Compare commits
31 Commits
Author | SHA1 | Date |
---|---|---|
Fabio Sinibaldi | f031d68224 | |
Fabio Sinibaldi | 13f9b12366 | |
Fabio Sinibaldi | 7bd61985f7 | |
Fabio Sinibaldi | f4096a3e97 | |
Fabio Sinibaldi | 95a837ba48 | |
Fabio Sinibaldi | a1f284eae0 | |
Fabio Sinibaldi | 00413916f7 | |
Fabio Sinibaldi | c917eb76a4 | |
Fabio Sinibaldi | 4d7b97c5e1 | |
Fabio Sinibaldi | 8271d0b973 | |
Fabio Sinibaldi | 1459d8b64c | |
Fabio Sinibaldi | fed8b3cbef | |
Fabio Sinibaldi | 8e204019c8 | |
Fabio Sinibaldi | 502b0d30aa | |
Fabio Sinibaldi | ce3f825cb9 | |
Fabio Sinibaldi | a2c07335aa | |
Fabio Sinibaldi | 2f23e571fc | |
Fabio Sinibaldi | d4d4a5e376 | |
Fabio Sinibaldi | 9f91758a82 | |
Fabio Sinibaldi | 252e273556 | |
Fabio Sinibaldi | 8512f573ba | |
Fabio Sinibaldi | 94064f17f7 | |
Fabio Sinibaldi | 96e2f61b03 | |
Fabio Sinibaldi | 6e05cba2ec | |
Fabio Sinibaldi | b431076650 | |
Fabio Sinibaldi | 77abccd9cd | |
Fabio Sinibaldi | e0cc9af6ee | |
Fabio Sinibaldi | d70b7a6347 | |
Fabio Sinibaldi | 8981b3ffd6 | |
Fabio Sinibaldi | 05ff46dc6f | |
Fabio Sinibaldi | 8d8005f0c0 |
36
.classpath
36
.classpath
|
@ -1,36 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<classpath>
|
||||
<classpathentry kind="src" output="target/classes" path="src/main/java">
|
||||
<attributes>
|
||||
<attribute name="optional" value="true"/>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="src" output="target/test-classes" path="src/test/java">
|
||||
<attributes>
|
||||
<attribute name="optional" value="true"/>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
|
||||
<attributes>
|
||||
<attribute name="maven.pomderived" value="true"/>
|
||||
</attributes>
|
||||
</classpathentry>
|
||||
<classpathentry kind="output" path="target/classes"/>
|
||||
</classpath>
|
|
@ -0,0 +1 @@
|
|||
/org.eclipse.jdt.core.prefs
|
|
@ -1,5 +0,0 @@
|
|||
eclipse.preferences.version=1
|
||||
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
|
||||
org.eclipse.jdt.core.compiler.compliance=1.8
|
||||
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.source=1.8
|
11
CHANGELOG.md
11
CHANGELOG.md
|
@ -2,6 +2,17 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
|
|||
|
||||
# Changelog for org.gcube.data.transfer.sis-geotk-plugin
|
||||
|
||||
## [v1.3.1] 2021-03-25
|
||||
Fixes [#20760](https://support.d4science.org/issues/20760) https endpoints
|
||||
|
||||
|
||||
## [v1.3.0] 2021-03-25
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||||
Use of EPSG Dataset
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||||
Proxy support
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||||
|
||||
## [v1.2.0] 2020-09-07
|
||||
Upgrade to apache-sis 1.0
|
||||
|
||||
## [v1.1.3] 2020-09-07
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||||
|
||||
### Fixes
|
||||
|
|
95
pom.xml
95
pom.xml
|
@ -1,4 +1,5 @@
|
|||
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
<project xmlns="http://maven.apache.org/POM/4.0.0"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
|
||||
<modelVersion>4.0.0</modelVersion>
|
||||
<parent>
|
||||
|
@ -8,14 +9,15 @@
|
|||
</parent>
|
||||
<groupId>org.gcube.data.transfer</groupId>
|
||||
<artifactId>sis-geotk-plugin</artifactId>
|
||||
<version>1.1.3</version>
