Revision de8249cf
Added by Andreas Müller over 3 years ago
| cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/ExcelUtils.java | ||
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import java.io.FileNotFoundException; |
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import java.io.InputStream; |
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import java.net.URI; |
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import java.text.DateFormat; |
| 15 | 14 |
import java.text.Format; |
| 16 | 15 |
import java.util.ArrayList; |
| cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/URI.java | ||
|---|---|---|
| 1 |
/** |
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* Copyright (C) 2021 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.common; |
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import java.io.File; |
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import java.net.MalformedURLException; |
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import java.net.URISyntaxException; |
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import java.net.URL; |
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/** |
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* See https://dev.e-taxonomy.eu/redmine/issues/9114 |
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* |
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* @author a.mueller |
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* @since 05.01.2021 |
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*/ |
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public class URI implements java.io.Serializable {
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private static final long serialVersionUID = -8002215586516542076L; |
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private final java.net.URI javaUri; |
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// ***************************** FACTORY METHODS ***************************************/ |
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public static URI fromString(String uri) throws URISyntaxException {
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return new URI(uri); |
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} |
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/** |
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* Factory method. |
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* |
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* @see java.net.URI#create(String) |
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*/ |
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public static URI create(String uri) {
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try {
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return new URI(uri); |
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} catch (URISyntaxException e) {
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throw new IllegalArgumentException(e); |
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} |
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} |
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public static URI fromUrl(URL url) throws URISyntaxException {
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return new URI(url); |
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} |
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public static URI fromFile(File file) {
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return new URI(file.toURI()); |
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} |
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// ******************************* CONSTRUCTOR ************************************/ |
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@SuppressWarnings("unused")
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private URI(){javaUri = null;} //empty constructor required for JAXB (not tested but copied from DOI)
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public URI(String uriString) throws URISyntaxException {
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javaUri = parseUriString(uriString); |
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} |
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public URI(java.net.URI javaUri) {
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this.javaUri = javaUri; |
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} |
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//TODO maybe we can do encoding in between |
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public URI(URL url) throws URISyntaxException {
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this.javaUri = url.toURI(); |
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} |
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/** |
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* @see java.net.URI#URI(String, String, String, int, String, String, String) |
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*/ |
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public URI(String protocol, String userInfo, String host, int port, String path, String query, String ref) throws URISyntaxException {
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javaUri = new java.net.URI(protocol, userInfo, host, port, path, query, ref); |
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} |
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//************************************ GETTER ***********************************/ |
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public java.net.URI getJavaUri(){
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return javaUri; |
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} |
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//************************************ METHODS ************************************/ |
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private java.net.URI parseUriString(String uriString) throws URISyntaxException {
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java.net.URI javaUri = null; |
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if(uriString != null){
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try{
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javaUri = new java.net.URI(uriString); |
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}catch(Exception e){
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try {
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String encodedUri = uriString; |
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URL url = new URL(encodedUri); |
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String[] pathElements = url.getPath().split("/");
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for (String element: pathElements){
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if(element.contains("\\")){
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//TODO needs discussion if backslash should be converted to slash instead, for now we keep it more strict |
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throw new URISyntaxException(uriString, "URI path must not contain backslash ('\')");
