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The IO bundle for Geneweaver.
/*-
*
* Copyright 2018, 2020 The Jackson Laboratory Inc.
*
* 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.
*
* @author Matthew Gerring
*/
package org.geneweaver.io.reader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Objects;
import java.util.regex.Matcher;
import java.util.zip.GZIPInputStream;
import javax.annotation.processing.Generated;
import org.geneweaver.domain.Entity;
import com.fasterxml.jackson.annotation.JsonIgnore;
/**
* Get a reader for a given request. This object holds all the required information
* for determining which concrete reader should be used for a given format.
*
* @author gerrim
*
*/
@Generated("POJO")
public class ReaderRequest {
/**
* Name of the source e.g. species or name of data source.
*/
private String source;
/**
* The file in which the data is in.
*/
private File file;
/**
* Instead of file, the data may be an input stream.
*/
@JsonIgnore
private InputStream stream;
/**
* Name of the data, usually the file name.
*/
private String name;
/**
* Some readers can be verbose or truncated.
*/
private boolean includeAll = true;
/**
* If the reader is reading a zip or tar file, setting the filter
* means that if the entry has more files than required,
* those not matching the filter can be ignored when the reader
* streams the data from the file.
* e.g. "^.+\\.egenes\\.txt(\\.gz)?$" to take only egenes files.
*/
private String fileFilter;
/**
* Used only testing, this field marks size for RepeatedLineReader which
* pumps the same line through the stream in order to test it.
*/
private int expectedSize;
/**
* Set to allow no inputstream request. In which case the file source will not
* setup an input stream.
*/
private boolean noInputStream = false;
/**
* Normallly we would like to close the input stream
* as we read from it. In the case of reading from a tar or
* zip, we do not want to close the stream at reader time because
* other files will be read from it.
*/
private boolean closeInputStream = true;
/**
* objType is only used for test requests.
*/
@JsonIgnore
private Class objType;
/**
* Calling init can be turned off.
*/
private boolean initRequired = true;
@JsonIgnore
private transient Matcher matcher;
/**
* Delimiter for parsing text files.
*/
private String delimiter = null; // Use the default of the reader.
/**
* The hint for which reader to use. It should be the full class name,
* the simple name or a string which is contained in the name for instance:
* "org.geneweaver.io.reader.MapCSVReader"
* "MapCSVReader"
* "Map"
* Obviously if hinting with a simpler string, you are a bit less likely to get the
* reader you prefer but more likely to be future proof if underlying readers change.
*/
private String readerHint;
public ReaderRequest() {
}
public ReaderRequest(File file) {
this(null, file, true);
}
public ReaderRequest(File file, String fileFilter) {
this(null, file, true);
this.fileFilter = fileFilter;
}
public ReaderRequest(URL url) throws IOException {
this.stream = url.openStream();
this.name = Paths.get(url.toString()).getFileName().toString();
this.file = null; // It's not a file.
}
public ReaderRequest(String source, File file) {
this(source, file, true);
}
public ReaderRequest(String source, File file, String delimiter) {
this(source, file, true);
setDelimiter(delimiter);
}
public ReaderRequest(String source, Path path) throws IOException{
this.source = source;
if (path.startsWith("http:/") || path.startsWith("ftp:/")) {
String spath = path.toString().replaceAll(":/", "://");
URL url = new URL(spath);
this.stream = url.openStream();
this.name = Paths.get(url.toString()).getFileName().toString();
this.file = null; // It's not a file.
