gCubeSystem
/
dataminer
15
0
Fork 0
Code Issues Pull Requests Releases 2 Wiki Activity

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173499 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Lucio Lelii 2018-10-15 17:41:21 +00:00
parent 30749c37e3
commit 8e7edbb075
2 changed files with 231 additions and 233 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

16
pom.xml
View File

@ -124,7 +124,7 @@
<artifactId>javassist</artifactId> <artifactId>javassist</artifactId>
<version>3.12.1.GA</version> <version>3.12.1.GA</version>
</dependency> </dependency>
<dependency> <!-- <dependency>
<groupId>org.gcube.common</groupId> <groupId>org.gcube.common</groupId>
<artifactId>home-library-jcr</artifactId> <artifactId>home-library-jcr</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version> <version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
@ -134,8 +134,18 @@
<groupId>org.gcube.common</groupId> <groupId>org.gcube.common</groupId>
<artifactId>home-library</artifactId> <artifactId>home-library</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version> <version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
</dependency> </dependency> -->
<dependency >
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-client-library</artifactId>
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
</dependency>
<dependency >
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-model</artifactId>
<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
</dependency>
<dependency> <dependency>
<groupId>xerces</groupId> <groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId> <artifactId>xercesImpl</artifactId>

448
src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/DataspaceManager.java
View File

@ -13,16 +13,14 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.UUID; import java.util.UUID;
import org.gcube.common.homelibrary.home.Home; import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.homelibrary.home.HomeLibrary; import org.gcube.common.storagehub.client.dsl.FolderContainer;
import org.gcube.common.homelibrary.home.HomeManager; import org.gcube.common.storagehub.client.dsl.ItemContainer;
import org.gcube.common.homelibrary.home.HomeManagerFactory; import org.gcube.common.storagehub.client.dsl.StorageHubClient;
import org.gcube.common.homelibrary.home.User; import org.gcube.common.storagehub.model.Metadata;
import org.gcube.common.homelibrary.home.workspace.Workspace; import org.gcube.common.storagehub.model.items.FolderItem;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder; import org.gcube.common.storagehub.model.items.GCubeItem;
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem; import org.gcube.common.storagehub.model.items.Item;
import org.gcube.common.homelibrary.home.workspace.folder.FolderItem;
import org.gcube.common.homelibrary.util.WorkspaceUtil;
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools; import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper; import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper;
@ -88,43 +86,55 @@ public class DataspaceManager implements Runnable {
} }
public void createFoldersNetwork(Workspace ws, WorkspaceFolder root) throws Exception { public FolderContainer createFoldersNetwork() throws Exception {
LOGGER.debug("Dataspace->Creating folders for DataMiner"); LOGGER.debug("Dataspace->Creating folders for DataMiner");
// manage folders: create the folders network StorageHubClient shc = new StorageHubClient();
if (!ws.exists(dataminerFolder, root.getId())) {
LOGGER.debug("Dataspace->Creating DataMiner main folder");
root.createFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
}
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
if (!ws.exists(importedDataFolder, dataminerFolderWS.getId())) { FolderContainer root =shc.getWSRoot();
List<ItemContainer<? extends Item>> dataminerItems = root.findByName(dataminerFolder).getContainers();
FolderContainer dataminerFolderContainer;
// manage folders: create the folders network
if (dataminerItems.isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner main folder");
dataminerFolderContainer = root.newFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
//((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
} else if (dataminerItems.size()>1) throw new Exception("found more than one dataminer folder (impossible!!!)");
else dataminerFolderContainer = (FolderContainer) dataminerItems.get(0);
if (dataminerFolderContainer.findByName(importedDataFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner imported data folder"); LOGGER.debug("Dataspace->Creating DataMiner imported data folder");
dataminerFolderWS.createFolder(importedDataFolder, "A folder collecting DataMiner imported data"); dataminerFolderContainer.newFolder(importedDataFolder, "A folder collecting DataMiner imported data");
} }
if (!ws.exists(computedDataFolder, dataminerFolderWS.getId())) {
