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Processing HL7 Records

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Processing HL7 Records

Learn how to ingest and convert HL7 records to usable Apache Hive tables for SQL queries, machine learning, and analysis in your Hadoop data lake.

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Dec. 08, 17 · Big Data Zone ·
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Let's explore a step-by-step method for ingesting and converting HL7 records to usable Apache Hive tables for SQL queries, machine learning, and analysis in your Hadoop data lake.

Step 1

Collect HL7 health records.

Get Python to send JSON data to MQTT (data generated by Mockaroo):

import paho.mqtt.client as mqtt    
import json    
# MQTT    
client = mqtt.Client()    
client.connect("localhost", 14162, 60)    
row = [{"PID_SSNNumberPatient":823456789,"email":"ahospital0@census.gov","gender":"Male","ip_address":"138.135.180.206","drug_provider":"OrchidPharma Inc","icd9":"94140","icd9_description":"Deep necrosis of underlying tissues [deep third degree] without mention of loss of a body part, face and head, unspecified site","icd9P_proc":"7942","icd9_proc_description":"Closed reduction of separated epiphysis, radius and ulna","user_agent":"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_5_8) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.801.0 Safari/535.1","drug_used":"Naratriptan"}]    
json_string = json.dumps(row)    
client.publish("patientdata",payload=json_string,qos=1,retain=False)    
client.disconnect()

Step 2

Get to Apache NiFi via FTP, sFTP, File, Apache Kafka, MQTT, REST API, TCP/IP, or any other preferred option.

Schema:

