org.molgenis.studymanager.StudyManagerController Maven / Gradle / Ivy
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package org.molgenis.studymanager;
import java.io.IOException;
import java.lang.reflect.Array;
import java.text.SimpleDateFormat;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletResponse;
import javax.validation.Valid;
import javax.validation.constraints.NotNull;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.log4j.Logger;
import org.molgenis.catalog.Catalog;
import org.molgenis.catalog.CatalogItem;
import org.molgenis.catalog.CatalogModelBuilder;
import org.molgenis.catalog.UnknownCatalogException;
import org.molgenis.catalogmanager.CatalogManagerService;
import org.molgenis.data.Entity;
import org.molgenis.data.Writable;
import org.molgenis.data.excel.ExcelWriter;
import org.molgenis.data.support.MapEntity;
import org.molgenis.framework.server.MolgenisSettings;
import org.molgenis.framework.ui.MolgenisPluginController;
import org.molgenis.omx.study.StudyDataRequest;
import org.molgenis.security.core.MolgenisPermissionService;
import org.molgenis.security.core.Permission;
import org.molgenis.study.StudyDefinition;
import org.molgenis.study.StudyDefinitionImpl;
import org.molgenis.study.UnknownStudyDefinitionException;
import org.molgenis.util.ErrorMessageResponse;
import org.molgenis.util.ErrorMessageResponse.ErrorMessage;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.ExceptionHandler;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.bind.annotation.ResponseStatus;
import com.google.common.base.Function;
import com.google.common.collect.Lists;
@Controller
@RequestMapping(StudyManagerController.URI)
public class StudyManagerController extends MolgenisPluginController
{
private static final Logger logger = Logger.getLogger(StudyManagerController.class);
public static final String ID = "studymanager";
public static final String URI = MolgenisPluginController.PLUGIN_URI_PREFIX + ID;
public static final String VIEW_NAME = "view-studymanager";
private final StudyManagerService studyDefinitionManagerService;
private final CatalogManagerService catalogManagerService;
private final MolgenisPermissionService molgenisPermissionService;
public static final String EXPORT_BTN_TITLE = "plugin.studymanager.export.title";
public static final String EXPORT_ENABLED = "plugin.studymanager.export.enabled";
@Autowired
private MolgenisSettings molgenisSettings;
@Autowired
public StudyManagerController(StudyManagerService studyDefinitionManagerService,
CatalogManagerService catalogManagerService, MolgenisPermissionService molgenisPermissionService)
{
super(URI);
if (studyDefinitionManagerService == null) throw new IllegalArgumentException(
"Study definition manager service is null");
if (catalogManagerService == null) throw new IllegalArgumentException("Catalog manager service is null");
this.studyDefinitionManagerService = studyDefinitionManagerService;
this.catalogManagerService = catalogManagerService;
this.molgenisPermissionService = molgenisPermissionService;
}
/**
* Show the available studydefinitions.
*
* StudyDefinitions are exposed via a 'studyDefinitions' model attribute that contains a list of
* StudyDefinitionModel objects.
*
* @param model
* @return
*/
@RequestMapping(method = RequestMethod.GET)
public String getStudyDefinitions(Model model)
{
model.addAttribute("dataLoadingEnabled", studyDefinitionManagerService.canLoadStudyData());
if (molgenisSettings.getBooleanProperty(EXPORT_ENABLED, false))
{
model.addAttribute("studyDefinitionStates", StudyDefinition.Status.values());
}
else
{
model.addAttribute("studyDefinitionStates",
ArrayUtils.removeElement(StudyDefinition.Status.values(), StudyDefinition.Status.EXPORTED));
}
model.addAttribute("studyDefinitionUpdateStates",
ArrayUtils.removeElement(StudyDefinition.Status.values(), StudyDefinition.Status.EXPORTED));
model.addAttribute("defaultStudyDefinitionState", StudyDefinition.Status.SUBMITTED);
model.addAttribute("exportedStudyDefinitionState", StudyDefinition.Status.EXPORTED);
model.addAttribute("writePermission",
molgenisPermissionService.hasPermissionOnEntity(StudyDataRequest.ENTITY_NAME, Permission.WRITE));
model.addAttribute("exportTitle", molgenisSettings.getProperty(EXPORT_BTN_TITLE, "Export"));
model.addAttribute("exportEnabled", molgenisSettings.getBooleanProperty(EXPORT_ENABLED, false));
return VIEW_NAME;
}
/**
* Returns a list of meta data for each study definition
*
* @return
*/
@RequestMapping(value = "/list")
@ResponseBody
public StudyDefinitionsMetaResponse getStudyDefinitionsMeta(@RequestParam("state") StudyDefinition.Status status,
@RequestParam(value = "search", required = false) String search)
{
List studyDefinitions = studyDefinitionManagerService.findStudyDefinitions(status, search);
