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statistical-algorithms-importer
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1452: Implement a GUI for StatMan Algorithms Importer 

Task-Url: https://support.d4science.org/issues/1452

Fixed InputStream on Annotations

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/portlets/user/statistical-algorithms-importer@122714 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Giancarlo Panichi 2016-02-02 10:17:20 +00:00
parent b308f1c32b
commit 3afec34257
2 changed files with 98 additions and 46 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

91
src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/annotation/WPS4RParser.java
View File

@ -2,6 +2,10 @@ package org.gcube.portlets.user.statisticalalgorithmsimporter.server.annotation;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
import java.nio.file.StandardOpenOption;
import java.util.ArrayList;
import java.util.List;
@ -18,6 +22,7 @@ import org.gcube.portlets.user.statisticalalgorithmsimporter.shared.workspace.It
import org.n52.wps.server.r.R_Config;
import org.n52.wps.server.r.metadata.RAnnotationParser;
import org.n52.wps.server.r.syntax.RAnnotation;
import org.n52.wps.server.r.syntax.RAnnotationException;
import org.n52.wps.server.r.syntax.RAnnotationType;
import org.n52.wps.server.r.syntax.RAttribute;
import org.slf4j.Logger;
@ -30,11 +35,10 @@ import org.slf4j.LoggerFactory;
*
*/
public class WPS4RParser {
public static final Logger logger = LoggerFactory
.getLogger(WPS4RParser.class);
private Project project;
private ASLSession aslSession;
@ -44,56 +48,88 @@ public class WPS4RParser {
}
public Project parse() throws StatAlgoImporterServiceException {
logger.debug("MainCode: " + project.getMainCode());
ItemDescription mainCode = project.getMainCode().getItemDescription();
FilesStorage fileStorage = new FilesStorage();
InputStream is = fileStorage.retrieveItemOnWorkspace(
aslSession.getUsername(), mainCode.getId());
R_Config config = R_Config.getInstance();
List<RAnnotation> annotations;
logger.debug("MainCode InputStream: " + is);
Path tempFile=null;
try {
RAnnotationParser parser = new RAnnotationParser(config);
annotations = parser.parseAnnotationsfromScript(is);
} catch (Throwable e) {
tempFile = Files.createTempFile("RCodeToParse", ".R");
Files.copy(is, tempFile, StandardCopyOption.REPLACE_EXISTING);
} catch (IOException e) {
e.printStackTrace();
throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
} finally {
try {
is.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
logger.debug("" + tempFile);
R_Config config = R_Config.getInstance();
logger.debug("R_Config: " + config);
List<RAnnotation> annotations;
try {
RAnnotationParser parser = new RAnnotationParser(config);
logger.debug("RAnnotations Parser:" + parser);
annotations = parser.parseAnnotationsfromScript(Files.newInputStream(tempFile, StandardOpenOption.READ));
} catch (RAnnotationException e) {
e.printStackTrace();
throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
} catch (Throwable e) {
e.printStackTrace();
throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
}
try {
Files.delete(tempFile);
} catch (IOException e) {
e.printStackTrace();
}
logger.debug("RAnnotations: " + annotations);
WPSAlgorithmInfo wpsAlgorithmInfo = mapAnnotations(annotations);
logger.debug("wpsAlgorithmInfo: "+wpsAlgorithmInfo);
if (wpsAlgorithmInfo.getAlgorithmName() == null)
logger.debug("wpsAlgorithmInfo: " + wpsAlgorithmInfo);
if (wpsAlgorithmInfo==null || wpsAlgorithmInfo.getAlgorithmName() == null)
return project;
else
return mapToProject(wpsAlgorithmInfo);
}
private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo) throws StatAlgoImporterServiceException {
if(project==null){
private Project mapToProject(WPSAlgorithmInfo wpsAlgorithmInfo)
throws StatAlgoImporterServiceException {
if (project == null) {
throw new StatAlgoImporterServiceException("Open project before!");
}
if(project.getInputData()==null){
ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
InputData inputData=new InputData(projectInfo, null, null, wpsAlgorithmInfo.getInputOutputVariables());
if (project.getInputData() == null) {
ProjectInfo projectInfo = new ProjectInfo(
wpsAlgorithmInfo.getAlgorithmName(),
wpsAlgorithmInfo.getDescription(), null);
InputData inputData = new InputData(projectInfo, null, null,
wpsAlgorithmInfo.getInputOutputVariables());
project.setInputData(inputData);
} else {
InputData inputData=project.getInputData();
ProjectInfo projectInfo=new ProjectInfo(wpsAlgorithmInfo.getAlgorithmName(), wpsAlgorithmInfo.getDescription(), null);
InputData inputData = project.getInputData();
ProjectInfo projectInfo = new ProjectInfo(
wpsAlgorithmInfo.getAlgorithmName(),
wpsAlgorithmInfo.getDescription(), null);
inputData.setProjectInfo(projectInfo);
inputData.setListInputOutputVariables(wpsAlgorithmInfo.getInputOutputVariables());
inputData.setListInputOutputVariables(wpsAlgorithmInfo
.getInputOutputVariables());
inputData.setListGlobalVariables(null);
}
return project;
}
private WPSAlgorithmInfo mapAnnotations(List<RAnnotation> annotations)
@ -102,15 +138,18 @@ public class WPS4RParser {
WPSAlgorithmInfo wpsAlgorithmInfo = new WPSAlgorithmInfo();
ArrayList<InputOutputVariables> inputOutputVariables = new ArrayList<>();
int index=1;
int index = 1;
for (RAnnotation rAnnotation : annotations) {
logger.debug("RAnnotation: " + rAnnotation);
if (rAnnotation.getType().equals(RAnnotationType.DESCRIPTION)) {
wpsAlgorithmInfo.setVersion(rAnnotation
.getStringValue(RAttribute.VERSION));
wpsAlgorithmInfo.setDescription(rAnnotation
.getStringValue(RAttribute.ABSTRACT));
wpsAlgorithmInfo.setAlgorithmName(rAnnotation
.getStringValue(RAttribute.TITLE));
String algorithmName=rAnnotation
.getStringValue(RAttribute.TITLE);
algorithmName=algorithmName.replaceAll("[^A-Za-z0-9]", "_");
wpsAlgorithmInfo.setAlgorithmName(algorithmName);
wpsAlgorithmInfo.setVersion(rAnnotation
.getStringValue(RAttribute.VERSION));
} else if (rAnnotation.getType().equals(RAnnotationType.OUTPUT)
@ -144,8 +183,8 @@ public class WPS4RParser {
dataType = DataType.ENUMERATED;
InputOutputVariables ioVariable = new InputOutputVariables(
index, name, description, defaultValue, dataType, ioType,
"");
index, name, description, defaultValue, dataType,
ioType, "");
inputOutputVariables.add(ioVariable);
index++;
}