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} |
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String replacement = UrlUtf8Coder.encode(element); |
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encodedUri = encodedUri.replace(element, replacement); |
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} |
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if (url.getQuery() != null){
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encodedUri = encodedUri.replace(url.getQuery(), UrlUtf8Coder.encode(url.getQuery())); |
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} |
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url = new URL(encodedUri); |
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javaUri = url.toURI(); |
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} catch (MalformedURLException e1) {
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throw new URISyntaxException(uriString, e1.getMessage()); |
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} |
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} |
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} |
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return javaUri; |
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} |
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//******************************** Wrapper methods *********************/ |
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public URL toURL() throws MalformedURLException{
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return javaUri.toURL(); |
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} |
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public String getHost() {
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return javaUri.getHost(); |
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} |
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public int getPort() {
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return javaUri.getPort(); |
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} |
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public String getScheme() {
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return javaUri.getScheme(); |
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} |
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public boolean isAbsolute() {
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return javaUri.isAbsolute(); |
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} |
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public String getPath() {
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return javaUri.getPath(); |
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} |
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public String getFragment() {
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return javaUri.getFragment(); |
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} |
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public Object getQuery() {
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return javaUri.getQuery(); |
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} |
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//****************************** equals *****************************/ |
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@Override |
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public int hashCode() {
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return javaUri.hashCode(); |
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} |
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@Override |
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public boolean equals(Object obj) {
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if (obj instanceof URI){
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return javaUri.equals(((URI)obj).javaUri); |
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} |
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return false; |
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} |
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//********************** clone ***********************************/ |
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@Override |
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protected URI clone() throws CloneNotSupportedException {
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return new URI(this.javaUri); |
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} |
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//******************************** toString ****************************/ |
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@Override |
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public String toString() {
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return javaUri.toString(); |
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} |
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} |
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| cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/UriUtils.java | ||
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import java.net.InetAddress; |
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import java.net.MalformedURLException; |
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import java.net.Socket; |
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import java.net.URI; |
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import java.net.URISyntaxException; |
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import java.net.URL; |
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import java.net.UnknownHostException; |
| ... | ... | |
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throw new HttpException("HTTP Reponse code is not = 200 (OK): " + UriUtils.getStatus(response));
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} |
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}else if (uri.getScheme().equals("file")){
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File file = new File(uri); |
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File file = new File(uri.getJavaUri());
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return new FileInputStream(file); |
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}else{
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throw new RuntimeException("Protocol not handled yet: " + uri.getScheme());
|
| ... | ... | |
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throw new HttpException("HTTP Reponse code is not = 200 (OK): " + UriUtils.getStatus(response));
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} |
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}else if ("file".equals(uri.getScheme())){
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File file = new File(uri); |
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File file = new File(uri.getJavaUri());
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return file.length(); |
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}else{