|
||||
<version>1.3.1</version>
|
||||
<name>Sis/GeoToolkit plugin</name>
|
||||
<description>Apache Sis/Geotk plugin for data-transfer-service</description>
|
||||
|
||||
<properties>
|
||||
<sis.version>0.7</sis.version>
|
||||
<sis.version>1.0</sis.version>
|
||||
<sis.utils.modules>${sis.version}</sis.utils.modules>
|
||||
<gitBaseUrl>https://code-repo.d4science.org/gCubeSystem</gitBaseUrl>
|
||||
<netcdfJavaVersion>5.3.3</netcdfJavaVersion>
|
||||
</properties>
|
||||
|
||||
<scm>
|
||||
|
@ -30,14 +32,22 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-smartgears-bom</artifactId>
|
||||
<version>2.0.0</version>
|
||||
<version>2.2.0</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-bom</artifactId>
|
||||
<version>2.0.0</version>
|
||||
<version>2.1.0</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
<!-- https://mvnrepository.com/artifact/org.apache.sis/storage -->
|
||||
<dependency>
|
||||
<groupId>org.apache.sis</groupId>
|
||||
<artifactId>storage</artifactId>
|
||||
<version>1.0</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
|
@ -48,7 +58,7 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.data.transfer</groupId>
|
||||
<artifactId>data-transfer-plugin-framework</artifactId>
|
||||
<version>[1.0.2,2.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.2,2.0.0)</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
|
@ -69,7 +79,8 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.spatial.data</groupId>
|
||||
<artifactId>sdi-library</artifactId>
|
||||
<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
|
||||
<version>[1.0.0,1.0.2]</version>
|
||||
<!-- <version>[1.0.0,2.0)</version> -->
|
||||
</dependency>
|
||||
|
||||
<!-- SMARTGEARS -->
|
||||
|
@ -96,6 +107,48 @@
|
|||
<artifactId>sis-netcdf</artifactId>
|
||||
<version>${sis.utils.modules}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.sis.storage</groupId>
|
||||
<artifactId>sis-earth-observation</artifactId>
|
||||
<version>${sis.utils.modules}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.sis.storage</groupId>
|
||||
<artifactId>sis-geotiff</artifactId>
|
||||
<version>${sis.utils.modules}</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
<!-- SIS EXTERNALS -->
|
||||
<!-- https://mvnrepository.com/artifact/com.esri.geometry/esri-geometry-api -->
|
||||
<!-- <dependency> -->
|
||||
<!-- <groupId>com.esri.geometry</groupId> -->
|
||||
<!-- <artifactId>esri-geometry-api</artifactId> -->
|
||||
<!-- </dependency> -->
|
||||
|
||||
<!-- https://mvnrepository.com/artifact/edu.ucar/cdm -->
|
||||
<dependency>
|
||||
<groupId>edu.ucar</groupId>
|
||||
<artifactId>cdm</artifactId>
|
||||
<scope>compile</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
<!-- EPSG DATASET -->
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.sis.non-free</groupId>
|
||||
<artifactId>sis-embedded-data</artifactId>
|
||||
<version>${sis.version}</version>
|
||||
<scope>runtime</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.derby</groupId>
|
||||
<artifactId>derby</artifactId>
|
||||
<scope>runtime</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
|
||||
<!-- TEST -->
|
||||
<dependency>
|
||||
|
@ -107,21 +160,43 @@
|
|||
<dependency>
|
