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dataminer
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feature/23054 #2

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giancarlo.panichi merged 3 commits from feature/23054 into master 2022-04-01 10:27:41 +02:00
Conversation 0 Commits 3 Files Changed 3 +53 -68
3 changed files with 53 additions and 68 deletions
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35
CHANGELOG.md
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@ -1,92 +1,67 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
# Changelog for "dataminer"
## [v1.8.1-SNAPSHOT] - 2022-03-21
### Fixes
- Update wps service to support not writing of the computation status to the user's workspace [#23054]
- Fixed protocol parameter when persistence is disabled
## [v1.8.0] - 2022-01-24
### Fixes
- Fixed max computations support [#22700]
## [v1.7.1] - 2021-05-24
### Fixes
- Fixed obsolete short urls [#20971]
## [v1.7.0] - 2020-11-20
### Fixes
- import range modified to resolve old repositories invalid url
## [v1.6.0] - 2020-05-12
### Fixes
## [v1.6.0] - 2020-05-12
- Added storagehub retry in InputsManager class, getLocalFile method [#19253]
## [v1.5.9] - 2019-11-20
### Fixes
- Fixed Content-Type support for files in the results of computations [#18096]
## [v1.5.8] - 2019-10-01
### Fixes
- Fixed https link for output parameter [#17659]
## [v1.5.7] - 2019-03-01
### Features
- Updated https support [#13024]
## [v1.5.2] - 2017-12-13
### Fixes
- added the right extension on output file
- lock file created on execution
## [v1.5.1] - 2017-09-14
### Features
- added accounting on algorithm execution
## [v1.5.0] - 2017-07-31
### Features
- service interface classes moved to wps project
## [v1.1.0] - 2016-10-03
- First Release
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

33
src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/AbstractEcologicalEngineMapper.java
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@ -53,12 +53,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
private static final int COMPUTATION_WAIT_FOR_RUN_REQUEST = 20000;
/**
* Deploying procedure: 1 - modify configuration files 2 - modify resource
* file: resources/templates/setup.cfg 3 - generate classes with
* ClassGenerator 4 - add new classes in the wps_config.xml on the wps web
* app config folder 5 - produce the Jar file of this project 6 - copy the
* jar file in the lib folder of the wps web app change the server
* parameters in the wps_config.xml file
* Deploying procedure: 1 - modify configuration files 2 - modify resource file:
* resources/templates/setup.cfg 3 - generate classes with ClassGenerator 4 -
* add new classes in the wps_config.xml on the wps web app config folder 5 -
* produce the Jar file of this project 6 - copy the jar file in the lib folder
* of the wps web app change the server parameters in the wps_config.xml file
*/
private static final Logger LOGGER = LoggerFactory.getLogger(AbstractEcologicalEngineMapper.class);
@ -538,15 +537,25 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
}
private boolean checkWriteAuthorization(String username) {
if (env != null && env.getShubUsersExcluded() != null) {
if (env.getShubUsersExcluded().isEmpty()) {
return false;
}
if (env.getShubUsersExcluded().contains(username)) {
if (env != null) {
if (env.getShubUsersExcluded() != null) {
if (env.getShubUsersExcluded().isEmpty()) {
// all users write
return true;
}
if (env.getShubUsersExcluded().contains(username)) {
return false;
} else {
// username write
return true;
}
} else {
//This is the * case, no users write.
return false;
}
} else {
return false;
}
return true;
}
private void accountAlgorithmExecution(long start, long end, OperationResult result) {

