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wow-such-codewow-such-code
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version 1.5.0
2 parents e86b96e + fb246d7 commit 9369d84

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3 files changed

+88
-54
lines changed

3 files changed

+88
-54
lines changed

‎pom.xml

+1-1
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
<version>1.4.0</version>
99
</parent>
1010
<artifactId>user-db-portlet</artifactId>
11-
<version>1.4.0</version>
11+
<version>1.5.0</version>
1212
<name>User Database Portlet</name>
1313
<url>http://github.com/qbicsoftware/user-db-portlet</url>
1414
<packaging>war</packaging>

‎src/main/java/life/qbic/portal/portlet/UserDBPortletUI.java

+24-13
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
import java.util.HashMap;
66
import java.util.List;
77
import java.util.Map;
8+
import java.util.Objects;
89
import java.util.Set;
910

1011
import org.apache.commons.lang3.StringUtils;
@@ -66,7 +67,7 @@ public class UserDBPortletUI extends QBiCPortletUI {
6667
private Map<String, Integer> affiMap;
6768
private Map<String, Integer> personMap;
6869
private Map<String, ProjectInfo> projectMap;
69-
70+
7071
private TabSheet options;
7172

7273
private ConfigurationManager manager;
@@ -86,9 +87,10 @@ protected Layout getPortletContent(final VaadinRequest request) {
8687

8788
String userID = "";
8889
boolean success = true;
90+
manager = ConfigurationManagerFactory.getInstance();
91+
8992
if (PortalUtils.isLiferayPortlet()) {
9093
// read in the configuration file
91-
manager = ConfigurationManagerFactory.getInstance();
9294

9395
logger.info("User DB portlet is running on Liferay and user is logged in.");
9496
userID = PortalUtils.getUser().getScreenName();
@@ -107,6 +109,7 @@ protected Layout getPortletContent(final VaadinRequest request) {
107109
// establish connection to the OpenBIS API
108110
try {
109111
logger.debug("trying to connect to openbis");
112+
110113
this.openbis = new OpenBisClient(manager.getDataSourceUser(), manager.getDataSourcePassword(),
111114
manager.getDataSourceUrl());
112115
this.openbis.login();
@@ -129,7 +132,7 @@ protected Layout getPortletContent(final VaadinRequest request) {
129132
dbControl = new DBManager(config);
130133

131134
initTabs();
132-
135+
133136
layout.addComponent(options);
134137
return layout;
135138
}
@@ -214,12 +217,18 @@ private void initTabs() {
214217

215218
Map<String, ProjectInfo> allProjects = dbControl.getProjectMap();
216219
for (Project p : openbisProjects) {
220+
String desc = Objects.toString(p.getDescription(), "");
221+
desc = desc.replace("\n", ";");
217222
String projectID = p.getIdentifier();
218223
String code = p.getCode();
219224
if (allProjects.get(projectID) == null)
220-
userProjects.put(projectID, new ProjectInfo(p.getSpaceCode(), code, "", "", -1));
221-
else
222-
userProjects.put(projectID, allProjects.get(projectID));
225+
userProjects.put(projectID, new ProjectInfo(p.getSpaceCode(), code, desc, "", -1));
226+
else {
227+
ProjectInfo info = allProjects.get(projectID);
228+
info.setDescription(desc);
229+
userProjects.put(projectID, info);
230+
}
231+
223232
}
224233

225234
projectMap = new HashMap<>();
@@ -360,17 +369,19 @@ public void valueChange(ValueChangeEvent event) {
360369
collaborators.add(c);
361370
}
362371
projects.setCollaboratorsOfProject(collaborators);
363-
}
364-
365-
Person investigator = getPersonOrNull(projectMap.get(item).getInvestigator());
366-
Person manager = getPersonOrNull(projectMap.get(item).getManager());
367-
Person contact = getPersonOrNull(projectMap.get(item).getContact());
368372

369-
projects.handleProjectValueChange(item, investigator, contact, manager);
373+
Person investigator = getPersonOrNull(projectMap.get(item).getInvestigator());
374+
Person manager = getPersonOrNull(projectMap.get(item).getManager());
375+
Person contact = getPersonOrNull(projectMap.get(item).getContact());
376+
377+
projects.handleProjectValueChange(item, investigator, contact, manager);
378+
} else {
379+
projects.handleProjectDeselect();
380+
}
370381
}
371382

372383
private Person getPersonOrNull(String name) {
373-
if(personMap.get(name)!=null) {
384+
if (personMap.get(name) != null) {
374385
return dbControl.getPersonWithAffiliations(personMap.get(name)).get(0);
375386
}
376387
return null;

‎src/main/java/life/qbic/userdb/views/ProjectView.java

+63-40
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
import java.util.HashMap;
2525
import java.util.List;
2626
import java.util.Map;
27+
import java.util.Objects;
2728

