Selective reporting for extrapolated antibiotics

docs/changelog.rst

@@ -4,6 +4,7 @@ Changelog
 1.0.0 (unreleased)
 ------------------
 
+- #17 Selective reporting for extrapolated antibiotics
 - #15 Support for extrapolated antibiotics
 - #13 Allow addition of new antibiotics to submitted/verified AST analyses
 - #12 Negative values for diameter and zone size tests not permitted

src/senaite/ast/adapters/guards.py

@@ -92,8 +92,10 @@ def guard_submit(self):
         # Check that all interim fields have non-empty values
         keyword = self.context.getKeyword()
         for interim in self.context.getInterimFields():
-            if utils.is_interim_empty(interim):
-                return False
+
+            if utils.is_extrapolated_interim(interim):
+                # Skip extrapolated interims
+                continue
 
             if keyword in [ZONE_SIZE_KEY, DISK_CONTENT_KEY]:
                 # Negative values are not permitted

src/senaite/ast/browser/addpanel.py

@@ -24,9 +24,11 @@
 from senaite.ast import utils
 from senaite.ast.config import BREAKPOINTS_TABLE_KEY
 from senaite.ast.config import DISK_CONTENT_KEY
+from senaite.ast.config import REPORT_EXTRAPOLATED_KEY
+from senaite.ast.config import REPORT_KEY
 from senaite.ast.config import RESISTANCE_KEY
 from senaite.ast.config import ZONE_SIZE_KEY
-from senaite.ast.config import REPORT_KEY
+from senaite.ast.utils import get_extrapolated_antibiotics
 from senaite.ast.utils import update_breakpoint_tables_choices
 
 
@@ -49,6 +51,7 @@ def __call__(self):
         microorganisms = filter(lambda m: m in identified, microorganisms)
 
         # Create an analysis for each microorganism
+        add = self.add_ast_analysis
         for microorganism in microorganisms:
 
             # Create/Update the breakpoints table analysis
@@ -57,18 +60,24 @@ def __call__(self):
 
             # Create/Update the disk content (potency) analysis
             if panel.disk_content:
-                self.add_ast_analysis(DISK_CONTENT_KEY, microorganism, antibiotics)
+                add(DISK_CONTENT_KEY, microorganism, antibiotics)
 
             # Create/Update the zone size analysis
             if panel.zone_size:
-                self.add_ast_analysis(ZONE_SIZE_KEY, microorganism, antibiotics)
+                add(ZONE_SIZE_KEY, microorganism, antibiotics)
 
             # Create/Update the sensitivity result analysis
             self.add_ast_analysis(RESISTANCE_KEY, microorganism, antibiotics)
 
-            # Create/Update the selective reporting analysis
+            # Create/Update the selective reporting analyses
             if panel.selective_reporting:
-                self.add_ast_analysis(REPORT_KEY, microorganism, antibiotics)
+                add(REPORT_KEY, microorganism, antibiotics)
+
+                # If there are extrapolated antibiotics defined, add the
+                # analysis for selective reporting of extrapolated
+                extra = get_extrapolated_antibiotics(antibiotics, uids=True)
+                if extra:
+                    add(REPORT_EXTRAPOLATED_KEY, microorganism, antibiotics)
 
         return "{} objects affected".format(len(panel.microorganisms))
 

src/senaite/ast/browser/reporting.py

@@ -25,6 +25,7 @@
 from senaite.ast import messageFactory as _
 from senaite.ast import utils
 from senaite.ast.browser.panel import ASTPanelView
+from senaite.ast.config import REPORT_EXTRAPOLATED_KEY
 from senaite.ast.config import REPORT_KEY
 
 
@@ -138,6 +139,13 @@ def update_analyses(self, microorganism, antibiotics):
             rep_analyses = [utils.create_ast_analysis(self.context, REPORT_KEY,
                                                       microorganism, all_abx)]
 
+            # Create the selective reporting for extrapolated if required
+            extra = utils.get_extrapolated_antibiotics(all_abx, uids=True)
+            if extra:
+                utils.create_ast_analysis(self.context,
+                                          REPORT_EXTRAPOLATED_KEY,
+                                          microorganism, all_abx)
+
         # Reporting is true for the given antibiotics
         selected = map(lambda o: o.abbreviation, antibiotics)
         for analysis in rep_analyses:

src/senaite/ast/calc.py

@@ -18,12 +18,14 @@
 # Copyright 2020-2021 by it's authors.
 # Some rights reserved, see README and LICENSE.
 
