Browse Source

moved to Storagehub

feature/21995
lucio.lelii 3 months ago
parent
commit
3519fc2888
  1. 15
      .settings/org.eclipse.wst.common.component
  2. 5
      CHANGELOG.md
  3. 21
      pom.xml
  4. 76
      src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java
  5. 57
      src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/csv/ManageTimeSeriesThread.java
  6. 134
      src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java

15
.settings/org.eclipse.wst.common.component

@ -1,12 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="grsf-publisher-ws">
<wb-module deploy-name="grsf-publisher-ws-1.12.1-SNAPSHOT">
<wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
<dependent-module archiveName="grsf-common-library-1.0.3-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/grsf-common-library/grsf-common-library">
<dependent-module archiveName="storagehub-model-1.1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/storagehub-model/storagehub-model">
<dependency-type>uses</dependency-type>
</dependent-module>
<dependent-module archiveName="common-gcube-calls-1.3.1-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/common-gcube-calls/common-gcube-calls">
<dependency-type>uses</dependency-type>
</dependent-module>
<property name="context-root" value="grsf-publisher-ws"/>
<property name="java-output-path" value="/grsf-publisher-ws/target/classes"/>
</wb-module>
</project-modules>

5
CHANGELOG.md

@ -3,13 +3,14 @@
All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [v1.12.1-SNAPSHOT]
## [v1.13.0-SNAPSHOT]
### Changed
- Switched dependency management to gcube-bom 2.0.0
- moved to storagehub
## [v1.12.0] [r4.24.0] - 2020-06-19
## [v1.12.0] - 2020-06-19
### Added

21
pom.xml

@ -11,7 +11,7 @@
<groupId>org.gcube.data-catalogue</groupId>
<artifactId>grsf-publisher-ws</artifactId>
<version>1.12.1-SNAPSHOT</version>
<version>1.13.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>grsf-publisher-ws</name>
<description>Utility library to publish GRSF products on GRSF catalogue.</description>
@ -52,6 +52,11 @@
<artifactId>grsf-common-library</artifactId>
<version>[1-0-0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-client-library</artifactId>
<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
</dependency>
<!-- jsoup HTML parser library @ http://jsoup.org/ -->
<dependency>
<groupId>org.jsoup</groupId>
@ -100,12 +105,7 @@
<artifactId>authorization-client</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>home-library-jcr</artifactId>
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>common-authorization</artifactId>
@ -157,12 +157,7 @@
<artifactId>common-smartgears</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>home-library</artifactId>
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.test-framework.providers</groupId>
<artifactId>jersey-test-framework-provider-jetty</artifactId>