2829
import org.apache.logging.log4j.LogManager;
2930
import org.apache.logging.log4j.Logger;
@@ -62,7 +63,7 @@ public class ProjectView extends VerticalLayout {
6263
private Button downloadProjectInfo;
6364
private FileDownloader tsvDL;
6465

65-
private Table projectPersons;
66+
private Table experimentPersons;
6667
private Button submitPersons;
6768
private Map<String, CollaboratorWithResponsibility> experimentMap;
6869

@@ -98,15 +99,15 @@ public ProjectView(Map<String, ProjectInfo> projectMap, Map<String, Integer> per
9899
addComponent(downloadProjectInfo);
99100
initProjectInfos();
100101

101-
projectPersons = new Table("Experiment Collaborators (optional)");
102-
projectPersons.setVisible(false);
103-
projectPersons.setStyleName(ValoTheme.TABLE_SMALL);
104-
projectPersons.addContainerProperty("Name", ComboBox.class, null);
105-
projectPersons.addContainerProperty("Experiment", String.class, null);
106-
projectPersons.addContainerProperty("Responsibility", String.class, null);
107-
projectPersons.setColumnWidth("Responsibility", 150);
108-
projectPersons.setPageLength(1);
109-
addComponent(projectPersons);
102+
experimentPersons = new Table("Experiment Collaborators (optional)");
103+
experimentPersons.setVisible(false);
104+
experimentPersons.setStyleName(ValoTheme.TABLE_SMALL);
105+
experimentPersons.addContainerProperty("Name", ComboBox.class, null);
106+
experimentPersons.addContainerProperty("Experiment", String.class, null);
107+
experimentPersons.addContainerProperty("Responsibility", String.class, null);
108+
experimentPersons.setColumnWidth("Responsibility", 150);
109+
experimentPersons.setPageLength(1);
110+
addComponent(experimentPersons);
110111

111112
submitPersons = new Button("Submit Experiment");
112113
addComponent(submitPersons);
@@ -212,15 +213,21 @@ public void initProjectInfos() {
212213
private String createTSV(String subProject, Person PI, Person contact, Person manager)
213214
throws FileNotFoundException, UnsupportedEncodingException {
214215

215-
String secondaryName = projectMap.get(subProject).getSecondaryName();
216+
ProjectInfo proj = projectMap.get(subProject);
217+
String secondaryName = proj.getSecondaryName();
216218
secondaryName = secondaryName == null ? "" : secondaryName;
217-
String space = projectMap.get(subProject).getSpace();
218-
219-
List<String> header = new ArrayList<>(
220-
Arrays.asList("Sub-Project", "Short Title", "Project", "Principal Investigator",
221-
"PI Affiliation", "PI Adress", "Contact Person", "Contact Affiliation",
222-
"Contact Adress", "Project Manager", "Manager Affiliation", "Manager Adress"));
223-
List<String> data = new ArrayList<>(Arrays.asList(subProject, secondaryName, space));
219+
String space = proj.getSpace();
220+
String description = proj.getDescription();
221+
System.out.println(description);
222+
223+
List<String> summaryHeader =
224+
new ArrayList<>(Arrays.asList("Sub-Project", "Short Title", "Description", "Project",
225+
"Principal Investigator", "PI E-Mail", "PI Group", "PI Institute", "PI Organization",
226+
"PI Address", "Contact Person", "Contact E-Mail", "Contact Group", "Contact Institute",
227+
"Contact Organization", "Contact Address", "Project Manager", "Manager E-Mail",
228+
"Manager Group", "Manager Institute", "Manager Organization", "Manager Address"));
229+
List<String> data =
230+
new ArrayList<>(Arrays.asList(subProject, secondaryName, description, space));
224231

225232
addPersonInfos(data, PI);
226233
addPersonInfos(data, contact);
@@ -230,39 +237,50 @@ private String createTSV(String subProject, Person PI, Person contact, Person ma
230237
for (CollaboratorWithResponsibility col : experimentMap.values()) {
231238
String name = col.getPerson();
232239
if (name != null && !name.isEmpty()) {
233-
header.add(col.getOpenbisCode() + " Experiment Collaborator");
234-
header.add(col.getOpenbisCode() + " Experiment Role");
240+
summaryHeader.add(col.getOpenbisCode() + " Experiment Collaborator");
241+
summaryHeader.add(col.getOpenbisCode() + " Experiment Role");
235242
data.add(name);
236243
data.add(col.getRole());
237244
}
238245
}
239246

240-
String headerLine = String.join("\t", header);
241-
String dataLine = String.join("\t", data);
247+
String headerLine = String.join("\t", summaryHeader);
248+
String dataLine = replaceSpecialSymbols(String.join("\t", data));
242249

