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Fix bugs: #Q946031 #Q195987 #Q189427
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@christopher-mohr
christopher-mohr committed Jul 5, 2017
1 parent 02320af commit 73a8242
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Showing 6 changed files with 380 additions and 342 deletions.
158 changes: 117 additions & 41 deletions QBiCMainPortlet/src/de/uni_tuebingen/qbic/qbicmainportlet/DataHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,6 @@
*******************************************************************************/
package de.uni_tuebingen.qbic.qbicmainportlet;

import helpers.AlternativeSecondaryNameCreator;
import helpers.Utils;
import life.qbic.openbis.openbisclient.OpenBisClient;

import java.io.Serializable;
import java.sql.Timestamp;
import java.text.ParseException;
Expand All @@ -39,30 +35,6 @@

import javax.xml.bind.JAXBException;

import logging.Log4j2Logger;
import model.DBManager;
import model.DatasetBean;
import model.ExperimentBean;
import model.ExperimentStatusBean;
import model.ExperimentType;
import model.NewIvacSampleBean;
import model.ProjectBean;
import model.SampleBean;
import parser.PersonParser;
import persons.Qperson;
import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;

import com.vaadin.data.util.BeanItemContainer;
import com.vaadin.data.util.HierarchicalContainer;
import com.vaadin.data.util.IndexedContainer;
Expand All @@ -75,8 +47,34 @@
import com.vaadin.ui.VerticalLayout;
import com.vaadin.ui.themes.ValoTheme;

import ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.dto.QueryTableModel;
import de.uni_tuebingen.qbic.main.LiferayAndVaadinUtils;
import de.uni_tuebingen.qbic.util.DashboardUtil;
import helpers.AlternativeSecondaryNameCreator;
import helpers.Utils;
import life.qbic.openbis.openbisclient.OpenBisClient;
import logging.Log4j2Logger;
import model.DBManager;
import model.DatasetBean;
import model.ExperimentBean;
import model.ExperimentStatusBean;
import model.ExperimentType;
import model.NewIvacSampleBean;
import model.ProjectBean;
import model.SampleBean;
import parser.PersonParser;
import persons.Qperson;


public class DataHandler implements Serializable {
Expand Down Expand Up @@ -544,8 +542,32 @@ else if (assignedProperties.keySet().contains("Q_WF_STATUS")) {

newProjectBean.setLongDescription(longDesc);

newProjectBean.setContainsData(this.getOpenBisClient()
.getDataSetsOfProjectByIdentifierWithSearchCriteria(projectIdentifier).size() != 0);
List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> projectData = this
.getOpenBisClient().getDataSetsOfProjectByIdentifierWithSearchCriteria(projectIdentifier);

Boolean containsData = false;
Boolean containsResults = false;
Boolean attachmentResult = false;
// Boolean containsAttachments = false;

for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet ds : projectData) {
attachmentResult = false;
if (ds.getDataSetTypeCode().equals("Q_PROJECT_DATA")) {
attachmentResult = ds.getProperties().get("Q_ATTACHMENT_TYPE").equals("RESULT");
}

if (!(ds.getDataSetTypeCode().equals("Q_PROJECT_DATA"))
&& !(ds.getDataSetTypeCode().contains("RESULTS"))) {
containsData = true;
} else if (ds.getDataSetTypeCode().contains("RESULTS") || attachmentResult) {
containsResults = true;
} // else if (ds.getDataSetTypeCode() == "Q_PROJECT_DATA") {
// containsAttachments = true;
// }
}

newProjectBean.setContainsData(containsData);
newProjectBean.setContainsResults(containsResults);

newProjectBean.setExperiments(experimentBeans);
newProjectBean.setMembers(new HashSet<String>());
Expand Down Expand Up @@ -676,8 +698,33 @@ else if (assignedProperties.keySet().contains("Q_WF_STATUS")) {
experimentBeans.addBean(newExperimentBean);
}

newProjectBean.setContainsData(this.getOpenBisClient()
.getDataSetsOfProjectByIdentifierWithSearchCriteria(projectIdentifier).size() != 0);
List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet> projectData = this
.getOpenBisClient().getDataSetsOfProjectByIdentifierWithSearchCriteria(projectIdentifier);