{
  "type": "record",
  "name": "hl7oru",
  "fields": [
    {
      "name": "OBX_1_UserDefinedAccessChecks",
      "type": "string",
      "doc": "Type inferred from '\"20150101000100\"'"
    },
    {
      "name": "OBR_1_OrderingProvider_FamilyName",
      "type": "string",
      "doc": "Type inferred from '\"Johnson\"'"
    },
    {
      "name": "MSH_MessageControlID",
      "type": "string",
      "doc": "Type inferred from '\"Q1111111111111111111\"'"
    },
    {
      "name": "OBX_1_ObservationIdentifier_Text",
      "type": "string",
      "doc": "Type inferred from '\"Glucose Lvl\"'"
    },
    {
      "name": "MSH_SendingApplication_NamespaceID",
      "type": "string",
      "doc": "Type inferred from '\"XXXXXX\"'"
    },
    {
      "name": "OBR_1_UniversalServiceIdentifier_Text",
      "type": "string",
      "doc": "Type inferred from '\"Basic Metabolic Panel\"'"
    },
    {
      "name": "MSH_ReceivingApplication_NamespaceID",
      "type": "string",
      "doc": "Type inferred from '\"HealthOrg01\"'"
    },
    {
      "name": "MSH_ProcessingID_ProcessingID",
      "type": "string",
      "doc": "Type inferred from '\"P\"'"
    },
    {
      "name": "PID_SSNNumberPatient",
      "type": "string",
      "doc": "Type inferred from '\"123456789\"'"
    },
    {
      "name": "OBR_1_FillerOrderNumber_EntityIdentifier",
      "type": "string",
      "doc": "Type inferred from '\"000000000000000000\"'"
    },
    {
      "name": "PID_PatientAccountNumber_ID",
      "type": "string",
      "doc": "Type inferred from '\"999999999999\"'"
    },
    {
      "name": "PID_DateOfBirth",
      "type": "string",
      "doc": "Type inferred from '\"19700101\"'"
    },
    {
      "name": "PD1_PatientPrimaryCareProviderNameIDNo_IDNumber",
      "type": "string",
      "doc": "Type inferred from '\"1234567890\"'"
    },
    {
      "name": "PID_Sex",
      "type": "string",
      "doc": "Type inferred from '\"M\"'"
    },
    {
      "name": "MSH_MessageType_MessageType",
      "type": "string",
      "doc": "Type inferred from '\"ORU\"'"
    },
    {
      "name": "OBX_1_ReferencesRange",
      "type": "string",
      "doc": "Type inferred from '\"H\"'"
    },
    {
      "name": "OBR_1_OrderingProvider_IDNumber",
      "type": "string",
      "doc": "Type inferred from '\"1620\"'"
    },
    {
      "name": "PD1_PatientPrimaryCareProviderNameIDNo_FamilyName",
      "type": "string",
      "doc": "Type inferred from '\"LAST\"'"
    },
    {
      "name": "OBX_1_Units_NameOfCodingSystem",
      "type": "string",
      "doc": "Type inferred from '\"99\"'"
    },
    {
      "name": "OBX_1_Units_Identifier",
      "type": "string",
      "doc": "Type inferred from '\"65-99\"'"
    },
    {
      "name": "PID_PatientName_GivenName",
      "type": "string",
      "doc": "Type inferred from '\"JOHN\"'"
    },
    {
      "name": "OBX_1_ObservationSubID",
      "type": "string",
      "doc": "Type inferred from '\"159\"'"
    },
    {
      "name": "PD1_PatientPrimaryCareProviderNameIDNo_GivenName",
      "type": "string",
      "doc": "Type inferred from '\"FIRST\"'"
    },
    {
      "name": "OBR_1_PlacerOrderNumber_NamespaceID",
      "type": "string",
      "doc": "Type inferred from '\"HNAM_ORDERID\"'"
    },
    {
      "name": "MSH_MessageType_TriggerEvent",
      "type": "string",
      "doc": "Type inferred from '\"R01\"'"
    },
    {
      "name": "PD1_PatientPrimaryCareProviderNameIDNo_AssigningAuthority",
      "type": "string",
      "doc": "Type inferred from '\"NPI\"'"
    },
    {
      "name": "OBR_1_ResultStatus",
      "type": "string",
      "doc": "Type inferred from '\"M\"'"
    },
    {
      "name": "PID_PatientName_FamilyName",
      "type": "string",
      "doc": "Type inferred from '\"SMITH\"'"
    },
    {
      "name": "MSH_EncodingCharacters",
      "type": "string",
      "doc": "Type inferred from '\"^~\\\\&\"'"
    },
    {
      "name": "MSH_VersionID",
      "type": "string",
      "doc": "Type inferred from '\"2.3\"'"
    },
    {
      "name": "OBR_1_UniversalServiceIdentifier_Identifier",
      "type": "string",
      "doc": "Type inferred from '\"648088\"'"
    },
    {
      "name": "OBR_1_ObservationDateTime",
      "type": "string",
      "doc": "Type inferred from '\"20150101000100\"'"
    },
    {
      "name": "OBR_1_ScheduledDateTime",
      "type": "string",
      "doc": "Type inferred from '\"20150101000100\"'"
    },
    {
      "name": "OBX_1_ObservationIdentifier_Identifier",
      "type": "string",
      "doc": "Type inferred from '\"GLU\"'"
    },
    {
      "name": "OBR_1_OrderingProvider_GivenName",
      "type": "string",
      "doc": "Type inferred from '\"John\"'"
    },
    {
      "name": "OBR_1_SetIDObservationRequest",
      "type": "string",
      "doc": "Type inferred from '\"1\"'"
    },
    {
      "name": "OBR_1_ResultsRptStatusChngDateTime",
      "type": "string",
      "doc": "Type inferred from '\"20150101000100\"'"
    },
    {
      "name": "OBR_1_PlacerOrderNumber_EntityIdentifier",
      "type": "string",
      "doc": "Type inferred from '\"341856649\"'"
    },
    {
      "name": "OBX_1_NatureOfAbnormalTest",
      "type": "string",
      "doc": "Type inferred from '\"F\"'"
    },
    {
      "name": "OBX_1_SetIDOBX",
      "type": "string",
      "doc": "Type inferred from '\"1\"'"
    },
    {
      "name": "MSH_FieldSeparator",
      "type": "string",
      "doc": "Type inferred from '\"|\"'"
    },
    {
      "name": "PD1",
      "type": {
        "type": "record",
        "name": "PD1",
        "fields": [
          {
            "name": "PatientPrimaryCareProviderNameIDNo_MiddleInitialOrName",
            "type": "string",
            "doc": "Type inferred from '\"M\"'"
          }
        ]
      },
      "doc": "Type inferred from '{\"PatientPrimaryCareProviderNameIDNo_MiddleInitialOrName\":\"M\"}'"
    },
    {
      "name": "OBX_1_Units_Text",
      "type": "string",
      "doc": "Type inferred from '\"65\"'"
    },
    {
      "name": "OBX_1_ValueType",
      "type": "string",
      "doc": "Type inferred from '\"NM\"'"
    },
    {
      "name": "PID_PatientIDInternalID_ID",
      "type": "string",
      "doc": "Type inferred from '\"000000001\"'"
    },
    {
      "name": "OBX_1_ObservationValue",
      "type": "string",
      "doc": "Type inferred from '\"mg/dL\"'"
    },
    {
      "name": "OBR_1_OrderingProvider_MiddleInitialOrName",
      "type": "string",
      "doc": "Type inferred from '\"R\"'"
    }
  ]
}

