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NIFI-506: Fixed unit tests and resources, and added RAT exclusions

This commit is contained in:
Mark Payne 2015-04-10 14:25:53 -04:00
parent 3515f2c12f
commit c83c7afd98
15 changed files with 77 additions and 183 deletions
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10
nifi/nifi-commons/nifi-hl7-query-language/pom.xml
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@ -48,6 +48,16 @@
</execution> </execution>
</executions> </executions>
</plugin> </plugin>
<plugin>
<groupId>org.apache.rat</groupId>
<artifactId>apache-rat-plugin</artifactId>
<configuration>
<excludes>
<exclude>src/test/resources/hypoglycemia</exclude>
<exclude>src/test/resources/hyperglycemia</exclude>
</excludes>
</configuration>
</plugin>
</plugins> </plugins>
</build> </build>

17
nifi/nifi-commons/nifi-hl7-query-language/src/main/antlr3/org/apache/nifi/hl7/query/antlr/HL7QueryLexer.g
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@ -1,3 +1,20 @@
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
lexer grammar HL7QueryLexer; lexer grammar HL7QueryLexer;
@header { @header {

17
nifi/nifi-commons/nifi-hl7-query-language/src/main/antlr3/org/apache/nifi/hl7/query/antlr/HL7QueryParser.g
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@ -1,3 +1,20 @@
/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
parser grammar HL7QueryParser; parser grammar HL7QueryParser;
options { options {

52
nifi/nifi-commons/nifi-hl7-query-language/src/test/java/org/apache/nifi/hl7/query/TestHL7Query.java
View File