logger.debug("Got [" + studyDefinitions.size() + "] study definitions from service");
List models = Lists.transform(studyDefinitions,
new Function()
{
@Override
public StudyDefinitionMetaModel apply(StudyDefinition studyDefinition)
{
String id = studyDefinition.getId();
String name = studyDefinition.getName();
String email = studyDefinition.getAuthorEmail();
Date date = studyDefinition.getDateCreated();
boolean loaded;
boolean activated;
try
{
loaded = studyDefinitionManagerService.isStudyDataLoaded(id);
activated = studyDefinitionManagerService.isStudyDataActivated(id);
}
catch (UnknownStudyDefinitionException e)
{
throw new RuntimeException(e);
}
catch (UnknownCatalogException e)
{
throw new RuntimeException(e);
}
return new StudyDefinitionMetaModel(id, name, email, date, loaded, activated);
}
});
StudyDefinitionsMetaResponse studyDefinitionsResponse = new StudyDefinitionsMetaResponse();
studyDefinitionsResponse.setStudyDefinitions(models);
return studyDefinitionsResponse;
}
@RequestMapping(value = "/view/{id}", method = RequestMethod.GET)
@ResponseBody
public Map getStudyDefinitionAsCatalog(@PathVariable String id) throws UnknownCatalogException,
UnknownStudyDefinitionException
{
Map map = new HashMap();
// get study definition and catalog used to create study definition
StudyDefinition studyDefinition = studyDefinitionManagerService.getStudyDefinition(id);
Catalog catalog = catalogManagerService.getCatalogOfStudyDefinition(studyDefinition.getId());
map.put("catalog", CatalogModelBuilder.create(catalog, studyDefinition, true));
map.put("status", studyDefinition.getStatus());
return map;
}
@RequestMapping(value = "/edit/{id}", method = RequestMethod.GET)
@ResponseBody
public Map getCatalogWithStudyDefinition(@PathVariable String id) throws UnknownCatalogException,
UnknownStudyDefinitionException
{
Map map = new HashMap();
// get study definition and catalog used to create study definition
StudyDefinition studyDefinition = studyDefinitionManagerService.getStudyDefinition(id);
Catalog catalog = catalogManagerService.getCatalogOfStudyDefinition(studyDefinition.getId());
map.put("catalog", CatalogModelBuilder.create(catalog, studyDefinition, false));
map.put("status", studyDefinition.getStatus());
return map;
}
@RequestMapping(value = "/update/{id}", method = RequestMethod.POST)
@ResponseStatus(HttpStatus.NO_CONTENT)
public void updateStudyDefinition(@PathVariable String id,
@Valid @RequestBody StudyDefinitionUpdateRequest updateRequest) throws UnknownStudyDefinitionException,
UnknownCatalogException
{
// get study definition and catalog used to create study definition
StudyDefinition studyDefinition = studyDefinitionManagerService.getStudyDefinition(id);
if (!studyDefinition.getStatus().equals(StudyDefinition.Status.APPROVED))
{
final Catalog catalog = catalogManagerService.getCatalogOfStudyDefinition(studyDefinition.getId());
// create updated study definition
StudyDefinitionImpl updatedStudyDefinition = new StudyDefinitionImpl(studyDefinition);
updatedStudyDefinition.setItems(Lists.transform(updateRequest.getCatalogItemIds(),
new Function()
{
@Override
public CatalogItem apply(String catalogItemId)
{
CatalogItem catalogItem = catalog.findItem(catalogItemId);
if (catalogItem == null) throw new RuntimeException("unknown catalog item id: "
+ catalogItemId);
return catalogItem;
}
}));
updatedStudyDefinition.setStatus(updateRequest.getStatus());
// update study definition
studyDefinitionManagerService.updateStudyDefinition(updatedStudyDefinition);
}
else
{
throw new IllegalStateException("Cannot update APPROVED study definition");
}
}
@RequestMapping(value = "/export/{id}", method = RequestMethod.POST)
@ResponseStatus(HttpStatus.NO_CONTENT)
public void exportStudyDefinition(@PathVariable String id) throws UnknownStudyDefinitionException,
UnknownCatalogException
{
// get study definition and catalog used to create study definition
StudyDefinition studyDefinition = studyDefinitionManagerService.getStudyDefinition(id);
if (!studyDefinition.getStatus().equals(StudyDefinition.Status.EXPORTED))
{
final Catalog catalog = catalogManagerService.getCatalogOfStudyDefinition(studyDefinition.getId());
// export the studydefinition
studyDefinitionManagerService.exportStudyDefinition(studyDefinition.getId(), catalog.getId());
// update status for the study definition
StudyDefinitionImpl updatedStudyDefinition = new StudyDefinitionImpl(studyDefinition);
updatedStudyDefinition.setStatus(StudyDefinition.Status.EXPORTED);
// update study definition
studyDefinitionManagerService.updateStudyDefinition(updatedStudyDefinition);
}
else
{
throw new IllegalStateException("Cannot export already EXPORTED study definition");
}
}
/**
* Loads a studydefinition by it's id.