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throw new RuntimeException("Protocol not handled yet: " + uri.getScheme());
|
| ... | ... | |
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HttpUriRequest method; |
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switch (httpMethod) {
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case GET: |
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method = new HttpGet(uri); |
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method = new HttpGet(uri.getJavaUri());
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break; |
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case POST: |
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HttpPost httpPost = new HttpPost(uri); |
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HttpPost httpPost = new HttpPost(uri.getJavaUri());
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if(entity!=null){
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httpPost.setEntity(entity); |
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} |
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method = httpPost; |
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break; |
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default: |
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method = new HttpPost(uri); |
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method = new HttpPost(uri.getJavaUri());
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break; |
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} |
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|
| ... | ... | |
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uriBuilder.setPath(path); |
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uriBuilder.setQuery(query); |
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uriBuilder.setFragment(fragment); |
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return uriBuilder.build();
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return new URI(uriBuilder.build());
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} |
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/** |
| ... | ... | |
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//Http |
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CloseableHttpClient httpclient = HttpClients.createDefault(); |
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HttpGet httpget = new HttpGet(serviceUri); |
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HttpGet httpget = new HttpGet(serviceUri.getJavaUri());
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if(timeout!=null){
|
| ... | ... | |
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try {
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// this is the step that can fail, and so |
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// it should be this step that should be fixed |
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uri = url.toURI();
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uri = new URI(url);
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} catch (URISyntaxException e) {
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// OK if we are here, then obviously the URL did |
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// not comply with RFC 2396. This can only |
| ... | ... | |
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throw new IllegalArgumentException("broken URL: " + url);
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} |
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} |
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return new File(uri); |
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return new File(uri.getJavaUri());
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} |
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public static boolean checkServiceAvailable(String host, int port){
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| cdmlib-commons/src/main/java/eu/etaxonomy/cdm/common/media/CdmImageInfo.java | ||
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| 10 | 10 |
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import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
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import java.net.URI; |
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import java.util.HashMap; |
| 15 | 14 |
import java.util.Map; |
| 16 | 15 |
|
| ... | ... | |
| 26 | 25 |
import org.apache.log4j.Logger; |
| 27 | 26 |
|
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import eu.etaxonomy.cdm.common.CdmUtils; |
| 28 |
import eu.etaxonomy.cdm.common.URI; |
|
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import eu.etaxonomy.cdm.common.UriUtils; |
| 30 | 30 |
|
| 31 | 31 |
/** |
| cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/UriTest.java | ||
|---|---|---|
| 1 |
/** |
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* Copyright (C) 2021 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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| 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.common; |
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import java.net.URISyntaxException; |
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|
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import org.junit.Assert; |
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import org.junit.Test; |
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|
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/** |
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* @author a.mueller |
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* @since 05.01.2021 |
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*/ |
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public class UriTest {
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@Test |
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public void test() {
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try {
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//see example in #9111 |
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URI uri = new URI("https://bioone.org/journals/Cactus-and-Succulent-Journal/volume-78/issue-2/0007-9367(2006)78[66:FKASLA]2.0.CO;2/Finders-Keepers-and-some-Lavranian-Adjustments-in-Mesembryanthema/10.2985/0007-9367(2006)78[66:FKASLA]2.0.CO;2.full");
|
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Assert.assertEquals( |
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"/journals/Cactus-and-Succulent-Journal/volume-78/issue-2/0007-9367(2006)78[66:FKASLA]2.0.CO;2/Finders-Keepers-and-some-Lavranian-Adjustments-in-Mesembryanthema/10.2985/0007-9367(2006)78[66:FKASLA]2.0.CO;2.full", |
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uri.getPath()); |
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|
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} catch (URISyntaxException e) {
|
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Assert.fail("Parsing example URI from #9111 should not throw exception");
|
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| 33 |