if (dataminerFolderContainer.findByName(computedDataFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner computed data folder"); LOGGER.debug("Dataspace->Creating DataMiner computed data folder");
dataminerFolderWS.createFolder(computedDataFolder, "A folder collecting DataMiner computed data"); dataminerFolderContainer.newFolder(computedDataFolder, "A folder collecting DataMiner computed data");
} }
if (!ws.exists(computationsFolder, dataminerFolderWS.getId())) { if (dataminerFolderContainer.findByName(computationsFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner computations folder"); LOGGER.debug("Dataspace->Creating DataMiner computations folder");
dataminerFolderWS.createFolder(computationsFolder, "A folder collecting DataMiner computations information"); dataminerFolderContainer.newFolder(computationsFolder, "A folder collecting DataMiner computations information");
} }
return dataminerFolderContainer;
} }
public String uploadData(StoredData data, WorkspaceFolder wsFolder) throws Exception {
return uploadData(data, wsFolder, true); public String uploadData(StoredData data, FolderContainer destinationFolder) throws Exception {
return uploadData(data, destinationFolder, true);
} }
public String uploadData(StoredData data, WorkspaceFolder wsFolder, boolean changename) throws Exception { public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
LOGGER.debug("Dataspace->Analysing " + data); LOGGER.debug("Dataspace->Analysing " + data);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder); // String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder);
String filenameonwsString = data.name ; String filenameonwsString = data.name ;
if (changename) if (changename)
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload, data.type)); filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload, data.type));
InputStream in = null; InputStream in = null;
String url = ""; String url = "";
try { try {
@ -174,11 +184,13 @@ public class DataspaceManager implements Runnable {
properties.put(data_type, data.type); properties.put(data_type, data.type);
properties.put(payload, url); properties.put(payload, url);
FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size); FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
//TODO: add proprerty to file
//FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size);
//fileItem.getProperties().addProperties(properties); //fileItem.getProperties().addProperties(properties);
LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString); LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
url = fileItem.getPublicLink(false); url = fileContainer.getPublicLink().toString();
LOGGER.debug("Dataspace->WS OP url produced for the file " + url); LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
data.payload = url; data.payload = url;
@ -202,176 +214,167 @@ public class DataspaceManager implements Runnable {
return url; return url;
} }
public List<String> uploadInputData(List<StoredData> inputData, WorkspaceFolder dataminerFolder) throws Exception { public List<String> uploadInputData(List<StoredData> inputData, FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size()); LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size());
WorkspaceItem folderItem = dataminerFolder.find(importedDataFolder); FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder).getContainers().get(0);
List<String> urls = new ArrayList<String>(); List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) { for (StoredData input : inputData) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem; List<ItemContainer<? extends Item>> items = null;
for (StoredData input : inputData) {
WorkspaceItem item = null;
if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png")) if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png"))
item = destinationFolder.find(input.name); items = destinationFolder.findByName(input.name).getContainers();
if (item==null){ if (items==null || items.isEmpty()){
String url = uploadData(input, destinationFolder,false); String url = uploadData(input, destinationFolder,false);
LOGGER.debug("Dataspace->returning property "+url); LOGGER.debug("Dataspace->returning property "+url);
urls.add(url); urls.add(url);
}
else{
LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder");
String url = item.getPublicLink(false);
LOGGER.debug("Dataspace->returning WS url "+url);
urls.add(url);
}
} }
} else else{
LOGGER.debug("Dataspace->folder is not valid"); FileContainer item = (FileContainer) items.get(0);
LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder");
String url = item.getPublicLink().toString();
LOGGER.debug("Dataspace->returning WS url "+url);
urls.add(url);
}
}
LOGGER.debug("Dataspace->finished uploading input data"); LOGGER.debug("Dataspace->finished uploading input data");
return urls; return urls;
} }
