Support for Multiple component analysis

CHANGES.rst

@@ -4,6 +4,7 @@ Changelog
 2.6.0 (unreleased)
 ------------------
 
+- #2120 Support for Multiple component analysis
 - #2514 Added functions for easy update of workflows
 - #2512 Skip rendering of empty record fiels
 - #2510 Fix Add action of the Client located Analysis Profiles Listing

src/bika/lims/browser/analyses/view.py

@@ -81,6 +81,7 @@ def __init__(self, context, request, **kwargs):
             "portal_type": "Analysis",
             "sort_on": "sortable_title",
             "sort_order": "ascending",
+            "isAnalyte": False,
         })
 
         # set the listing view config
@@ -387,6 +388,10 @@ def is_result_edition_allowed(self, analysis_brain):
         # Get the ananylsis object
         obj = self.get_object(analysis_brain)
 
+        if obj.isMultiComponent():
+            # The results entry cannot be done directly, but for its analytes
+            return False
+
         if not obj.getDetectionLimitOperand():
             # This is a regular result (not a detection limit)
             return True
@@ -778,6 +783,11 @@ def folderitem(self, obj, item, index):
         # Renders the analysis conditions
         self._folder_item_conditions(obj, item)
 
+        # Analytes (if a multi component analysis)
+        obj = self.get_object(obj)
+        item["children"] = obj.getRawAnalytes()
+        item["parent"] = obj.getRawMultiComponentAnalysis()
+
         return item
 
     def folderitems(self):
@@ -940,6 +950,12 @@ def _folder_item_result(self, analysis_brain, item):
             item["before"]["Result"] = img
             return
 
+        # Get the analysis object
+        obj = self.get_object(analysis_brain)
+        if obj.isMultiComponent():
+            # Don't display the "NA" result of a multi-component analysis
+            return
+
         result = analysis_brain.getResult
         capture_date = analysis_brain.getResultCaptureDate
         capture_date_str = self.ulocalized_time(capture_date, long_format=0)
@@ -953,9 +969,6 @@ def _folder_item_result(self, analysis_brain, item):
         if unit:
             item["after"]["Result"] = self.render_unit(unit)
 
-        # Get the analysis object
-        obj = self.get_object(analysis_brain)
-
         # Edit mode enabled of this Analysis
         if self.is_analysis_edition_allowed(analysis_brain):
             # Allow to set Remarks
@@ -1167,6 +1180,12 @@ def _folder_item_unit(self, analysis_brain, item):
         if not self.is_analysis_edition_allowed(analysis_brain):
             return
 
+        obj = self.get_object(analysis_brain)
+        if obj.isMultiComponent():
+            # Leave units empty
+            item["Unit"] = ""
+            return
+
         # Edition allowed
         voc = self.get_unit_vocabulary(analysis_brain)
         if voc:
@@ -1179,7 +1198,11 @@ def _folder_item_method(self, analysis_brain, item):
         :param analysis_brain: Brain that represents an analysis
         :param item: analysis' dictionary counterpart that represents a row
         """
+        item["Method"] = ""
         obj = self.get_object(analysis_brain)
+        if obj.isAnalyte():
+            return
+
         is_editable = self.is_analysis_edition_allowed(analysis_brain)
         if is_editable:
             method_vocabulary = self.get_methods_vocabulary(analysis_brain)
@@ -1221,6 +1244,9 @@ def _folder_item_instrument(self, analysis_brain, item):
         :param item: analysis' dictionary counterpart that represents a row
         """
         item["Instrument"] = ""
+        obj = self.get_object(analysis_brain)
+        if obj.isAnalyte():
+            return
 
         # Instrument can be assigned to this analysis
         is_editable = self.is_analysis_edition_allowed(analysis_brain)
@@ -1261,7 +1287,13 @@ def _folder_item_analyst(self, obj, item):
         item["Analyst"] = self.get_user_name(analyst)
 
     def _folder_item_submitted_by(self, obj, item):
+        item["SubmittedBy"] = ""
+
         obj = self.get_object(obj)
+        if obj.isMultiComponent():
+            # Do not display submitter for multi-component analyses
+            return
+
         submitted_by = obj.getSubmittedBy()
         item["SubmittedBy"] = self.get_user_name(submitted_by)
 
@@ -1357,10 +1389,16 @@ def _folder_item_detection_limits(self, analysis_brain, item):
         if not obj.getDetectionLimitSelector():
             return None
 
+        # Display the column for the selector
+        self.columns["DetectionLimitOperand"]["toggle"] = True
+
+        # If multicomponent only render the selector for analytes
+        if obj.isMultiComponent():
+            return
+
         # Show Detection Limit Operand Selector
         item["DetectionLimitOperand"] = obj.getDetectionLimitOperand()
         item["allow_edit"].append("DetectionLimitOperand")
-        self.columns["DetectionLimitOperand"]["toggle"] = True
 
         # Prepare selection list for LDL/UDL
         choices = [
@@ -1583,6 +1621,9 @@ def _folder_item_report_visibility(self, analysis_brain, item):
             return
 
         full_obj = self.get_object(analysis_brain)
+        if full_obj.isMultiComponent():
+            return
+
         item['Hidden'] = full_obj.getHidden()
 
