Changeset 2501

Timestamp:

Jun 12, 2014, 11:31:00 AM (9 years ago)

Author:

olle

Message:

Refs #530. Case summary updated for specific event dates by optional addition of link to pop-up window with lab environment data for the given date in the lab where the event was performed. Initially, the link will be indicated by a thermometer icon:

1. The functionality uses LabEnv JSP file labenvironmentdatabaseeventpopup.jsp in resources/reports/, added in change set ​[2463] to LabEnv 1.1. Installation of LabEnv version 1.1 or higher is therefore required (otherwise no working lab environment event data links will be added).
2. JSP file case_summary.jsp in resources/reports/ updated by calling ExtensionsControl.getHomeUrl(...) to obtain the URL for "net.sf.basedb.labenv.service", and then add it attribute data-home-labenv in div tag with id = "page-data".
3. JavaScript case-summary.js in resources/reports/ updated:
   a. Call of cs.addColumn(...) for RNA, DNA, and FlowThrough extraction dates, mRNA cleanup date, cDNA synthesis date, library cleanup date, and pooled library pool date extended by calling new function cs.asLabEnvLink(sensor, date, title, icon) for the appropriate lab sensor and date.
   b. New function cs.asLabEnvLink(sensor, date, title, icon) added. It retrieves URL home-labenv from div tag with id = "page-data", and if the URL exists, a link is returned with class "link linked-labenv", and attribute data-sensor set to argument sensor, data-date to date, and data-title to title. The link is represented by the icon defined in the argument list.
   c. New event handler LabEnvs.viewDataOnClick is added to links of class "linked-labenv".
   d. New function LabEnvs.viewDataOnClick(event) added. It retrieves URL home-labenv from div tag with id = "page-data", and values for attributes sensor, date, and title from attributed with same name for event.currentTarget, after which a pop-up window is opened for a URL to LabEnv JSP file reports/labenvironmentdatabaseeventpopup.jsp, with added values for labSensorUrl, originDate, and pageTitle.
4. New icon image thermometer.png added to resources/images/.

Location:

extensions/net.sf.basedb.reggie/trunk/resources

Files:

• images/thermometer.png (added)
• reports/case-summary.js (modified) (10 diffs)
• reports/case_summary.jsp (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/reports/case-summary.js

@@ -278 +278 @@
         cs.addColumn('rna.storageBox', cs.asBioPlateLocation(r.bioWell));
         cs.addColumn('rna.usedQuantity', cs.asQuantity(r.usedQuantity, ' µg'));
-        cs.addColumn('rna.extractionDate', cs.asDate(r.extractionDate));
+        cs.addColumn('rna.extractionDate', cs.asDate(r.extractionDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.extractionDate, 'RNA extraction: ' + r.name, 'thermometer.png'));
         cs.addColumn('rna.extractionProtocol', cs.asLink('PROTOCOL', r.extractionProtocol, truncateAt));
         cs.addColumn('rna.remainingQuantity', cs.asQuantity(r.remainingQuantity, ' µg'));
@@ -318 +318 @@
         cs.addColumn('dna.registrationDate', cs.asDate(d.registrationDate));
         cs.addColumn('dna.storageBox', cs.asBioPlateLocation(d.bioWell));
-        cs.addColumn('dna.extractionDate', cs.asDate(d.extractionDate));
+        cs.addColumn('dna.extractionDate', cs.asDate(d.extractionDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', d.extractionDate, 'DNA extraction: ' + d.name, 'thermometer.png'));
         cs.addColumn('dna.extractionProtocol', cs.asLink('PROTOCOL', d.extractionProtocol, truncateAt));
         cs.addColumn('dna.remainingQuantity', cs.asQuantity(d.remainingQuantity, ' µg'));
@@ -349 +349 @@
         cs.addColumn('ft.registrationDate', cs.asDate(f.registrationDate));
         cs.addColumn('ft.storageBox', cs.asBioPlateLocation(f.bioWell));
-        cs.addColumn('ft.extractionDate', cs.asDate(f.extractionDate));
+        cs.addColumn('ft.extractionDate', cs.asDate(f.extractionDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', f.extractionDate, 'FlowThrough extraction: ' + f.name, 'thermometer.png'));
         cs.addColumn('ft.extractionProtocol', cs.asLink('PROTOCOL', f.extractionProtocol, truncateAt));
         cs.addColumn('ft.remainingQuantity', cs.asQuantity(f.remainingQuantity, ' µg'));
@@ -380 +380 @@
         cs.addColumn('mrna.storageBox', cs.asBioPlateLocation(r.bioWell)+cs.asFileLink(r.platePdf, 'pdffile.png'));
         cs.addColumn('mrna.result', (r.result && r.result != 'Successful') ? cs.asFailInfo(r.result, 'error.png') : null);
-        cs.addColumn('mrna.cleanupDate', cs.asDate(r.cleanupDate));
+        cs.addColumn('mrna.cleanupDate', cs.asDate(r.cleanupDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.cleanupDate, 'mRNA cleanup: ' + r.name, 'thermometer.png'));
         cs.addColumn('mrna.usedQuantity', cs.asQuantity(r.usedQuantity, ' µg'));
         cs.addColumn('mrna.comment', cs.truncate(r.comment, truncateAt));
@@ -409 +409 @@
         cs.addColumn('cdna.storageBox', cs.asBioPlateLocation(r.bioWell));
         cs.addColumn('cdna.result', (r.result && r.result != 'Successful') ? cs.asFailInfo(r.result, 'error.png') : null);
-        cs.addColumn('cdna.synthesisDate', cs.asDate(r.synthesisDate));
+        cs.addColumn('cdna.synthesisDate', cs.asDate(r.synthesisDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.synthesisDate, 'cDNA synthesis: ' + r.name, 'thermometer.png'));
         cs.addColumn('cdna.comment', cs.truncate(r.comment, truncateAt));
       }
@@ -437 +437 @@
         cs.addColumn('lib.storageBox', cs.asBioPlateLocation(r.bioWell));
         cs.addColumn('lib.result', (r.result && r.result != 'Successful') ? cs.asFailInfo(r.result, 'error.png') : null);
-        cs.addColumn('lib.cleanupDate', cs.asDate(r.cleanupDate));
+        cs.addColumn('lib.cleanupDate', cs.asDate(r.cleanupDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.cleanupDate, 'Library cleanup: ' + r.name, 'thermometer.png'));
         cs.addColumn('lib.remainingQuantity', cs.asQuantity(r.remainingQuantity, ' ng', 0.001));
         cs.addColumn('lib.originalQuantity', cs.asQuantity(r.originalQuantity, ' ng', 0.001));
@@ -470 +470 @@
         cs.addColumn('pooledlib.name', cs.asLink('EXTRACT', r));
         cs.addColumn('pooledlib.registrationDate', cs.asDate(r.registrationDate));
-        cs.addColumn('pooledlib.poolDate', cs.asDate(r.poolDate));
+        cs.addColumn('pooledlib.poolDate', cs.asDate(r.poolDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.poolDate, 'Pooled library pooling: ' + r.name, 'thermometer.png'));
         cs.addColumn('pooledlib.remainingQuantity', cs.asQuantity(r.remainingQuantity, ' ng', 0.001));
         cs.addColumn('pooledlib.originalQuantity', cs.asQuantity(r.originalQuantity, ' ng', 0.001));
@@ -531 +531 @@
     {
       Events.addEventHandler(linkedFiles[fileNo], 'click', Files.viewFileOnClick);
+    }
+    
+    var linkedLabEnvs = document.getElementsByClassName('linked-labenv');
+    for (var labEnvNo = 0; labEnvNo < linkedLabEnvs.length; labEnvNo++)
+    {
+      Events.addEventHandler(linkedLabEnvs[labEnvNo], 'click', LabEnvs.viewDataOnClick);
     }
     