@ -23,7 +23,6 @@ import static org.junit.Assert.assertTrue;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.List; import java.util.List;
@ -32,8 +31,6 @@ import java.util.Map;
import org.apache.nifi.hl7.hapi.HapiMessage; import org.apache.nifi.hl7.hapi.HapiMessage;
import org.apache.nifi.hl7.model.HL7Field; import org.apache.nifi.hl7.model.HL7Field;
import org.apache.nifi.hl7.model.HL7Message; import org.apache.nifi.hl7.model.HL7Message;
import org.apache.nifi.hl7.query.HL7Query;
import org.apache.nifi.hl7.query.QueryResult;
import org.junit.Test; import org.junit.Test;
import ca.uhn.hl7v2.DefaultHapiContext; import ca.uhn.hl7v2.DefaultHapiContext;
@ -99,7 +96,7 @@ public class TestHL7Query {
@Test @Test
public void testSelectMessage() throws HL7Exception, IOException { public void testSelectMessage() throws HL7Exception, IOException {
final HL7Query query = HL7Query.compile("SELECT MESSAGE"); final HL7Query query = HL7Query.compile("SELECT MESSAGE");
final HL7Message msg = createMessage(new File("src/test/resources/vaers-message-long")); final HL7Message msg = createMessage(new File("src/test/resources/hypoglycemia"));
final QueryResult result = query.evaluate(msg); final QueryResult result = query.evaluate(msg);
assertTrue(result.isMatch()); assertTrue(result.isMatch());
final List<String> labels = result.getLabels(); final List<String> labels = result.getLabels();
@ -114,7 +111,7 @@ public class TestHL7Query {
@SuppressWarnings({ "unchecked", "rawtypes" }) @SuppressWarnings({ "unchecked", "rawtypes" })
public void testSelectField() throws HL7Exception, IOException { public void testSelectField() throws HL7Exception, IOException {
final HL7Query query = HL7Query.compile("SELECT PID.5"); final HL7Query query = HL7Query.compile("SELECT PID.5");
final HL7Message msg = createMessage(new File("src/test/resources/unsolicited-vaccine-update-short")); final HL7Message msg = createMessage(new File("src/test/resources/hypoglycemia"));
final QueryResult result = query.evaluate(msg); final QueryResult result = query.evaluate(msg);
assertTrue(result.isMatch()); assertTrue(result.isMatch());
final List<String> labels = result.getLabels(); final List<String> labels = result.getLabels();
@ -126,7 +123,7 @@ public class TestHL7Query {
final List<Object> nameList = (List) names; final List<Object> nameList = (List) names;
assertEquals(1, nameList.size()); assertEquals(1, nameList.size());
final HL7Field nameField = (HL7Field) nameList.get(0); final HL7Field nameField = (HL7Field) nameList.get(0);
assertEquals("KENNEDY^JOHN^FITZGERALD^JR", nameField.getValue()); assertEquals("SMITH^JOHN", nameField.getValue());
} }
@Test @Test
@ -134,8 +131,8 @@ public class TestHL7Query {
final String query = "DECLARE result AS REQUIRED OBX SELECT result WHERE result.7 != 'N' AND result.1 = 1"; final String query = "DECLARE result AS REQUIRED OBX SELECT result WHERE result.7 != 'N' AND result.1 = 1";
final HL7Query hl7Query = HL7Query.compile(query); final HL7Query hl7Query = HL7Query.compile(query);
final QueryResult result = hl7Query.evaluate(createMessage(new File("src/test/resources/vaers-message-long"))); final QueryResult result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia")));
assertFalse( result.isMatch() ); assertTrue( result.isMatch() );
} }
@ -224,18 +221,6 @@ public class TestHL7Query {
QueryResult result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia"))); QueryResult result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia")));
assertTrue( result.isMatch() ); assertTrue( result.isMatch() );
assertEquals(1, result.getHitCount()); assertEquals(1, result.getHitCount());
hl7Query = HL7Query.compile("DECLARE result AS REQUIRED OBX SELECT result WHERE result.1 = 1");
HL7Message msg = createMessage(new File("src/test/resources/vaers-message-long"));
result = hl7Query.evaluate(msg);
assertTrue( result.isMatch() );
assertEquals(9, result.getHitCount());
hl7Query = HL7Query.compile("DECLARE result AS REQUIRED OBX SELECT result WHERE result.1 = 1 AND result.3.1.1 = '30961-7'");
result = hl7Query.evaluate(msg);
assertTrue( result.isMatch() );
assertEquals(1, result.getHitCount());
} }
@Test @Test
@ -288,10 +273,6 @@ public class TestHL7Query {
hl7Query = HL7Query.compile("SELECT MESSAGE WHERE OBX IS NULL"); hl7Query = HL7Query.compile("SELECT MESSAGE WHERE OBX IS NULL");
result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia"))); result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia")));
assertFalse( result.isMatch() ); assertFalse( result.isMatch() );
hl7Query = HL7Query.compile("SELECT MESSAGE WHERE NK1.1 = '1' AND NK1.8 IS NULL");
result = hl7Query.evaluate(createMessage(new File("src/test/resources/unsolicited-vaccine-update-long")));
assertTrue( result.isMatch() );
} }
@ -312,14 +293,6 @@ public class TestHL7Query {
hl7Query = HL7Query.compile("SELECT MESSAGE WHERE OBX NOT NULL"); hl7Query = HL7Query.compile("SELECT MESSAGE WHERE OBX NOT NULL");
result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia"))); result = hl7Query.evaluate(createMessage(new File("src/test/resources/hypoglycemia")));
assertTrue( result.isMatch() ); assertTrue( result.isMatch() );
hl7Query = HL7Query.compile("SELECT MESSAGE WHERE NK1.1 = '1' AND NK1.33 NOT NULL");
result = hl7Query.evaluate(createMessage(new File("src/test/resources/unsolicited-vaccine-update-long")));
assertTrue( result.isMatch() );
hl7Query = HL7Query.compile("SELECT MESSAGE WHERE NK1.1 = 1 AND NK1.33 NOT NULL");
result = hl7Query.evaluate(createMessage(new File("src/test/resources/unsolicited-vaccine-update-long")));
assertTrue( result.isMatch() );
} }
private HL7Message createMessage(final File file) throws HL7Exception, IOException { private HL7Message createMessage(final File file) throws HL7Exception, IOException {
@ -334,19 +307,4 @@ public class TestHL7Query {
return new HapiMessage(message); return new HapiMessage(message);
} }
@Test
@SuppressWarnings("unused")
public void createMessage() throws IOException, HL7Exception {
final byte[] bytes = Files.readAllBytes(Paths.get("src/test/resources/vaers-message-long"));
final String msgText = new String(bytes, "UTF-8");
final HapiContext hapiContext = new DefaultHapiContext();
hapiContext.setValidationContext(ValidationContextFactory.noValidation());
final PipeParser parser = hapiContext.getPipeParser();
final Message message = parser.parse(msgText);
final HL7Message hl7Msg = new HapiMessage(message);
}
} }