} else {
this.file = path.toFile();
this.name = file.getName();
}
}
public ReaderRequest(String source, File file, boolean includeAll) {
this.source = source;
this.file = file;
this.name = file.getName();
this.includeAll = includeAll;
}
public ReaderRequest(InputStream stream, String name) {
if (stream instanceof GZIPInputStream) throw new IllegalArgumentException("There is no need to wrap inputstream in compressed streams!");
this.stream = stream;
this.name = name;
}
public ReaderRequest(InputStream stream, String name, boolean close) {
if (stream instanceof GZIPInputStream) throw new IllegalArgumentException("There is no need to wrap inputstream in compressed streams!");
this.stream = stream;
this.name = name;
this.closeInputStream = close;
}
public ReaderRequest(String source, InputStream stream, String name) {
if (stream instanceof GZIPInputStream) throw new IllegalArgumentException("There is no need to wrap inputstream in compressed streams!");
this.source = source;
this.stream = stream;
this.name = name;
}
public ReaderRequest(String source, int expectedSize, Class objType) {
this.source = source;
this.expectedSize = expectedSize;
this.objType = objType;
}
public ReaderRequest(String name) {
this.name = name;
}
/**
* @return the species
*/
public String getSource() {
return source;
}
/**
* @param species the species to set
*/
public ReaderRequest setSource(String species) {
this.source = species;
return this;
}
/**
* @return the file
*/
public File getFile() {
return file;
}
/**
* @param file the file to set
*/
public ReaderRequest setFile(File file) {
this.file = file!=null ? file.getAbsoluteFile() : null;
return this;
}
/**
* @return the stream
*/
@JsonIgnore
public InputStream getStream() {
return stream;
}
/**
* @param stream the stream to set
*/
@JsonIgnore
public ReaderRequest setStream(InputStream stream) {
this.stream = stream;
return this;
}
/**
* @return the name
*/
public String getName() {
return name;
}
/**
* @param name the name to set
*/
public ReaderRequest setName(String name) {
this.name = name;
return this;
}
/**
* @return the includeAll
*/
public boolean isIncludeAll() {
return includeAll;
}
/**
* @param includeAll the includeAll to set
*/
public ReaderRequest setIncludeAll(boolean includeAll) {
this.includeAll = includeAll;
return this;
}
@Override
public int hashCode() {
return Objects.hash(closeInputStream, expectedSize, file, fileFilter, includeAll, initRequired, name,
noInputStream, source);
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (!(obj instanceof ReaderRequest))
return false;
ReaderRequest other = (ReaderRequest) obj;
return closeInputStream == other.closeInputStream && expectedSize == other.expectedSize
&& Objects.equals(file, other.file) && Objects.equals(fileFilter, other.fileFilter)
&& includeAll == other.includeAll && initRequired == other.initRequired
&& Objects.equals(name, other.name) && noInputStream == other.noInputStream
&& Objects.equals(source, other.source);
}
@JsonIgnore
String name() {
if (file!=null) return file.getName();
if (name!=null) return name;
throw new IllegalArgumentException("A reader request must have a name for the resource!");
}
@JsonIgnore
String path() {
if (file!=null) return file.getAbsolutePath();
return toString();
}
@JsonIgnore
public InputStream stream() throws FileNotFoundException {
if (file!=null) return new FileInputStream(file);
if (stream!=null) return stream;
return null;
}
@JsonIgnore
public boolean isFileRequest() {
return file!=null;
}
@JsonIgnore
public void close() throws IOException {
if (!isCloseInputStream()) return;
if (stream!=null) stream.close();
stream = null;
}
/**
* @return the objType
*/
@JsonIgnore
protected Class getObjType() {
return objType;
}
/**
* @param objType the objType to set
*/
@JsonIgnore
protected void setObjType(Class objType) {
this.objType = objType;
}
/**
* @return the expectedSize
*/
public int getExpectedSize() {
return expectedSize;
}
/**
* @param expectedSize the expectedSize to set
*/
public ReaderRequest setExpectedSize(int expectedSize) {
this.expectedSize = expectedSize;
return this;
}
@Override
public String toString() {
return "ReaderRequest [source=" + source + ", file=" + file + ", stream=" + stream
+ ", name=" + name + ", includeAll=" + includeAll + ", fileFilter=" + fileFilter + ", expectedSize="
+ expectedSize + ", noInputStream=" + noInputStream + ", objType=" + objType + "]";
}
/**
* @return the noInputStream
*/
public boolean isNoInputStream() {
return noInputStream;
}
/**
* @param noInputStream the noInputStream to set
*/
public ReaderRequest setNoInputStream(boolean noInputStream) {
this.noInputStream = noInputStream;
return this;
}
/**
* @return the closeInputStream
*/
public boolean isCloseInputStream() {
return closeInputStream;
}
/**
* @param closeInputStream the closeInputStream to set
*/
public ReaderRequest setCloseInputStream(boolean closeInputStream) {
this.closeInputStream = closeInputStream;
return this;
}
/**
* @return the initRequired
*/
public boolean isInitRequired() {
return initRequired;
}
/**
* @param initRequired the initRequired to set
*/
public ReaderRequest setInitRequired(boolean initRequired) {
this.initRequired = initRequired;
return this;
}
/**
* @return the fileFilter
*/
public String getFileFilter() {
return fileFilter;
}
/**
* @param fileFilter the fileFilter to set
*/
public ReaderRequest setFileFilter(String fileFilter) {
this.fileFilter = fileFilter;
return this;
}
@JsonIgnore
public Matcher getMatcher() {
return matcher;
}
/**
* @param matcher the matcher to set
*/
@JsonIgnore
public void setMatcher(Matcher matcher) {
this.matcher = matcher;
}
/**
* @return the delimiter
*/
public String getDelimiter() {
return delimiter;
}
/**
* @param delimiter the delimiter to set
*/
public void setDelimiter(String delimiter) {
this.delimiter = delimiter;
}
/**
* @return the readerHint
*/
public String getReaderHint() {
return readerHint;
}
/**
* @param readerHint the readerHint to set
*/
public void setReaderHint(String readerHint) {
this.readerHint = readerHint;
}
}