Boolean containsData = false;
Boolean containsResults = false;
Boolean attachmentResult = false;
// Boolean containsAttachments = false;

for (ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet ds : projectData) {
attachmentResult = false;
if (ds.getDataSetTypeCode().equals("Q_PROJECT_DATA")) {
attachmentResult = ds.getProperties().get("Q_ATTACHMENT_TYPE").equals("RESULT");
}

if (!(ds.getDataSetTypeCode().equals("Q_PROJECT_DATA"))
&& !(ds.getDataSetTypeCode().contains("RESULTS"))) {
containsData = true;
} else if (ds.getDataSetTypeCode().contains("RESULTS") || attachmentResult) {
containsResults = true;
} // else if (ds.getDataSetTypeCode() == "Q_PROJECT_DATA") {
// containsAttachments = true;
// }
}

newProjectBean.setContainsData(containsData);
newProjectBean.setContainsResults(containsResults);
// newProjectBean.setContainsAttachments(containsAttachments);

newProjectBean.setExperiments(experimentBeans);
newProjectBean.setMembers(new HashSet<String>());
Expand Down Expand Up @@ -1827,7 +1874,7 @@ public Map<String, Integer> computeProjectStatuses(ProjectBean projectBean) {
BeanItemContainer<ExperimentBean> cont = projectBean.getExperiments();

// project was planned (otherwise it would hopefully not exist :) )
res.put("Project Planned", 1);
res.put("Project planned", 1);

// design is pre-registered to the test sample level
int prereg = 0;
Expand All @@ -1839,14 +1886,20 @@ public Map<String, Integer> computeProjectStatuses(ProjectBean projectBean) {
break;
}
}
res.put("Experimental Design registered", prereg);
res.put("Experimental design registered", prereg);
// data is uploaded
// TODO fix that
// if (datasetMap.get(p.getIdentifier()) != null)
// res.put("Data Registered", 1);
// else
int dataregistered = projectBean.getContainsData() ? 1 : 0;
res.put("Data Registered", dataregistered);
int resultsregistered = projectBean.getContainsResults() ? 1 : 0;
// int attachmentsregistered = projectBean.getContainsAttachments() ? 1 : 0;

// res.put("Attachments registered", attachmentsregistered);
res.put("Raw data registered", dataregistered);
res.put("Results registered", resultsregistered);

return res;
}

Expand Down Expand Up @@ -2330,6 +2383,7 @@ public void registerNewPatients(int numberPatients, List<String> secondaryNames,
*
* @param statusValues
* @return
* @deprecated
*/
public VerticalLayout createProjectStatusComponent(Map<String, Integer> statusValues) {
VerticalLayout projectStatusContent = new VerticalLayout();
Expand Down Expand Up @@ -2379,6 +2433,11 @@ public VerticalLayout createProjectStatusComponentNew(Map<String, Integer> statu
projectStatusContent.setMargin(true);
projectStatusContent.setSpacing(true);

Label planned = new Label();
Label design = new Label();
Label raw = new Label();
Label results = new Label();

Iterator<Entry<String, Integer>> it = statusValues.entrySet().iterator();

while (it.hasNext()) {
Expand All @@ -2389,7 +2448,15 @@ public VerticalLayout createProjectStatusComponentNew(Map<String, Integer> statu
statusLabel.setStyleName(ValoTheme.LABEL_FAILURE);
statusLabel.setResponsive(true);
// statusLabel.addStyleName("redicon");
projectStatusContent.addComponent(statusLabel);
if (pairs.getKey().equals("Project planned")) {
planned = statusLabel;
} else if (pairs.getKey().equals("Experimental design registered")) {
design = statusLabel;
} else if (pairs.getKey().equals("Raw data registered")) {
raw = statusLabel;
} else if (pairs.getKey().equals("Results registered")) {
results = statusLabel;
}
}

else {
Expand All @@ -2399,14 +2466,23 @@ public VerticalLayout createProjectStatusComponentNew(Map<String, Integer> statu

// statusLabel.addStyleName("greenicon");

if (pairs.getKey().equals("Project Planned")) {
projectStatusContent.addComponentAsFirst(statusLabel);
} else {
projectStatusContent.addComponent(statusLabel);

if (pairs.getKey().equals("Project planned")) {
planned = statusLabel;
} else if (pairs.getKey().equals("Experimental design registered")) {
design = statusLabel;
} else if (pairs.getKey().equals("Raw data registered")) {
raw = statusLabel;
} else if (pairs.getKey().equals("Results registered")) {
results = statusLabel;
}
}
}

projectStatusContent.addComponent(planned);
projectStatusContent.addComponent(design);
projectStatusContent.addComponent(raw);
projectStatusContent.addComponent(results);

// ProgressBar progressBar = new ProgressBar();
// progressBar.setValue((float) finishedExperiments / statusValues.keySet().size());
// projectStatusContent.addComponent(progressBar);
Expand Down
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