8
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/hyperglycemia
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@ -1,5 +1,5 @@
MSH|^~\&|CERNER||PriorityHealth||||ORU^R01|Q479004375T431430612|P|2.3| MSH|^~\&|XXXXXXXX||HealthProvider||||ORU^R01|Q1111111111111111111|P|2.3|
PID|||001677980||SMITH^CURTIS||19680219|M||||||||||929645156318|123456789| PID|||111111111||SMITH^JOHN||19700100|M||||||||||111111111111|123456789|
PD1||||1234567890^LAST^FIRST^M^^^^^NPI| PD1||||1234567890^LAST^FIRST^M^^^^^NPI|
OBR|1|341856649^HNAM_ORDERID|000002006326002362|648088^Basic Metabolic Panel|||20061122151600|||||||||1620^Hooker^Robert^L||||||20061122154733|||F|||||||||||20061122140000| OBR|1|341856649^HNAM_ORDERID|000000000000000000|648088^Basic Metabolic Panel|||20150101000000|||||||||1620^Johnson^Corey^A||||||20150101000000|||F|||||||||||20150101000000|
OBX|1|NM|GLU^Glucose Lvl|159|mg/dL|65-99^65^99|H|||F|||20061122154733| OBX|1|NM|GLU^Glucose Lvl|159|mg/dL|65-99^65^99|H|||F|||20150102000000|

8
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/hypoglycemia
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@ -1,5 +1,5 @@
MSH|^~\&|CERNER||PriorityHealth||||ORU^R01|Q479004375T431430612|P|2.3| MSH|^~\&|XXXXXXXX||HealthProvider||||ORU^R01|Q1111111111111111111|P|2.3|
PID|||001677980||SMITH^CURTIS||19680219|M||||||||||929645156318|123456789| PID|||111111111||SMITH^JOHN||19700100|M||||||||||111111111111|123456789|
PD1||||1234567890^LAST^FIRST^M^^^^^NPI| PD1||||1234567890^LAST^FIRST^M^^^^^NPI|
OBR|1|341856649^HNAM_ORDERID|000002006326002362|648088^Basic Metabolic Panel|||20061122151600|||||||||1620^Hooker^Robert^L||||||20061122154733|||F|||||||||||20061122140000| OBR|1|341856649^HNAM_ORDERID|000000000000000000|648088^Basic Metabolic Panel|||20150101000000|||||||||1620^Johnson^Corey^A||||||20150101000000|||F|||||||||||20150101000000|
OBX|1|NM|GLU^Glucose Lvl|59|mg/dL|65-99^65^99|L|||F|||20061122154733| OBX|1|NM|GLU^Glucose Lvl|59|mg/dL|65-99^65^99|L|||F|||20150102000000|

