
+        // Inits <code>ILineTokenizer</code>
+        lineTokenizer.init();
+        String line;
+        // 
+        if (mapperFactory.getHeaderLine() < 0)
+        {
+            
+        }
+    }
+    
+    ///////////////////////////////////////////////////////
+    // Parser
+    ///////////////////////////////////////////////////////
+
+    public final List<E> parse(Reader reader)
+    {
+        return parse(reader, COMMENT_AND_EMPTY_LINE_FILTER);
+    }
+
+    public final List<E> parse(Reader reader, ILineFilter lineFilter)
+    {
+        BufferedReader bufferedReader;
+        if (reader instanceof BufferedReader)
+        {
+            bufferedReader = (BufferedReader) reader;
+        } else
+        {
+            bufferedReader = new BufferedReader(reader);
+        }
+        List<E> elements = new ArrayList<E>();
+        synchronized (lineTokenizer)
+        {
+            initParsing();
+            String line;
+            try
+            {
+                for (int lineNumber = 0; (line = bufferedReader.readLine()) != null; lineNumber++)
+                {
+                    if (mapperFactory.getHeaderLine() > -1)
+                    {
+                        String[] tokens = parseLine(lineNumber, line);
+                        factory.setPropertyMapper(mapperFactory.createPropertyMapper(tokens));
+                        continue;
+                    }
+                    if (lineFilter.acceptLine(line))
+                    {
+                        String[] tokens = parseLine(lineNumber, line);
+                        elements.add(createObject(tokens));
+                    }
+                }
+                return elements;
+            } catch (IOException ex)
+            {
+                throw new CheckedExceptionTunnel(ex);
+            } finally
+            {
+                // Destroys line tokenizer.
+                lineTokenizer.destroy();
+            }
+
+        }
+
+    }
+
+    public final void setObjectFactory(IParserObjectFactory<E> factory)
+    {
+        this.factory = factory;
+    }
+
+    public final void setPropertyMapperFactory(IPropertyMapperFactory mapperFactory)
+    {
+        this.mapperFactory = mapperFactory;
+    }
+}
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/HeaderFilePropertyMapper.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * 
+ *
+ * @author Christian Ribeaud
+ */
+public class HeaderFilePropertyMapper implements IPropertyMapper
+{
+    public final static char NAME_FORMAT_SEPARATOR = ',';
+    
+    private final Map<String, Property> properties;
+    
+    HeaderFilePropertyMapper(String[] headerTokens) {
+        this.properties = tokensToMap(headerTokens);
+    }
+    
+    private final static Map<String, Property> tokensToMap(String[] tokens)
+    {
+        Map<String, Property> map = new HashMap<String, Property>(tokens.length);
+        for (int i = 0; i < tokens.length; i++)
+        {
+            String token = tokens[i];
+            String[] split = StringUtils.split(token, NAME_FORMAT_SEPARATOR);
+            String format = null;
+            if (split.length > 1)
+            {
+                format = split[1];
+            }
+            map.put(token, new Property(i, split[0], format));
+        }
+        return map;
+    }
+    
+    
+    ///////////////////////////////////////////////////////
+    // IPropertyMapper
+    ///////////////////////////////////////////////////////
+
+    public Property getProperty(String name)
+    {
+        return properties.get(name);
+    }
+
+}

common/source/java/ch/systemsx/cisd/common/parser/ILineFilter.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+/**
+ * A line filter for <code>ReaderParser</code>.
+ * 
+ * @author Christian Ribeaud
+ */
+public interface ILineFilter
+{
+
+    /** A default <code>LineFilter</code> implementation that accepts any line. */
+    public final static ILineFilter ALWAYS_ACCEPT_LINE = new ILineFilter()
+        {
+
+            ///////////////////////////////////////////////////////
+            // LineFilter
+            ///////////////////////////////////////////////////////
+
+            public boolean acceptLine(String line)
+            {
+                return true;
+            }
+        };
+
+    /**
+     * If given <code>line</code> should be accepted or not.
+     * 
+     * @param line the line read from the <code>Reader</code>. Can not be <code>null</code>.
+     */
+    public boolean acceptLine(String line);
+}

