offers and alternate api that for the spark lines summary panel in th…

…e infection summary

elcid/assets/js/elcid/services/lab_test_summary_loader.js

@@ -2,7 +2,8 @@ angular.module('opal.services').factory('LabTestSummaryLoader', function($q, $ht
 
     "use strict";
 
-    var url = '/labtest/v0.1/lab_test_summary_api/';
+    // var url = '/labtest/v0.1/lab_test_summary_api/';
+    var url = '/api/v0.1/infection_test_summary/';
 
     var load = function(patientId){
       var deferred = $q.defer();

lab/api.py

@@ -0,0 +1,124 @@
+from collections import OrderedDict, defaultdict
+import itertools
+import re
+from django.conf import settings
+from opal.core.api import patient_from_pk, LoginRequiredViewset
+from opal.core.views import json_response
+from lab import models
+
+
+def clean_ref_range(ref_range):
+    return ref_range.replace("]", "").replace("[", "").strip()
+
+
+def extract_observation_value(observation_value):
+    """
+        if an observation is numeric, return it as a float
+        if its >12 return >12
+        else return None
+    """
+    regex = r'^[-0-9][0-9.]*$'
+    obs_result = observation_value.strip()
+    obs_result = obs_result.split("~")[0].strip("<").strip(">").strip()
+    if re.match(regex, obs_result):
+        return round(float(obs_result), 3)
+
+
+def is_empty_observation_value(self, observation_value):
+    """ we don't care about empty strings or
+        ' - ' or ' # '
+    """
+    if isinstance(observation_value, str):
+        return not observation_value.strip().strip("-").strip("#").strip()
+    else:
+        return observation_value is None
+
+
+def to_date_str(some_date):
+    if some_date:
+        return some_date[:10]
+
+
+def datetime_to_str(dt):
+    return dt.strftime(
+        settings.DATETIME_INPUT_FORMATS[0]
+    )
+
+
+class InfectionTestSummary(LoginRequiredViewset):
+    base_name = "infection_test_summary"
+    RELEVANT_TESTS = OrderedDict((
+        ("FULL BLOOD COUNT", ["WBC", "Lymphocytes", "Neutrophils"]),
+        ("C REACTIVE PROTEIN", ["C Reactive Protein"]),
+        ("LIVER PROFILE", [
+            "ALT", "AST", "Alkaline Phosphatase"
+        ]),
+    ),)
+
+    def get_queryset_for_obs(self, patient, test_name, obs_name):
+        """
+        Returns all observations for a patient/lab_test/observation
+        """
+        return models.Obs.objects.filter(
+            test__patient = patient
+        ).filter(
+            observation_name=obs_name
+        ).filter(
+            test__test_name=test_name
+        ).order_by("-test__datetime_ordered")
+
+    def get_observations(self, patient):
+        """
+        Looks at all the obs in relevant tests
+        it returns the latest 6 dates we have results for
+        """
+        dates_to_obs = defaultdict(list)
+
+        # get the latest 6 results for all observations
+        for test_name, obs_names in self.RELEVANT_TESTS.items():
+            for obs_name in obs_names:
+                qs = self.get_queryset_for_obs(
+                    patient, test_name, obs_name
+                )[:5]
+                for obs in qs:
+                    dates_to_obs[obs.test.datetime_ordered].append(obs)
+
+        # get the highest 6 results of all the observations
+        recent_dates = sorted(dates_to_obs.keys())
+        recent_dates = recent_dates[-5:]
+
+        # for each observation we want an array of 6 corresponding
+        # to the dates in recent dates, if there is no
+        # observation for the date it should be empty
+        obs_names = [i for i in itertools.chain(*self.RELEVANT_TESTS.values())]
+        latest_results = defaultdict(dict)
+
+        recent_dates_str = []
+
+        for recent_date in recent_dates:
+            recent_date_str = to_date_str(datetime_to_str(recent_date))
+            recent_dates_str.append(recent_date_str)
+            obs_name_to_obs = {o.observation_name: o for o in dates_to_obs[recent_date]}
+            for obs_name in obs_names:
+                obs = obs_name_to_obs.get(obs_name, None)
+
+                # get a rounded float version
+                if obs:
+                    obs_value = extract_observation_value(obs.observation_value)
+                    latest_results[obs_name][recent_date_str] = obs_value
+
+        obs_values = []
+        for obs_name in obs_names:
+            obs_values.append({
+                "name": obs_name,
+                "latest_results": latest_results[obs_name]
+            })
+        return {"obs_values": obs_values, "recent_dates": recent_dates_str}
+
+
+    @patient_from_pk
+    def retrieve(self, request, patient):
+        result = self.get_observations(patient)
+        return json_response(result)
+
+

lab/plugin.py

@@ -2,11 +2,15 @@
 Plugin definition for the lab OPAL plugin
 """
 from opal.core import plugins
-
 from lab.urls import urlpatterns
+from lab import api
 
 class LabPlugin(plugins.OpalPlugin):
     """
     Main entrypoint to expose this plugin to our OPAL application.
     """
     urls = urlpatterns
+
+    apis = [
+        ('infection_test_summary', api.InfectionTestSummary,),
+    ]