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AKTIN
dwh-import
Commits
1f44cbb6
Commit
1f44cbb6
authored
Apr 16, 2019
by
R.W.Majeed
Browse files
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Plain Diff
generalize xml transformation lookup to include root ns and element,
test case for no birthdate
parent
fdc22f9b
Changes
9
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9 changed files
with
870 additions
and
13 deletions
+870
-13
cda-import/src/main/java/org/aktin/cda/etl/AbstractCDAImporter.java
.../src/main/java/org/aktin/cda/etl/AbstractCDAImporter.java
+3
-1
cda-import/src/main/java/org/aktin/cda/etl/transform/TransformationFactory.java
...va/org/aktin/cda/etl/transform/TransformationFactory.java
+1
-1
cda-import/src/test/java/org/aktin/cda/etl/TestTransformToEAV.java
...t/src/test/java/org/aktin/cda/etl/TestTransformToEAV.java
+4
-3
cda-import/src/test/java/org/aktin/cda/etl/TestTransformationLoader.java
...test/java/org/aktin/cda/etl/TestTransformationLoader.java
+1
-1
cda-import/src/test/resources/basismodul-minimal.xml
cda-import/src/test/resources/basismodul-minimal.xml
+851
-0
cda-server/pom.xml
cda-server/pom.xml
+1
-1
cda-server/src/main/java/org/aktin/cda/etl/fhir/Binary.java
cda-server/src/main/java/org/aktin/cda/etl/fhir/Binary.java
+3
-3
demo-server/src/main/java/org/aktin/cda/etl/demo/NoOpStatistics.java
.../src/main/java/org/aktin/cda/etl/demo/NoOpStatistics.java
+4
-3
demo-server/src/main/java/org/aktin/cda/etl/demo/Server.java
demo-server/src/main/java/org/aktin/cda/etl/demo/Server.java
+2
-0
No files found.
cda-import/src/main/java/org/aktin/cda/etl/AbstractCDAImporter.java
View file @
1f44cbb6
...
...
@@ -23,6 +23,7 @@ import org.aktin.cda.etl.transform.Transformation;
import
org.aktin.cda.etl.transform.TransformationFactory
;
import
org.aktin.dwh.Anonymizer
;
import
org.w3c.dom.Document
;
import
org.w3c.dom.Element
;
import
de.sekmi.histream.Observation
;
import
de.sekmi.histream.ObservationFactory
;
...
...
@@ -114,7 +115,8 @@ public abstract class AbstractCDAImporter implements CDAProcessor{
@Override
public
final
Path
transform
(
Document
document
,
String
templateId
)
throws
CDAException
,
UnsupportedTemplateException
{
try
{
Transformation
t
=
cdaToDataWarehouse
.
getTransformation
(
templateId
);
Element
rootEl
=
(
Element
)
document
.
getDocumentElement
();
Transformation
t
=
cdaToDataWarehouse
.
getTransformation
(
rootEl
.
getNamespaceURI
(),
rootEl
.
getLocalName
(),
templateId
);
if
(
t
==
null
){
throw
new
UnsupportedTemplateException
(
templateId
);
}
...
...
cda-import/src/main/java/org/aktin/cda/etl/transform/TransformationFactory.java
View file @
1f44cbb6
...
...
@@ -113,7 +113,7 @@ public class TransformationFactory {
public
Anonymizer
getAnonymizer
()
{
return
anonymizer
;
}
public
Transformation
getTransformation
(
String
templateId
)
throws
IOException
,
TransformerConfigurationException
,
TransformerFactoryConfigurationError
{
public
Transformation
getTransformation
(
String
documentRootNS
,
String
documentRootName
,
String
templateId
)
throws
IOException
,
TransformerConfigurationException
,
TransformerFactoryConfigurationError
{
// look in cache
Transformation
transform
=
cache
.
get
(
templateId
);
if
(
transform
==
null
){
...
...
cda-import/src/test/java/org/aktin/cda/etl/TestTransformToEAV.java
View file @
1f44cbb6
...
...
@@ -53,7 +53,7 @@ public class TestTransformToEAV {
public
void
transformExample1
()
throws
Exception
{
CDAParser
parser
=
new
CDAParser
();
CDAImporterMockUp
t
=
new
CDAImporterMockUp
();
try
(
InputStream
in
=
CDAParser
.
class
.
getResourceAsStream
(
"/
Additional Examples/basismodul-v2-beispiel-storyboard01-complete
.xml"
)
){
try
(
InputStream
in
=
CDAParser
.
class
.
getResourceAsStream
(
"/
basismodul-minimal
.xml"
)
){
Document
dom
=
parser
.
buildDOM
(
new
StreamSource
(
in
));
...
...
@@ -65,7 +65,8 @@ public class TestTransformToEAV {
// verify patient birth date
Patient
p
=
o
.
getExtension
(
Patient
.
class
);
Assert
.
assertNotNull
(
p
);
Assert
.
assertEquals
(
DateTimeAccuracy
.
parsePartialIso8601
(
"1996-05-31"
,
t
.
getDefaultZoneId
()),
p
.
getBirthDate
());
// no birthdate should be available
Assert
.
assertNull
(
p
.
getBirthDate
());
// verify visit start date
Visit
v
=
o
.
getExtension
(
Visit
.
class
);
Assert
.
assertNotNull
(
v
);
...
...