76
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java

@ -5,7 +5,6 @@ import static org.gcube.resources.discovery.icclient.ICFactory.client;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
@ -20,15 +19,11 @@ import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
import org.gcube.common.homelibrary.home.workspace.exceptions.InsufficientPrivilegesException;
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemAlreadyExistException;
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException;
import org.gcube.common.homelibrary.home.workspace.folder.items.ExternalFile;
import org.gcube.common.resources.gcore.utils.XPathHelper;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.storagehub.client.dsl.FolderContainer;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogue;
import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogueFactory;
import org.gcube.datacatalogue.common.caches.CacheImpl;
@ -74,7 +69,6 @@ public abstract class HelperMethods {
public static final String MANAGE_CONTEX_KEY = "ManageVRE";
public static final String PREVALIDATE_CONTEX_KEY = "PreValidateVRE";
public static final String PUBLIC_CONTEX_KEY = "PublicVRE";
private static final String CSV_MIME = "text/csv";
private static final String PATH_SEPARATOR = "/";
// caches
@ -258,29 +252,20 @@ public abstract class HelperMethods {
* @param csvFile
* @return
*/
public static ExternalFile uploadExternalFile(WorkspaceFolder resourceFormatFolder, String resourceToAttachName, String description, File csvFile) {
public static FileContainer uploadExternalFile(FolderContainer resourceFormatFolder, String resourceToAttachName, String description, File csvFile) {
try {
WorkspaceItem existsFile = resourceFormatFolder.find(resourceToAttachName);
if(existsFile == null)
return resourceFormatFolder.createExternalFileItem(resourceToAttachName, description, CSV_MIME, csvFile);
else{
InputStream targetStream = new FileInputStream(csvFile);
existsFile.updateItem(targetStream);
return (ExternalFile)existsFile;
}
} catch (InsufficientPrivilegesException | ItemAlreadyExistException
| InternalErrorException e) {
logger.error("Failed to upload the file into the workspace shared folder for " + resourceToAttachName, e);
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ItemNotFoundException e) {
try (InputStream is= new FileInputStream(csvFile)) {
FileContainer fileContainer = resourceFormatFolder.uploadFile(is , resourceToAttachName, description);
return fileContainer;
}
} catch (StorageHubException she) {
logger.error("Failed to upload the file into the workspace shared folder for " + resourceToAttachName, she);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
return null;
}
@ -291,9 +276,10 @@ public abstract class HelperMethods {
* @param subPath
* @return null if an error occurred
*/
public static WorkspaceFolder createOrGetSubFoldersByPath(WorkspaceFolder folder, String subPath){
WorkspaceFolder parentFolder = folder;
public static FolderContainer createOrGetSubFoldersByPath(FolderContainer folder, String subPath){
FolderContainer parentFolder = folder;
if(folder == null)
throw new IllegalArgumentException("Root folder is null!");
@ -312,8 +298,9 @@ public abstract class HelperMethods {
String[] splittedPaths = subPath.split(PATH_SEPARATOR);
for (String path : splittedPaths) {
WorkspaceFolder createdFolder = getFolderOrCreate(parentFolder, path, "");
logger.debug("Created subfolder with path " + createdFolder.getPath());
FolderContainer createdFolder = getFolderOrCreate(parentFolder, path, "");
logger.debug("Created subfolder with path " + createdFolder.get().getPath());
parentFolder = createdFolder;
}
@ -329,23 +316,18 @@ public abstract class HelperMethods {
* Get a folder within the catalogue folder or create it if it doesn't exist.
* @return
*/
public static WorkspaceFolder getFolderOrCreate(WorkspaceFolder folder, String relativePath, String descriptionFolder){
WorkspaceFolder result = null;
public static FolderContainer getFolderOrCreate(FolderContainer folder, String relativePath, String descriptionFolder){
FolderContainer result = null;
try {
WorkspaceItem foundFolder = folder.find(relativePath);
if(foundFolder != null && foundFolder.isFolder())
result = (WorkspaceFolder)foundFolder;
if(result != null)
logger.debug("Folder found with name " + result.getName() + ", it has id " + result.getId());
else
throw new Exception("There is no folder with name " + relativePath + " under folder " + folder.getName());
result = folder.openByRelativePath(relativePath).asFolder();
} catch (Exception e) {
logger.debug("Probably the folder doesn't exist");
try{
result = folder.createFolder(relativePath, descriptionFolder);
} catch (InsufficientPrivilegesException | InternalErrorException | ItemAlreadyExistException e2) {
logger.error("Failed to get or generate this folder", e2);
result = folder.newFolder(relativePath, descriptionFolder);
} catch (StorageHubException se) {
logger.error("Failed to get or generate this folder", se);
}
}
return result;

57
src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/csv/ManageTimeSeriesThread.java