243250
return headerLine + "\n" + dataLine + "\n";
244251
}
245252

253+
private String replaceSpecialSymbols(String string) {
254+
string = string.replace("ß", "ss");
255+
string = string.replace("ä", "ae").replace("ü", "ue").replace("ö", "oe");
256+
string = string.replace("Ä", "Ae").replace("Ü", "Ue").replace("Ö", "Oe");
257+
return string;
258+
}
259+
246260
private void addPersonInfos(List<String> data, Person p) {
247261
if (p != null) {
248262
data.add(getFullName(p));
249-
String affi = p.getAffiliations().get(0).getGroupName();
250-
if (affi != null) {
251-
data.add(affi);
252-
}
253-
data.add(generatePersonAdress(p));
263+
data.add(p.getEmail());
264+
Affiliation affi = p.getAffiliations().get(0);
265+
data.add(Objects.toString(affi.getGroupName(), ""));
266+
data.add(Objects.toString(affi.getInstitute(), ""));
267+
data.add(Objects.toString(affi.getOrganization(), ""));
268+
data.add(generatePersonAddress(p));
254269
} else {
255270
data.add("");
256271
data.add("");
257272
data.add("");
273+
data.add("");
274+
data.add("");
275+
data.add("");
258276
}
259277
}
260278

261279
private String getFullName(Person person) {
262280
return person.getFirstName() + " " + person.getLastName();
263281
}
264282

265-
private String generatePersonAdress(Person person) {
283+
private String generatePersonAddress(Person person) {
266284
Affiliation af = person.getAffiliations().get(0);
267285
StringBuilder b = new StringBuilder(af.getStreet());
268286
b.append(" ");
@@ -367,13 +385,13 @@ public FilterTable getProjectTable() {
367385
}
368386

369387
public Table getCollaboratorTable() {
370-
return projectPersons;
388+
return experimentPersons;
371389
}
372390

373391
public void setCollaboratorsOfProject(List<CollaboratorWithResponsibility> collaborators) {
374392
experimentMap = new HashMap<String, CollaboratorWithResponsibility>();
375-
projectPersons.removeAllItems();
376-
projectPersons.setVisible(false);
393+
experimentPersons.removeAllItems();
394+
experimentPersons.setVisible(false);
377395

378396
for (CollaboratorWithResponsibility c : collaborators) {
379397
String code = c.getOpenbisCode();
@@ -387,17 +405,17 @@ public void setCollaboratorsOfProject(List<CollaboratorWithResponsibility> colla
387405
row.add(persons);
388406
row.add(c.getOpenbisCode());
389407
row.add(c.getOpenbisType());
390-
projectPersons.addItem(row.toArray(new Object[row.size()]), code);
391-
projectPersons.setVisible(true);
408+
experimentPersons.addItem(row.toArray(new Object[row.size()]), code);
409+
experimentPersons.setVisible(true);
392410
}
393411

394412
// sort ascending by Experiment ID
395413
Object[] properties = {"Experiment"};
396414
boolean[] ordering = {true};
397-
projectPersons.sort(properties, ordering);
415+
experimentPersons.sort(properties, ordering);
398416

399-
projectPersons.sort();
400-
projectPersons.setPageLength(collaborators.size());
417+
experimentPersons.sort();
418+
experimentPersons.setPageLength(collaborators.size());
401419
}
402420

403421
/**
@@ -406,9 +424,10 @@ public void setCollaboratorsOfProject(List<CollaboratorWithResponsibility> colla
406424
*/
407425
public List<CollaboratorWithResponsibility> getNewResponsibilities() {
408426
List<CollaboratorWithResponsibility> res = new ArrayList<CollaboratorWithResponsibility>();
409-
for (Object code : projectPersons.getItemIds()) {
427+
logger.debug("ids: " + experimentPersons.getItemIds());
428+
for (Object code : experimentPersons.getItemIds()) {
410429
ComboBox personBox =
411-
(ComboBox) projectPersons.getItem(code).getItemProperty("Name").getValue();
430+
(ComboBox) experimentPersons.getItem(code).getItemProperty("Name").getValue();
412431
String name = "";
413432
if (personBox.getValue() != null)
414433
name = personBox.getValue().toString();
@@ -434,6 +453,12 @@ public void updateChangedInfo(ProjectInfo info) {
434453
projectTable.sort(new Object[] {"Sub-Project"}, new boolean[] {true});
435454
}
436455

456+
public void handleProjectDeselect() {
457+
projectInfoLayout.setVisible(false);
458+
downloadProjectInfo.setVisible(false);
459+
experimentPersons.setVisible(false);
460+
}
461+
437462
public void handleProjectValueChange(Object item, Person PI, Person contact, Person manager) {
438463
projectInfoLayout.setVisible(false);
439464
downloadProjectInfo.setVisible(false);
@@ -450,10 +475,8 @@ public void handleProjectValueChange(Object item, Person PI, Person contact, Per
450475
armDownloadButton(item, PI, contact, manager);
451476
downloadProjectInfo.setVisible(true);
452477
} catch (FileNotFoundException e) {
453-
// TODO Auto-generated catch block
454478
e.printStackTrace();
455479
} catch (UnsupportedEncodingException e) {
456-
// TODO Auto-generated catch block
457480
e.printStackTrace();
458481
}
459482
projectInfoLayout.setVisible(true);

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