||||
<groupId>junit</groupId>
|
||||
<artifactId>junit</artifactId>
|
||||
<version>4.12</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.data.transfer</groupId>
|
||||
<artifactId>data-transfer-library</artifactId>
|
||||
<version>[1.2.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
|
||||
<version>[1.2.0,2.0.0-SNAPSHOT)</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>javax.xml.bind</groupId>
|
||||
<artifactId>jaxb-api</artifactId>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.opengis</groupId>
|
||||
<artifactId>geoapi-conformance</artifactId>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
|
||||
</dependencies>
|
||||
|
||||
<repositories>
|
||||
<repository>
|
||||
<id>unidata-all</id>
|
||||
<name>Unidata All</name>
|
||||
|
||||
<url>https://nexus.d4science.org/nexus/content/repositories/unidata/</url>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
|
||||
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
|
|
|
@ -0,0 +1 @@
|
|||
/.DS_Store
|
|
@ -0,0 +1,74 @@
|
|||
package org.gcube.data.transfer.plugins.thredds;
|
||||
|
||||
import static java.util.Collections.singletonMap;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
import javax.xml.transform.stream.StreamResult;
|
||||
|
||||
import org.apache.sis.xml.MarshallerPool;
|
||||
import org.apache.sis.xml.XML;
|
||||
import org.opengis.metadata.Metadata;
|
||||
|
||||
import lombok.Synchronized;
|
||||
import lombok.extern.slf4j.Slf4j;
|
||||
|
||||
@Slf4j
|
||||
public class ISOMetadataMarshalling {
|
||||
|
||||
|
||||
private static MarshallerPool pool=null;
|
||||
|
||||
// static {
|
||||
//
|
||||
// File temp=new File(System.getProperty("java.io.tmpdir")+"/EPSG");
|
||||
// temp.mkdirs();
|
||||
//
|
||||
// EmbeddedConnectionPoolDataSource ds = new EmbeddedConnectionPoolDataSource();
|
||||
// ds.setConnectionAttributes("create=true");
|
||||
//
|
||||
// ds.setDatabaseName(temp.getAbsolutePath()+"/SpatialMetadata");
|
||||
//
|
||||
//// ds.setDataSourceName(arg0);
|
||||
//// ds.setServerName("someHost");
|
||||
//// ds.setPortNumber("1527");
|
||||
//// ds.setDatabaseName("someDB");
|
||||
//
|
||||
// Configuration.current().setDatabase(new Supplier<DataSource>() {
|
||||
// @Override
|
||||
// public DataSource get() {
|
||||
// return ds;
|
||||
// }
|
||||
// });
|
||||
//
|
||||
//
|
||||
// }
|
||||
|
||||
|
||||
|
||||
@Synchronized
|
||||
private static MarshallerPool getPool() throws JAXBException {
|
||||
if(pool==null)
|
||||
pool=new MarshallerPool(
|
||||
singletonMap(XML.METADATA_VERSION,"2007"));
|
||||
|
||||
return pool;
|
||||
}
|
||||
|
||||
public static final File asXML(Metadata meta) throws JAXBException, IOException {
|
||||
File tmp=File.createTempFile("tmp_meta_", ".xml");
|
||||
try (FileWriter fw=new FileWriter(tmp)){
|
||||
|
||||
getPool().acquireMarshaller().marshal(meta,new StreamResult(fw));
|
||||
|
||||
// XML.marshal(meta, new StreamResult(fw), singletonMap(XML.METADATA_VERSION,"2007"));
|
||||
}
|
||||
return tmp;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
|
@ -71,7 +71,18 @@ public class ThreddsInstanceManager {
|
|||
protected ThreddsInstanceManager(DataTransferContext context) {
|
||||