common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+/**
+ * 
+ *
+ * @author Christian Ribeaud
+ */
+public interface ILineTokenizer
+{
+
+    /**
+     * Inits this <code>ILineTokenizer</code>.
+     * <p>
+     * Just gets called before parsing starts.
+     * </p>
+     */
+    public void init();
+    
+    public abstract String[] tokenize(int lineNumber, String line);
+
+    /**
+     * Destroys resources used by this <code>IParserObjectFactory</code>.
+     * <p>
+     * Just gets called when parsing has finished.
+     * </p>
+     */
+    public void destroy();
+}
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+/**
+ * Implementation know how to deal with given parsed text line and convert it into an appropriate <code>Object</code>.
+ * A <code>IParserObjectFactory</code> needs a <code>IPropertyMapper</code> to do its job. This
+ * <code>IPropertyMapper</code> helps to map <code>Object</code> properties to given tokens.
+ * <p>
+ * A <code>IParserObjectFactory</code> is typically registered in {@link IReaderParser}.
+ * </p>
+ * 
+ * @author Christian Ribeaud
+ */
+public interface IParserObjectFactory<E>
+{
+
+    /**
+     * This <code>IParserObjectFactory</code> implementation does nothing and returns the passed
+     * <code>lineTokens</code> as <code>String[]</code>.
+     * 
+     * @author Christian Ribeaud
+     */
+    public final static IParserObjectFactory<String[]> DO_NOTHING_OBJECT_FACTORY = new IParserObjectFactory<String[]>()
+        {
+
+            // /////////////////////////////////////////////////////
+            // IParserObjectFactory
+            // /////////////////////////////////////////////////////
+
+            public String[] createObject(String[] lineTokens)
+            {
+                return lineTokens;
+            }
+
+            public void setPropertyMapper(IPropertyMapper propertyMapper)
+            {
+            }
+        };
+
+    /**
+     * Parses given text line and returns an appropriate <i>Object</i>.
+     */
+    public E createObject(String[] lineTokens);
+
+    public void setPropertyMapper(IPropertyMapper propertyMapper);
+}
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+/**
+ * 
+ *
+ * @author Christian Ribeaud
+ */
+public interface IPropertyMapper
+{
+    
+    public Property getProperty(String name);
+    
+    ///////////////////////////////////////////////////////
+    // Helper Classes
+    ///////////////////////////////////////////////////////
+
+    /**
+     *
+     * 
+     * @author Christian Ribeaud
+     */
+    public final static class Property {
+        
+        public final int column;
+        
+        public final String name;
+        
+        public final String format;
+
+        protected Property(final int column, final String name, final String format)
+        {
+            this.column = column;
+            this.name = name;
+            this.format = format;
+        }
+        
+        ///////////////////////////////////////////////////////
+        // Object
+        ///////////////////////////////////////////////////////
+        
+        @Override
+        public final String toString()
+        {
+            return ToStringBuilder.reflectionToString(this);
+        }
+        
+    }
+}
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapperFactory.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+/**
+ * 
+ *
+ * @author Christian Ribeaud
+ */
+public interface IPropertyMapperFactory
+{
+    public int getHeaderLine();
+
+    public IPropertyMapper createPropertyMapper(String[] tokens);
+}

common/source/java/ch/systemsx/cisd/common/parser/IReaderParser.java

+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.parser;
+
+import java.io.BufferedReader;
+import java.io.Reader;
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
+
+/**
+ * <code>IReaderParser</code> is able to parse a given {@link Reader} and to returns <code>Object</code> instances.
+ * 
+ * @author Christian Ribeaud
+ */
+public interface IReaderParser<E>
+{
+
+    /**
+     * Parses given <code>Reader</code>. Encapsulates given <code>Reader</code> in a {@link BufferedReader} for
+     * better performance (if not already done).
+     * <p>
+     * Note that this does not close given <code>Parser</code>. It is your responsability to do so.
+     * </p>
+     * 
+     * @param lineFilter you could define a filter for the lines found in given <code>reader</code>.
+     * @return a <code>List</code> of elements.
+     * @throws CheckedExceptionTunnel if an <code>IOException</code> occurs.
+     */
+    public List<E> parse(Reader reader, ILineFilter lineFilter) throws CheckedExceptionTunnel;
+
+    /**
+     * Parses given <code>Reader</code>. Encapsulates given <code>Reader</code> in a {@link BufferedReader} for
+     * better performance (if not already done).
+     * <p>
+     * Note that this does not close given <code>Parser</code>. It is your responsability to do so.
+     * </p>
+     * 
+     * @return a <code>List</code> of elements.
+     * @throws CheckedExceptionTunnel if an <code>IOException</code> occurs.
+     */
+    public List<E> parse(Reader reader) throws CheckedExceptionTunnel;
+
+    /**
+     * Sets the <code>IParserObjectFactory</code>.
+     * <p>
+     * Typically, the given <code>factory</code> transforms a line into an element.
+     * </p>
+     */
+    public void setObjectFactory(IParserObjectFactory<E> factory);
+
+    public void setPropertyMapperFactory(IPropertyMapperFactory factory);
+}