@@ -76,7 +77,7 @@ public class TestTransformToEAV {
Optional
<
Observation
>
opt
=
suppl
.
stream
().
filter
(
x
->
x
.
getConceptId
().
equals
(
"ICD10GM:S80.1"
)).
findFirst
();
Assert
.
assertTrue
(
opt
.
isPresent
());
o
=
opt
.
get
();
Assert
.
assertEquals
(
DateTimeAccuracy
.
parsePartialIso8601
(
"2015-01-17T1
5:56
+0100"
),
o
.
getStartTime
());
Assert
.
assertEquals
(
DateTimeAccuracy
.
parsePartialIso8601
(
"2015-01-17T1
6:03
+0100"
),
o
.
getStartTime
());
suppl
.
close
();
}
finally
{
...
...
cda-import/src/test/java/org/aktin/cda/etl/TestTransformationLoader.java
View file @
1f44cbb6
...
...
@@ -13,7 +13,7 @@ public class TestTransformationLoader {
f
.
setAnonymizer
(
new
ConcatAnonymizer
());
//XMLStreamReader xsr = inputFactory.createXMLStreamReader(getClass().getResourceAsStream("/cda-eav.xsl"));
// InputSource input = new InputSource(getClass().getResourceAsStream("/cda-eav.xsl"));
Transformation
t
=
f
.
getTransformation
(
"1.2.276.0.76.10.1019"
);
Transformation
t
=
f
.
getTransformation
(
"
..."
,
"ClinicalDocument"
,
"
1.2.276.0.76.10.1019"
);
Assert
.
assertNotNull
(
t
);
System
.
out
.
println
(
"template="
+
t
.
getTemplateId
());
System
.
out
.
println
(
"module="
+
t
.
getModuleId
());
...
...
cda-import/src/test/resources/basismodul-minimal.xml
0 → 100644
View file @
1f44cbb6
This diff is collapsed.
Click to expand it.
cda-server/pom.xml
View file @
1f44cbb6
...
...
@@ -77,7 +77,7 @@
<dependency>
<groupId>
org.aktin
</groupId>
<artifactId>
dwh-api
</artifactId>
<version>
0.
4
</version>
<version>
0.
5-SNAPSHOT
</version>
</dependency>
<!-- dependency injection -->
...
...
cda-server/src/main/java/org/aktin/cda/etl/fhir/Binary.java
View file @
1f44cbb6
...
...
@@ -161,13 +161,13 @@ public class Binary implements ExternalInterface{
location
=
URI
.
create
(
"Binary/"
+
stat
.
getDocumentId
()+
"/_history/0"
);
response
=
Response
.
created
(
location
);
hallihallo2
.
addCreated
();
hallihallo2
.
addCreated
(
templateId
);
importSuccessful
=
true
;
}
else
if
(
stat
.
getStatus
()
==
Status
.
Updated
){
response
=
Response
.
ok
();
location
=
URI
.
create
(
"Binary/"
+
stat
.
getDocumentId
());
// Location header not allowed for status 200
hallihallo2
.
addUpdated
();
hallihallo2
.
addUpdated
(
templateId
);
importSuccessful
=
true
;
}
else
if
(
stat
.
getStatus
()
==
Status
.
Rejected
)
{
response
=
Response
.
status
(
409
);
// HTTP conflict
...
...
@@ -211,7 +211,7 @@ public class Binary implements ExternalInterface{
// should add a Location header with the created id and version
// Location: [base]/Binary/[id]/_history/[vid]
if
(
false
==
importSuccessful
){
hallihallo2
.
addRejected
(
isValid
,
outcome
.
toString
());
hallihallo2
.
addRejected
(
templateId
,
isValid
,
outcome
.
toString
());
}
if
(
cda
!=
null
){
tryDebugProcessing
(
cda
,
outcome
);
...
...
demo-server/src/main/java/org/aktin/cda/etl/demo/NoOpStatistics.java
View file @
1f44cbb6
...
...
@@ -58,20 +58,21 @@ public class NoOpStatistics implements ImportSummary{
return
null
;
}
@Override
public
void
add
Rejected
(
boolean
valid
,
String
cause
)
{
public
void
add
Created
(
String
templateId
)
{
// TODO Auto-generated method stub
}
@Override
public
void
add
Created
(
)
{
public
void
add
Rejected
(
String
templateId
,
boolean
valid
,
String
cause
)
{
// TODO Auto-generated method stub
}
@Override
public
void
addUpdated
()
{
public
void
addUpdated
(
String
templateId
)
{
// TODO Auto-generated method stub
}
...
...
demo-server/src/main/java/org/aktin/cda/etl/demo/Server.java
View file @
1f44cbb6
...
...
@@ -6,6 +6,7 @@ import java.net.InetSocketAddress;
import
java.net.URI
;
import
java.net.URISyntaxException
;
import
java.net.UnknownHostException
;
import
java.util.Objects
;
import
java.util.logging.Logger
;
import
javax.xml.transform.TransformerConfigurationException
;
...
...
@@ -102,6 +103,7 @@ public class Server{
// publish XDS.b end point
Objects
.
requireNonNull
(
xdsService
);
xdsEndpoint
=
Endpoint
.
create
(
SOAPBinding
.
SOAP11HTTP_MTOM_BINDING
,
xdsService
);
xdsEndpoint
.
publish
(
server
.
createContext
(
XDS_CONTEXT_PATH
));
// enable MTOM for efficient binary transfer
...
...
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