log.warn("Instance Creation. Should happen only once. Loading information from context..");
|
||||
this.ctx=context;
|
||||
currentHostname=ctx.getCtx().container().configuration().hostname();
|
||||
try {
|
||||
log.info("Loading proxy configuration..");
|
||||
currentHostname=ctx.getCtx().configuration().proxyAddress().hostname();
|
||||
if(currentHostname==null||currentHostname.isEmpty()) throw new Exception("Proxy is : "+currentHostname);
|
||||
}catch(Exception e) {
|
||||
log.info("Unable to get proxy..",e);
|
||||
currentHostname=ctx.getCtx().container().configuration().hostname();
|
||||
}
|
||||
log.info("Hostname to be used is "+currentHostname);
|
||||
|
||||
|
||||
|
||||
currentGHNId=ctx.getCtx().container().id();
|
||||
String tomcatSecurityPath=System.getenv("WEB_CONTAINER_HOME")+"/conf/tomcat-users.xml";
|
||||
|
||||
|
@ -121,7 +132,7 @@ public class ThreddsInstanceManager {
|
|||
info.setHostname(currentHostname);
|
||||
info.setGhnId(currentGHNId);
|
||||
info.setLocalBasePath(threddsPersistenceLocation);
|
||||
info.setInstanceBaseUrl("http://"+info.getHostname()+"/thredds");
|
||||
info.setInstanceBaseUrl("https://"+info.getHostname()+"/thredds");
|
||||
|
||||
|
||||
String mainCatalogPath=threddsContentRoot+"/catalog.xml";
|
||||
|
|
|
@ -20,7 +20,7 @@ public class SISPluginFactory extends AbstractPluginFactory<SisPlugin> {
|
|||
|
||||
|
||||
|
||||
static final String PLUGIN_ID="SIS/GEOTK";
|
||||
public static final String PLUGIN_ID="SIS/GEOTK";
|
||||
|
||||
public static final String SOURCE_PARAMETER="SOURCE_FILE";
|
||||
public static final String GEONETWORK_CATEGORY="GEONETWORK_CATEGORY";
|
||||
|
|
|
@ -16,6 +16,7 @@ import org.gcube.data.transfer.model.plugins.thredds.ThreddsCatalog;
|
|||
import org.gcube.data.transfer.plugin.AbstractPlugin;
|
||||
import org.gcube.data.transfer.plugin.fails.PluginCleanupException;
|
||||
import org.gcube.data.transfer.plugin.fails.PluginExecutionException;
|
||||
import org.gcube.data.transfer.plugins.thredds.ISOMetadataMarshalling;
|
||||
import org.gcube.data.transfer.plugins.thredds.ThreddsInstanceManager;
|
||||
import org.gcube.spatial.data.sdi.model.metadata.MetadataPublishOptions;
|
||||
import org.gcube.spatial.data.sdi.model.metadata.MetadataReport;
|
||||
|
@ -69,9 +70,7 @@ public class SisPlugin extends AbstractPlugin {
|
|||
log.debug("Extracting meta from {} ",dataStore.getAbsolutePath());
|
||||
Metadata meta=getMetaFromFile(dataStore);
|
||||
|
||||
tmp=File.createTempFile("tmp_meta_", ".xml");
|
||||
|
||||
XML.marshal(meta,tmp);
|
||||
tmp=ISOMetadataMarshalling.asXML(meta);
|
||||
|
||||
org.gcube.spatial.data.sdi.interfaces.Metadata metadataInterface=SDIAbstractPlugin.metadata().build();
|
||||
|
||||
|
|
|
@ -0,0 +1,80 @@
|
|||
package org.gcube.data.transfer.plugins.sis;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FilenameFilter;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.Collections;
|
||||
import java.util.Set;
|
||||
|
||||
import org.gcube.data.transfer.library.DataTransferClient;
|
||||
import org.gcube.data.transfer.library.TransferResult;
|
||||
import org.gcube.data.transfer.library.faults.DestinationNotSetException;
|
||||
import org.gcube.data.transfer.library.faults.FailedTransferException;
