Fix conditions are not set when adding analyses manually via manage a…

…nalyses view (#1997)

* Add (pre)conditions when adding analysis from Manage analyses view

* Sort conditions to match with same order as defined in services

* Changelog

CHANGES.rst

@@ -4,6 +4,7 @@ Changelog
 2.2.0 (unreleased)
 ------------------
 
+- #1997 Fix conditions not set when adding analyses via "Manage Analyses" view
 - #1995 Dynamic assingment of "Owner" role for Client Contacts
 - #1994 Support for dynamic assignment of Local Roles for context and principal
 - #1992 Fix Generic Setup XML export/import adapters for Dexterity fields

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

@@ -381,7 +381,7 @@ def is_analysis_conditions_edition_allowed(self, analysis_brain):
             return False
 
         # Omit analysis does not have conditions set
-        if not obj.getConditions():
+        if not obj.getConditions(empties=True):
             return False
 
         return True

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

@@ -214,6 +214,35 @@ def resolve_uid(self, result_range):
         value["uid"] = uid
         return value
 
+    def resolve_conditions(self, analysis):
+        """Returns the conditions to be applied to this analysis by merging
+        those already set at sample level with defaults
+        """
+        service = analysis.getAnalysisService()
+        default_conditions = service.getConditions()
+
+        # Extract the conditions set for this analysis already
+        existing = analysis.getConditions()
+        existing_titles = [cond.get("title") for cond in existing]
+
+        def is_missing(condition):
+            return condition.get("title") not in existing_titles
+
+        # Add only those conditions that are missing
+        missing = filter(is_missing, default_conditions)
+
+        # Sort them to match with same order as in service
+        titles = [condition.get("title") for condition in default_conditions]
+
+        def index(condition):
+            cond_title = condition.get("title")
+            if cond_title in titles:
+                return titles.index(cond_title)
+            return len(titles)
+
+        conditions = existing + missing
+        return sorted(conditions, key=lambda con: index(con))
+
     def add_analysis(self, instance, service, **kwargs):
         service_uid = api.get_uid(service)
 
@@ -269,6 +298,11 @@ def add_analysis(self, instance, service, **kwargs):
             # 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)
+
             analysis.reindexObject()
 
     def generate_analysis_id(self, instance, service):

src/bika/lims/content/abstractroutineanalysis.py

@@ -449,19 +449,21 @@ def setInternalUse(self, internal_use):
         else:
             noLongerProvides(self, IInternalUse)
 
-    def getConditions(self):
+    def getConditions(self, empties=False):
         """Returns the conditions of this analysis. These conditions are usually
-        set on sample registration and are stored at sample level
+        set on sample registration and are stored at sample level. Do not return
+        conditions with empty value unless `empties` is True
         """
         sample = self.getRequest()
         service_uid = self.getRawAnalysisService()
 
         def is_valid(condition):
             uid = condition.get("uid")
             if api.is_uid(uid) and uid == service_uid:
+                if empties:
+                    return True
                 value = condition.get("value", None)
-                if value:
-                    return "title" in condition
+                return value not in [None, ""]
             return False
 
         conditions = sample.getServiceConditions()
@@ -483,4 +485,28 @@ def setConditions(self, conditions):
         # Keep the conditions from sample for analyses other than this one
         other_conditions = filter(lambda c: c.get("uid") != service_uid,
                                   sample_conditions)
+
+        def to_condition(condition):
+            # Type and title are required
+            title = condition.get("title")
+            cond_type = condition.get("type")
+            if not all([title, cond_type]):
+                return None
+
+            condition_info = {
+                "uid": service_uid,
+                "type": cond_type,
+                "title": title,
+                "description": "",
+                "choices": "",
+                "default": "",
+                "required": "",
+                "value": "",
+            }
+            condition = dict(condition)
+            condition_info.update(condition)
+            return condition_info
+
+        # Sanitize the conditions
+        conditions = filter(None, [to_condition(cond) for cond in conditions])
         sample.setServiceConditions(other_conditions + conditions)

src/senaite/core/browser/modals/analysis.py

@@ -69,7 +69,10 @@ def get_analysis_name(self):
         return api.get_title(analysis)
 