@ -1,6 +1,5 @@
package org.gcube.data_catalogue.grsf_publish_ws.utils.csv;
import java.beans.IntrospectionException;
import java.beans.PropertyDescriptor;
import java.io.File;
import java.lang.reflect.Field;
@ -8,18 +7,11 @@ import java.lang.reflect.InvocationTargetException;
import java.util.List;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.homelibrary.home.HomeLibrary;
import org.gcube.common.homelibrary.home.exceptions.HomeNotFoundException;
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
import org.gcube.common.homelibrary.home.exceptions.UserNotFoundException;
import org.gcube.common.homelibrary.home.workspace.Workspace;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
import org.gcube.common.homelibrary.home.workspace.WorkspaceSharedFolder;
import org.gcube.common.homelibrary.home.workspace.catalogue.WorkspaceCatalogue;
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException;
import org.gcube.common.homelibrary.home.workspace.exceptions.WorkspaceFolderNotFoundException;
import org.gcube.common.homelibrary.home.workspace.folder.items.ExternalFile;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.storagehub.client.dsl.FolderContainer;
import org.gcube.common.storagehub.client.dsl.StorageHubClient;
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CustomField;
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.TimeSeries;
import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.Common;
@ -42,13 +34,15 @@ public class ManageTimeSeriesThread extends Thread{
private static final String PATH_SEPARATOR = "/";
private static final String CATALOGUE_FOLDER = ".catalogue";
// Logger
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(ManageTimeSeriesThread.class);
// try to attach the source at most CHANCES times ..
private static final int CHANCES = 10;
private static CacheInterface<String, WorkspaceCatalogue> vreFolderCache = new CacheImpl<String, WorkspaceCatalogue>(1000 * 60 * 60 * 24);
private static CacheInterface<String, FolderContainer> vreFolderCache = new CacheImpl<String, FolderContainer>(1000 * 60 * 60 * 24);
private static final int MAX_NAME_CSV_FILE_WITHOUT_MEASURE = 50;
@ -96,17 +90,7 @@ public class ManageTimeSeriesThread extends Thread{
logger.error("Error was " + e.getMessage());
} catch (InvocationTargetException e) {
logger.error("Error was " + e.getMessage());
} catch (WorkspaceFolderNotFoundException e) {
logger.error("Error was " + e.getMessage());
} catch (ItemNotFoundException e) {
logger.error("Error was " + e.getMessage());
} catch (IntrospectionException e) {
logger.error("Error was " + e.getMessage());
} catch (InternalErrorException e) {
logger.error("Error was " + e.getMessage());
} catch (HomeNotFoundException e) {
logger.error("Error was " + e.getMessage());
} catch (UserNotFoundException e) {
} catch (StorageHubException e) {
logger.error("Error was " + e.getMessage());
} catch (Exception e) {
logger.error("Error was " + e.getMessage());
@ -130,17 +114,26 @@ public class ManageTimeSeriesThread extends Thread{
if(record == null)
throw new IllegalArgumentException("The given record is null!!");
StorageHubClient shClient = new StorageHubClient();
String token = SecurityTokenProvider.instance.get();
WorkspaceCatalogue catalogueFolder = null;
FolderContainer catalogueFolder = null;
//WorkspaceCatalogue catalogueFolder = null;
if((catalogueFolder = vreFolderCache.get(token)) == null){
Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
WorkspaceSharedFolder vreFolder = ws.getVREFolderByScope(ScopeProvider.instance.get());
catalogueFolder = vreFolder.getVRECatalogue();
//Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
FolderContainer vreFolder = shClient.openVREFolder();
try {
catalogueFolder = vreFolder.openByRelativePath(CATALOGUE_FOLDER).asFolder();
}catch (StorageHubException e) {
catalogueFolder = vreFolder.newHiddenFolder(CATALOGUE_FOLDER, "catalogue folder");
}
vreFolderCache.insert(token, catalogueFolder);
}
logger.debug("Catalogue folder in vre has path " + catalogueFolder.getPath());
logger.debug("Catalogue folder in vre has path " + catalogueFolder.get().getPath());
// the structure under the .catalogue will be as follows:
// .catalogue:
@ -167,7 +160,7 @@ public class ManageTimeSeriesThread extends Thread{
// the whole path of the directory is going to be...
String csvDirectoryForThisProduct = recordTypeFolderName + PATH_SEPARATOR + firstLetter + PATH_SEPARATOR + replaceIllegalChars(uuidKB, "_") + PATH_SEPARATOR + CSVUtils.CSV_EXTENSION.replace(".", "");
logger.debug("The path under which the time series are going to be saved is " + csvDirectoryForThisProduct);
WorkspaceFolder csvFolder = HelperMethods.createOrGetSubFoldersByPath(catalogueFolder, csvDirectoryForThisProduct);
FolderContainer csvFolder = HelperMethods.createOrGetSubFoldersByPath(catalogueFolder, csvDirectoryForThisProduct);
if(csvFolder == null)
logger.error("Failed to create directory where csv files will be deployed in the workspace!!");
@ -192,7 +185,7 @@ public class ManageTimeSeriesThread extends Thread{
String resourceToAttachOnCkanDescription = productName;
CkanResourceBase ckanResource = null;
ExternalFile createdFileOnWorkspace = null;
FileContainer createdFileOnWorkspace = null;
String[] relevantSources = new String[1];
File csvFile = CSVUtils.listToCSV(asList, relevantSources);
if(csvFile != null){
@ -212,7 +205,7 @@ public class ManageTimeSeriesThread extends Thread{
+ customAnnotation.key() + CSVUtils.CSV_EXTENSION, resourceToAttachOnCkanDescription, csvFile);
if(createdFileOnWorkspace != null){
String publicUrlToSetOnCkan = createdFileOnWorkspace.getPublicLink(true);
String publicUrlToSetOnCkan = createdFileOnWorkspace.getPublicLink().toString();
// wait for patching..
Thread.sleep(1500);