|
||||
import org.gcube.data.transfer.library.faults.InitializationException;
|
||||
import org.gcube.data.transfer.library.faults.InvalidDestinationException;
|
||||
import org.gcube.data.transfer.library.faults.InvalidSourceException;
|
||||
import org.gcube.data.transfer.library.faults.SourceNotSetException;
|
||||
import org.gcube.data.transfer.model.Destination;
|
||||
import org.gcube.data.transfer.model.DestinationClashPolicy;
|
||||
import org.gcube.data.transfer.model.PluginInvocation;
|
||||
import org.gcube.data.transfer.plugins.thredds.sis.SISPluginFactory;
|
||||
|
||||
|
||||
public class PublishTest {
|
||||
|
||||
public static void main(String[] args) throws MalformedURLException, Exception, InvalidSourceException, SourceNotSetException, FailedTransferException, InitializationException, InvalidDestinationException, DestinationNotSetException {
|
||||
|
||||
TokenSetter.set("/pred4s/preprod/preVRE");
|
||||
|
||||
|
||||
|
||||
String hostname="";
|
||||
// Not yet released sdi refactoring
|
||||
// new URL(SDIAbstractPlugin.management().build().getConfiguration().getByEngine(Engine.TH_ENGINE).get(0).getBaseEndpoint()).getHost();
|
||||
|
||||
DataTransferClient client=DataTransferClient.getInstanceByEndpoint("https://"+hostname);
|
||||
|
||||
|
||||
File metadata=Paths.get("src/test/resources/toPublishMeta").toFile();
|
||||
// for(File f:metadata.listFiles(new FilenameFilter() {
|
||||
// @Override
|
||||
// public boolean accept(File dir, String name) {
|
||||
// return name.endsWith(".xml");
|
||||
// }
|
||||
// })) {
|
||||
// for(File f:new File[] {
|
||||
// new File("/Users/FabioISTI/Downloads/NASA_Surface_Air_Temperature_1950_2100_rcp45.nc")
|
||||
// }) {
|
||||
|
||||
for(URL url:new URL[] {
|
||||
new URL("https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Precipitations_1950_2100_rcp45.nc")
|
||||
}) {
|
||||
|
||||
// if not present, generate with sis/geotk
|
||||
Destination toSetDestination=new Destination();
|
||||
toSetDestination.setCreateSubfolders(true);
|
||||
toSetDestination.setDestinationFileName("another_dataset");
|
||||
toSetDestination.setOnExistingFileName(DestinationClashPolicy.REWRITE);
|
||||
toSetDestination.setOnExistingSubFolder(DestinationClashPolicy.APPEND);
|
||||
toSetDestination.setPersistenceId("thredds");
|
||||
|
||||
//NB ITEM IS SUPPOSED TO HAVE REMOTE PATH
|
||||
String fileLocation="public/netcdf/test_"+System.currentTimeMillis();
|
||||
toSetDestination.setSubFolder(fileLocation);
|
||||
|
||||
PluginInvocation inv=new PluginInvocation(SISPluginFactory.PLUGIN_ID);
|
||||
inv.setParameters(Collections.singletonMap(SISPluginFactory.VALIDATE_PARAMETER, "false"));
|
||||
|
||||
System.out.println(
|
||||
// client.localFile(f, toSetDestination, Collections.singleton(new PluginInvocation(SISPluginFactory.PLUGIN_ID))));
|
||||
client.httpSource(url, toSetDestination, inv));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
|
@ -2,67 +2,144 @@ package org.gcube.data.transfer.plugins.sis;
|
|||
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.io.OutputStream;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.StandardCopyOption;
|
||||