+import json
 from bika.lims import api
 from bika.lims.interfaces import IAuditable
 from bika.lims.interfaces import ISubmitted
 from senaite.ast import utils
 from senaite.ast.config import BREAKPOINTS_TABLE_KEY
 from senaite.ast.config import DISK_CONTENT_KEY
+from senaite.ast.config import REPORT_EXTRAPOLATED_KEY
 from senaite.ast.config import REPORT_KEY
 from senaite.ast.config import RESISTANCE_KEY
 from senaite.ast.config import ZONE_SIZE_KEY
@@ -102,7 +104,10 @@ def calc_sensitivity_categories(analysis):
 
     # Update sensitivity categories
     for category in categories:
-        abx_uid = category["uid"]
+        # If extrapolated, assume same zone size as representative
+        abx_uid = category.get("primary")
+        if not api.is_uid(abx_uid):
+            abx_uid = category["uid"]
 
         # Get the zone size
         zone_size = zone_sizes.get(abx_uid)
@@ -161,7 +166,10 @@ def calc_disk_dosages(analysis):
     # Dosages are stored as interim fields
     disk_dosages = disk_dosages_analysis.getInterimFields()
     for dosage in disk_dosages:
-        abx_uid = dosage["uid"]
+        # If extrapolated, assume same zone size as representative
+        abx_uid = dosage.get("primary")
+        if not api.is_uid(abx_uid):
+            abx_uid = dosage["uid"]
 
         # Get the selected Breakpoints Table for this category
         breakpoints_uid = breakpoints.get(abx_uid)
@@ -181,14 +189,14 @@ def calc_disk_dosages(analysis):
 
 
 def update_extrapolated_antibiotics(analysis):
-    """Updates the sensitivity categories (R/I/S) and reporting option (Y/N) of
-    extrapolated antibiotics assigned to the analysis passed-in.
+    """Updates the sensitivity categories (R/I/S) of extrapolated antibiotics
+    assigned to the analysis passed-in.
 
     The sensitivity result (category) obtained for a particular antibiotic is
     extrapolated to extrapolated antibiotics
     """
-    keyword = analysis.getKeyword()
-    if keyword not in [BREAKPOINTS_TABLE_KEY, RESISTANCE_KEY, REPORT_KEY]:
+    keys = [BREAKPOINTS_TABLE_KEY, ZONE_SIZE_KEY, RESISTANCE_KEY, REPORT_KEY]
+    if analysis.getKeyword() not in keys:
         return
 
     def update_extrapolated(target):
@@ -210,6 +218,11 @@ def update_extrapolated(target):
     # Get the analysis (keyword: analysis) from same sample and microorganism
     analyses = utils.get_ast_group(analysis)
 
+    # Update the analysis that stores the zone diameter category
+    zone_diameter = analyses.get(ZONE_SIZE_KEY)
+    if zone_diameter:
+        update_extrapolated(zone_diameter)
+
     # Update the analysis that stores the sensitivity category
     sensitivity = analyses.get(RESISTANCE_KEY)
     if sensitivity:
@@ -261,7 +274,7 @@ def to_report(option):
 
     # Set the final result
     capture_date = sensitivity.getResultCaptureDate()
-    sensitivity.setResult(result)
+    sensitivity.setResult(json.dumps(result))
     sensitivity.setResultCaptureDate(capture_date)
 
     # Re-enable the audit for this analysis
@@ -279,19 +292,41 @@ def get_reportable_antibiotics(analysis):
     sensitivity = analyses.get(RESISTANCE_KEY)
     results = sensitivity.getInterimFields()
 
+    # The analysis "Report Extrapolated" is used to identify the antibiotics
+    # their sensitivity category has been extrapolated from representative
+    # antibiotics. Build a mapping with keys as the UIDs of the representatives
+    # and values as the UIDs of the extrapolated antibiotics to report
+    reportable = {}
+    extrapolated = analyses.get(REPORT_EXTRAPOLATED_KEY)
+    if extrapolated:
+        for interim in extrapolated.getInterimFields():
+            try:
+                selected = json.loads(interim.get("value", "[]"))
+            except:
+                selected = []
+            reportable[interim.get("uid")] = selected
+
+    def is_reportable(interim):
+        primary = interim.get("primary", None)
+        if primary:
+            # Check if the primary is reportable
+            uid = interim.get("uid")
+            return uid in reportable.get(primary)
+        return interim.get("value") == "1"
+
     # The analysis "Report" is used to identify the results from the sensitivity
     # category analysis that need to be reported
     report = analyses.get(REPORT_KEY)
     if report:
         # The results to be reported are defined by the Y/N values
         # XXX senaite.app.listing has no support boolean type for interim fields
         report_values = report.getInterimFields()
-        to_report = filter(lambda k: k.get("value") == "1", report_values)
+        to_report = filter(is_reportable, report_values)
 
-        # Get the abbreviation of microorganisms (keyword)
-        microorganisms = map(lambda k: k.get("keyword"), to_report)
+        # Get the abbreviation of antibiotics (keyword)
+        antibiotics = map(lambda k: k.get("keyword"), to_report)
 