134
src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java

@ -13,17 +13,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.homelibrary.home.HomeLibrary;
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
import org.gcube.common.homelibrary.home.workspace.Workspace;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
import org.gcube.common.homelibrary.home.workspace.WorkspaceSharedFolder;
import org.gcube.common.homelibrary.home.workspace.catalogue.WorkspaceCatalogue;
import org.gcube.common.homelibrary.home.workspace.exceptions.InsufficientPrivilegesException;
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemAlreadyExistException;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CustomField;
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Group;
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Tag;
@ -238,129 +227,8 @@ public class JTests {
instance.uploadResourceFile(csvFile, datasetName, instance.getApiKeyFromUsername("costantino.perciante"), "random_name.csv", null, null, null);
}
// @Test
public void sharedVREFolderWriteTest() throws Exception{
String token = "";
String context = "/gcube/devNext/NextNext";
ScopeProvider.instance.set(context);
SecurityTokenProvider.instance.set(token);
Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
// Get a VRE folder by scope
WorkspaceSharedFolder vreFolder = ws.getVREFolderByScope(context);
//Get the VRE Folder catalogue
WorkspaceCatalogue catalogueFolder = vreFolder.getVRECatalogue();
logger.debug("Catalogue folder retrieved " + catalogueFolder.getName());
// WorkspaceItem stockFolder = catalogueFolder.find("stock");
// vreFolder.removeChild(stockFolder);
/**
* Test is
* .catalogue:
* -test
* - a
* -aproductwiththisname
* - csv
* - testfile.csv
*/
String allSubPath = "/test/a/aproductwiththisname/";
//WorkspaceFolder lastFolder = createGetSubFoldersByPath(catalogueFolder, allSubPath);
// WorkspaceFolder recordFolder = (WorkspaceFolder)getFolderOrCreate(catalogueFolder, "test", "");
// String firstLetter = "a";
// WorkspaceFolder firstLetterFolder = (WorkspaceFolder)getFolderOrCreate(recordFolder, firstLetter, "");
// String folderPath = "aproductwiththisname";
// WorkspaceFolder productFolder = (WorkspaceFolder)getFolderOrCreate(firstLetterFolder, folderPath, "");
//logger.debug("Test folder created/get..its path is " + lastFolder.getPath());
// String ccsvUnderProductFolderName = productFolderName + "/" + "csv";
// WorkspaceFolder csvUnderProductFolder = (WorkspaceFolder)getFolderOrCreate(catalogueFolder, ccsvUnderProductFolderName, "");
//
// logger.debug("FOLDERS created " + csvUnderProductFolder.getPath());
// treeCheck(catalogueFolder);
}
public void treeCheck(WorkspaceFolder rootFolder) throws InternalErrorException{
List<WorkspaceItem> children = rootFolder.getChildren();
for (WorkspaceItem workspaceItem : children) {
if(workspaceItem.isFolder()){
logger.debug("children folder is " + workspaceItem.getName());
treeCheck((WorkspaceFolder)workspaceItem);
}
}
}
/**
* Create subfolders in cascade, returning the last created ones
* It could be also used for getting them if they already exists
* @param folder
* @param subPath
* @return
*/
private static WorkspaceFolder createGetSubFoldersByPath(WorkspaceFolder folder, String subPath){
String pathSeparator = "/";
WorkspaceFolder parentFolder = folder;
if(folder == null)
throw new IllegalArgumentException("Root folder is null!");
if(subPath == null || subPath.isEmpty())
throw new IllegalArgumentException("subPath is null/empty!");
try{
if(subPath.startsWith(pathSeparator))
subPath = subPath.replaceFirst(pathSeparator, "");
if(subPath.endsWith(subPath))
subPath = subPath.substring(0, subPath.length() - 1);
logger.debug("Splitting path " + subPath);
String[] splittedPaths = subPath.split(pathSeparator);
for (String path : splittedPaths) {
WorkspaceFolder createdFolder = getFolderOrCreate(parentFolder, path, "");
logger.debug("Created subfolder with path " + createdFolder.getPath());
parentFolder = createdFolder;
}
}catch(Exception e){
logger.error("Failed to create the subfolders by path " + subPath);
}
return parentFolder;
}
/**
* Get a folder within the catalogue folder or create it if it doesn't exist.
* @return
*/
private static WorkspaceFolder getFolderOrCreate(WorkspaceFolder folder, String relativePath, String descriptionFolder){
WorkspaceFolder result = null;
try {
if(folder.exists(relativePath) && folder.find(relativePath).isFolder())
result = (WorkspaceFolder) folder.find(relativePath);
if(result != null)
logger.debug("Folder found with name " + result.getName() + ", it has id " + result.getId());
else
throw new Exception("There is no folder with name " + relativePath + " under foler " + folder.getName());
} catch (Exception e) {
logger.debug("Probably the folder doesn't exist", e);
try{
result = folder.createFolder(relativePath, descriptionFolder);
} catch (InsufficientPrivilegesException | InternalErrorException | ItemAlreadyExistException e2) {
logger.error("Failed to get or generate this folder", e2);
}
}
return result;
}
//@Test
public void GRSFServiceUrl() throws Exception{

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