public List<String> uploadOutputData(List<StoredData> outputData, WorkspaceFolder dataminerFolder) throws Exception { public List<String> uploadOutputData(List<StoredData> outputData,FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size()); LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size());
WorkspaceItem folderItem = dataminerFolder.find(computedDataFolder); FolderContainer destinationFolder = (FolderContainer)dataminerFolder.findByName(computedDataFolder).getContainers().get(0);
List<String> urls = new ArrayList<String>(); List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) { for (StoredData output : outputData) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
for (StoredData output : outputData) {
String url = uploadData(output, destinationFolder); String url = uploadData(output, destinationFolder);
urls.add(url); urls.add(url);
} }
} else
LOGGER.debug("Dataspace->folder is not valid");
LOGGER.debug("Dataspace->finished uploading output data"); LOGGER.debug("Dataspace->finished uploading output data");
return urls; return urls;
} }
public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, WorkspaceFolder dataminerFolder, Workspace ws) throws Exception { public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading computation data"); LOGGER.debug("Dataspace->uploading computation data");
WorkspaceItem folderItem = dataminerFolder.find(computationsFolder); FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder).getContainers().get(0);
if (folderItem != null && folderItem.isFolder()) { // create a folder in here
// create a folder in here LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
LOGGER.debug("Dataspace->Creating computation folder " + computation.id); String cfoldername = computation.id;
WorkspaceFolder cfolder = ((WorkspaceFolder) folderItem); FolderContainer newcomputationFolder = null;
String cfoldername = computation.id; try{
WorkspaceFolder newcomputationFolder = null; newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
try{ }catch(java.lang.ClassCastException e){
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription); LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
}catch(java.lang.ClassCastException e){ deleteRunningComputationData();
LOGGER.debug("Dataspace->concurrency exception - deleting remaining item"); newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
deleteRunningComputationData();
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
}
//String itemType = "COMPUTATION";
// create IO folders
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
newcomputationFolder.createFolder(importedDataFolder, importedDataFolder);
newcomputationFolder.createFolder(computedDataFolder, computedDataFolder);
// copy IO in those folders
LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****adding properties to the folder*****");
LOGGER.debug("Dataspace->creating Folder Properties");
// write a computation item for the computation
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre);
properties.put(operator_name, config.getAgent());
properties.put(operator_id, computation.operatorId);
properties.put(operator_description, computation.operatorDescription);
properties.put(start_date, computation.startDate);
properties.put(end_date, computation.endDate);
properties.put(status, getStatus(computation.status));
properties.put(execution_platform, computation.infrastructure);
int ninput = inputurls.size();
int noutput = outputurls.size();
LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.payload.contains("|")){
String payload = input .payload;
LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload);
//delete the names that are not useful
for (StoredData subinput:inputData){
if (input.description.equals(subinput.description)){
payload = payload.replace(subinput.name,subinput.payload);
subinput.name=null;
}
}
input.name = null;
//delete last pipe character
if (payload.endsWith("|"))
payload = payload.substring(0,payload.length()-1);
LOGGER.debug("Dataspace->Complex input after processing "+payload);
properties.put("input" + i + "_" + input.description, payload);
input.payload=payload;
}
}
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.name!=null){
properties.put("input" + i + "_" + input.name, inputurls.get(i - 1));
}
}
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
for (int i = 1; i <= noutput; i++) {
properties.put("output" + i + "_" + outputData.get(i - 1).name, outputurls.get(i - 1));
}
LOGGER.debug("Dataspace->Properties of the folder: " + properties);
LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs");
/*
* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
*/
try {
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
InputStream sis = new FileInputStream(xmltosave);
WorkspaceUtil.createExternalFile(newcomputationFolder, computation.id + ".xml", computation.operatorDescription, sis,null,"text/xml",xmltosave.length());