23
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/metabolic-panel
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@ -1,23 +0,0 @@
MSH|^~\&|Lab1^1234^CLIA|^1234^CLIA|ELR^2.16.840.1.113883.19.3.2^ISO|SPH^2.16.840.1.113883.19.3.2^ISO|20110410140502-0500||ORU^R01^ORU_R01|1234567890|P^T|2.5.1|||NE|NE|USA||||USELR1.0^^2.16.840.1.114222.4.10.3^ISO
SFT|1|Level Seven Healthcare Software, Inc.^L^^^^&2.16.840.1.113883.19.4.6^ISO^XX^^^1234|1.2|An Lab System|56734||20080817
PID|1||36363636^^^MPI&2.16.840.1.113883.19.3.2.1&ISO^MR^A&2.16.840.1.113883.19.3.2.1&ISO~444333333^^^&2.16.840.1.113883.4.1^IS O^SS||Everyman^Adam^A^^^^L^^^^^^^BS|Mum^Martha^M^^^^M|19800602|M||2106-3^White^CDCREC^^^^04/24/2007|2222 Home Street^^Ann Arbor^MI^99999^USA^H||^PRN^PH^^1^555^5552004|^WPN^PH^^1^955^5551009|eng^English^ISO6392^^^^3/29/2007|M^Married^HL70002^^^^2.5.1||||||N^Not Hispanic or Latino^HL70189^^^^2.5.1||||||||N|||200808151000-0700| Reliable^2.16.840.1.113883.19.3.1^ISO
ORC|RE|23456^EHR^2.16.840.1.113883.19.3.2.3^ISO|9700123^Lab^2.16.840.1.113883.19.3.1.6^ISO|||||||||1234^Admit^Alan^A^III^Dr^^^&2.16.840.1.113883.19.4.6^ISO^L^^^EI^&2.16.840.1.113883.19.4.6^ISO^^^^^^^^MD||^WPN^PH^^1^555^5551005|||||||Level Seven Healthcare, Inc.^L^^^^&2.16.840.1.113883.19.4.6^ISO^XX^^^1234|1005 Healthcare Drive^^Ann Arbor^MI^99999^USA^B|^WPN^PH^^1^555^5553001|4444 Healthcare Drive^Suite 123^Ann Arbor^MI^99999^USA^B
OBR|1|23456^EHR^2.16.840.1.113883.19.3.2.3^ISO|9700123^Lab^2.16.840.1.113883.19.3.1.6^ISO|24323-8^Comprehensive metabolic 2000 panel in Serum or Plasma^LN^3436442^Metaboloic Panel 2000, Comprehensive^99USI|||201104101130-0500||||||angina|||1234^Admit^Alan^A^III^Dr^^^&2.16.840.1.113883.19.4.6^ISO^L^^^EI^&2.16.840.1.113883.19.4.6^ISO^^^^^^^^MD|^WPN^PH^^1^555^5551005|||||201104101405-0500|||F||||||413^Angina pectoris^I9CDX^^^^07/09/2008|1235&Slide&Stan&S&&Dr&MD&&DOC&2.16.840.1.113883.19.4.6&ISO
OBX|1|NM|17861-6^Calcium [Mass/volume] in Serum or Plasma^LN||27.3|mg/dL^milligrams per deciliter^UCUM|8.7-10.7|HH|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|2|NM|3094-0^Urea nitrogen [Mass/volume] in Serum of Plasma^LN||15|mg/dL^milligrams per deciliter^UCUM|6 to 23|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|3|NM|2160-0^Creatinine [Mass/volume] in Serum or Plasma^LN||1.8|mg/dL^milligrams per deciliter^UCUM|0.7 to 1.2|H|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|4|NM|3097-3^Urea nitrogen/Creatinine [Mass ratio] in Serum or Plasma^LN||15||6 to 25|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|5|NM|2885-2^Protein [Mass/volume] in Serum or Plasma^LN||8.9|gm/dL^grams per deciliter^UCUM|6.3 to 8.2|H|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|6|NM|1751-7^Albumin [Mass/volume] in Serum or Plasma^LN||5.7|gm/dL^grams per deciliter^UCUM|3.5 to 5.0|H|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|7|NM|2336-6^Globulin [Mass/volume] in Serum or Plasma^LN||4.7|gm/dL^grams per deciliter^UCUM|2.2 to 4.2|H|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|8|NM|1759-0^Albumin/Globulin [Mass ratio] in Serum or Plasma^LN||1.7||0.8 to 2.0|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|9|NM|1975-2^Bilirubin.total [Mass/volume] in Serum or Plasma^LN||0.7|mg/dL^milligrams per deciliter^UCUM|0.3 to 1.9|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|10|NM|2345-7^Glucose [Mass/volume] in Serum or Plasma^LN||55|mg/dL^milligrams per deciliter^UCUM|60 to 109|L|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|11|NM|6768-6^Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma^LN||64|U/L^units per liter^UCUM|32 to 110|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|12|NM|1920-8^Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma^LN||6|U/L^units per liter^UCUM|6 to 18|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|13|NM|1742-6^Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma^LN||10|U/L^units per liter^UCUM|5 to 35|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|14|NM|2951-2^Sodium [Moles/volume] in Serum or Plasma^LN||140|mmol/L^millimoles per liter^UCUM|137 to 147|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|15|NM|2823-3^Potassium [Moles/volume] in Serum or Plasma^LN||4.5|mmol/L^millimoles per liter^UCUM|3.4 to 5.3|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|16|NM|2075-0^Chloride [Moles/volume] in Serum or Plasma^LN||99|mmol/L^millimoles per liter^UCUM|99 to 108|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
OBX|17|NM|2028-9^Carbon dioxide, total [Moles/volume] in Serum or Plasma^LN||27|mmol/L^millimoles per liter^UCUM|22 to 29|N|||F|||201104101130-0500|||||201104101325-0500||||GHH Lab^L^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^1236|3434 Industrial Loop^^Ann Arbor^MI^99999^USA^B|9876543^Slide^Stan^S^^^^^NPPES&2.16.840.1.113883.19.4.6&ISO^L^^^NPI
SPM|1|23456&EHR&2.16.840.1.113883.19.3.2.3&ISO^9700122&Lab&2.16.840.1.113883.19.3.1.6&ISO||119364003^Serum specimen^SCT^^^^20080131|||||||||||||201104101130-0500|201104101130-0500