Jolt Scripts

{  
   "OBX_1.UserDefinedAccessChecks":"OBX_1_UserDefinedAccessChecks",
   "OBR_1.OrderingProvider.FamilyName":"OBR_1_OrderingProvider_FamilyName",
   "MSH.MessageControlID":"MSH_MessageControlID",
   "OBX_1.ObservationIdentifier.Text":"OBX_1_ObservationIdentifier_Text",
   "MSH.SendingApplication.NamespaceID":"MSH_SendingApplication_NamespaceID",
   "OBR_1.UniversalServiceIdentifier.Text":"OBR_1_UniversalServiceIdentifier_Text",
   "MSH.ReceivingApplication.NamespaceID":"MSH_ReceivingApplication_NamespaceID",
   "MSH.ProcessingID.ProcessingID":"MSH_ProcessingID_ProcessingID",
   "PID.SSNNumberPatient":"PID_SSNNumberPatient",
   "OBR_1.FillerOrderNumber.EntityIdentifier":"OBR_1_FillerOrderNumber_EntityIdentifier",
   "PID.PatientAccountNumber.ID":"PID_PatientAccountNumber_ID",
   "PID.DateOfBirth":"PID_DateOfBirth",
   "PD1.PatientPrimaryCareProviderNameIDNo.IDNumber":"PD1_PatientPrimaryCareProviderNameIDNo_IDNumber",
   "PID.Sex":"PID_Sex",
   "MSH.MessageType.MessageType":"MSH_MessageType_MessageType",
   "OBX_1.ReferencesRange":"OBX_1_ReferencesRange",
   "OBR_1.OrderingProvider.IDNumber":"OBR_1_OrderingProvider_IDNumber",
   "PD1.PatientPrimaryCareProviderNameIDNo.FamilyName":"PD1_PatientPrimaryCareProviderNameIDNo_FamilyName",
   "OBX_1.Units.NameOfCodingSystem":"OBX_1_Units_NameOfCodingSystem",
   "OBX_1.Units.Identifier":"OBX_1_Units_Identifier",
   "PID.PatientName.GivenName":"PID_PatientName_GivenName",
   "OBX_1.ObservationSubID":"OBX_1_ObservationSubID",
   "PD1.PatientPrimaryCareProviderNameIDNo.GivenName":"PD1_PatientPrimaryCareProviderNameIDNo_GivenName",
   "OBR_1.PlacerOrderNumber.NamespaceID":"OBR_1_PlacerOrderNumber_NamespaceID",
   "MSH.MessageType.TriggerEvent":"MSH_MessageType_TriggerEvent",
   "PD1.PatientPrimaryCareProviderNameIDNo.AssigningAuthority":"PD1_PatientPrimaryCareProviderNameIDNo_AssigningAuthority",
   "OBR_1.ResultStatus":"OBR_1_ResultStatus",
   "PID.PatientName.FamilyName":"PID_PatientName_FamilyName",
   "MSH.EncodingCharacters":"MSH_EncodingCharacters",
   "MSH.VersionID":"MSH_VersionID",
   "OBR_1.UniversalServiceIdentifier.Identifier":"OBR_1_UniversalServiceIdentifier_Identifier",
   "OBR_1.ObservationDateTime":"OBR_1_ObservationDateTime",
   "OBR_1.ScheduledDateTime":"OBR_1_ScheduledDateTime",
   "OBX_1.ObservationIdentifier.Identifier":"OBX_1_ObservationIdentifier_Identifier",
   "OBR_1.OrderingProvider.GivenName":"OBR_1_OrderingProvider_GivenName",
   "OBR_1.SetIDObservationRequest":"OBR_1_SetIDObservationRequest",
   "OBR_1.ResultsRptStatusChngDateTime":"OBR_1_ResultsRptStatusChngDateTime",
   "OBR_1.PlacerOrderNumber.EntityIdentifier":"OBR_1_PlacerOrderNumber_EntityIdentifier",
   "OBX_1.NatureOfAbnormalTest":"OBX_1_NatureOfAbnormalTest",
   "OBX_1.SetIDOBX":"OBX_1_SetIDOBX",
   "MSH.FieldSeparator":"MSH_FieldSeparator",
   "PD1.PatientPrimaryCareProviderNameIDNo.MiddleInitialOrName":"PD1_PatientPrimaryCareProviderNameIDNo_MiddleInitialOrName",
   "OBX_1.Units.Text":"OBX_1_Units_Text",
   "OBX_1.ValueType":"OBX_1_ValueType",
   "PID.PatientIDInternalID.ID":"PID_PatientIDInternalID_ID",
   "OBX_1.ObservationValue":"OBX_1_ObservationValue",
   "OBR_1.OrderingProvider.MiddleInitialOrName":"OBR_1_OrderingProvider_MiddleInitialOrName"