@@ -641 +647 @@
   }
 
+  cs.asLabEnvLink = function(sensor, date, title, icon)
+  {
+    var link = '';
+    // Check if BASE extension LabEnv is installed
+    var homeLabEnv = Data.get('page-data', 'home-labenv');
+    if (homeLabEnv)
+    {
+      if (date)
+      {
+        if (sensor)
+        {
+          // Link to pop-up window with lab environment data for the chosen sensor and date
+          link = '<span class="link linked-labenv" data-sensor="'+sensor+'" data-date="'+date+'" data-title="'+title+'"><img src="../images/'+icon+'"></span>';
+        }
+      }
+    }
+    return link;
+  }
+
   cs.asCaseList = function(allCases, mainCase)
   {
@@ -838 +863 @@
 }();
 
+var LabEnvs = function()
+{
+  var labenvs = {};
+
+  /**
+    Event handler that calls 'labenv.jar/reports/labenvironmentdatabaseeventpopup.jsp'
+    when clicking on the attached target. The sensor id should be stored
+    in attribute 'data-sensor', the date in 'data-date',
+    and the title in 'data-title'.
+  */
+  labenvs.viewDataOnClick = function(event)
+  {
+    var homeLabEnv = Data.get('page-data', 'home-labenv');
+    var title = Data.get(event.currentTarget, 'title');
+    var sensor = Data.get(event.currentTarget, 'sensor');
+    var date = Data.get(event.currentTarget, 'date');
+    var url = homeLabEnv;
+    url += '/reports/labenvironmentdatabaseeventpopup.jsp';
+    url += '?ID='+App.getSessionId();
+    url += '&pageTitle='+encodeURIComponent(title);
+    url += '&labSensorUrl='+encodeURIComponent(sensor);
+    url += '&originDate='+encodeURIComponent(date);
+    Dialogs.openPopup(url, title, 820, 768);
+  }
+  
+  return labenvs;
+}();
+
 Doc.onLoad(CaseSummary.initPage);

extensions/net.sf.basedb.reggie/trunk/resources/reports/case_summary.jsp

@@ -26 +26 @@
 final float scale = Base.getScale(sc);
 final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
+final String homeLabEnv = ExtensionsControl.getHomeUrl("net.sf.basedb.labenv.service");
 DbControl dc = null;
 try
@@ -75 +76 @@
     data-patient-curator="<%=isPatientCurator ? 1 : 0%>"
     data-page-type="<%=pageType%>"
+    data-home-labenv="<%=HTML.encodeTags(homeLabEnv)%>"
   ></div>
   <div id="all-content">