Changeset 5832


Ignore:
Timestamp:
Feb 21, 2020, 4:19:57 PM (22 months ago)
Author:
olle
Message:

Refs #1029. FFPE section (specimen) registration wizard updated by removing input fields for tumour cell percentage for H&E glass items, since these should be moved to a separate wizard. Also, created FFPE sections (specimens) now made children of the FFPE block instead of the case item:

  1. Javascript file ffpe_section_registration_alt_rec.js in resources/personal/ updated by removing code related to input fields for tumour cell percentage for H&E glass items.
  2. Java servlet class/file BaseLineRegistrationServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doPost(HttpServletRequest req, HttpServletResponse resp) for command "RegisterFFPESections" to not set tumour cell percentage for H&E glass items. Also, created FFPE sections (specimens) now made children of the FFPE block instead of the case item.
Location:
extensions/net.sf.basedb.meludi/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.meludi/trunk/resources/personal/ffpe_section_registration_alt_rec.js

    r5214 r5832  
    167167      var yellowLabelMsg = 'Assigned yellow label for '+ffpeSectionName+' (selected for processing).';
    168168      var nofSectionsMsg = 'Number of sections for '+ffpeSectionName+'.';
    169       var pctViabTumourCellsMsg = '% Viable tumour cells for '+ffpeSectionName+'.';
     169      //var pctViabTumourCellsMsg = '% Viable tumour cells for '+ffpeSectionName+'.';
    170170      var opDelCmtMsg = 'In this field, enter information specific for for '+ffpeSectionName+'.';
    171171      var disabledAttribute = '';
     
    209209      var heGlassEBoxMsg = 'Box-number and position where the H&E glass "E" will be placed.';
    210210      var disabledAttribute = '';
    211       var pctTumourCellsFMsg = '% Tumour cells for '+ffpeSectionName+'.F.'
    212       var pctTumourCellsEMsg = '% Tumour cells for '+ffpeSectionName+'.E.'
     211      //var pctTumourCellsFMsg = '% Tumour cells for '+ffpeSectionName+'.F.'
     212      //var pctTumourCellsEMsg = '% Tumour cells for '+ffpeSectionName+'.E.'
    213213
    214214/*
     
    282282      html += '</tr>';
    283283
     284/*
    284285      // H&E glass "Front" percentage of tumor cells
    285286      html += '<tr>';
     
    291292      html += '<td class="help"><span id="pctTumourCellsF.'+i+'.message" class="message"></span>'+pctTumourCellsFMsg+'<span id="pctTumourCellsF.'+i+'.message" class="message"></span></td>';
    292293      html += '</tr>';
     294*/
    293295
    294296      // H&E glass "End"
     
    304306      html += '</tr>';
    305307
     308/*
    306309      // H&E glass "End" percentage of tumor cells
    307310      html += '<tr>';
     
    313316      html += '<td class="help"><span id="pctTumourCellsE.'+i+'.message" class="message"></span>'+pctTumourCellsEMsg+'<span id="pctTumourCellsE.'+i+'.message" class="message"></span></td>';
    314317      html += '</tr>';
     318*/
    315319    }
    316320    Doc.element('ffpe-sections').innerHTML = html;
     
    854858      ffpeSection.heGlassFBox = frm['heGlassFBox.'+i].value;
    855859      ffpeSection.heGlassFPosition = frm['heGlassFPosition.'+i].value;
    856       ffpeSection.pctTumourCellsF = frm['pctTumourCellsF.'+i].value;
     860      //ffpeSection.pctTumourCellsF = frm['pctTumourCellsF.'+i].value;
    857861
    858862      ffpeSection.heGlassEBox = frm['heGlassEBox.'+i].value;
    859863      ffpeSection.heGlassEPosition = frm['heGlassEPosition.'+i].value;
    860       ffpeSection.pctTumourCellsE = frm['pctTumourCellsE.'+i].value;
     864      //ffpeSection.pctTumourCellsE = frm['pctTumourCellsE.'+i].value;
    861865      //
    862866      ffpeSectionInfo.ffpeSections[i] = ffpeSection;
  • extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/BaseLineRegistrationServlet.java

    r5756 r5832  
    19241924            String heGlassFBox = (String)jsonFfpeSection.get("heGlassFBox");
    19251925            String heGlassFPosition = (String)jsonFfpeSection.get("heGlassFPosition");
    1926             int pctTumourCellsF = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsF"));
     1926            //int pctTumourCellsF = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsF"));
    19271927
    19281928            String heGlassEBox = (String)jsonFfpeSection.get("heGlassEBox");
    19291929            String heGlassEPosition = (String)jsonFfpeSection.get("heGlassEPosition");
    1930             int pctTumourCellsE = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsE"));
     1930            //int pctTumourCellsE = Integer.parseInt((String)jsonFfpeSection.get("pctTumourCellsE"));
    19311931
    19321932            // Find case name from FFPE block
     
    19581958
    19591959            BioMaterialEvent creationEvent = specimen.getCreationEvent();
     1960            /*
    19601961            // Link the specimen with the case
    19611962            if (theCase != null)
    19621963            {
    19631964              creationEvent.setSource(theCase.getSample());
     1965            }
     1966            creationEvent.setEventDate(createDate);
     1967            */
     1968
     1969            // Link the specimen with the FFPE block
     1970            if (ffpeBlock != null)
     1971            {
     1972              creationEvent.setSource(ffpeBlock.getSample());
    19641973            }
    19651974            creationEvent.setEventDate(createDate);
     
    20662075            dc.saveItem(stained);
    20672076
    2068             Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsF);
     2077            //Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsF);
    20692078            // Get location for stain on glass plate
    20702079            BioWell stainedFWell = heGlassF.getBioWell(0, 0);
     
    21122121            dc.saveItem(stained);
    21132122
    2114             Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsE);
     2123            //Annotationtype.TUMOUR_CELLS_PERCENT.setAnnotationValue(dc, stained, pctTumourCellsE);
    21152124            // Get location for stain on glass plate
    21162125            BioWell stainedEWell = heGlassE.getBioWell(0, 0);
Note: See TracChangeset for help on using the changeset viewer.