import java.security.MessageDigest;
|
||||
import java.security.NoSuchAlgorithmException;
|
||||
|
||||
import javax.xml.bind.JAXBException;
|
||||
|
||||
import org.apache.sis.storage.DataStoreException;
|
||||
import org.apache.sis.storage.UnsupportedStorageException;
|
||||
import org.gcube.data.transfer.model.TransferTicket.Status;
|
||||
import org.gcube.data.transfer.plugins.thredds.ISOMetadataMarshalling;
|
||||
import org.gcube.data.transfer.plugins.thredds.sis.SisPlugin;
|
||||
|
||||
import ucar.nc2.NetcdfFile;
|
||||
import ucar.nc2.dataset.NetcdfDataset;
|
||||
|
||||
public class TestGetMetadata {
|
||||
|
||||
public static void main(String[] args) throws UnsupportedStorageException, DataStoreException, IOException, NoSuchAlgorithmException {
|
||||
public static void main(String[] args) throws UnsupportedStorageException, DataStoreException, IOException, NoSuchAlgorithmException, JAXBException {
|
||||
String[] toCheckFiles=new String[] {
|
||||
|
||||
|
||||
// ********** HDF - NETCDF 4
|
||||
"/Users/FabioISTI/Downloads/NASA_Surface_Air_Temperature_1950_2100_rcp45.nc",
|
||||
|
||||
// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Precipitations_1950_2100_rcp45.nc",
|
||||
// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Precipitations_1950_2100_rcp85.nc",
|
||||
// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Surface_Air_Temperature_1950_2100_rcp45.nc",
|
||||
// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/NASA_Surface_Air_Temperature_1950_2100_rcp85.nc",
|
||||
// "https://thredds.d4science.org/thredds/fileServer/public/netcdf/ClimateChange/hcaf_v6_1950_2100.nc",
|
||||
|
||||
|
||||
// *********** NETCDF 3
|
||||
|
||||
"/Users/FabioISTI/Downloads/Aaptos_aaptos.nc",
|
||||
"/Users/FabioISTI/Downloads/dataset-armor-3d-rep-monthly_20181115T1200Z_P20190301T0000Z.nc",
|
||||
//"/Users/FabioISTI/Downloads/data_retro_Run_10026_911.nc",
|
||||
//"/Users/FabioISTI/Downloads/2BPR6_2021_a_NRT_Gosud_V3.nc",
|
||||
"/Users/FabioISTI/Downloads/GO_WTEP_2015_TRAJ.nc"
|
||||
|
||||
};
|
||||
|
||||
File temp=File.createTempFile("temp", ".temp");
|
||||
File original=new File("/home/fabio/Downloads/oscar_vel2011_180.nc");
|
||||
File copied=File.createTempFile("copied", ".nc");
|
||||
transferStream(new FileInputStream(original),new FileOutputStream(temp));
|
||||
System.out.println("copied. Moving..");
|
||||
|
||||
System.out.println("Checksum original : "+getChecksum(original));
|
||||
System.out.println("Checksum temp : "+getChecksum(temp));
|
||||
for(String f:toCheckFiles) {
|
||||
System.out.println("checking "+f);
|
||||
try{
|
||||
check(false,f);
|
||||
}catch(Exception e) {
|
||||
System.err.println(e.getMessage());
|
||||
System.out.println("Trying opening "+f+" manually");
|
||||
open(f);
|
||||
}
|
||||
}
|
||||
System.out.println("Done");
|
||||
}
|
||||
|
||||
|
||||
private static void open(String path) throws IOException, UnsupportedStorageException, DataStoreException {
|
||||
System.out.println("Opening "+path);
|
||||
NetcdfFile f=NetcdfFile.open(path);
|
||||
System.out.println(f.getFileTypeDescription()+"\t"+f.getFileTypeId());
|
||||
|
||||
|
||||
NetcdfDataset ncDs=NetcdfDataset.openDataset(path);
|
||||
// NcMLReaderNew.