}{  
   "OBX_1.UserDefinedAccessChecks":"OBX_1.UserDefinedAccessChecks",
   "OBR_1.OrderingProvider.FamilyName":"OBR_1.OrderingProvider.FamilyName",
   "MSH.MessageControlID":"MSH.MessageControlID",
   "OBX_1.ObservationIdentifier.Text":"OBX_1.ObservationIdentifier.Text",
   "MSH.SendingApplication.NamespaceID":"MSH.SendingApplication.NamespaceID",
   "OBR_1.UniversalServiceIdentifier.Text":"OBR_1.UniversalServiceIdentifier.Text",
   "MSH.ReceivingApplication.NamespaceID":"MSH.ReceivingApplication.NamespaceID",
   "MSH.ProcessingID.ProcessingID":"MSH.ProcessingID.ProcessingID",
   "PID.SSNNumberPatient":"PID.SSNNumberPatient",
   "OBR_1.FillerOrderNumber.EntityIdentifier":"OBR_1.FillerOrderNumber.EntityIdentifier",
   "PID.PatientAccountNumber.ID":"PID.PatientAccountNumber.ID",
   "PID.DateOfBirth":"PID.DateOfBirth",
   "PD1.PatientPrimaryCareProviderNameIDNo.IDNumber":"PD1.PatientPrimaryCareProviderNameIDNo.IDNumber",
   "PID.Sex":"PID.Sex",
   "MSH.MessageType.MessageType":"MSH.MessageType.MessageType",
   "OBX_1.ReferencesRange":"OBX_1.ReferencesRange",
   "OBR_1.OrderingProvider.IDNumber":"OBR_1.OrderingProvider.IDNumber",
   "PD1.PatientPrimaryCareProviderNameIDNo.FamilyName":"PD1.PatientPrimaryCareProviderNameIDNo.FamilyName",
   "OBX_1.Units.NameOfCodingSystem":"OBX_1.Units.NameOfCodingSystem",
   "OBX_1.Units.Identifier":"OBX_1.Units.Identifier",
   "PID.PatientName.GivenName":"PID.PatientName.GivenName",
   "OBX_1.ObservationSubID":"OBX_1.ObservationSubID",
   "PD1.PatientPrimaryCareProviderNameIDNo.GivenName":"PD1.PatientPrimaryCareProviderNameIDNo.GivenName",
   "OBR_1.PlacerOrderNumber.NamespaceID":"OBR_1.PlacerOrderNumber.NamespaceID",
   "MSH.MessageType.TriggerEvent":"MSH.MessageType.TriggerEvent",
   "PD1.PatientPrimaryCareProviderNameIDNo.AssigningAuthority":"PD1.PatientPrimaryCareProviderNameIDNo.AssigningAuthority",
   "OBR_1.ResultStatus":"OBR_1.ResultStatus",
   "PID.PatientName.FamilyName":"PID.PatientName.FamilyName",
   "MSH.EncodingCharacters":"MSH.EncodingCharacters",
   "MSH.VersionID":"MSH.VersionID",
   "OBR_1.UniversalServiceIdentifier.Identifier":"OBR_1.UniversalServiceIdentifier.Identifier",
   "OBR_1.ObservationDateTime":"OBR_1.ObservationDateTime",
   "OBR_1.ScheduledDateTime":"OBR_1.ScheduledDateTime",
   "OBX_1.ObservationIdentifier.Identifier":"OBX_1.ObservationIdentifier.Identifier",
   "OBR_1.OrderingProvider.GivenName":"OBR_1.OrderingProvider.GivenName",
   "OBR_1.SetIDObservationRequest":"OBR_1.SetIDObservationRequest",
   "OBR_1.ResultsRptStatusChngDateTime":"OBR_1.ResultsRptStatusChngDateTime",
   "OBR_1.PlacerOrderNumber.EntityIdentifier":"OBR_1.PlacerOrderNumber.EntityIdentifier",
   "OBX_1.NatureOfAbnormalTest":"OBX_1.NatureOfAbnormalTest",
   "OBX_1.SetIDOBX":"OBX_1.SetIDOBX",
   "MSH.FieldSeparator":"MSH.FieldSeparator",
   "PD1.PatientPrimaryCareProviderNameIDNo.MiddleInitialOrName":"PD1.PatientPrimaryCareProviderNameIDNo.MiddleInitialOrName",
   "OBX_1.Units.Text":"OBX_1.Units.Text",
   "OBX_1.ValueType":"OBX_1.ValueType",
   "PID.PatientIDInternalID.ID":"PID.PatientIDInternalID.ID",
   "OBX_1.ObservationValue":"OBX_1.ObservationValue",
   "OBR_1.OrderingProvider.MiddleInitialOrName":"OBR_1.OrderingProvider.MiddleInitialOrName"
}