*
* If an error occurred an 'errorMessage' model attribute is exposed.
*
* If the studydefinition was successfully loaded a 'successMessage' model attribute is exposed.
*
* @param id
* @param model
* @return
*/
@RequestMapping(value = "/load", method = RequestMethod.POST)
public String loadStudyDefinition(@RequestParam(value = "id", required = false) String id, Model model)
{
try
{
if (id != null)
{
studyDefinitionManagerService.loadStudyData(id);
model.addAttribute("successMessage", "Studydefinition loaded");
logger.info("Loaded studydefinition with id [" + id + "]");
}
else
{
model.addAttribute("errorMessage", "Please select a studydefinition");
}
}
catch (UnknownStudyDefinitionException e)
{
model.addAttribute("errorMessage", e.getMessage());
}
return getStudyDefinitions(model);
}
@RequestMapping(value = "/download/{id}", method = RequestMethod.GET)
public void downloadStudyDefinition(@PathVariable String id, HttpServletResponse response)
throws UnknownStudyDefinitionException, IOException
{
StudyDefinition studyDefinition = studyDefinitionManagerService.getStudyDefinition(id);
// write response headers
String fileName = "variables_" + new SimpleDateFormat("yyyy-MM-dd_HH.mm").format(new Date()) + ".xls";
response.setContentType("application/vnd.ms-excel");
response.setHeader("Content-Disposition", "attachment; filename=" + fileName);
// TODO remove code duplication (see ProtocolViewerController)
// write excel file
List header = Arrays.asList("Id", "Variable", "Description");
List catalogItems = Lists.newArrayList(studyDefinition.getItems());
if (catalogItems != null)
{
Collections.sort(catalogItems, new Comparator()
{
@Override
public int compare(CatalogItem catalogItem1, CatalogItem catalogItem2)
{
return catalogItem1.getId().compareTo(catalogItem2.getId());
}
});
}
ExcelWriter excelWriter = new ExcelWriter(response.getOutputStream());
try
{
Writable sheetWriter = excelWriter.createWritable("Variables", header);
try
{
if (catalogItems != null)
{
for (CatalogItem catalogItem : catalogItems)
{
Entity entity = new MapEntity();
entity.set(header.get(0), catalogItem.getId());
entity.set(header.get(1), catalogItem.getName());
entity.set(header.get(2), catalogItem.getDescription());
sheetWriter.add(entity);
}
}
}
finally
{
sheetWriter.close();
}
}
finally
{
excelWriter.close();
}
}
public static class StudyDefinitionUpdateRequest
{
@NotNull
private StudyDefinition.Status status;
@NotNull
private List catalogItemIds;
public List getCatalogItemIds()
{
return catalogItemIds;
}
public void setCatalogItemIds(List catalogItemIds)
{
this.catalogItemIds = catalogItemIds;
}
public StudyDefinition.Status getStatus()
{
return status;
}
public void setStatus(StudyDefinition.Status status)
{
this.status = status;
}
}
public static class StudyDefinitionsMetaResponse
{
private List studyDefinitions;
public List getStudyDefinitions()
{
return studyDefinitions;
}
public void setStudyDefinitions(List studyDefinitions)
{
this.studyDefinitions = studyDefinitions;
}
}
@ExceptionHandler(RuntimeException.class)
@ResponseStatus(HttpStatus.INTERNAL_SERVER_ERROR)
@ResponseBody
public ErrorMessageResponse handleRuntimeException(RuntimeException e)
{
logger.error(null, e);
return new ErrorMessageResponse(Collections.singletonList(new ErrorMessage(
"An error occured. Please contact the administrator.
Message:" + e.getMessage())));
}
@ExceptionHandler(Exception.class)
@ResponseBody
@ResponseStatus(HttpStatus.BAD_REQUEST)
public ErrorMessageResponse handleException(Exception e)
{
logger.debug(null, e);
return new ErrorMessageResponse(Collections.singletonList(new ErrorMessage(e.getMessage())));
}
}
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