|
||||
//
|
||||
System.out.println(ncDs.getFileTypeDescription()+"\t"+ncDs.getFileTypeId());
|
||||
|
||||
// NetcdfDatasets.openFile(path,null);
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static void check(boolean checkCopy,String src) throws UnsupportedStorageException, DataStoreException, IOException, NoSuchAlgorithmException, JAXBException {
|
||||
|
||||
File original=new File(src);
|
||||
|
||||
File dataset=original;
|
||||
|
||||
if(checkCopy) {
|
||||
File temp=File.createTempFile("temp", ".temp");
|
||||
File copied=File.createTempFile("copied", ".nc");
|
||||
transferStream(new FileInputStream(original),new FileOutputStream(temp));
|
||||
System.out.println("copied. Moving..");
|
||||
|
||||
System.out.println("Checksum original : "+getChecksum(original));
|
||||
System.out.println("Checksum temp : "+getChecksum(temp));
|
||||
|
||||
|
||||
|
||||
Files.move(temp.toPath(), copied.toPath(),StandardCopyOption.ATOMIC_MOVE,StandardCopyOption.REPLACE_EXISTING);
|
||||
if(copied.length()<original.length()) throw new RuntimeException("Different size after moving");
|
||||
|
||||
dataset=copied;
|
||||
|
||||
}
|
||||
|
||||
|
||||
if(dataset.exists())
|
||||
System.out.println(
|
||||
ISOMetadataMarshalling.asXML(SisPlugin.getMetaFromFile(dataset)).getAbsolutePath());
|
||||
else {
|
||||
System.out.println(
|
||||
ISOMetadataMarshalling.asXML(SisPlugin.getMetaFromFile(new URL(src))).getAbsolutePath());
|
||||
}
|
||||
|
||||
Files.move(temp.toPath(), copied.toPath(),StandardCopyOption.ATOMIC_MOVE,StandardCopyOption.REPLACE_EXISTING);
|
||||
if(copied.length()<original.length()) throw new RuntimeException("Different size after moving");
|
||||
System.out.println(SisPlugin.getMetaFromFile(copied));
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
private static String getChecksum(File datafile) throws NoSuchAlgorithmException, IOException {
|
||||
MessageDigest md = MessageDigest.getInstance("SHA1");
|
||||
FileInputStream fis = new FileInputStream(datafile);
|
||||
byte[] dataBytes = new byte[1024];
|
||||
FileInputStream fis = new FileInputStream(datafile);
|
||||
byte[] dataBytes = new byte[1024];
|
||||
|
||||
int nread = 0;
|
||||
int nread = 0;
|
||||
|
||||
while ((nread = fis.read(dataBytes)) != -1) {
|
||||
md.update(dataBytes, 0, nread);
|
||||
};
|
||||
while ((nread = fis.read(dataBytes)) != -1) {
|
||||
md.update(dataBytes, 0, nread);
|
||||
};
|
||||
|
||||
byte[] mdbytes = md.digest();
|
||||
byte[] mdbytes = md.digest();
|
||||
|
||||
//convert the byte to hex format
|
||||
StringBuffer sb = new StringBuffer("");
|
||||
for (int i = 0; i < mdbytes.length; i++) {
|
||||
sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
|
||||
}
|
||||
//convert the byte to hex format
|
||||
StringBuffer sb = new StringBuffer("");
|
||||
for (int i = 0; i < mdbytes.length; i++) {
|
||||
sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
|
||||
}
|
||||
|
||||
return sb.toString();
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static void transferStream(InputStream in, OutputStream out){
|
||||
|
||||
|
@ -74,12 +151,12 @@ public class TestGetMetadata {
|
|||
while ((received=in.read(internalBuf))!=-1){
|
||||
out.write(internalBuf,0,received);
|
||||
receivedTotal+=received;
|
||||
|
||||
|
||||
}
|
||||
out.flush();
|
||||
}catch(IOException e){
|
||||
throw new RuntimeException("Unable to read from source.");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
@ -0,0 +1,33 @@
|
|||
package org.gcube.data.transfer.plugins.sis;
|
||||
|
||||
import java.util.Properties;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
|
||||
import lombok.extern.slf4j.Slf4j;
|
||||
@Slf4j
|
||||
public class TokenSetter {
|
||||
|
||||
|
||||
private static Properties props=new Properties();
|
||||
|
||||
static{
|
||||
try {
|
||||
props.load(TokenSetter.class.getResourceAsStream("/tokens.properties"));
|
||||
} catch (Exception e) {
|
||||
throw new RuntimeException("YOU NEED TO SET TOKEN FILE IN CONFIGURATION");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public static void set(String scope){
|
||||
try{
|
||||
if(!props.containsKey(scope)) throw new RuntimeException("No token found for scope : "+scope);
|
||||
SecurityTokenProvider.instance.set(props.getProperty(scope));
|
||||
}catch(Throwable e){
|
||||
log.warn("Unable to set token for scope "+scope,e);
|
||||
}
|
||||
ScopeProvider.instance.set(scope);
|
||||
}
|
||||
}
|
Loading…
Reference in New Issue