The following images depict the results:

Step 3

Profit! Let's build a big data environment for our data.

Build HDFS directories:

su hdfs     
hdfs dfs -mkdir -p /hl7/hl7-mdm    
hdfs dfs -mkdir -p /hl7/hl7-adt   
hdfs dfs -mkdir -p /hl7/hl7-orm    
hdfs dfs -mkdir -p /hl7/hl7-oru    
hdfs dfs -mkdir -p /hl7/json/hl7-mdm    
hdfs dfs -mkdir -p /hl7/json/hl7-adt    
hdfs dfs -mkdir -p /hl7/json/hl7-orm    
hdfs dfs -mkdir -p /hl7/json/hl7-oru    
hdfs dfs -mkdir -p /hl7/flat/oru    
hdfs dfs -mkdir -p /patientdata    
hdfs dfs -chmod -R 777 /hl7    
hdfs dfs -chmod -R 777 /patientdata   
hdfs dfs -ls -R /hl7   
hdfs dfs -ls -R /patientdata

Build Hive DDL:

CREATE EXTERNAL TABLE IF NOT EXISTS patientdata 
(PID_SSNNumberPatient INT, email STRING, gender STRING, ip_address STRING,   
 drug_provider STRING, icd9 STRING, icd9_description STRING,
 icd9P_proc STRING, icd9_proc_description STRING, user_agent STRING,
 drug_used STRING)     STORED AS ORC LOCATION '/patientdata'    