     def get_conditions(self):
-        conditions = self.get_analysis().getConditions()
+        """Returns the conditions to display in the form, those with empty or
+        non-set value included
+        """
+        conditions = self.get_analysis().getConditions(empties=True)
         conditions = copy.deepcopy(conditions)
         for condition in conditions:
             choices = condition.get("choices", "")

src/senaite/core/browser/modals/templates/set_analysis_conditions.pt

@@ -14,13 +14,10 @@
            tal:define="conditions python:view.get_conditions()"
            tal:condition="nocall:conditions">
         <div class="col-sm-12">
-          <h3>
+          <h3 class="mb-4">
             <i class="fas fa-list"/>
             <span i18n:translate="" tal:content="python:view.get_analysis_name()"/>
           </h3>
-          <h4>
-            <span i18n:translate="">Set analysis conditions</span>
-          </h4>
           <form name="set-analysis-conditions-form"
                 class="form"
                 method="POST"
@@ -32,7 +29,9 @@
                 <col style="width:20%"/>
               </colgroup>
               <tal:condition repeat="condition python:view.get_conditions()">
-                <tr tal:define="required python:condition.get('required') == 'on';">
+                <tr tal:define="required python:condition.get('required') == 'on';
+                                is_checkbox python:condition.get('type') == 'checkbox';
+                                required python:required and not is_checkbox;">
                   <td>
                     <label class="formQuestion">
                       <span tal:content="structure condition/title"/>
@@ -61,10 +60,16 @@
                            tal:attributes="value condition/required"/>
 
                     <select tal:condition="options"
+                            tal:define="value condition/value|nothing"
                             name="conditions.value:records">
-                      <option tal:condition="required"/>
-                      <option tal:repeat="option options"
-                              tal:content="option"/>
+                      <option tal:condition="not:required"/>
+                      <tal:option repeat="option options">
+                        <option tal:content="option"
+                                tal:condition="python:option == value"
+                                selected="selected"/>
+                        <option tal:content="option"
+                                tal:condition="python:option != value" />
+                      </tal:option>
                     </select>
 
                     <tal:non_select condition="not:options">
@@ -77,7 +82,6 @@
                       <input tal:attributes="type condition/type;
                                              value condition/value"
                              tal:condition="not:required"
-                             required="required"
                              name="conditions.value:records"/>
                     </tal:non_select>
 

src/senaite/core/upgrade/v02_02_000.py

@@ -82,6 +82,9 @@ def upgrade(tool):
     # Remove explicit owner role for contacts
     remove_contacts_ownership(portal)
 
+    # Fix analyses conditions
+    fix_analyses_conditions(portal)
+
     logger.info("{0} upgraded to version {1}".format(product, version))
     return True
 
@@ -280,3 +283,52 @@ def remove_owner_role(obj, usernames):
         remove_owner_role(client, usernames)
 
     logger.info("Removing Contacts explicit ownership [DONE]")
+
+
+def fix_analyses_conditions(portal):
+    """Fixes the analyses conditions
+    """
+    def to_condition(condition):
+        # UID, type and title are required
+        uid = condition.get("uid")
+        title = condition.get("title")
+        cond_type = condition.get("type")
+        if not all([api.is_uid(uid), title, cond_type]):
+            return None
+
+        condition_info = {
+            "uid": uid,
+            "title": title,
+            "type": cond_type,
+            "description": "",
+            "choices": "",
+            "default": "",
+            "required": "",
+            "value": "",
+        }
+        condition = dict(condition)
+        condition_info.update(condition)
+        return condition_info
+
+    logger.info("Reassign analyses conditions ...")
+    query = {
+        "portal_type": "Analysis",
+        "review_state": ["registered", "unassigned", "assigned",
+                         "to_be_verified"]
+    }
+    brains = api.search(query, ANALYSIS_CATALOG)
+    for brain in brains:
+        analysis = api.get_object(brain)
+        if not IRequestAnalysis.providedBy(analysis):
+            continue
+
+        sample = analysis.getRequest()
+        conditions = sample.getServiceConditions()
+        if not conditions:
+            continue
+
+        # Sanitize and reassign the conditions
+        conditions = filter(None, map(to_condition, conditions))
+        sample.setServiceConditions(conditions)
+
+    logger.info("Reassign analyses conditions [DONE]")