} |
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| 34 |
|
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| 35 |
try {
|
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| 36 |
//see example in #9111 |
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URI uri = new URI("http:\\www.fail.de");
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Assert.fail("Using backslash in URI instead of slash should fail");
|
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} catch (URISyntaxException e) {
|
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//OK |
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| 41 |
} |
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| 42 |
|
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| 43 |
} |
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|
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| 45 |
} |
|
| cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/UriUtilsTest.java | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
import java.io.IOException; |
| 4 | 4 |
import java.net.MalformedURLException; |
| 5 |
import java.net.URI; |
|
| 6 | 5 |
import java.net.URISyntaxException; |
| 7 | 6 |
import java.net.URL; |
| 8 | 7 |
import java.util.ArrayList; |
| cdmlib-commons/src/test/java/eu/etaxonomy/cdm/common/media/CdmImageInfoTest.java | ||
|---|---|---|
| 6 | 6 |
import static org.junit.Assert.fail; |
| 7 | 7 |
|
| 8 | 8 |
import java.io.IOException; |
| 9 |
import java.net.URI; |
|
| 10 | 9 |
import java.net.URL; |
| 11 | 10 |
import java.util.Map; |
| 12 | 11 |
|
| ... | ... | |
| 16 | 15 |
import org.junit.Before; |
| 17 | 16 |
import org.junit.Test; |
| 18 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.common.URI; |
|
| 19 | 19 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 20 | 20 |
|
| 21 | 21 |
/** |
| ... | ... | |
| 38 | 38 |
@Before |
| 39 | 39 |
public void setUp() throws Exception {
|
| 40 | 40 |
URL jpegUrl = CdmImageInfoTest.class.getResource("/images/OregonScientificDS6639-DSC_0307-small.jpg");
|
| 41 |
jpegUri = jpegUrl.toURI();
|
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| 41 |
jpegUri = new URI(jpegUrl);
|
|
| 42 | 42 |
|
| 43 | 43 |
URL tiffUrl = CdmImageInfoTest.class.getResource("/images/OregonScientificDS6639-DSC_0307-small.tif");
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| 44 |
tiffUri = tiffUrl.toURI();
|
|
| 44 |
tiffUri = new URI(tiffUrl);
|
|
| 45 | 45 |
|
| 46 | 46 |
remotePngUri = URI.create("https://dev.e-taxonomy.eu/trac_htdocs/logo_edit.png");
|
| 47 | 47 |
} |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/BciSchemaAdapter.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 |
import java.net.URISyntaxException; |
|
| 15 | 13 |
import java.util.ArrayList; |
| 16 | 14 |
import java.util.List; |
| 17 | 15 |
|
| ... | ... | |
| 23 | 21 |
import org.xml.sax.SAXException; |
| 24 | 22 |
import org.xml.sax.helpers.DefaultHandler; |
| 25 | 23 |
|
| 24 |
import eu.etaxonomy.cdm.common.URI; |
|
| 26 | 25 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 27 | 26 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 28 | 27 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/bci/BciServiceWrapper.java | ||
|---|---|---|
| 14 | 14 |
import java.io.InputStreamReader; |
| 15 | 15 |
import java.net.HttpURLConnection; |
| 16 | 16 |
import java.net.MalformedURLException; |
| 17 |
import java.net.URI; |
|
| 18 | 17 |
import java.net.URISyntaxException; |
| 19 | 18 |
import java.net.URL; |
| 20 | 19 |
import java.util.ArrayList; |
| ... | ... | |
| 32 | 31 |
|
| 33 | 32 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 34 | 33 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 34 |
import eu.etaxonomy.cdm.common.URI; |
|
| 35 | 35 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 36 | 36 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/common/SchemaAdapterBase.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 | 13 |
import java.util.List; |
| 15 | 14 |
|
| 16 | 15 |
import org.apache.log4j.Logger; |
| 17 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.common.URI; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 19 | 19 |
|
| 20 | 20 |
/** |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/common/ServiceWrapperBase.java | ||
|---|---|---|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 | 13 |
import java.net.MalformedURLException; |
| 14 |
import java.net.URI; |
|
| 15 | 14 |
import java.net.URISyntaxException; |
| 16 | 15 |
import java.net.URL; |
| 17 | 16 |
import java.util.HashMap; |
| ... | ... | |
| 25 | 24 |
import org.apache.http.message.BasicNameValuePair; |
| 26 | 25 |
import org.apache.log4j.Logger; |
| 27 | 26 |
|
| 27 |
import eu.etaxonomy.cdm.common.URI; |
|
| 28 | 28 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 29 | 29 |
import eu.etaxonomy.cdm.common.UriUtils.HttpMethod; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/dc/DublinCoreSchemaAdapter.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 |
import java.net.URISyntaxException; |
|
| 15 | 13 |
import java.util.ArrayList; |
| 16 | 14 |
import java.util.List; |
| 17 | 15 |
|
| ... | ... | |
| 23 | 21 |
import org.xml.sax.SAXException; |
| 24 | 22 |
import org.xml.sax.helpers.DefaultHandler; |
| 25 | 23 |
|
| 24 |
import eu.etaxonomy.cdm.common.URI; |
|
| 26 | 25 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 27 | 26 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 28 | 27 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/ipni/IpniService.java | ||
|---|---|---|
| 14 | 14 |
import java.io.InputStreamReader; |
| 15 | 15 |
import java.net.HttpURLConnection; |
| 16 | 16 |
import java.net.MalformedURLException; |
| 17 |
import java.net.URI; |
|
| 18 | 17 |
import java.net.URISyntaxException; |
| 19 | 18 |
import java.net.URL; |
| 20 | 19 |
import java.text.ParseException; |
| ... | ... | |
| 35 | 34 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 36 | 35 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 37 | 36 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 37 |
import eu.etaxonomy.cdm.common.URI; |
|
| 38 | 38 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.agent.Team; |
| ... | ... | |
| 278 | 278 |
serviceUrl.getPath() |
| 279 | 279 |
+ "?" + request); |
| 280 | 280 |
|
| 281 |
URI newUri = newUrl.toURI();
|
|
| 281 |
URI newUri = URI.fromUrl(newUrl);
|
|
| 282 | 282 |
logger.info("Firing request for URI: " + newUri);
|
| 283 | 283 |
HttpResponse response = UriUtils.getResponse(newUri, null); |
| 284 | 284 |
|
| ... | ... | |
| 323 | 323 |
serviceUrl.getPath() |
| 324 | 324 |
+ "?" + request); |
| 325 | 325 |
|
| 326 |
|
|
| 327 |
URI newUri = newUrl.toURI(); |
|
| 328 |
|
|
| 326 |
URI newUri = URI.fromUrl(newUrl); |
|
| 329 | 327 |
logger.info("Firing request for URI: " + newUri);
|
| 330 | 328 |
|
| 331 | 329 |
HttpResponse response = UriUtils.getResponse(newUri, null); |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/DataResponse.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence; |
| 10 | 10 |
|
| 11 |
import java.net.URI;
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI;
|
|
| 12 | 12 |
|
| 13 | 13 |
/** |
| 14 | 14 |