53
src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/DataspaceManager.java
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@ -64,7 +64,7 @@ public class DataspaceManager implements Runnable {
public static String payload = "payload";
private String statusComputationName;
private static final String STATUS_POSTFIX="-STATUS";
private static final String STATUS_POSTFIX = "-STATUS";
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
List<StoredData> outputData, List<File> generatedFiles) {
@ -73,7 +73,7 @@ public class DataspaceManager implements Runnable {
this.inputData = inputData;
this.outputData = outputData;
this.generatedFiles = generatedFiles;
this.statusComputationName = this.computation.id+STATUS_POSTFIX;
this.statusComputationName = this.computation.id + STATUS_POSTFIX;
LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
@ -142,25 +142,26 @@ public class DataspaceManager implements Runnable {
}
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
LOGGER.debug("Dataspace->Analysing " + data);
LOGGER.debug("Dataspace->Uploaddata:"
+ " [data={},destinationFolder={}, changename={}] ", data, destinationFolder,
changename);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
// wsFolder);
String filenameonwsString = data.name;
if (changename)
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
getExtension(data.payload));
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload));
InputStream in = null;
String url = "";
try {
//long size = 0;
// long size = 0;
if (data.type.equals("text/csv") || data.type.equals("application/d4science")
|| data.type.equals("image/png")) {
if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
LOGGER.debug("Dataspace->Uploading file {}", data.payload);
in = new FileInputStream(new File(data.payload));
//size = new File(data.payload).length();
// size = new File(data.payload).length();
} else {
LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
int tries = 10;
@ -188,7 +189,7 @@ public class DataspaceManager implements Runnable {
// LOGGER.debug("Dataspace->final file name on ws " +
// data.name+" description "+data.description);
LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
LOGGER.debug("Dataspace->WS OP saving the following file on the WS: " + filenameonwsString);
Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, data.computationId);
@ -203,9 +204,11 @@ public class DataspaceManager implements Runnable {
properties.put(payload, url);
FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
fileContainer.setMetadata(new Metadata(properties));
LOGGER.debug("Dataspace->WS OP file uploaded on WS: " + filenameonwsString);
Metadata metadata = new Metadata(properties);
fileContainer.setMetadata(metadata);
LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
LOGGER.debug("Dataspace->WS OP file set metadata: " + metadata);
url = fileContainer.getPublicLink().toString();
LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
@ -395,10 +398,9 @@ public class DataspaceManager implements Runnable {
}
/*
* List<String> scopes = new ArrayList<String>();
* scopes.add(config.getGcubeScope());
* ws.createGcubeItem(computation.id, computation.operatorDescription,
* scopes, computation.user, itemType, properties,
* newcomputationFolder.getId());
* scopes.add(config.getGcubeScope()); ws.createGcubeItem(computation.id,
* computation.operatorDescription, scopes, computation.user, itemType,
* properties, newcomputationFolder.getId());
*/
newcomputationFolder.setMetadata(new Metadata(properties));
@ -465,8 +467,8 @@ public class DataspaceManager implements Runnable {
List<String> scopes = new ArrayList<String>();
scopes.add(config.getGcubeScope());
//TODO: update gcubeItem not recreate it...
// TODO: update gcubeItem not recreate it...
GCubeItem gcubeItem = new GCubeItem();
gcubeItem.setName(this.statusComputationName);
gcubeItem.setDescription(computation.operatorDescription);
@ -509,7 +511,8 @@ public class DataspaceManager implements Runnable {
.getContainers().get(0);
LOGGER.debug("Dataspace->removing computation data");
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName).getContainers();
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName)
.getContainers();
if (!wi.isEmpty()) {
for (ItemContainer<? extends Item> container : wi) {
boolean retry = false;
@ -517,25 +520,23 @@ public class DataspaceManager implements Runnable {
try {
container.forceDelete();
retry = false;
}catch (ItemLockedException e) {
} catch (ItemLockedException e) {
LOGGER.warn("item locked, retrying");
Thread.sleep(1000);
retry = true;
}
}while (retry);
} while (retry);
}
} else
LOGGER.debug("Dataspace->Warning Could not find {} under {}", this.statusComputationName,
computationContainer.get().getName());
/*
* TODO: ASK GIANPAOLO int maxtries = 3; int i =1; while
* (ws.exists(computation.id,computationsFolderWs.getId()) &&
* i<maxtries){
* LOGGER.debug("Dataspace->computation data still exist... retrying "+i
* ); Thread.sleep(1000);
* computationsFolderWs.find(computation.id).remove(); i++; }
* (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
* LOGGER.debug("Dataspace->computation data still exist... retrying "+i );
* Thread.sleep(1000); computationsFolderWs.find(computation.id).remove(); i++;
* }
*/
LOGGER.debug("Dataspace->finished removing computation data ");
@ -544,7 +545,7 @@ public class DataspaceManager implements Runnable {
// TODO
public static String getExtension(String payload) {
LOGGER.debug("DataSpace->Get Extension from: " + payload);
String extension="";
String extension = "";
if (payload.toLowerCase().startsWith("http")) {
try {
URL obj = new URL(payload);