Repository: nifi Updated Branches: refs/heads/master c9097e7db -> 443803e72
NIFI-2564 This closes #854. Add support for HL7 composite component names Signed-off-by: joewitt <[email protected]> Project: http://git-wip-us.apache.org/repos/asf/nifi/repo Commit: http://git-wip-us.apache.org/repos/asf/nifi/commit/c1e47f9b Tree: http://git-wip-us.apache.org/repos/asf/nifi/tree/c1e47f9b Diff: http://git-wip-us.apache.org/repos/asf/nifi/diff/c1e47f9b Branch: refs/heads/master Commit: c1e47f9b44a57304962b12524f999360e0faf365 Parents: c9097e7 Author: Joey Frazee <[email protected]> Authored: Thu Mar 9 13:00:05 2017 -0600 Committer: joewitt <[email protected]> Committed: Thu Mar 9 21:50:02 2017 -0500 ---------------------------------------------------------------------- .../nifi-hl7-bundle/nifi-hl7-processors/pom.xml | 11 +-- .../processors/hl7/ExtractHL7Attributes.java | 62 ++++++++++++----- .../hl7/TestExtractHL7Attributes.java | 72 ++++++++++---------- nifi-nar-bundles/nifi-hl7-bundle/pom.xml | 15 ++++ 4 files changed, 103 insertions(+), 57 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/nifi/blob/c1e47f9b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml index d2daccc..b86d71d 100644 --- a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml +++ b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/pom.xml @@ -55,14 +55,17 @@ <dependency> <groupId>org.apache.nifi</groupId> <artifactId>nifi-hl7-query-language</artifactId> - <version>1.2.0-SNAPSHOT</version> </dependency> - + <dependency> + <groupId>commons-beanutils</groupId> + <artifactId>commons-beanutils</artifactId> + <version>1.9.2</version> + </dependency> <dependency> <groupId>ca.uhn.hapi</groupId> <artifactId>hapi-base</artifactId> <version>2.2</version> - </dependency> + </dependency> <dependency> <groupId>ca.uhn.hapi</groupId> <artifactId>hapi-structures-v21</artifactId> @@ -103,7 +106,7 @@ <artifactId>hapi-structures-v26</artifactId> <version>2.2</version> </dependency> - + <dependency> <groupId>org.apache.nifi</groupId> <artifactId>nifi-mock</artifactId> http://git-wip-us.apache.org/repos/asf/nifi/blob/c1e47f9b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java index 40a7cf9..4ceb12e 100644 --- a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java +++ b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java @@ -27,7 +27,10 @@ import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; +import java.util.regex.Matcher; +import java.util.regex.Pattern; +import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.text.WordUtils; @@ -218,7 +221,7 @@ public class ExtractHL7Attributes extends AbstractProcessor { // These maybe should used the escaped values, but that would // change the existing non-broken behavior of the processor if (parseFields && (field instanceof Composite) && !isTimestamp(field)) { - for (final Map.Entry<String, Type> componentEntry : getAllComponents(fieldKey, field).entrySet()) { + for (final Map.Entry<String, Type> componentEntry : getAllComponents(fieldKey, field, useNames).entrySet()) { final String componentKey = componentEntry.getKey(); final Type component = componentEntry.getValue(); final String componentValue = HL7_ESCAPING.unescape(component.encode(), HL7_ENCODING); @@ -298,25 +301,50 @@ public class ExtractHL7Attributes extends AbstractProcessor { return fields; } - private static Map<String, Type> getAllComponents(final String fieldKey, final Type field) throws HL7Exception { + private static Map<String, Type> getAllComponents(final String fieldKey, final Type field, final boolean useNames) throws HL7Exception { final Map<String, Type> components = new TreeMap<>(); if (!isEmpty(field) && (field instanceof Composite)) { - final Type[] types = ((Composite) field).getComponents(); - for (int i = 0; i < types.length; i++) { - final Type type = types[i]; - if (!isEmpty(type)) { - String fieldName = field.getName(); - if (fieldName.equals("CM_MSG")) { - fieldName = "CM"; + if (useNames) { + final Pattern p = Pattern.compile("^(cm_msg|[a-z][a-z][a-z]?)