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Merge branch 'develop' into fb_fileLike3
2 parents d4e59ee + 63a78ba commit a08023a

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13 files changed

+197
-55
lines changed

13 files changed

+197
-55
lines changed

‎panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java‎

Lines changed: 10 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -6879,6 +6879,11 @@ private ExperimentAnnotations getCopiedExperimentFor(ExperimentAnnotations expAn
68796879
return null;
68806880
}
68816881

6882+
if (_journalSubmission.hasPendingSubmission())
6883+
{
6884+
errors.reject(ERROR_MSG, String.format("There is a pending re-submit request for this experiment on '%s'", _journal.getName()));
6885+
return null;
6886+
}
68826887
if (expAnnot.isJournalCopy())
68836888
{
68846889
if (!_journalSubmission.isLatestExperimentCopy(_expAnnot.getId()))
@@ -7010,12 +7015,10 @@ public void validateCommand(PublicationDetailsForm form, Errors errors)
70107015
return;
70117016
}
70127017
}
7013-
if (!form.hasNewPublicationDetails(_copiedExperiment))
7014-
{
7015-
errors.reject(ERROR_MSG, String.format("Publication details are the same as the ones associated with the data on %s at %s",
7016-
_journal.getName(), _copiedExperiment.getShortUrl().renderShortURL()));
7017-
return;
7018-
}
7018+
// Validation removed: no need to ensure that publication details entered in the form differ from the
7019+
// publication details already associated with the experiment. The user may have entered the
7020+
// correct PubMedID etc. when submitting but forgot to make the data public.
7021+
// (See commit history for the original logic.)
70197022
}
70207023
else if (_copiedExperiment.isPublic())
70217024
{
@@ -7359,13 +7362,6 @@ public boolean hasLinkAndCitation()
73597362
{
73607363
return !(StringUtils.isBlank(_link) || StringUtils.isBlank(_citation));
73617364
}
7362-
7363-
public boolean hasNewPublicationDetails(ExperimentAnnotations copiedExperiment)
7364-
{
7365-
return !(Objects.equals(_pubmedId, copiedExperiment.getPubmedId())
7366-
&& Objects.equals(_link, copiedExperiment.getPublicationLink())
7367-
&& Objects.equals(_citation, copiedExperiment.getCitation()));
7368-
}
73697365
}
73707366

73717367
public static abstract class PanoramaPublicExperimentAction<T extends ExperimentIdForm> extends FormViewAction<T>
@@ -9852,7 +9848,7 @@ private MessageExampleBean createExampleMessage(List<Integer> experimentIds, Pan
98529848
{
98539849
continue;
98549850
}
9855-
Announcement announcement = announcementSvc.getAnnouncement(announcementsContainer, getUser(), submission.getAnnouncementId());
9851+
Announcement announcement = submission.getAnnouncement(announcementSvc, announcementsContainer, getUser());
98569852
if (announcement == null)
98579853
{
98589854
continue; // old data before we started posting submission requests to a message board

‎panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicNotification.java‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -396,14 +396,15 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
396396
message.append("Dear ").append(getUserName(submitter)).append(",").append(NL2)
397397
.append("We are reaching out regarding your data on Panorama Public (").append(shortUrl).append("), which has been private since ")
398398
.append(dateString).append(".")
399-
.append("\n\n**Is the paper associated with this work already published?**")
400-
.append("\n- If yes: Please make your data public by clicking the \"Make Public\" button in your folder or by clicking this link: ")
399+
.append(NL2).append(bold("Title:")).append(" ").append(escape(exptAnnotations.getTitle()))
400+
.append(NL2).append(bold("Is the paper associated with this work already published?"))
401+
.append(NL).append("- If yes: Please make your data public by clicking the \"Make Public\" button in your folder or by clicking this link: ")
401402
.append(bold(link("Make Data Public", makePublicLink)))
402403
.append(". This helps ensure that your valuable research is easily accessible to the community.")
403-
.append("\n- If not: You have a couple of options:")
404-
.append("\n - **Request an Extension** - If your paper is still under review, or you need additional time, please let us know by clicking ")
404+
.append(NL).append("- If not: You have a couple of options:")
405+
.append(NL).append(" - ").append(bold("Request an Extension")).append(" - If your paper is still under review, or you need additional time, please let us know by clicking ")
405406
.append(bold(link("Request Extension", requestExtensionUrl.getURIString()))).append(".")
406-
.append("\n - **Delete from Panorama Public** - If you no longer wish to host your data on Panorama Public, please click ")
407+
.append(NL).append(" - ").append(bold("Delete from Panorama Public")).append(" - If you no longer wish to host your data on Panorama Public, please click ")
407408
.append(bold(link("Request Deletion", requesDeletionUrl.getURIString()))).append(". ")
408409
.append("We will remove your data from Panorama Public.");
409410
if (sourceExperiment != null)
@@ -413,9 +414,9 @@ public static String getDataStatusReminderMessage(@NotNull ExperimentAnnotations
413414
.append(") will remain intact, allowing you to resubmit your data in the future if you wish.");
414415
}
415416