16
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/unsolicited-vaccine-update-long
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@ -1,16 +0,0 @@
MSH|^~\&||MA0000||GA0000|19970901||VXU^V04|19970522MA53|T|2.3.1|||AL
PID|||1234^^^^SR^~1234-12^^^^LR^~3872^^^^MR~221345671^^^^SS^~430078856^^^^MA^ ||KENNEDY^JOHN^FITZGERALD^JR^^^L|BOUVIER^^^^^^M|19900607|M|KENNEDY^BABY BOY^^^^^^ B|W^WHITE^NY8 RACE CODES^W^WHITE^HL70005|123 MAIN ST^APT 3B^LEXINGTON^MA^00210^ ^M^MSA CODE^MA034~345 ELM ST^^BOSTON^MA^00314^^BLD~^^^^^^BR^^MA002| |(617) 555-1212 ^PRN^PH^^^617^5551212^^||EN^ENGLISH^HL70296^^^|||||||WN^NOT HISPANIC^LOCAL CODE SET^NH^NOT OF HISPANIC ORIGIN^HL70189|CHILDREN=S HOSPITAL
PD1|||CHILDREN=S HOSPITAL^^1234^^^^XX~LEXINGTON CLINIC^^1234A^^^^FI|12345^CARE^ PRIMARY^^^DR^MD^^^L^^^DN|||||||03^REMINDER/RECALL - NO CALLS^HL70215|Y
NK1|1|KENNEDY^JACQUELINE^LEE|32^MOTHER^HL70063||||||||||||||||||||||||||||||898666725^^^^SS
NK1|2|KENNEDY^JOHN^FITZGERALD|33^FATHER^HL70063||||||||||||||||||||||||||||||822546618^^^^SS
PV1||R|||||||||||||||A|||V02^19900607~H02^19900607
RXA|0|1|19900607|19900607|08^HEPB-PEDIATRIC/ADOLESCENT^CVX^90744^HEPB-PEDATRIC/ADOLESCENT^CPT|.5|ML^^ISO+||03^HISTORICAL INFORMATION - FROM PARENT=S WRITTEN RECORD^NIP0001|^JONES^LISA|^^^CHILDREN=S HOSPITAL||5|MCG^^ISO+|MRK12345| 199206|MSD^MERCK^MVX
RXA|0|4|19910907|19910907|50^DTAP-HIB^CVX^90721^DTAP-HIB^CPT|.5|ML^^ISO+||00^NEW IMMUNIZATION RECORD^NIP0001|1234567890^SMITH^SALLY^S^^^^^^^^^VEI~1234567891 ^O=BRIAN^ROBERT^A^^DR^MD^^^^^^OEI|^^^CHILD HEALTHCARE CLINIC^^^^^101 MAIN STREET^^ BOSTON^MA||||W46932777|199208|PMC^PASTEUR MERIEUX CONNAUGHT^MVX|||CP|A| 19910907120030
RXR|IM^INTRAMUSCULAR^HL70162|LA^LEFT ARM^HL70163
RXA|0|1|19910907|19910907|03^MMR^CVX|.5|ML^^ISO+|||1234567890^SMITH^SALLY^S^^^^^^^^^VEI~1234567891^O=BRIAN^ROBERT^A^^DR^MD^^^^^^OEI|^^^CHILD HEALTHCARE CLINIC^^^^^101 MAIN STREET^^BOSTON^MA||||W2348796456|19920731|MSD^MERCK^MVX
RXR|SC^SUBCUTANEOUS^HL70162|LA^LEFT ARM^HL70163
RXA|0|5|19950520|19950520|20^DTAP^CVX|.5|ML^^ISO+|||1234567891^O=BRIAN^ROBERT^A^^DR|^^^CHILD HEALTHCARE CLINIC^^^^^101 MAIN STREET^^BOSTON^MA||||W22532806|19950705|PMC^ PASTEUR MERIEUX CONNAUGHT^MVX
RXR|IM^INTRAMUSCULAR^HL70162|LA^LEFT ARM^HL70163
NTE|PATIENT DEVELOPED HIGH FEVER APPROX 3 HRS AFTER VACCINE INJECTION
RXA|0|2|19950520|19950520|03^MMR^CVX|.5|ML^^ISO+|||1234567891^O=BRIAN^ROBERT^A^^DR|^^^CHILD HEALTHCARE CLINIC^^^^^101 MAIN STREET^^BOSTON^MA||||W2341234567|19950630| MSD^MERCK^MVX
RXR|SC^SUBCUTANEOUS^HL70162|LA^LEFT ARM^HL70163