([0-9]+)_(\\w+)$"); + try { + final java.beans.PropertyDescriptor[] properties = PropertyUtils.getPropertyDescriptors(field); + for (final java.beans.PropertyDescriptor property : properties) { + final String propertyName = property.getName(); + final Matcher matcher = p.matcher(propertyName); + if (matcher.find()) { + final Type type = (Type) PropertyUtils.getProperty(field, propertyName); + if (!isEmpty(type)) { + final String componentName = matcher.group(3); + final String typeKey = new StringBuilder() + .append(fieldKey) + .append(".") + .append(componentName) + .toString(); + components.put(typeKey, type); + } + } + } + } catch (Exception e) { + throw new RuntimeException(e.getMessage(), e); + } + } else { + final Type[] types = ((Composite) field).getComponents(); + for (int i = 0; i < types.length; i++) { + final Type type = types[i]; + if (!isEmpty(type)) { + String fieldName = field.getName(); + if (fieldName.equals("CM_MSG")) { + fieldName = "CM"; + } + final String typeKey = new StringBuilder() + .append(fieldKey) + .append(".") + .append(fieldName) + .append(".") + .append(i+1) + .toString(); + components.put(typeKey, type); } - final String typeKey = new StringBuilder() - .append(fieldKey) - .append(".") - .append(fieldName) - .append(".") - .append(i+1) - .toString(); - components.put(typeKey, type); } } } http://git-wip-us.apache.org/repos/asf/nifi/blob/c1e47f9b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java index 51ebf96..64517df 100644 --- a/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java +++ b/nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java @@ -213,64 +213,64 @@ public class TestExtractHL7Attributes { expectedAttributes.put("MSH.FieldSeparator", "|"); expectedAttributes.put("MSH.EncodingCharacters", "^~\\&"); - expectedAttributes.put("MSH.SendingApplication.HD.1", "XXXXXXXX"); - expectedAttributes.put("MSH.ReceivingApplication.HD.1", "HealthProvider"); - expectedAttributes.put("MSH.MessageType.CM.1", "ORU"); - expectedAttributes.put("MSH.MessageType.CM.2", "R01"); + expectedAttributes.put("MSH.SendingApplication.NamespaceID", "XXXXXXXX"); + expectedAttributes.put("MSH.ReceivingApplication.NamespaceID", "HealthProvider"); + expectedAttributes.put("MSH.MessageType.MessageType", "ORU"); + expectedAttributes.put("MSH.MessageType.TriggerEvent", "R01"); expectedAttributes.put("MSH.MessageControlID", "Q1111111111111111111"); - expectedAttributes.put("MSH.ProcessingID.PT.1", "P"); + expectedAttributes.put("MSH.ProcessingID.ProcessingID", "P"); expectedAttributes.put("MSH.VersionID", "2.3"); expectedAttributes.put("ORC_1.OrderControl", "NW"); - expectedAttributes.put("ORC_1.PlacerOrderNumber.EI.1", "987654321"); - expectedAttributes.put("ORC_1.PlacerOrderNumber.EI.2", "EPC"); - expectedAttributes.put("ORC_1.FillerOrderNumber.EI.1", "123456789"); - expectedAttributes.put("ORC_1.FillerOrderNumber.EI.2", "EPC"); + expectedAttributes.put("ORC_1.PlacerOrderNumber.EntityIdentifier", "987654321"); + expectedAttributes.put("ORC_1.PlacerOrderNumber.NamespaceID", "EPC"); + expectedAttributes.put("ORC_1.FillerOrderNumber.EntityIdentifier", "123456789"); + expectedAttributes.put("ORC_1.FillerOrderNumber.NamespaceID", "EPC"); expectedAttributes.put("ORC_1.DateTimeOfTransaction", "20161003000000"); - expectedAttributes.put("ORC_1.OrderingProvider.XCN.1", "SMITH"); + expectedAttributes.put("ORC_1.OrderingProvider.IDNumber", "SMITH"); expectedAttributes.put("OBR_1.SetIDObservationRequest", "1"); - expectedAttributes.put("OBR_1.PlacerOrderNumber.EI.1", "341856649"); - expectedAttributes.put("OBR_1.PlacerOrderNumber.EI.2", "HNAM_ORDERID"); - expectedAttributes.put("OBR_1.FillerOrderNumber.EI.1", "000000000000000000"); - expectedAttributes.put("OBR_1.UniversalServiceIdentifier.CE.1", "648088"); - expectedAttributes.put("OBR_1.UniversalServiceIdentifier.CE.2", "Basic Metabolic Panel"); + expectedAttributes.put("OBR_1.PlacerOrderNumber.EntityIdentifier", "341856649"); + expectedAttributes.put("OBR_1.PlacerOrderNumber.NamespaceID", "HNAM_ORDERID"); + expectedAttributes.put("OBR_1.FillerOrderNumber.EntityIdentifier", "000000000000000000"); + expectedAttributes.put("OBR_1.UniversalServiceIdentifier.Identifier", "648088"); + expectedAttributes.put("OBR_1.UniversalServiceIdentifier.Text", "Basic Metabolic