 CREATE EXTERNAL TABLE IF NOT EXISTS hl7oru    
 (OBX_1 STRUCT<UserDefinedAccessChecks:STRING, 
  ObservationIdentifier:STRUCT<Text:STRING,    
  Identifier:STRING>,     ReferencesRange:STRING,  
  Units:STRUCT<NameOfCodingSystem:STRING,     Identifier:STRING,     
  Text:STRING>,     ObservationSubID:STRING,   
  NatureOfAbnormalTest:STRING,     SetIDOBX:STRING,   
  ValueType:STRING,     ObservationValue:STRING>,    
  OBR_1 STRUCT<OrderingProvider:STRUCT<FamilyName:STRING,   
  IDNumber:STRING,     GivenName:STRING,     MiddleInitialOrName:STRING>,   
  UniversalServiceIdentifier:STRUCT<Text:STRING,    
  Identifier:STRING>,   
  FillerOrderNumber:STRUCT<EntityIdentifier:STRING>,    
  PlacerOrderNumber:STRUCT<NamespaceID:STRING,     
  EntityIdentifier:STRING>,     ResultStatus:STRING,    
  ObservationDateTime:STRING,     ScheduledDateTime:STRING,     SetIDObservationRequest:STRING,     ResultsRptStatusChngDateTime:STRING>,     MSH STRUCT<MessageControlID:STRING,     SendingApplication:STRUCT<NamespaceID:STRING>,     ReceivingApplication:STRUCT<NamespaceID:STRING>,     ProcessingID:STRUCT<ProcessingID:STRING>,     MessageType:STRUCT<MessageType:STRING,     TriggerEvent:STRING>,     EncodingCharacters:STRING,     VersionID:STRING,     FieldSeparator:STRING>,     PID STRUCT<SSNNumberPatient:STRING,     PatientAccountNumber:STRUCT<ID:STRING>,     DateOfBirth:STRING,     Sex:STRING,     PatientName:STRUCT<GivenName:STRING,     FamilyName:STRING>,     PatientIDInternalID:STRUCT<ID:STRING>>,     PD1 STRUCT<PatientPrimaryCareProviderNameIDNo:STRUCT<IDNumber:STRING,     FamilyName:STRING,     GivenName:STRING,     AssigningAuthority:STRING,     MiddleInitialOrName:STRING>>)      STORED AS ORC    LOCATION '/hl7/hl7-oru'    CREATE EXTERNAL TABLE IF NOT EXISTS hl7_oru_flat     (OBX_1_UserDefinedAccessChecks STRING,     OBR_1_OrderingProvider_FamilyName STRING,     MSH_MessageControlID STRING,     OBX_1_ObservationIdentifier_Text STRING,     MSH_SendingApplication_NamespaceID STRING,     OBR_1_UniversalServiceIdentifier_Text STRING,     MSH_ReceivingApplication_NamespaceID STRING,     MSH_ProcessingID_ProcessingID STRING,     PID_SSNNumberPatient STRING,     OBR_1_FillerOrderNumber_EntityIdentifier STRING,     PID_PatientAccountNumber_ID STRING,     PID_DateOfBirth STRING,     PD1_PatientPrimaryCareProviderNameIDNo_IDNumber STRING,     PID_Sex STRING,     MSH_MessageType_MessageType STRING,     OBX_1_ReferencesRange STRING,     OBR_1_OrderingProvider_IDNumber STRING,     PD1_PatientPrimaryCareProviderNameIDNo_FamilyName STRING,     OBX_1_Units_NameOfCodingSystem STRING,     OBX_1_Units_Identifier STRING,     PID_PatientName_GivenName STRING,     OBX_1_ObservationSubID STRING,     PD1_PatientPrimaryCareProviderNameIDNo_GivenName STRING,     OBR_1_PlacerOrderNumber_NamespaceID STRING,     MSH_MessageType_TriggerEvent STRING,     PD1_PatientPrimaryCareProviderNameIDNo_AssigningAuthority STRING,     OBR_1_ResultStatus STRING,     PID_PatientName_FamilyName STRING,     MSH_EncodingCharacters STRING,     MSH_VersionID STRING,     OBR_1_UniversalServiceIdentifier_Identifier STRING,     OBR_1_ObservationDateTime STRING,     OBR_1_ScheduledDateTime STRING,     OBX_1_ObservationIdentifier_Identifier STRING,     OBR_1_OrderingProvider_GivenName STRING,     OBR_1_SetIDObservationRequest STRING,     OBR_1_ResultsRptStatusChngDateTime STRING,     OBR_1_PlacerOrderNumber_EntityIdentifier STRING,     OBX_1_NatureOfAbnormalTest STRING,     OBX_1_SetIDOBX STRING,     MSH_FieldSeparator STRING,     PD1_PatientPrimaryCareProviderNameIDNo_MiddleInitialOrName STRING,     OBX_1_Units_Text STRING,     OBX_1_ValueType STRING,     PID_PatientIDInternalID_ID STRING,     OBX_1_ObservationValue STRING,     OBR_1_OrderingProvider_MiddleInitialOrName STRING)     STORED AS ORC    LOCATION '/hl7/flat/oru'    CREATE EXTERNAL TABLE IF NOT EXISTS patientdata (PID_SSNNumberPatient INT, email STRING, gender STRING, ip_address STRING,     drug_provider STRING, icd9 STRING, icd9_description STRING, icd9P_proc STRING, icd9_proc_description STRING, user_agent STRING, drug_used STRING)     STORED AS ORC LOCATION '/patientdata'    CREATE EXTERNAL TABLE IF NOT EXISTS hl7-oru (OBX_1 STRUCT<UserDefinedAccessChecks:STRING, ObservationIdentifier:STRUCT<Text:STRING, Identifier:STRING>,     ReferencesRange:STRING, Units:STRUCT<NameOfCodingSystem:STRING, Identifier:STRING, Text:STRING>,     ObservationSubID:STRING, NatureOfAbnormalTest:STRING, SetIDOBX:STRING, ValueType:STRING, ObservationValue:STRING>,     OBR_1 STRUCT<OrderingProvider:STRUCT<FamilyName:STRING, IDNumber:STRING, GivenName:STRING, MiddleInitialOrName:STRING>,     UniversalServiceIdentifier:STRUCT<Text:STRING, Identifier:STRING>, FillerOrderNumber:STRUCT<EntityIdentifier:STRING>,     PlacerOrderNumber:STRUCT<NamespaceID:STRING, EntityIdentifier:STRING>, ResultStatus:STRING, ObservationDateTime:STRING,     ScheduledDateTime:STRING, SetIDObservationRequest:STRING, ResultsRptStatusChngDateTime:STRING>, MSH STRUCT<MessageControlID:STRING,     SendingApplication:STRUCT<NamespaceID:STRING>, ReceivingApplication:STRUCT<NamespaceID:STRING>, ProcessingID:STRUCT<ProcessingID:STRING>,     MessageType:STRUCT<MessageType:STRING, TriggerEvent:STRING>, EncodingCharacters:STRING, VersionID:STRING, FieldSeparator:STRING>,     PID STRUCT<SSNNumberPatient:STRING, PatientAccountNumber:STRUCT<ID:STRING>, DateOfBirth:STRING, Sex:STRING, PatientName:STRUCT<GivenName:STRING,     FamilyName:STRING>, PatientIDInternalID:STRUCT<ID:STRING>>, PD1 STRUCT<PatientPrimaryCareProviderNameIDNo:STRUCT<IDNumber:STRING, FamilyName:STRING,      GivenName:STRING, AssigningAuthority:STRING, MiddleInitialOrName:STRING>>) STORED AS ORC    LOCATION '/hl7/hl7oru'