4
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/unsolicited-vaccine-update-short
View File

@ -1,4 +0,0 @@
MSH|^~\&|||||||VXU^V04|19970522MA53|P|2.3.1
PID|||221345671^^^^SS||KENNEDY^JOHN^FITZGERALD^JR|BOUVIER^^^^^^M|19900607|M|||^^^^MA^^^BLD
NK1|1|KENNEDY^JACQUELINE^LEE|32^MOTHER^HL70063
RXA|0|1|19900607|19900607|08^HEPB-PEDIATRIC/ADOLESCENT^CVX|.5|ML^^ISO+||||||||MRK12345||MSD^MERCK^MVX

3
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/vaccine-query
View File

@ -1,3 +0,0 @@
MSH|^~\&||GA0000||MA0000|199705221605||VXQ^V01|19970522GA40|T|2.3.1|||AL
QRD|199705221605|R|I|19970522GA05|||25^RD|^KENNEDY^JOHN^FITZGERALD^JR|VXI^VACCINE INFORMATION^HL70048|^SIIS
QRF|MA0000||||256946789~19900607~MA~MA99999999~88888888~KENNEDY^JACQUELINE^LEE~BOUVIER~898666725~KENNEDY^JOHN^FITZGERALD~822546618

60
nifi/nifi-commons/nifi-hl7-query-language/src/test/resources/vaers-message-long
View File