53
src/main/java/org/gcube/portlets/user/statisticalalgorithmsimporter/server/generator/ProjectBuilder.java
View File

@ -84,6 +84,19 @@ public class ProjectBuilder {
createAlgorithm();
createIntegrationInfo();
createProjectJarFile();
try {
if (algorithmJava != null)
Files.delete(algorithmJava);
} catch (IOException e) {
e.printStackTrace();
}
try {
if (infoTXT != null)
Files.delete(infoTXT);
} catch (IOException e) {
e.printStackTrace();
}
return project;
@ -128,24 +141,23 @@ public class ProjectBuilder {
throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
}
filesStorage.saveInputStreamInItem(
aslSession.getUsername(), project.getProjectTarget()
.getProjectDeploy().getPackageProject().getId(),
inputStream);
WorkspaceItem packageProject=filesStorage.retrieveItemInfoOnWorkspace(aslSession.getUsername(), project.getProjectTarget()
.getProjectDeploy().getPackageProject().getId());
filesStorage.saveInputStreamInItem(aslSession.getUsername(), project
.getProjectTarget().getProjectDeploy().getPackageProject()
.getId(), inputStream);
WorkspaceItem packageProject = filesStorage
.retrieveItemInfoOnWorkspace(aslSession.getUsername(), project
.getProjectTarget().getProjectDeploy()
.getPackageProject().getId());
ItemDescription packageProjectItemDescription;
try {
packageProjectItemDescription = new ItemDescription(packageProject.getId(),
packageProject.getName(), packageProject
.getOwner().getPortalLogin(),
packageProject.getPath(), packageProject
.getType().name());
packageProjectItemDescription.setPublicLink(packageProject.getPublicLink(true));
packageProjectItemDescription = new ItemDescription(
packageProject.getId(), packageProject.getName(),
packageProject.getOwner().getPortalLogin(),
packageProject.getPath(), packageProject.getType().name());
packageProjectItemDescription.setPublicLink(packageProject
.getPublicLink(true));
} catch (InternalErrorException e) {
logger.error(e.getLocalizedMessage());
e.printStackTrace();
@ -153,11 +165,11 @@ public class ProjectBuilder {
}
project.getProjectTarget().getProjectDeploy().setPackageProject(packageProjectItemDescription);
project.getProjectTarget().getProjectDeploy()
.setPackageProject(packageProjectItemDescription);
logger.debug("ProjectDeploy: "
+ project.getProjectTarget().getProjectDeploy());
}
private void copyJarInDeploy() throws StatAlgoImporterServiceException {
@ -447,7 +459,8 @@ public class ProjectBuilder {
throw new StatAlgoImporterServiceException(e.getLocalizedMessage());
}
project.getProjectTarget().getProjectDeploy().setPackageProject(packageUrl);
project.getProjectTarget().getProjectDeploy()
.setPackageProject(packageUrl);
}
private void createTargetFolder() throws StatAlgoImporterServiceException {