Build Kafka topics:

/usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic patientboth    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-mdm    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-adt    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-orm    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-oru    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic simple    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-mdm_avro    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-adt_avro    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-orm_avro    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic hl7-oru_avro    /usr/hdp/current/kafka-broker/bin/kafka-topics.sh --create --zookeeper localhost:2181 --replication-factor 1 --partitions 1 --topic patientdata

Script to send a file to Kafka:

/usr/hdp/current/kafka-broker/bin/kafka-console-producer.sh --broker-list localhost:6667 --topic hl7-oru < hl7sampledata.txt

HBase DDL

hbase shell    
create 'patient_observations', 'obs'    
list

Running a Mosquitto MQTT Broker (OSX):

/usr/local/Cellar/mosquitto/1.4.14_2/sbin/mosquitto  --daemon --verbose --port 14162

Removing unneeded HDFS files:

hdfs dfs -rm -r -f -skipTrash $1

Example data from internet:

MSH|^~\&|XXXXXX||HealthOrg01||||ORU^R01|Q1111111111111111111|P|2.3|<cr>PID|||000000001||SMITH^JOHN||19700101|M||||||||||999999999999|123456789|<cr>PD1||||1234567890^LAST^FIRST^M^^^^^NPI|<cr>OBR|1|341856649^HNAM_ORDERID|000000000000000000|648088^Basic Metabolic Panel|||20150101000100|||||||||1620^Johnson^John^R||||||20150101000100|||M|||||||||||20150101000100|<cr>OBX|1|NM|GLU^Glucose Lvl|159|mg/dL|65-99^65^99|H|||F|||20150101000100|

See this article for some helpful info.

Code:

      Map < String, String > attributes = flowFile.getAttributes();
      Map < String, String > attributesClean = new HashMap < > ();
      String tempKey = "";
      for (Map.Entry < String, String > entry: attributes.entrySet()) {
       tempKey = entry.getKey().replaceFirst("[^A-Za-z]", ""); < br > tempKey = tempKey.replaceAll("[^A-Za-z0-9_]", ""); < br > attributesClean.put(tempKey, entry.getValue()); < br > session.removeAttribute(flowFile, entry.getKey()); < br >
      } < br > session.putAllAttributes(flowFile, attributesClean);

Lastly, you can find the Apache NiFi FlowFile here.

Learn how taking a DataOps approach will help you speed up processes and increase data quality by providing streamlined analytics pipelines via automation and testing. Learn More.

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Big Data Partner Resources

Whitepaper: Scaling Capabilities to Build a Homogeneous Big Data Ecosystem
Eckerson Group Report - DataOps: Industrializing Data and Analytics Strategies for Streamlining the Delivery of Insights
White Paper: 6 Simple Steps for Replatforming in the Age of the Data Lake
Data Lakes: A Serious Consideration for Serious Data Science

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