@ -1,60 +0,0 @@
MSH|^~\&||GA0000||VAERS PROCESSOR|20010331605||ORU^R01|20010422GA03|T|2.3.1|||AL|
PID|||1234^^^^SR~1234-12^^^^LR~00725^^^^MR||Doe^John^Fitzgerald^JR^^^L||20001007|M||2106-3^White^HL70005|123 Peachtree St^APT 3B^Atlanta^GA^30210^^M^^GA067||(678) 555-1212^^PRN|
NK1|1|Jones^Jane^Lee^^RN|VAB^Vaccine administered by (Name)^HL70063|
NK1|2|Jones^Jane^Lee^^RN|FVP^Form completed by (Name)-Vaccine provider^HL70063|101 Main Street^^Atlanta^GA^38765^^O^^GA121||(404) 554-9097^^WPN|
ORC|CN|||||||||||1234567^Welby^Marcus^J^Jr^Dr.^MD^L|||||||||Peachtree Clinic|101 Main Street^^Atlanta^GA^38765^^O^^GA121|(404) 554-9097^^WPN|101 Main Street^^Atlanta^GA^38765^^O^^GA121|
OBR|1|||^CDC VAERS-1 (FDA) Report|||20010316|
OBX|1|NM|21612-7^Reported Patient Age^LN||05|mo^month^ANSI|
OBX|1|TS|30947-6^Date form completed^LN||20010316|
OBX|2|FT|30948-4^Vaccination adverse events and treatment, if any^LN|1|fever of 106F, with vomiting, seizures, persistent crying lasting over 3 hours, loss of appetite|
OBX|3|CE|30949-2^Vaccination adverse event outcome^LN|1|E^required emergency room/doctor visit^NIP005|
OBX|4|CE|30949-2^Vaccination adverse event outcome^LN|1|H^required hospitalization^NIP005|
OBX|5|NM|30950-0^Number of days hospitalized due to vaccination adverse event^LN|1|02|d^day^ANSI|
OBX|6|CE|30951-8^Patient recovered^LN||Y^Yes^ HL70239|
OBX|7|TS|30952-6^Date of vaccination^LN||20010216|
OBX|8|TS|30953-4^Adverse event onset date and time^LN||200102180900|
OBX|9|FT|30954-2^Relevant diagnostic tests/lab data^LN||Electrolytes, CBC, Blood culture|
OBR|2|||30955-9^All vaccines given on date listed in #10^LN|
OBX|1|CE30955-9&30956-7^Vaccine type^LN|1|08^HepB-Adolescent/pediatric^CVX|
OBX|2|CE|30955-9&30957-5^Manufacturer^LN|1|MSD^Merck^MVX|
OBX|3|ST|30955-9&30959-1^Lot number^LN|1|MRK12345|
OBX|4|CE|30955-9&30958-3^ Route^LN|1|IM^Intramuscular ^HL70162|
OBX|5|CE|30955-9&31034-2^Site^LN|1|LA^Left arm^ HL70163|
OBX|6|NM|30955-9&30960-9^Number of previous doses^LN|1|01I
OBX|7|CE|CE|30955-9&30956-7^Vaccine type^LN|2|50^DTaP-Hib^CVX|
OBX|8|CE|30955-9&30957-5^ Manufacturer^LN|2|WAL^Wyeth_Ayerst^MVX|
OBX|9|ST|30955-9&30959-1^Lot number^LN|2|W46932777|
OBX|10|CE|30955-9&30958-3^ Route^LN|2|IM^Intramuscular^HL70162|
OBX|11|CE|30955-9&31034-2^Site^LN|2|LA^Left arm^HL70163|
OBX|12|NM|30955-9&30960-9^Number of previous doses^LN|2|01|
OBR|3|||30961-7^Any other vaccinations within 4 weeks prior to the date listed in #10|
OBX|1|CE|30961-7&30956-7^Vaccine type^LN|1|10^IPV^CVX|
OBX|2|CE|30961-7&30957-5^Manufacturer^LN|1|PMC^Aventis Pasteur ^MVX|
OBX|3|ST|30961-7&30959-1^Lot number^LN|1|PMC123456|
OBX|4|CE|30961-7&30958-3^Route^LN|1|SC^Subcutaneaous^HL70162|
OBX|5|CE|30961-7&31034-2^Site^LN|1|LA^Left arm^HL70163|
OBX|6|NM|30961-7&30960-9^Number of previous doses^LN|1|01|
OBX|7|TS|30961-7&31035-9^date given^LN|1|20001216|
OBX|8|CE|30962-^Vaccinated at^LN||PVT^Private doctor<6F>s office/hospital^NIP009|
OBX|9|CE|30963-3^Vaccine purchased with^LN||PBF^Public funds^NIP008|
OBX|10|FT|30964-1^Other medications^LN||None|
OBX|11|FT|30965-8^Illness at time of vaccination (specify)^LN||None|
OBX|12|FT|30966-6^Pre-existing physician diagnosed allergies, birth defects, medical conditions^LN||Past conditions convulsions|
OBX|13|CE|30967-4^Was adverse event reported previously^LN||N^no^NIP009|
OBR|4||30968-2^Adverse event following prior vaccination in patient^LN|
OBX|1|TX|30968-2&30971-6^Adverse event^LN||None|
OBR|5||30969-0^Adverse event following prior vaccination in brother^LN|
OBX|1|TX||30969-0&30971-6^Adverse event^LN||vomiting, fever, otitis media|
OBX|2|NM||30969-0&30972-4^Onset age^LN||04|mo^month^ANSI|
OBX|3|CE||30969-0&30956-7^Vaccine Type ^LN||10^IPV^CVX|
OBX|4|NM||30969-0&30973-2^Dose number in series^LN||02|
OBR|6|||30970-8^Adverse event following prior vaccination in sister^LN|
OBX|1|TX|30970-8&30971-6^Adverse event^LN||None|
OBR|7||^For children 5 and under|
OBX|1|NM|8339-4^Body weight at birth^LN||82|oz^ounces^ANSI|
OBX|2|NM|30974-0^Number of brothers and sisters^LN||2|
OBR|8|||^Only for reports submitted by manufacturer/immunization project|
OBX|1|ST|30975-7^Mfr./Imm. Proj. report no.^LN||12345678|
OBX|2|TS|30976-5^Date received by manufacturer/immunization project^LN||12345678|
OBX|3|CE|30977-3^15 day report^LN||N^No^HL70136|
OBX|4|CE|30978-1^Report type^LN||IN^Initial^NIP010|

14
nifi/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml
View File

@ -25,6 +25,20 @@
<artifactId>nifi-hl7-processors</artifactId> <artifactId>nifi-hl7-processors</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<build>
<plugins>
<plugin>
<groupId>org.apache.rat</groupId>
<artifactId>apache-rat-plugin</artifactId>
<configuration>
<excludes>
<exclude>src/test/resources/hypoglycemia.hl7</exclude>
</excludes>
</configuration>
</plugin>
</plugins>
</build>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>org.apache.nifi</groupId> <groupId>org.apache.nifi</groupId>