* @author k.luther |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/bioCase/BioCaseQueryServiceWrapper.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 | 13 |
import java.util.ArrayList; |
| 15 | 14 |
import java.util.HashMap; |
| 16 | 15 |
import java.util.List; |
| ... | ... | |
| 35 | 34 |
import org.xml.sax.SAXException; |
| 36 | 35 |
|
| 37 | 36 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 37 |
import eu.etaxonomy.cdm.common.URI; |
|
| 38 | 38 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 39 | 39 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
| 40 | 40 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/bioCase/BioCaseResponse.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence.bioCase; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 13 | 11 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 12 |
import eu.etaxonomy.cdm.common.URI; |
|
| 14 | 13 |
import eu.etaxonomy.cdm.ext.occurrence.DataResponse; |
| 15 | 14 |
|
| 16 | 15 |
/** |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/DataSetResponse.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence.gbif; |
| 10 | 10 |
|
| 11 |
import java.net.URI;
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI;
|
|
| 12 | 12 |
|
| 13 | 13 |
/** |
| 14 | 14 |
* Wrapper object for the parameters that are parsed from a GBIF dataset query |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifJsonOccurrenceParser.java | ||
|---|---|---|
| 12 | 12 |
import java.io.InputStream; |
| 13 | 13 |
import java.io.StringWriter; |
| 14 | 14 |
import java.net.MalformedURLException; |
| 15 |
import java.net.URI; |
|
| 16 | 15 |
import java.net.URISyntaxException; |
| 17 | 16 |
import java.net.URL; |
| 18 | 17 |
import java.nio.charset.Charset; |
| ... | ... | |
| 25 | 24 |
import org.apache.log4j.Logger; |
| 26 | 25 |
|
| 27 | 26 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 27 |
import eu.etaxonomy.cdm.common.URI; |
|
| 28 | 28 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 29 | 29 |
import eu.etaxonomy.cdm.common.media.CdmImageInfo; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.agent.Institution; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifQueryServiceWrapper.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence.gbif; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.Calendar; |
| 15 | 14 |
import java.util.Collection; |
| ... | ... | |
| 19 | 18 |
import org.apache.http.client.ClientProtocolException; |
| 20 | 19 |
import org.apache.http.client.utils.URIBuilder; |
| 21 | 20 |
|
| 21 |
import eu.etaxonomy.cdm.common.URI; |
|
| 22 | 22 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 23 | 23 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
| 24 | 24 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| ... | ... | |
| 65 | 65 |
|
| 66 | 66 |
if(UriUtils.isServiceAvailable(uri, 10000)){
|
| 67 | 67 |
logger.info("Querying GBIF service with " + builder.build());
|
| 68 |
return GbifJsonOccurrenceParser.parseJsonRecords(executeHttpGet(builder.build(), null));
|
|
| 68 |
return GbifJsonOccurrenceParser.parseJsonRecords(executeHttpGet(new URI(builder.build()), null));
|
|
| 69 | 69 |
} |
| 70 | 70 |
else{
|
| 71 | 71 |
logger.error("Querying " + uri + " got a timeout!");
|
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifResponse.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence.gbif; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 13 | 11 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 12 |
import eu.etaxonomy.cdm.common.URI; |
|
| 14 | 13 |
import eu.etaxonomy.cdm.ext.occurrence.DataResponse; |
| 15 | 14 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| 16 | 15 |
|
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/openurl/MobotOpenUrlQuery.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.openurl; |
| 10 | 10 |
|
| 11 |
import java.net.URI;
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI;
|
|
| 12 | 12 |
|
| 13 | 13 |
/** |
| 14 | 14 |
* @author a.kohlbecker |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/openurl/MobotOpenUrlResponseSchemaAdapter.java | ||
|---|---|---|
| 12 | 12 |
import java.io.InputStream; |
| 13 | 13 |
import java.io.InputStreamReader; |
| 14 | 14 |
import java.io.Reader; |
| 15 |
import java.net.URI; |
|
| 16 | 15 |
import java.net.URISyntaxException; |
| 17 | 16 |
import java.util.ArrayList; |
| 18 | 17 |
import java.util.List; |
| ... | ... | |
| 26 | 25 |
import org.xml.sax.SAXException; |
| 27 | 26 |
import org.xml.sax.helpers.DefaultHandler; |
| 28 | 27 |
|
| 28 |
import eu.etaxonomy.cdm.common.URI; |
|
| 29 | 29 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.agent.Team; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/openurl/MobotOpenUrlServiceWrapper.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 | 13 |
import java.net.URISyntaxException; |
| 15 | 14 |
import java.util.ArrayList; |
| 16 | 15 |
import java.util.HashMap; |
| ... | ... | |
| 20 | 19 |
import org.apache.http.NameValuePair; |
| 21 | 20 |
import org.apache.http.message.BasicNameValuePair; |
| 22 | 21 |
|
| 22 |
import eu.etaxonomy.cdm.common.URI; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 24 | 24 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/openurl/OpenUrlReference.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.openurl; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.net.URISyntaxException; |
| 13 | 12 |
|
| 14 | 13 |
import org.apache.log4j.Logger; |
| 15 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.ext.openurl.MobotOpenUrlServiceWrapper.ReferenceType; |
| 17 | 17 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 18 | 18 |
|
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/scratchpads/ScratchpadsService.java | ||
|---|---|---|
| 14 | 14 |
import java.io.IOException; |
| 15 | 15 |
import java.io.InputStream; |
| 16 | 16 |
import java.io.InputStreamReader; |
| 17 |
import java.net.URI; |
|
| 18 | 17 |
import java.net.URISyntaxException; |
| 19 | 18 |
import java.net.URL; |
| 20 | 19 |
import java.util.Iterator; |
| ... | ... | |
| 28 | 27 |
import com.fasterxml.jackson.databind.JsonNode; |
| 29 | 28 |
import com.fasterxml.jackson.databind.ObjectMapper; |
| 30 | 29 |
|
| 30 |
import eu.etaxonomy.cdm.common.URI; |
|
| 31 | 31 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 32 | 32 |
|
| 33 | 33 |
|
| ... | ... | |
| 52 | 52 |
|
| 53 | 53 |
try {
|
| 54 | 54 |
URL url = new URL(SCRATCHPADS_JSON_ENDPOINT); |
| 55 |
boolean isAvailable = UriUtils.isServiceAvailable(url.toURI());
|
|
| 55 |
boolean isAvailable = UriUtils.isServiceAvailable(URI.fromUrl(url));
|
|
| 56 | 56 |
|
| 57 | 57 |
if (isAvailable) {
|
| 58 |
inputStream = UriUtils.getInputStream(url.toURI());
|
|
| 58 |
inputStream = UriUtils.getInputStream(URI.fromUrl(url));
|
|
| 59 | 59 |
} |
| 60 | 60 |
|
| 61 | 61 |
BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream, "iso-8859-1"), 8); |
| ... | ... | |
| 85 | 85 |
if (fieldWebsite.startsWith("http")) {
|
| 86 | 86 |
|
| 87 | 87 |
url = new URL(fieldWebsite + "/dwca.zip"); |
| 88 |
URI uri = url.toURI();
|
|
| 88 |
URI uri = URI.fromUrl(url);
|
|
| 89 | 89 |
isAvailable = UriUtils.isServiceAvailable(uri); |
