Merge pull request #788 from openhealthcare/new-pathology-database

New pathology database

elcid/settings.py

@@ -189,9 +189,9 @@
 # this needs to be set to true on prod
 ASYNC_API = False
 
-# if the intrahospital api is prod, we need
-# an ip address, a database, a username and a password for
-# the hospital db
+# if the intrahospital api is prod
+# there 2 databases
+# the hopstial DB does demographics, appointments and ITU
 HOSPITAL_DB = dict(
     ip_address=None,
     database=None,
@@ -200,6 +200,15 @@
     view=None
 )
 
+# the trust DB does lab tests
+TRUST_DB = dict(
+    ip_address=None,
+    database=None,
+    username=None,
+    password=None,
+    view=None
+)
+
 
 # search with external demographics when adding a patient
 ADD_PATIENT_DEMOGRAPHICS = True

intrahospital_api/apis/dev_api.py

@@ -74,6 +74,10 @@
     u'Patient_Class': u'NHS',
     u'Patient_ID_External': u'7060976728',
     u'Patient_Number': u'20552710',
+    'PV1_7_C_NUMBER': '',
+    'PV1_7_CONSULTANT_NAME': '',
+    'PV1_3_5': None,
+    'PV1_3_9': None,
     u'Relevant_Clinical_Info': u'testing',
     u'Reported_date': datetime(2015, 7, 18, 16, 26),
     u'Request_Date': datetime(2015, 7, 18, 16, 15),
@@ -90,6 +94,8 @@
     u'date_inserted': datetime(2015, 7, 18, 17, 0, 2, 240000),
     u'id': 5949264,
     u'last_updated': datetime(2015, 7, 18, 17, 0, 2, 240000),
+    'obr_id': 2000000,
+    'result_source': 'RF',
     u'visible': u'Y'
 }
 

intrahospital_api/apis/prod_api.py

@@ -20,21 +20,21 @@
 MAIN_DEMOGRAPHICS_VIEW = "VIEW_CRS_Patient_Masterfile"
 
 PATHOLOGY_DEMOGRAPHICS_QUERY = "SELECT top(1) * FROM {view} WHERE Patient_Number = \
-@hospital_number ORDER BY last_updated DESC;"
+@hospital_number ORDER BY date_inserted DESC;"
 
 MAIN_DEMOGRAPHICS_QUERY = "SELECT top(1) * FROM {view} WHERE Patient_Number = \
 @hospital_number ORDER BY last_updated DESC;"
 
 ALL_DATA_QUERY_FOR_HOSPITAL_NUMBER = "SELECT * FROM {view} WHERE Patient_Number = \
-@hospital_number AND last_updated > @since ORDER BY last_updated DESC;"
+@hospital_number AND date_inserted > @since ORDER BY date_inserted DESC;"
 
 ALL_DATA_QUERY_WITH_LAB_NUMBER = "SELECT * FROM {view} WHERE Patient_Number = \
-@hospital_number AND last_updated > @since and Result_ID = @lab_number ORDER BY last_updated DESC;"
+@hospital_number AND date_inserted > @since and Result_ID = @lab_number ORDER BY date_inserted DESC;"
 
 ALL_DATA_QUERY_WITH_LAB_TEST_TYPE = "SELECT * FROM {view} WHERE Patient_Number = \
-@hospital_number AND last_updated > @since and OBR_exam_code_Text = @test_type ORDER BY last_updated DESC;"
+@hospital_number AND date_inserted > @since and OBR_exam_code_Text = @test_type ORDER BY date_inserted DESC;"
 
-ALL_DATA_SINCE = "SELECT * FROM {view} WHERE last_updated > @since ORDER BY Patient_Number, last_updated DESC;"
+ALL_DATA_SINCE = "SELECT * FROM {view} WHERE date_inserted > @since ORDER BY Patient_Number, date_inserted DESC;"
 
 
 ETHNICITY_MAPPING = {
@@ -253,7 +253,7 @@ def get_status(self):
 
     def get_site(self):
         site = self.db_row.get('Specimen_Site')
-        if "^" in site and "-" in site:
+        if site and "^" in site and "-" in site:
             return site.split("^")[1].strip().split("-")[0].strip()
         return site
 
@@ -329,59 +329,89 @@ def get_all_fields(self):
 
 class ProdApi(base_api.BaseApi):
     def __init__(self):
-        self.ip_address = settings.HOSPITAL_DB.get("ip_address")
-        self.database = settings.HOSPITAL_DB.get("database")
-        self.username = settings.HOSPITAL_DB.get("username")
-        self.password = settings.HOSPITAL_DB.get("password")
-        self.view = settings.HOSPITAL_DB.get("view")
+        self.hospital_settings = settings.HOSPITAL_DB
+        self.trust_settings = settings.TRUST_DB
         if not all([
-            self.ip_address,
-            self.database,
-            self.username,
-            self.password,
-            self.view
+            self.hospital_settings.get("ip_address"),
+            self.hospital_settings.get("database"),
+            self.hospital_settings.get("username"),
+            self.hospital_settings.get("password"),
+            self.hospital_settings.get("view"),
+            self.trust_settings.get("ip_address"),
+            self.trust_settings.get("database"),
+            self.trust_settings.get("username"),
+            self.trust_settings.get("password"),
+            self.trust_settings.get("view"),
         ]):
             raise ValueError(
                 "You need to set proper credentials to use the prod api"
             )
 