2
nifi/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java
View File

@ -34,7 +34,7 @@ public class TestExtractHL7Attributes {
public void testExtract() throws IOException { public void testExtract() throws IOException {
System.setProperty("org.slf4j.simpleLogger.log.org.apache.nifi", "DEBUG"); System.setProperty("org.slf4j.simpleLogger.log.org.apache.nifi", "DEBUG");
final TestRunner runner = TestRunners.newTestRunner(ExtractHL7Attributes.class); final TestRunner runner = TestRunners.newTestRunner(ExtractHL7Attributes.class);
runner.enqueue(Paths.get("src/test/resources/1.hl7")); runner.enqueue(Paths.get("src/test/resources/hypoglycemia.hl7"));
runner.run(); runner.run();
runner.assertAllFlowFilesTransferred(ExtractHL7Attributes.REL_SUCCESS, 1); runner.assertAllFlowFilesTransferred(ExtractHL7Attributes.REL_SUCCESS, 1);

16
nifi/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/resources/1.hl7
View File

@ -1,16 +0,0 @@
MSH|^~`&|ECG REPORTING|ROCHESTER|ERIS|ROCHESTER|20110621050440||ORU^R01|20110621050440|P|2.1
PID|||999999999||TEST^PATIENT||18450101|F
OBR|||211088491|0^ADULT^ROCHECG|||20110620170631|||||||||M999999^^^^^^^RACFID||||||20110621060232||EC|F|||||||M999999^LASTNAME MD^FIRSTNAME^^^^^RACFID
OBX||ST|93000.2^VENTRICULAR RATE EKG/MIN^CPT4|1|52|/SEC
OBX||ST|93000.4^PR INTERVAL(MSEC)^CPT4|2|208|MSEC
OBX||ST|93000.5^QRS - INTERVAL(MSEC)^CPT4|3|88|MSEC
OBX||ST|93000.6^QT - INTERVAL(MSEC)^CPT4|4|466|MSEC
OBX||ST|93000&PTL^PHYSICAL TEST LOCATION^CPT4|5|STMA
OBX||ST|93000&PTR^PHYSICAL TEST ROOM^CPT4|6|04254
OBX||CE|93000.17^^CPT4|7|21&101^Sinus bradycardia`T`with 1st degree A-V block^MEIECG
OBX||CE|93000.17^^CPT4|8|1687^Otherwise normal ECG^MEIECG
OBX||CE|93000&CMP^^CPT4|9|1301^When compared with ECG of^MEIECG
OBX||TS|93000&CMD^EKG COMPARISON DATE^CPT4|10|201106171659
OBX||CE|93000&CMP^^CPT4|11|1305^No significant change was found^MEIECG
OBX||TX|93000.48^EKG COMMENT^CPT4|12|9917^LASTNAME MD^FIRSTNAME
OBX||FT|93000^ECG 12-LEAD^CPT4|13|{\rtf1\ansi \deff1\deflang1033\ {\fonttbl{\f1\fmodern\fcharset0 Courier;}{\f2\fmodern\fcharset0 Courier;}} \pard\plain \f1\fs18\par 20Jun2011 17:06\par VENTRICULAR RATE 52\par Sinus bradycardia with 1st degree A-V block\par Otherwise normal ECG\par When compared with ECG of 17-JUN-2011 16:59,\par No significant change was found\par 47507`S`'LASTNAME MD`S`'FIRSTNAME \par }

8
nifi/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/resources/hypoglycemia.hl7
View File

@ -1,5 +1,5 @@
MSH|^~\&|CERNER||PriorityHealth||||ORU^R01|Q479004375T431430612|P|2.3| MSH|^~\&|XXXXXXXX||HealthProvider||||ORU^R01|Q1111111111111111111|P|2.3|
PID|||001677980||SMITH^CURTIS||19680219|M||||||||||929645156318|123456789| PID|||111111111||SMITH^JOHN||19700100|M||||||||||111111111111|123456789|
PD1||||1234567890^LAST^FIRST^M^^^^^NPI| PD1||||1234567890^LAST^FIRST^M^^^^^NPI|
OBR|1|341856649^HNAM_ORDERID|000002006326002362|648088^Basic Metabolic Panel|||20061122151600|||||||||1620^Hooker^Robert^L||||||20061122154733|||F|||||||||||20061122140000| OBR|1|341856649^HNAM_ORDERID|000000000000000000|648088^Basic Metabolic Panel|||20150101000000|||||||||1620^Johnson^Corey^A||||||20150101000000|||F|||||||||||20150101000000|
OBX|1|NM|GLU^Glucose Lvl|59|mg/dL|65-99^65^99|L|||F|||20061122154733| OBX|1|NM|GLU^Glucose Lvl|59|mg/dL|65-99^65^99|L|||F|||20150102000000|