| 90 | 90 |
logger.debug("Is " + fieldWebsite + " available :" + isAvailable);
|
| 91 | 91 |
|
| ... | ... | |
| 117 | 117 |
logger.debug("There is a dwca " + websiteName);
|
| 118 | 118 |
|
| 119 | 119 |
try {
|
| 120 |
inputStream = UriUtils.getInputStream(url.toURI()); |
|
| 121 |
|
|
| 120 |
inputStream = UriUtils.getInputStream(URI.fromUrl(url)); |
|
| 122 | 121 |
num++; |
| 123 | 122 |
if (inputStream != null) {
|
| 124 | 123 |
copyDwcaZip(inputStream, websiteName); |
| cdmlib-ext/src/main/java/eu/etaxonomy/cdm/ext/sru/SruServiceWrapper.java | ||
|---|---|---|
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 |
import java.net.URI; |
|
| 14 | 13 |
import java.net.URISyntaxException; |
| 15 | 14 |
import java.util.ArrayList; |
| 16 | 15 |
import java.util.HashMap; |
| ... | ... | |
| 20 | 19 |
import org.apache.http.NameValuePair; |
| 21 | 20 |
import org.apache.http.message.BasicNameValuePair; |
| 22 | 21 |
|
| 22 |
import eu.etaxonomy.cdm.common.URI; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.ext.common.SchemaAdapterBase; |
| 24 | 24 |
import eu.etaxonomy.cdm.ext.common.ServiceWrapperBase; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/geo/EditGeoServiceTest.java | ||
|---|---|---|
| 17 | 17 |
import java.io.InputStreamReader; |
| 18 | 18 |
import java.net.HttpURLConnection; |
| 19 | 19 |
import java.net.MalformedURLException; |
| 20 |
import java.net.URI; |
|
| 21 | 20 |
import java.net.URL; |
| 22 | 21 |
import java.util.ArrayList; |
| 23 | 22 |
import java.util.Collection; |
| ... | ... | |
| 42 | 41 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
| 43 | 42 |
import eu.etaxonomy.cdm.api.utility.DescriptionUtility; |
| 44 | 43 |
import eu.etaxonomy.cdm.common.StreamUtils; |
| 44 |
import eu.etaxonomy.cdm.common.URI; |
|
| 45 | 45 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 46 | 46 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 47 | 47 |
import eu.etaxonomy.cdm.model.common.Language; |
| cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/occurrence/bioCase/BioCaseQueryServiceWrapperTest.java | ||
|---|---|---|
| 16 | 16 |
import java.io.IOException; |
| 17 | 17 |
import java.io.InputStream; |
| 18 | 18 |
import java.io.InputStreamReader; |
| 19 |
import java.net.URI; |
|
| 20 | 19 |
import java.util.HashSet; |
| 21 | 20 |
import java.util.Set; |
| 22 | 21 |
|
| ... | ... | |
| 24 | 23 |
import org.apache.log4j.Logger; |
| 25 | 24 |
import org.junit.Test; |
| 26 | 25 |
|
| 26 |
import eu.etaxonomy.cdm.common.URI; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 28 | 28 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| 29 | 29 |
|
| cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/occurrence/gbif/GbifQueryServiceWrapperTest.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.ext.occurrence.gbif; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.IOException; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.Collection; |
| 15 | 14 |
import java.util.GregorianCalendar; |
| ... | ... | |
| 22 | 21 |
import org.junit.Ignore; |
| 23 | 22 |
import org.junit.Test; |
| 24 | 23 |
|
| 24 |
import eu.etaxonomy.cdm.common.URI; |
|
| 25 | 25 |
import eu.etaxonomy.cdm.ext.occurrence.OccurenceQuery; |
| 26 | 26 |
|
| 27 | 27 |
/** |
| cdmlib-ext/src/test/java/eu/etaxonomy/cdm/ext/openurl/MobotOpenUrlServiceWrapperTest.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.ext.openurl; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.net.URISyntaxException; |
| 13 | 12 |
import java.util.List; |
| 14 | 13 |
|
| ... | ... | |
| 19 | 18 |
import org.junit.Ignore; |
| 20 | 19 |
import org.junit.Test; |
| 21 | 20 |
|
| 21 |
import eu.etaxonomy.cdm.common.URI; |
|
| 22 | 22 |
import eu.etaxonomy.cdm.common.UriUtils; |
| 23 | 23 |
|
| 24 | 24 |
/** |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/CdmImportBase.java | ||
|---|---|---|
| 10 | 10 |
package eu.etaxonomy.cdm.io.common; |
| 11 | 11 |
|
| 12 | 12 |
import java.net.MalformedURLException; |
| 13 |
import java.net.URI; |
|
| 14 | 13 |
import java.net.URISyntaxException; |
| 15 | 14 |
import java.sql.ResultSet; |
| 16 | 15 |
import java.sql.SQLException; |
| ... | ... | |
| 24 | 23 |
|
| 25 | 24 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 26 | 25 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 26 |
import eu.etaxonomy.cdm.common.URI; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.common.media.CdmImageInfo; |
| 28 | 28 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 29 | 29 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/XmlImportBase.java | ||
|---|---|---|
| 12 | 12 |
import java.io.FileInputStream; |
| 13 | 13 |
import java.io.IOException; |
| 14 | 14 |
import java.io.InputStream; |
| 15 |
import java.net.URI; |
|
| 16 | 15 |
import java.util.NoSuchElementException; |
| 17 | 16 |
|
| 18 | 17 |
import javax.xml.namespace.QName; |
| ... | ... | |
| 28 | 27 |
import org.apache.log4j.Logger; |
| 29 | 28 |
import org.xml.sax.SAXException; |
| 30 | 29 |
|
| 30 |
import eu.etaxonomy.cdm.common.URI; |
|
| 31 | 31 |
import eu.etaxonomy.cdm.io.common.events.IIoEvent; |
| 32 | 32 |
import eu.etaxonomy.cdm.io.common.events.IIoObserver; |
| 33 | 33 |
|
| ... | ... | |
| 123 | 123 |
protected InputStream getInputStream(CONFIG config) {
|
| 124 | 124 |
try {
|
| 125 | 125 |
URI uri = config.getSource(); |
| 126 |
File file = new File(uri); |
|
| 126 |
File file = new File(uri.getJavaUri());
|
|
| 127 | 127 |
InputStream is = new FileInputStream(file); |
| 128 | 128 |
return is; |
| 129 | 129 |
}catch (Exception e) {
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/XmlImportConfiguratorBase.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.common; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI; |
|
| 13 | 12 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 14 | 13 |
|
| 15 | 14 |
/** |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportImageGalleryMapper.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.common.mapping; |
| 11 | 11 |
|
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.sql.ResultSet; |
| 15 | 14 |
import java.sql.SQLException; |
| ... | ... | |
| 19 | 18 |
import org.apache.log4j.Logger; |
| 20 | 19 |
|
| 21 | 20 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 22 |
import eu.etaxonomy.cdm.common.CdmUtils;
|
|
| 21 |
import eu.etaxonomy.cdm.common.URI;
|
|
| 23 | 22 |
import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException; |
| 24 | 23 |
import eu.etaxonomy.cdm.io.common.DbImportStateBase; |
| 25 | 24 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportMediaMapper.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.common.mapping; |
| 11 | 11 |
|
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.sql.ResultSet; |
| 15 | 14 |
import java.sql.SQLException; |
| 16 | 15 |
|
| 17 | 16 |
import org.apache.log4j.Logger; |
| 18 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.common.URI; |
|
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.DbImportStateBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.media.Media; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/berlinModel/CdmUriMapper.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.common.mapping.berlinModel; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI; |
