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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| package org.molgenis.io; | ||
|
|
||
| import java.io.IOException; | ||
| import java.io.InputStreamReader; | ||
| import java.io.Reader; | ||
| import java.nio.charset.Charset; | ||
| import java.util.Enumeration; | ||
| import java.util.Iterator; | ||
| import java.util.LinkedHashMap; | ||
| import java.util.Map; | ||
| import java.util.zip.ZipEntry; | ||
| import java.util.zip.ZipFile; | ||
|
|
||
| import javax.annotation.Nullable; | ||
|
|
||
| import org.molgenis.io.csv.CsvReader; | ||
|
|
||
| import com.google.common.base.Function; | ||
| import com.google.common.collect.Iterators; | ||
|
|
||
| public class ZipTableReader implements TableReader | ||
| { | ||
| private final ZipFile zipFile; | ||
| private final Map<String, ZipEntry> tableNameMap; | ||
|
|
||
| public ZipTableReader(ZipFile zipFile) throws IOException | ||
| { | ||
| if (zipFile == null) throw new IllegalArgumentException("zip file is null"); | ||
| this.zipFile = zipFile; | ||
|
|
||
| // init table name map | ||
| tableNameMap = new LinkedHashMap<String, ZipEntry>(); | ||
| for (Enumeration<? extends ZipEntry> e = zipFile.entries(); e.hasMoreElements();) | ||
| { | ||
| ZipEntry zipEntry = e.nextElement(); | ||
|
|
||
| // remove extension from filename | ||
| int pos = zipEntry.getName().lastIndexOf('.'); | ||
| String tableName = pos != -1 ? zipEntry.getName().substring(0, pos) : zipEntry.getName(); | ||
|
|
||
| tableNameMap.put(tableName, zipEntry); | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public Iterator<TupleReader> iterator() | ||
| { | ||
| return Iterators.transform(tableNameMap.values().iterator(), new Function<ZipEntry, TupleReader>() | ||
| { | ||
| @Override | ||
| @Nullable | ||
| public TupleReader apply(@Nullable | ||
| ZipEntry zipEntry) | ||
| { | ||
| try | ||
| { | ||
| return toTupleReader(zipEntry); | ||
| } | ||
| catch (IOException e) | ||
| { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
| }); | ||
| } | ||
|
|
||
| @Override | ||
| public void close() throws IOException | ||
| { | ||
| // noop | ||
| } | ||
|
|
||
| @Override | ||
| public TupleReader getTupleReader(String tableName) throws IOException | ||
| { | ||
| ZipEntry zipEntry = tableNameMap.get(tableName); | ||
| return zipEntry != null ? toTupleReader(zipEntry) : null; | ||
| } | ||
|
|
||
| @Override | ||
| public Iterable<String> getTableNames() throws IOException | ||
| { | ||
| return tableNameMap.keySet(); | ||
| } | ||
|
|
||
| private TupleReader toTupleReader(ZipEntry zipEntry) throws IOException | ||
| { | ||
| String name = zipEntry.getName(); | ||
| if (name.endsWith(".csv") || name.endsWith(".txt")) | ||
| { | ||
| Reader reader = new InputStreamReader(zipFile.getInputStream(zipEntry), Charset.forName("UTF-8")); | ||
| return new CsvReader(reader); | ||
| } | ||
| else if (name.endsWith(".tsv")) | ||
| { | ||
| Reader reader = new InputStreamReader(zipFile.getInputStream(zipEntry), Charset.forName("UTF-8")); | ||
| return new CsvReader(reader, '\t'); | ||
| } | ||
| else | ||
| { | ||
| throw new IOException("unknown file type: " + name); | ||
| } | ||
| } | ||
| } |
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