         # Bail out (Sensitivity) "Category" results to not report
-        results = filter(lambda r: r.get("keyword") in microorganisms, results)
+        results = filter(lambda r: r.get("keyword") in antibiotics, results)
 
     return results

src/senaite/ast/config.py

@@ -63,6 +63,10 @@
 # is not present, the system assign all microorganisms from the panel
 IDENTIFICATION_KEY = "senaite_ast_identification"
 
+# Keyword of the Analysis Service used to choose the extrapolated antibiotics
+# to be reported in results report
+REPORT_EXTRAPOLATED_KEY = "senaite_ast_report_extrapolated"
+
 # Title for the AST calculation object. This calculation allows AST machinery
 # to assign a final result by its own, without prompting the user
 AST_CALCULATION_TITLE = "senaite_ast_calc"
@@ -84,6 +88,9 @@
               u"(Susceptible, increased exposure) and R (Resistant)"),
         "choices": "0:|1:S|2:I|3:R",
         "sort_key": 530,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
     },
 
     BREAKPOINTS_TABLE_KEY: {
@@ -96,6 +103,9 @@
         # XXX This is a choices field, but choices are populated on creation
         "choices": "",
         "sort_key": 505,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
     },
 
     DISK_CONTENT_KEY: {
@@ -108,12 +118,18 @@
               u"charge."),
         "size": "1",
         "sort_key": 510,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
     },
 
     ZONE_SIZE_KEY: {
         "title": "{} - " + _(u"Zone diameter (mm)"),
         "size": "1",
         "sort_key": 520,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
     },
 
     REPORT_KEY: {
@@ -122,11 +138,35 @@
         # XXX senaite.app.listing has no support for boolean types (interim)
         "type": "boolean",
         "sort_key": 540,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
+    },
+
+    REPORT_EXTRAPOLATED_KEY: {
+        "title": "{} - " + _(u"Report extrapolated"),
+        "description":
+            _(u"Selection of the antibiotics to be included in results report "
+              u"that their sensitivity is extrapolated from antibiotic "
+              u"representatives"),
+        # XXX This is a choices field, but choices are populated on creation
+        "choices": "",
+        "type": "multichoice",
+        "sort_key": 550,
+        "string_result": True,
+        "point_of_capture": AST_POINT_OF_CAPTURE,
+        "calculation": AST_CALCULATION_TITLE,
     },
 
     IDENTIFICATION_KEY: {
         "title": _(u"Microorganism identification"),
         "sort_key": 500,
+        # The options are the list of microorganisms and are automatically
+        # added when the corresponding analysis is initialized
+        "options_type": "multiselect",
+        "string_result": False,
+        "point_of_capture": "lab",
+        "calculation": None,
     }
 
 }

src/senaite/ast/setuphandlers.py

@@ -172,11 +172,6 @@ def setup_ast_services(portal):
         categories = setup.bika_analysiscategories.objectValues()
         category = filter(lambda c: api.get_title(c) == cat_name, categories)[0]
 
-        # Get the calculation
-        calc_name = AST_CALCULATION_TITLE
-        calcs = setup.bika_calculations.objectValues()
-        calc = filter(lambda c: api.get_title(c) == calc_name, calcs)[0]
-
         title = settings["title"]
         if "{}" in title:
             title = title.format(_("Antibiotic Sensitivity"))
@@ -190,20 +185,25 @@ def setup_ast_services(portal):
             service = api.create(folder, "AnalysisService", Category=category,
                                  title=title, Keyword=key)
 
+        description = settings.get("description", AUTOGENERATED)
+        sort_key = settings.get("sort_key", 1000)
+        options_type = settings.get("options_type", "select")
+        string_result = settings.get("string_result", False)
+        poc = settings.get("point_of_capture", AST_POINT_OF_CAPTURE)
+        calc_name = settings.get("calculation", AST_CALCULATION_TITLE)
+
         service.setKeyword(key)
         service.setTitle(title)
-        description = settings.get("description", AUTOGENERATED)
         service.setDescription(description)
-        service.setSortKey(settings["sort_key"])
-        if key == IDENTIFICATION_KEY:
-            # This is the lab analysis for the identification of microorganisms
-            # The options are the list of microorganisms and are automatically
-            # added when the corresponding analysis is initialized
-            service.setResultOptionsType("multiselect")
-        else:
-            # These are "ast" analyses
-            service.setStringResult(True)
-            service.setPointOfCapture(AST_POINT_OF_CAPTURE)
+        service.setSortKey(sort_key)
+        service.setResultOptionsType(options_type)
+        service.setStringResult(string_result)
+        service.setPointOfCapture(poc)
+
+        # Get the calculation
+        if calc_name:
+            calcs = setup.bika_calculations.objectValues()
+            calc = filter(lambda c: api.get_title(c) == calc_name, calcs)[0]
             service.setCalculation(calc)
 
         # Do not allow the modification of this service