-    def execute_query(self, query, params=None):
+    def execute_hospital_query(self, query, params=None):
+        result = []
+        with pytds.connect(
+            self.hospital_settings["ip_address"],
+            self.hospital_settings["database"],
+            self.hospital_settings["username"],
+            self.hospital_settings["password"],
+            as_dict=True
+        ) as conn:
+            with conn.cursor() as cur:
+                logger.info(
+                    "Running upstream query {} {}".format(query, params)
+                )
+                cur.execute(query, params)
+                result.extend(cur.fetchmany(1000))
+        logger.debug(result)
+        return result
+
+    def execute_trust_query(self, query, params=None):
+        result = []
         with pytds.connect(
-            self.ip_address,
-            self.database,
-            self.username,
-            self.password,
+            self.trust_settings["ip_address"],
+            self.trust_settings["database"],
+            self.trust_settings["username"],
+            self.trust_settings["password"],
             as_dict=True
         ) as conn:
             with conn.cursor() as cur:
                 logger.info(
                     "Running upstream query {} {}".format(query, params)
                 )
                 cur.execute(query, params)
-                result = cur.fetchall()
+                result.extend(cur.fetchmany(1000))
         logger.debug(result)
         return result
 
     @property
     def pathology_demographics_query(self):
-        return PATHOLOGY_DEMOGRAPHICS_QUERY.format(view=self.view)
+        return PATHOLOGY_DEMOGRAPHICS_QUERY.format(
+            view=self.trust_settings["view"]
+        )
 
     @property
     def all_data_for_hospital_number_query(self):
-        return ALL_DATA_QUERY_FOR_HOSPITAL_NUMBER.format(view=self.view)
+        return ALL_DATA_QUERY_FOR_HOSPITAL_NUMBER.format(
+            view=self.trust_settings["view"]
+        )
 
     @property
     def all_data_since_query(self):
-        return ALL_DATA_SINCE.format(view=self.view)
+        return ALL_DATA_SINCE.format(
+            view=self.trust_settings["view"]
+        )
 
     @property
     def all_data_query_for_lab_number(self):
-        return ALL_DATA_QUERY_WITH_LAB_NUMBER.format(view=self.view)
+        return ALL_DATA_QUERY_WITH_LAB_NUMBER.format(
+            view=self.trust_settings["view"]
+        )
 
     @property
     def all_data_query_for_lab_test_type(self):
-        return ALL_DATA_QUERY_WITH_LAB_TEST_TYPE.format(view=self.view)
-
+        return ALL_DATA_QUERY_WITH_LAB_TEST_TYPE.format(
+            view=self.trust_settings["view"]
+        )
 
     @property
     def main_demographics_query(self):
@@ -399,11 +429,10 @@ def demographics(self, hospital_number):
             demographics_result["external_system"] = EXTERNAL_SYSTEM
             return demographics_result
 
-
     @timing
     @db_retry
     def main_demographics(self, hospital_number):
-        rows = list(self.execute_query(
+        rows = list(self.execute_hospital_query(
             self.main_demographics_query,
             params=dict(hospital_number=hospital_number)
         ))
@@ -412,11 +441,10 @@ def main_demographics(self, hospital_number):
 
         return MainDemographicsRow(rows[0]).get_demographics_dict()
 
-
     @timing
     @db_retry
     def pathology_demographics(self, hospital_number):
-        rows = list(self.execute_query(
+        rows = list(self.execute_trust_query(
             self.pathology_demographics_query,
             params=dict(hospital_number=hospital_number)
         ))
@@ -431,7 +459,7 @@ def raw_data(self, hospital_number, lab_number=None, test_type=None):
         db_date = datetime.date.today() - datetime.timedelta(365)
 
         if lab_number:
-            return self.execute_query(
+            return self.execute_trust_query(
                 self.all_data_query_for_lab_number,
                 params=dict(
                     hospital_number=hospital_number,
@@ -440,7 +468,7 @@ def raw_data(self, hospital_number, lab_number=None, test_type=None):
                 )
             )
         if test_type:
-            return self.execute_query(
+            return self.execute_trust_query(
                 self.all_data_query_for_lab_test_type,
                 params=dict(
                     hospital_number=hospital_number,
@@ -449,15 +477,15 @@ def raw_data(self, hospital_number, lab_number=None, test_type=None):
                 )
             )
         else:
-            return self.execute_query(
+            return self.execute_trust_query(
                 self.all_data_for_hospital_number_query,
                 params=dict(hospital_number=hospital_number, since=db_date)
             )
 
     @timing
     @db_retry
     def data_delta_query(self, since):
-        all_rows = self.execute_query(
+        all_rows = self.execute_trust_query(
             self.all_data_since_query,
             params=dict(since=since)
         )