|
| 13 | 12 |
import eu.etaxonomy.cdm.io.common.mapping.CdmSingleAttributeMapperBase; |
| 14 | 13 |
|
| 15 | 14 |
/** |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/out/DbImageMapper.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.common.mapping.out; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.sql.Types; |
| 13 | 12 |
import java.util.List; |
| 14 | 13 |
import java.util.Set; |
| 15 | 14 |
|
| 16 | 15 |
import org.apache.log4j.Logger; |
| 17 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.common.URI; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.description.TextData; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/out/DbUriMapper.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.common.mapping.out; |
| 11 | 11 |
|
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.sql.Types; |
| 14 | 13 |
|
| 15 | 14 |
import org.apache.log4j.Logger; |
| 16 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 19 | 19 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/in/CsvImportConfiguratorBase.java | ||
|---|---|---|
| 11 | 11 |
import java.io.IOException; |
| 12 | 12 |
import java.io.InputStream; |
| 13 | 13 |
import java.io.InputStreamReader; |
| 14 |
import java.net.URI; |
|
| 15 | 14 |
import java.net.URL; |
| 16 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 | 17 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 18 | 18 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoId.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.demo; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 14 | 13 |
import org.apache.log4j.Logger; |
| 15 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 17 | 17 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.LSID; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoMetaDataRecord.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.demo; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.ArrayList; |
| 13 | 12 |
import java.util.List; |
| 14 | 13 |
|
| 15 | 14 |
import org.apache.log4j.Logger; |
| 16 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 |
|
|
| 17 | 18 |
/** |
| 18 | 19 |
* @author a.mueller |
| 19 | 20 |
* @since 20.04.2011 |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/demo/CsvDemoRecordBase.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.demo; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.PrintWriter; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.ArrayList; |
| 15 | 14 |
import java.util.HashMap; |
| ... | ... | |
| 24 | 23 |
import org.joda.time.Partial; |
| 25 | 24 |
|
| 26 | 25 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 26 |
import eu.etaxonomy.cdm.common.URI; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.io.stream.terms.TermUri; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/out/CsvId.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.out; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 14 | 13 |
import org.apache.log4j.Logger; |
| 15 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 17 | 17 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.LSID; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/out/CsvMetaDataRecordRedlist.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.out; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.ArrayList; |
| 13 | 12 |
import java.util.List; |
| 14 | 13 |
|
| 15 | 14 |
import org.apache.log4j.Logger; |
| 16 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 |
|
|
| 17 | 18 |
/** |
| 18 | 19 |
* @author a.mueller |
| 19 | 20 |
* @since 20.04.2011 |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/csv/redlist/out/CsvRecordBaseRedlist.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.io.csv.redlist.out; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.PrintWriter; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.ArrayList; |
| 15 | 14 |
import java.util.HashMap; |
| ... | ... | |
| 24 | 23 |
import org.joda.time.Partial; |
| 25 | 24 |
|
| 26 | 25 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 26 |
import eu.etaxonomy.cdm.common.URI; |
|
| 27 | 27 |
import eu.etaxonomy.cdm.io.stream.terms.TermUri; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| 29 | 29 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/CharacterOwlImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.descriptive.owl.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.Arrays; |
| 13 | 12 |
|
| 14 | 13 |
import org.springframework.stereotype.Component; |
| ... | ... | |
| 16 | 15 |
import com.hp.hpl.jena.rdf.model.ResIterator; |
| 17 | 16 |
import com.hp.hpl.jena.rdf.model.Resource; |
| 18 | 17 |
|
| 18 |
import eu.etaxonomy.cdm.common.URI; |
|
| 19 | 19 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.io.descriptive.owl.OwlUtil; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.description.Character; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/OwlImportUtil.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.descriptive.owl.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.Arrays; |
| 13 | 12 |
import java.util.Collections; |
| 14 | 13 |
import java.util.HashSet; |
| ... | ... | |
| 22 | 21 |
|
| 23 | 22 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 24 | 23 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 24 |
import eu.etaxonomy.cdm.common.URI; |
|
| 25 | 25 |
import eu.etaxonomy.cdm.io.descriptive.owl.OwlUtil; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.common.Language; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/StructureTreeOwlImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.descriptive.owl.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 14 | 13 |
import org.springframework.stereotype.Component; |
| ... | ... | |
| 19 | 18 |
import com.hp.hpl.jena.rdf.model.Statement; |
| 20 | 19 |
import com.hp.hpl.jena.rdf.model.StmtIterator; |
| 21 | 20 |
|
| 21 |
import eu.etaxonomy.cdm.common.URI; |
|
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
| 23 | 23 |
import eu.etaxonomy.cdm.io.descriptive.owl.OwlUtil; |
| 24 | 24 |
import eu.etaxonomy.cdm.model.description.Feature; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/StructureTreeOwlImportConfigurator.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.descriptive.owl.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 11 |
import eu.etaxonomy.cdm.common.URI; |
|
| 13 | 12 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 14 | 13 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 15 | 14 |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/descriptive/owl/in/TermVocabularyOwlImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.descriptive.owl.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.Arrays; |
| 13 | 12 |
import java.util.Set; |
| 14 | 13 |
import java.util.UUID; |
| ... | ... | |
| 21 | 20 |
import com.hp.hpl.jena.rdf.model.Statement; |
| 22 | 21 |
import com.hp.hpl.jena.rdf.model.StmtIterator; |
| 23 | 22 |
|
| 23 |
import eu.etaxonomy.cdm.common.URI; |
|
| 24 | 24 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
| 26 | 26 |