sis.close();
xmltosave.delete();
} catch (Exception e) {
LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
}
//List<String> scopes = new ArrayList<String>();
//scopes.add(config.getGcubeScope());
//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
newcomputationFolder.getProperties().addProperties(properties);
} }
//String itemType = "COMPUTATION";
// create IO folders
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
newcomputationFolder.newFolder(importedDataFolder, importedDataFolder);
newcomputationFolder.newFolder(computedDataFolder, computedDataFolder);
// copy IO in those folders
LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****adding properties to the folder*****");
LOGGER.debug("Dataspace->creating Folder Properties");
// write a computation item for the computation
Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre);
properties.put(operator_name, config.getAgent());
properties.put(operator_id, computation.operatorId);
properties.put(operator_description, computation.operatorDescription);
properties.put(start_date, computation.startDate);
properties.put(end_date, computation.endDate);
properties.put(status, getStatus(computation.status));
properties.put(execution_platform, computation.infrastructure);
int ninput = inputurls.size();
int noutput = outputurls.size();
LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.payload.contains("|")){
String payload = input .payload;
LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload);
//delete the names that are not useful
for (StoredData subinput:inputData){
if (input.description.equals(subinput.description)){
payload = payload.replace(subinput.name,subinput.payload);
subinput.name=null;
}
}
input.name = null;
//delete last pipe character
if (payload.endsWith("|"))
payload = payload.substring(0,payload.length()-1);
LOGGER.debug("Dataspace->Complex input after processing "+payload);
properties.put("input" + i + "_" + input.description, payload);
input.payload=payload;
}
}
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.name!=null){
properties.put(String.format("input%d_%s",i, input.name), inputurls.get(i - 1));
}
}
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
for (int i = 1; i <= noutput; i++) {
properties.put(String.format("output%d_%s",i,outputData.get(i - 1).name), outputurls.get(i - 1));
}
LOGGER.debug("Dataspace->Properties of the folder: " + properties);
LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs");
/*
* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
*/
try {
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
try(InputStream sis = new FileInputStream(xmltosave)){
newcomputationFolder.uploadFile(sis,computation.id + ".xml", computation.operatorDescription);
}
xmltosave.delete();
} catch (Exception e) {
LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
}
//List<String> scopes = new ArrayList<String>();
//scopes.add(config.getGcubeScope());
//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
newcomputationFolder.setMetadata(new Metadata(properties));
LOGGER.debug("Dataspace->finished uploading computation data"); LOGGER.debug("Dataspace->finished uploading computation data");
} }
@ -389,23 +392,14 @@ public class DataspaceManager implements Runnable {
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception { public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception {
LOGGER.debug("Dataspace->connecting to Workspace"); LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
HomeManager manager = factory.getHomeManager();
LOGGER.debug("Dataspace->getting user");
User user = manager.createUser(computation.user);
Home home = manager.getHome(user);
LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
LOGGER.debug("Dataspace->create folders network"); LOGGER.debug("Dataspace->create folders network");
createFoldersNetwork(ws, root); FolderContainer dataminerFolder = createFoldersNetwork();
WorkspaceFolder dataminerItem = (WorkspaceFolder) root.find(dataminerFolder);
LOGGER.debug("Dataspace->****uploading input files****"); LOGGER.debug("Dataspace->****uploading input files****");
uploadInputData(inputData, dataminerItem); uploadInputData(inputData, dataminerFolder);
LOGGER.debug("Dataspace->****uploading output files****"); LOGGER.debug("Dataspace->****uploading output files****");
uploadOutputData(outputData, dataminerItem); uploadOutputData(outputData, dataminerFolder);
LOGGER.debug("Dataspace->****uploading computation files****"); LOGGER.debug("Dataspace->****uploading computation files****");
uploadComputationData(computation, inputData, outputData, dataminerItem, ws); uploadComputationData(computation, inputData, outputData, dataminerFolder);
LOGGER.debug("Dataspace->provenance management finished"); LOGGER.debug("Dataspace->provenance management finished");
LOGGER.debug("Dataspace->deleting generated files"); LOGGER.debug("Dataspace->deleting generated files");
AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles); AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles);
@ -418,27 +412,19 @@ public class DataspaceManager implements Runnable {
} catch (Exception e) { } catch (Exception e) {
LOGGER.debug("Dataspace->impossible to delete running computation : {} ",e.getMessage()); LOGGER.debug("Dataspace->impossible to delete running computation : {} ",e.getMessage());
} }
// LOGGER.debug("Dataspace->updating computation status"); StorageHubClient shc = new StorageHubClient();
// LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
HomeManager manager = factory.getHomeManager();
// LOGGER.debug("Dataspace->getting user");
User user = manager.createUser(computation.user);
Home home = manager.getHome(user);
// LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
// LOGGER.debug("Dataspace->create folders network"); // LOGGER.debug("Dataspace->create folders network");
createFoldersNetwork(ws, root); FolderContainer folderContainer = createFoldersNetwork();
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder); FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder).getContainers().get(0);
// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status); // LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status);
String itemType = "COMPUTATION"; String itemType = "COMPUTATION";
// write a computation item for the computation // write a computation item for the computation
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>(); Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, computation.id); properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname()); properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre); properties.put(vre, computation.vre);
@ -454,7 +440,15 @@ public class DataspaceManager implements Runnable {
List<String> scopes = new ArrayList<String>(); List<String> scopes = new ArrayList<String>();
scopes.add(config.getGcubeScope()); scopes.add(config.getGcubeScope());
ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, computationsFolderItem.getId()); GCubeItem gcubeItem = new GCubeItem();
gcubeItem.setName(computation.id);
gcubeItem.setDescription(computation.operatorDescription);
gcubeItem.setScopes(scopes.toArray(new String[scopes.size()]));
gcubeItem.setItemType(itemType);
gcubeItem.setProperty(new Metadata(properties));
computationsContainer.newGcubeItem(gcubeItem);
LOGGER.debug("Dataspace->finished uploading computation data"); LOGGER.debug("Dataspace->finished uploading computation data");
} }
@ -481,26 +475,20 @@ public class DataspaceManager implements Runnable {
LOGGER.debug("Dataspace->deleting computation item"); LOGGER.debug("Dataspace->deleting computation item");
LOGGER.debug("Dataspace->connecting to Workspace"); LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory(); StorageHubClient shc = new StorageHubClient();
HomeManager manager = factory.getHomeManager(); FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder).getContainers().get(0);
LOGGER.debug("Dataspace->getting user"); FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder).getContainers().get(0);
User user = manager.createUser(computation.user);
Home home = manager.getHome(user);
LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
LOGGER.debug("Dataspace->removing computation data"); LOGGER.debug("Dataspace->removing computation data");
WorkspaceFolder computationsFolderWs = ((WorkspaceFolder) computationsFolderItem);
WorkspaceItem wi = computationsFolderWs.find(computation.id); List<ItemContainer<? extends Item>> wi = computationContainer.findByName(computation.id).getContainers();
if (wi!=null){ if (wi.isEmpty()){
LOGGER.debug("Dataspace->Found "+computation.id+" under "+computationsFolderWs.getName()+" - removing"); for (ItemContainer<? extends Item> container : wi)
wi.remove(); container.delete();
} }
else else
LOGGER.debug("Dataspace->Warning Could not find "+computation.id+" under "+computationsFolderWs.getName()); LOGGER.debug("Dataspace->Warning Could not find "+computation.id+" under "+computationContainer.get().getName());
/*TODO: ASK GIANPAOLO
int maxtries = 3; int maxtries = 3;
int i =1; int i =1;
while (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){ while (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
@ -508,9 +496,9 @@ public class DataspaceManager implements Runnable {
Thread.sleep(1000); Thread.sleep(1000);
computationsFolderWs.find(computation.id).remove(); computationsFolderWs.find(computation.id).remove();
i++; i++;
} }*/
LOGGER.debug("Dataspace->finished removing computation data - success "+!ws.exists(computation.id,computationsFolderWs.getId())); LOGGER.debug("Dataspace->finished removing computation data ");
} }
public static String getExtension(String payload, String type){ public static String getExtension(String payload, String type){