416-
message.append("\n\nIf you have any questions or need further assistance, please do not hesitate to respond to this message by ")
417+
message.append(NL2).append("If you have any questions or need further assistance, please do not hesitate to respond to this message by ")
417418
.append(bold(link("clicking here", respondToMessageUrl.getURIString()))).append(".")
418-
.append("\n\nThank you for sharing your research on Panorama Public. We appreciate your commitment to open science and your contributions to the research community.")
419+
.append(NL2).append("Thank you for sharing your research on Panorama Public. We appreciate your commitment to open science and your contributions to the research community.")
419420
.append(NL2).append("Best regards,")
420421
.append(NL).append(getUserName(journalAdmin));
421422
return message.toString();

‎panoramapublic/src/org/labkey/panoramapublic/model/ExperimentAnnotations.java‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -224,6 +224,11 @@ public List<String> getInstruments()
224224
return instruments;
225225
}
226226

227+
public String getInstrumentsCommaSeparated()
228+
{
229+
return StringUtils.join(getInstruments(), ", ");
230+
}
231+
227232
public void setInstrument(String instrument)
228233
{
229234
_instrument = instrument;
@@ -504,12 +509,12 @@ public DataLicense getDataLicense()
504509

505510
/**
506511
* Returns true if the experiment is in an 'Experimental Data' folder that is public and the experiment is
507-
* associated with a published paper.
512+
* associated with a peer-reviewed paper (excludes biorxiv and medrxiv preprint servers).
508513
*/
509514
public boolean isFinal()
510515
{
511516
TargetedMSService.FolderType folderType = TargetedMSService.get().getFolderType(getContainer());
512-
return Experiment.equals(folderType) && isPublic() && isPublished();
517+
return Experiment.equals(folderType) && isPublic() && isPeerReviewed();
513518
}
514519

515520
public boolean hasCompletePublicationInfo()

‎panoramapublic/src/org/labkey/panoramapublic/model/JournalSubmission.java‎

Lines changed: 14 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,10 @@
22

33
import org.jetbrains.annotations.NotNull;
44
import org.jetbrains.annotations.Nullable;
5+
import org.labkey.api.announcements.api.Announcement;
6+
import org.labkey.api.announcements.api.AnnouncementService;
7+
import org.labkey.api.data.Container;
8+
import org.labkey.api.security.User;
59
import org.labkey.api.view.ShortURLRecord;
610
import org.labkey.panoramapublic.query.SubmissionManager;
711

@@ -69,11 +73,20 @@ public int getModifiedBy()
6973
return _journalExperiment.getModifiedBy();
7074
}
7175

72-
public Integer getAnnouncementId()
76+
public @Nullable Integer getAnnouncementId()
7377
{
7478
return _journalExperiment.getAnnouncementId();
7579
}
7680

81+
public @Nullable Announcement getAnnouncement(@NotNull AnnouncementService announcementSvc,
82+
@NotNull Container announcementsContainer,
83+
@NotNull User user)
84+
{
85+
return (getAnnouncementId() != null)
86+
? announcementSvc.getAnnouncement(announcementsContainer, user, getAnnouncementId())
87+
: null; // old data before we started posting submission requests to a message board
88+
}
89+
7790
public Integer getReviewerId()
7891
{
7992
return _journalExperiment.getReviewer();

‎panoramapublic/src/org/labkey/panoramapublic/pipeline/PostPanoramaPublicMessageJob.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,8 @@ private void postMessage()
102102
continue;
103103
}
104104