import eu.etaxonomy.cdm.io.descriptive.owl.OwlUtil; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/distribution/excelupdate/ExcelDistributionUpdateConfigurator.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.distribution.excelupdate; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 13 |
import eu.etaxonomy.cdm.common.URI; |
|
| 14 | 14 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 15 | 15 |
import eu.etaxonomy.cdm.io.common.ImportStateBase; |
| 16 | 16 |
import eu.etaxonomy.cdm.io.excel.common.ExcelImportConfiguratorBase; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcTaxonStreamItem2CdmTaxonConverter.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.ArrayList; |
| 13 | 12 |
import java.util.HashSet; |
| 14 | 13 |
import java.util.List; |
| ... | ... | |
| 22 | 21 |
import com.ibm.lsid.MalformedLSIDException; |
| 23 | 22 |
|
| 24 | 23 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 24 |
import eu.etaxonomy.cdm.common.URI; |
|
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 26 | 26 |
import eu.etaxonomy.cdm.io.stream.IPartitionableConverter; |
| 27 | 27 |
import eu.etaxonomy.cdm.io.stream.IReader; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcaDataImportConfiguratorBase.java | ||
|---|---|---|
| 10 | 10 |
package eu.etaxonomy.cdm.io.dwca.in; |
| 11 | 11 |
|
| 12 | 12 |
|
| 13 |
import java.net.URI; |
|
| 14 |
|
|
| 15 | 13 |
import org.apache.log4j.Logger; |
| 16 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 | 16 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 18 | 17 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
| 19 | 18 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcaImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 |
|
|
| 13 | 11 |
import org.apache.log4j.Logger; |
| 14 | 12 |
import org.springframework.stereotype.Component; |
| 15 | 13 |
|
| 14 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 15 |
import eu.etaxonomy.cdm.io.stream.CsvStream; |
| 17 | 16 |
import eu.etaxonomy.cdm.io.stream.IPartitionableConverter; |
| 18 | 17 |
import eu.etaxonomy.cdm.io.stream.IReader; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcaImportConfigurator.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.in; |
| 10 | 10 |
|
| 11 |
|
|
| 12 |
import java.net.URI; |
|
| 13 |
|
|
| 14 | 11 |
import org.apache.log4j.Logger; |
| 15 | 12 |
|
| 13 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 14 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 17 | 15 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
| 18 | 16 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/DwcaZipToStreamConverter.java | ||
|---|---|---|
| 14 | 14 |
import java.io.InputStreamReader; |
| 15 | 15 |
import java.io.Reader; |
| 16 | 16 |
import java.io.UnsupportedEncodingException; |
| 17 |
import java.net.URI; |
|
| 18 | 17 |
import java.util.ArrayList; |
| 19 | 18 |
import java.util.Arrays; |
| 20 | 19 |
import java.util.HashMap; |
| ... | ... | |
| 33 | 32 |
import au.com.bytecode.opencsv.CSVParser; |
| 34 | 33 |
import au.com.bytecode.opencsv.CSVReader; |
| 35 | 34 |
import au.com.bytecode.opencsv.CSVWriter; |
| 35 |
import eu.etaxonomy.cdm.common.URI; |
|
| 36 | 36 |
import eu.etaxonomy.cdm.io.dwca.jaxb.Archive; |
| 37 | 37 |
import eu.etaxonomy.cdm.io.dwca.jaxb.ArchiveEntryBase; |
| 38 | 38 |
import eu.etaxonomy.cdm.io.dwca.jaxb.Extension; |
| ... | ... | |
| 253 | 253 |
// |
| 254 | 254 |
|
| 255 | 255 |
private InputStream makeInputStream(String name) throws IOException {
|
| 256 |
File file = new File(dwcaZip); |
|
| 256 |
File file = new File(dwcaZip.getJavaUri());
|
|
| 257 | 257 |
if (! file.isFile() || ! file.exists()){
|
| 258 | 258 |
String message = "URI is not a file: %s"; |
| 259 | 259 |
throw new IOException(String.format(message, dwcaZip.toString())); |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/in/GbifReferenceCsv2CdmConverter.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.in; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.ArrayList; |
| 13 | 12 |
import java.util.HashSet; |
| 14 | 13 |
import java.util.List; |
| ... | ... | |
| 20 | 19 |
|
| 21 | 20 |
import com.ibm.lsid.MalformedLSIDException; |
| 22 | 21 |
|
| 22 |
import eu.etaxonomy.cdm.common.URI; |
|
| 23 | 23 |
import eu.etaxonomy.cdm.io.stream.IPartitionableConverter; |
| 24 | 24 |
import eu.etaxonomy.cdm.io.stream.IReader; |
| 25 | 25 |
import eu.etaxonomy.cdm.io.stream.ListReader; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaEmlRecord.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.out; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.PrintWriter; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.util.ArrayList; |
| 14 | 13 |
import java.util.List; |
| 15 | 14 |
import java.util.UUID; |
| ... | ... | |
| 17 | 16 |
import org.apache.log4j.Logger; |
| 18 | 17 |
import org.joda.time.DateTime; |
| 19 | 18 |
|
| 19 |
import eu.etaxonomy.cdm.common.URI; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.model.agent.InstitutionalMembership; |
| 21 | 21 |
import eu.etaxonomy.cdm.model.common.Language; |
| 22 | 22 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaId.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.out; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 14 | 13 |
import org.apache.log4j.Logger; |
| 15 | 14 |
|
| 15 |
import eu.etaxonomy.cdm.common.URI; |
|
| 16 | 16 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 17 | 17 |
import eu.etaxonomy.cdm.model.common.ICdmBase; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaImageRecord.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.out; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.PrintWriter; |
| 12 |
import java.net.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.Set; |
| 15 | 14 |
|
| 16 | 15 |
import org.apache.log4j.Logger; |
| 17 | 16 |
|
| 17 |
import eu.etaxonomy.cdm.common.URI; |
|
| 18 | 18 |
import eu.etaxonomy.cdm.io.stream.terms.TermUri; |
| 19 | 19 |
import eu.etaxonomy.cdm.model.agent.AgentBase; |
| 20 | 20 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaMetaDataExport.java | ||
|---|---|---|
| 11 | 11 |
|
| 12 | 12 |
import java.io.FileNotFoundException; |
| 13 | 13 |
import java.io.IOException; |
| 14 |
import java.net.URI;
|
|
| 14 |
import eu.etaxonomy.cdm.common.URI;
|
|
| 15 | 15 |
import java.util.List; |
| 16 | 16 |
|
| 17 | 17 |
import javax.xml.stream.XMLStreamException; |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaMetaDataRecord.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.out; |
| 10 | 10 |
|
| 11 |
import java.net.URI; |
|
| 12 | 11 |
import java.util.ArrayList; |
| 13 | 12 |
import java.util.List; |
| 14 | 13 |
|
| 15 | 14 |
import org.apache.log4j.Logger; |
| 16 | 15 |
|
| 16 |
import eu.etaxonomy.cdm.common.URI; |
|
| 17 |
|
|
| 17 | 18 |
/** |
| 18 | 19 |
* @author a.mueller |
| 19 | 20 |
* @since 20.04.2011 |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/dwca/out/DwcaRecordBase.java | ||
|---|---|---|
| 9 | 9 |
package eu.etaxonomy.cdm.io.dwca.out; |
| 10 | 10 |
|
| 11 | 11 |
import java.io.PrintWriter; |
| 12 |
import java.net.URI; |
|
Also available in: Unified diff
ref #9114 add URI Wrapper and replace all java.net.URI occurrences by the wrapper in cdmlib