         # Hidden checkbox is not reachable by tabbing

src/bika/lims/browser/analysisrequest/add2.py

@@ -927,6 +927,7 @@ def get_service_info(self, obj):
             "category": obj.getCategoryTitle(),
             "poc": obj.getPointOfCapture(),
             "conditions": self.get_conditions_info(obj),
+            "analytes": obj.getAnalytes(),
         })
 
         dependencies = get_calculation_dependencies_for(obj).values()

src/bika/lims/browser/analysisrequest/templates/ar_add2.pt

@@ -292,6 +292,44 @@
         </div>
       </script>
 
+      <!-- Service Analytes template -->
+      <script id="service-analytes" type="text/x-handlebars-template">
+        <div data-fieldname="ServiceAnalytes-{{arnum}}">
+          <table class="service-analytes-table table table-condensed table-bordered">
+            {{#each analytes}}
+            <tr data-subfield="{{title}}">
+              <td class="service-analytes-label">
+                <label class="formQuestion">
+                  <span class="">{{{title}}} ({{{keyword}}})</span>
+                </label>
+              </td>
+              <td class="service-analytes-value">
+                <input type='hidden'
+                       name="ServiceAnalytes-{{../arnum}}.uid:records"
+                       value="{{../uid}}"/>
+                <input type="hidden"
+                       name="ServiceAnalytes-{{../arnum}}.title:records"
+                       value="{{title}}"/>
+                <input type="hidden"
+                       name="ServiceAnalytes-{{../arnum}}.keyword:records"
+                       value="{{keyword}}"/>
+                <input type="hidden"
+                       name="ServiceAnalytes-{{../arnum}}.selected:records"
+                       value="{{selected}}"/>
+                {{# if selected}}
+                <input type="checkbox"
+                       name="ServiceAnalytes-{{../arnum}}.value:records"
+                       checked="checked"/>
+                {{else}}
+                <input type="checkbox"
+                       name="ServiceAnalytes-{{../arnum}}.value:records"/>
+                {{/if}}
+              </td>
+            </tr>
+            {{/each}}
+          </table>
+        </div>
+      </script>
     </metal:block>
   </head>
 
@@ -571,6 +609,11 @@
                                                class python:'{}-conditions service-conditions'.format(service_uid);">
                           </div>
 
+                          <!-- Service analytes -->
+                          <div tal:attributes="id python:'{}-analytes'.format(service_uid);
+                                               class python:'{}-analytes service-analytes'.format(service_uid);">
+                          </div>
+
                         </td>
                       </tal:columns>
                     </tr>

src/bika/lims/browser/fields/aranalysesfield.py

@@ -31,6 +31,7 @@
 from bika.lims.interfaces import ISubmitted
 from senaite.core.permissions import AddAnalysis
 from bika.lims.utils.analysis import create_analysis
+from bika.lims.utils.analysis import create_analytes
 from Products.Archetypes.public import Field
 from Products.Archetypes.public import ObjectField
 from Products.Archetypes.Registry import registerField
@@ -277,6 +278,10 @@ def add_analysis(self, instance, service, **kwargs):
             analysis = create_analysis(instance, service)
             analyses.append(analysis)
 
+            # Create the analytes if multi-component analysis
+            analytes = create_analytes(analysis)
+            analyses.extend(analytes)
+
         for analysis in analyses:
             # Set the hidden status
             analysis.setHidden(hidden)
@@ -288,18 +293,17 @@ def add_analysis(self, instance, service, **kwargs):
             parent_sample = analysis.getRequest()
             analysis.setInternalUse(parent_sample.getInternalUse())
 
-            # Set the default result to the analysis
-            if not analysis.getResult() and default_result:
-                analysis.setResult(default_result)
-                analysis.setResultCaptureDate(None)
+            # Set default result, but only if not a multi-component
+            self.set_default_result(analysis, default_result)
 
             # Set the result range to the analysis
             analysis_rr = specs.get(service_uid) or analysis.getResultsRange()
             analysis.setResultsRange(analysis_rr)
 
             # Set default (pre)conditions
-            conditions = self.resolve_conditions(analysis)
-            analysis.setConditions(conditions)
+            if not analysis.isAnalyte():
+                conditions = self.resolve_conditions(analysis)
+                analysis.setConditions(conditions)
 
             analysis.reindexObject()
 
@@ -368,6 +372,31 @@ def resolve_analyses(self, instance, service):
 
         return analyses
 
+    def set_default_result(self, analysis, default_result):
+        """Sets the default result to the analysis w/o updating the results
+        capture date. It does nothing if the instance is a multi-component
+        analysis or if the analysis has a result already set
+        """
+        if not default_result:
+            return
+        if analysis.getResult():
+            return
+        if analysis.isMultiComponent():
+            return
+
+        # keep track of original capture date of the multi-component the
+        # analysis belongs to
+        multi = analysis.getMultiComponentAnalysis()
+        multi_capture = multi.getResultCaptureDate() if multi else None
+
+        # set the default result and reset capture date
+        analysis.setResult(default_result)
+        analysis.setResultCaptureDate(None)
+
+        # if multi, restore the original capture date
+        if multi:
+            multi.setResultCaptureDate(multi_capture)
+
     def get_analyses_from_descendants(self, instance):
         """Returns all the analyses from descendants
         """

src/bika/lims/browser/worksheet/views/add_analyses.py

@@ -66,6 +66,7 @@ def __init__(self, context, request):
         self.contentFilter = {
             "portal_type": "Analysis",
             "review_state": "unassigned",
+            "isAnalyte": False,
             "isSampleReceived": True,
             "sort_on": "getPrioritySortkey",
         }

src/bika/lims/browser/worksheet/views/analyses.py

@@ -240,6 +240,10 @@ def folderitem(self, obj, item, index):
         item_obj = api.get_object(obj)
         uid = item["uid"]
 
+        # Analytes are rendered like the rest, as a flat list
+        item["parent"] = ""
+        item["children"] = ""
+
         # Slot is the row position where all analyses sharing the same parent
         # (eg. AnalysisRequest, SampleReference), will be displayed as a group
         slot = self.get_item_slot(uid)