105-
Announcement announcement = announcementSvc.getAnnouncement(announcementsContainer, getUser(), submission.getAnnouncementId());
105+
Announcement announcement = submission.getAnnouncement(announcementSvc, announcementsContainer, getUser());
106+
106107
if (announcement == null)
107108
{
108109
getLogger().error("Could not find the message thread for experiment Id: " + experimentAnnotationsId

‎panoramapublic/src/org/labkey/panoramapublic/pipeline/PrivateDataReminderJob.java‎

Lines changed: 8 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -100,6 +100,13 @@ private static ReminderDecision getReminderDecision(@NotNull ExperimentAnnotatio
100100
return ReminderDecision.skip("Not the current version of the experiment");
101101
}
102102

103+
// Make sure the data does not have a pending re-submission request
104+
JournalSubmission journalSubmission = SubmissionManager.getSubmissionForJournalCopy(exptAnnotations);
105+
if (journalSubmission != null && journalSubmission.hasPendingSubmission())
106+
{
107+
return ReminderDecision.skip("Data has a pending re-submission request");
108+
}
109+
103110
DatasetStatus datasetStatus = DatasetStatusManager.getForExperiment(exptAnnotations);
104111
if (datasetStatus != null)
105112
{
@@ -244,7 +251,7 @@ private void processExperiment(Integer experimentAnnotationsId, ProcessingContex
244251
}
245252

246253
Container announcementsFolder = context.getAnnouncementsFolder();
247-
Announcement announcement = context.getAnnouncementService().getAnnouncement(announcementsFolder, getUser(), submission.getAnnouncementId());
254+
Announcement announcement = submission.getAnnouncement(context.getAnnouncementService(), context.getAnnouncementsFolder(), getUser());
248255
if (announcement == null)
249256
{
250257
processingResults.addAnnouncementNotFound(experimentAnnotationsId, submission, announcementsFolder);

‎panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -301,7 +301,7 @@ void writePublicationList(ExperimentAnnotations experimentAnnotations)
301301
HtmlList publicationList = new HtmlList();
302302
if(experimentAnnotations.isPublished())
303303
{
304-
publicationList.addItem("Link: ", experimentAnnotations.getPublicationLink(), false);
304+
publicationList.addItem("Link", experimentAnnotations.getPublicationLink(), false);
305305

306306
if(experimentAnnotations.hasPubmedId())
307307
{

‎panoramapublic/src/org/labkey/panoramapublic/view/expannotations/experimentDetails.jsp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -337,7 +337,7 @@
337337
<li><strong>Organism:</strong> <%=h(annot.getOrganismsNoTaxId())%></li>
338338
<%}%>
339339
<%if(annot.getInstrument() != null){%>
340-
<li><strong>Instrument:</strong> <%=h(annot.getInstrument())%></li>
340+
<li><strong>Instrument:</strong> <%=h(annot.getInstrumentsCommaSeparated())%></li>
341341
<%}%>
342342
<%if(annot.getSpikeIn() != null){%>
343343
<li><strong>SpikeIn:</strong>

‎panoramapublic/src/org/labkey/panoramapublic/view/publish/copyExperimentForm.jsp‎