Panel"); expectedAttributes.put("OBR_1.ObservationDateTime", "20150101000000"); - expectedAttributes.put("OBR_1.OrderingProvider.XCN.1", "1620"); - expectedAttributes.put("OBR_1.OrderingProvider.XCN.2", "Johnson"); - expectedAttributes.put("OBR_1.OrderingProvider.XCN.3", "Corey"); - expectedAttributes.put("OBR_1.OrderingProvider.XCN.4", "A"); + expectedAttributes.put("OBR_1.OrderingProvider.IDNumber", "1620"); + expectedAttributes.put("OBR_1.OrderingProvider.FamilyName", "Johnson"); + expectedAttributes.put("OBR_1.OrderingProvider.GivenName", "Corey"); + expectedAttributes.put("OBR_1.OrderingProvider.MiddleInitialOrName", "A"); expectedAttributes.put("OBR_1.ResultsRptStatusChngDateTime", "20150101000000"); expectedAttributes.put("OBR_1.ResultStatus", "F"); expectedAttributes.put("OBR_1.ScheduledDateTime", "20150101000000"); expectedAttributes.put("OBX_1.SetIDOBX", "1"); expectedAttributes.put("OBX_1.ValueType", "NM"); - expectedAttributes.put("OBX_1.ObservationIdentifier.CE.1", "GLU"); - expectedAttributes.put("OBX_1.ObservationIdentifier.CE.2", "Glucose Lvl"); + expectedAttributes.put("OBX_1.ObservationIdentifier.Identifier", "GLU"); + expectedAttributes.put("OBX_1.ObservationIdentifier.Text", "Glucose Lvl"); expectedAttributes.put("OBX_1.ObservationSubID", "59"); expectedAttributes.put("OBX_1.ObservationValue", "mg/dL"); - expectedAttributes.put("OBX_1.Units.CE.1", "65-99"); - expectedAttributes.put("OBX_1.Units.CE.2", "65"); - expectedAttributes.put("OBX_1.Units.CE.3", "99"); + expectedAttributes.put("OBX_1.Units.Identifier", "65-99"); + expectedAttributes.put("OBX_1.Units.Text", "65"); + expectedAttributes.put("OBX_1.Units.NameOfCodingSystem", "99"); expectedAttributes.put("OBX_1.ReferencesRange", "L"); expectedAttributes.put("OBX_1.NatureOfAbnormalTest", "F"); expectedAttributes.put("OBX_1.UserDefinedAccessChecks", "20150102000000"); - expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.XCN.1", "1234567890"); - expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.XCN.2", "LAST"); - expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.XCN.3", "FIRST"); - expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.XCN.4", "M"); - expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.XCN.9", "NPI"); - - expectedAttributes.put("PID.PatientIDInternalID.CX.1", "12345"); - expectedAttributes.put("PID.PatientIDInternalID.CX.4", "XYZ"); - expectedAttributes.put("PID.PatientIDInternalID.CX.5", "MR"); - expectedAttributes.put("PID.PatientName.XPN.1", "SMITH"); - expectedAttributes.put("PID.PatientName.XPN.2", "JOHN"); + expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.IDNumber", "1234567890"); + expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.FamilyName", "LAST"); + expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.GivenName", "FIRST"); + expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.MiddleInitialOrName", "M"); + expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.AssigningAuthority", "NPI"); + + expectedAttributes.put("PID.PatientIDInternalID.ID", "12345"); + expectedAttributes.put("PID.PatientIDInternalID.AssigningAuthority", "XYZ"); + expectedAttributes.put("PID.PatientIDInternalID.IdentifierTypeCode", "MR"); + expectedAttributes.put("PID.PatientName.FamilyName", "SMITH"); + expectedAttributes.put("PID.PatientName.GivenName", "JOHN"); expectedAttributes.put("PID.DateOfBirth", "19700100"); expectedAttributes.put("PID.Sex", "M"); - expectedAttributes.put("PID.PatientAccountNumber.CX.1", "111111111111"); + expectedAttributes.put("PID.PatientAccountNumber.ID", "111111111111"); expectedAttributes.put("PID.SSNNumberPatient", "123456789"); runTests(message, expectedAttributes, true, true); http://git-wip-us.apache.org/repos/asf/nifi/blob/c1e47f9b/nifi-nar-bundles/nifi-hl7-bundle/pom.xml ---------------------------------------------------------------------- diff --git a/nifi-nar-bundles/nifi-hl7-bundle/pom.xml b/nifi-nar-bundles/nifi-hl7-bundle/pom.xml index 4ee8cd6..a0b8cdf 100644 --- a/nifi-nar-bundles/nifi-hl7-bundle/pom.xml +++ b/nifi-nar-bundles/nifi-hl7-bundle/pom.xml @@ -30,4 +30,19 @@ <module>nifi-hl7-nar</module> </modules> + <dependencyManagement> + <dependencies> + <dependency> + <groupId>org.apache.nifi</groupId> + <artifactId>nifi-hl7-processors</artifactId> + <version>1.2.0-SNAPSHOT</version> + </dependency> + <dependency> + <groupId>org.apache.nifi</groupId> + <artifactId>nifi-hl7-query-language</artifactId> + <version>1.2.0-SNAPSHOT</version> + </dependency> + </dependencies> + </dependencyManagement> + </project>