Lines changed: 29 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -52,6 +52,7 @@
5252
CopyExperimentForm form = bean.getForm();
5353
ExperimentAnnotations expAnnot = form.lookupExperiment();
5454
Journal journal = form.lookupJournal();
55+
Container folderTreeRoot = journal.getProject();
5556
JournalSubmission js = bean.getJournalSubmission();
5657
Submission currentSubmission = js.getLatestSubmission();
5758
ExperimentAnnotations previousCopy = ExperimentAnnotationsManager.getLatestCopyForSubmission(js);
@@ -93,15 +94,20 @@
9394
var folderTreeStore = Ext4.create('Ext.data.TreeStore', {
9495
proxy: {
9596
type: 'ajax',
96-
url: LABKEY.ActionURL.buildURL('core', 'getExtContainerAdminTree.api'),
97-
extraParams: {move: false, requiredPermission: <%=q(RoleManager.getPermission(AdminPermission.class).getUniqueName())%>, showContainerTabs: false}
97+
url: LABKEY.ActionURL.buildURL('core', 'getExtContainerTree.api'),
98+
extraParams: {
99+
annotateLeaf: true,
100+
requiredPermission: <%=q(RoleManager.getPermission(AdminPermission.class).getUniqueName())%>,
101+
}
98102
},
99103
root: {
100-
expanded: false
104+
id : <%=folderTreeRoot.getRowId()%>,
105+
expanded : true,
106+
expandable : false,
107+
text : <%=q(folderTreeRoot.getName())%>
101108
},
102109
folderSort: false,
103-
autoLoad: true,
104-
defaultRootId: <%=ContainerManager.getRoot().getRowId()%>
110+
autoLoad: true
105111
});
106112
107113
var form = Ext4.create('Ext.form.Panel', {
@@ -158,25 +164,33 @@
158164
xtype: 'treepanel',
159165
fieldLabel: 'Destination',
160166
store: folderTreeStore,
161-
rootVisible: false,
167+
rootVisible: true,
162168
enableDrag: false,
163-
useArrows : false,
169+
useArrows : true,
164170
autoScroll: true,
165171
title : '',
166172
border: true,
167173
width: 650,
168174
height:150,
169175
listeners: {
170176
select: function(node, record, index, eOpts){
171-
//console.log("the record is...");
172-
//console.log(record.get('id'));
173-
//console.log(record.get('text'));
174-
175-
var displayField = Ext4.ComponentQuery.query('#destParentContainer_DisplayField')[0];
176-
displayField.setValue(record.get('text'));
177+
const displayField = Ext4.ComponentQuery.query('#destParentContainer_DisplayField')[0];
178+
if (displayField) {
179+
displayField.setValue(record.getPath('text', '/'));
180+
}
177181
178-
var hiddenField = Ext4.ComponentQuery.query('#destParentContainer_Input')[0];
179-
hiddenField.setValue(record.get('id'));
182+
const hiddenField = Ext4.ComponentQuery.query('#destParentContainer_Input')[0];
183+
if (hiddenField) {
184+
hiddenField.setValue(record.get('id'));
185+
}
186+
},
187+
load : function(store, node) {
188+
// Data on Panorama Public is organized by year. Select the subfolder for the current year.
189+
const currentYear = new Date().getFullYear().toString();
190+
const target = store.getRootNode().findChild('text', currentYear, true);
191+
if (target) {
192+
this.getSelectionModel().select(target);
193+
}
180194
}
181195
}
182196
},

‎panoramapublic/src/org/labkey/panoramapublic/view/publish/dataDownloadInfo.jsp‎

Lines changed: 8 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -23,17 +23,20 @@
2323
%>
2424
<p>
2525
Select one or more files or folders in the browser above and click the download icon ( <span class="fa fa-download"></span> ).
26+
<br/>
27+
<br/>
2628
Data can also be downloaded by mapping this folder as a network drive in Windows Explorer, or by using a
2729
<%=simpleLink("WebDAV", "https://en.wikipedia.org/wiki/WebDAV")%>
2830
client such as <span class="nobr"><%=simpleLink("CyberDuck", "https://cyberduck.io")%></span>
2931
or <span class="nobr"><%=simpleLink("WinSCP", "https://winscp.net/eng/docs/introduction")%></span>.
30-
For details look at <%=simpleLink("Download data from Panorama Public", downloadDataDocHref)%>.
31-
Use the following URL, login email and password to connect to this folder:
32-
<br/>
32+
WebDAV downloads require an account on the PanoramaWeb server. Information on obtaining an account and other download options
33+
is available on the <%=simpleLink("Download data from Panorama Public", downloadDataDocHref)%> help page.
34+
Use the following URL to connect to this folder for WebDAV downloads:
3335
<br/>
3436
URL: <b class="bold"><span class="nobr" id="webdav_url_link"><%=h(webdavUrl)%></span></b>
3537
<br/>
36-
Login email: <b class="bold"><%=h(publicDataUser.getEmail())%></b>
3738
<br/>
38-
Password: <b class="bold"><%=h(publicDataUser.getPassword())%></b>
39+
<b class="bold">Note: </b> If you plan to download large volumes of data or datasets from multiple projects via WebDAV,
40+
please contact the PanoramaWeb team in advance so that we can coordinate the download to minimize load on the server
41+
and ensure reliable access.
3942
</p>

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