mirror of
https://github.com/pcvolkmer/mv64e-onkostar-plugin-export.git
synced 2025-09-13 05:02:52 +00:00
Initial commit
This commit is contained in:
44
.gitignore
vendored
Normal file
44
.gitignore
vendored
Normal file
@@ -0,0 +1,44 @@
|
|||||||
|
HELP.md
|
||||||
|
.gradle
|
||||||
|
build/
|
||||||
|
target/
|
||||||
|
!gradle/wrapper/gradle-wrapper.jar
|
||||||
|
!**/src/main/**/build/
|
||||||
|
!**/src/test/**/build/
|
||||||
|
!.mvn/wrapper/maven-wrapper.jar
|
||||||
|
!**/src/main/**/target/
|
||||||
|
!**/src/test/**/target/
|
||||||
|
|
||||||
|
### STS ###
|
||||||
|
.apt_generated
|
||||||
|
.classpath
|
||||||
|
.factorypath
|
||||||
|
.project
|
||||||
|
.settings
|
||||||
|
.springBeans
|
||||||
|
.sts4-cache
|
||||||
|
bin/
|
||||||
|
!**/src/main/**/bin/
|
||||||
|
!**/src/test/**/bin/
|
||||||
|
|
||||||
|
### IntelliJ IDEA ###
|
||||||
|
.idea
|
||||||
|
*.iws
|
||||||
|
*.iml
|
||||||
|
*.ipr
|
||||||
|
out/
|
||||||
|
!**/src/main/**/out/
|
||||||
|
!**/src/test/**/out/
|
||||||
|
|
||||||
|
### NetBeans ###
|
||||||
|
/nbproject/private/
|
||||||
|
/nbbuild/
|
||||||
|
/dist/
|
||||||
|
/nbdist/
|
||||||
|
/.nb-gradle/
|
||||||
|
|
||||||
|
### VS Code ###
|
||||||
|
.vscode/
|
||||||
|
|
||||||
|
### Onkostar Libs ###
|
||||||
|
libs/*.jar
|
||||||
165
LICENSE.txt
Normal file
165
LICENSE.txt
Normal file
@@ -0,0 +1,165 @@
|
|||||||
|
GNU LESSER GENERAL PUBLIC LICENSE
|
||||||
|
Version 3, 29 June 2007
|
||||||
|
|
||||||
|
Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
|
||||||
|
Everyone is permitted to copy and distribute verbatim copies
|
||||||
|
of this license document, but changing it is not allowed.
|
||||||
|
|
||||||
|
|
||||||
|
This version of the GNU Lesser General Public License incorporates
|
||||||
|
the terms and conditions of version 3 of the GNU General Public
|
||||||
|
License, supplemented by the additional permissions listed below.
|
||||||
|
|
||||||
|
0. Additional Definitions.
|
||||||
|
|
||||||
|
As used herein, "this License" refers to version 3 of the GNU Lesser
|
||||||
|
General Public License, and the "GNU GPL" refers to version 3 of the GNU
|
||||||
|
General Public License.
|
||||||
|
|
||||||
|
"The Library" refers to a covered work governed by this License,
|
||||||
|
other than an Application or a Combined Work as defined below.
|
||||||
|
|
||||||
|
An "Application" is any work that makes use of an interface provided
|
||||||
|
by the Library, but which is not otherwise based on the Library.
|
||||||
|
Defining a subclass of a class defined by the Library is deemed a mode
|
||||||
|
of using an interface provided by the Library.
|
||||||
|
|
||||||
|
A "Combined Work" is a work produced by combining or linking an
|
||||||
|
Application with the Library. The particular version of the Library
|
||||||
|
with which the Combined Work was made is also called the "Linked
|
||||||
|
Version".
|
||||||
|
|
||||||
|
The "Minimal Corresponding Source" for a Combined Work means the
|
||||||
|
Corresponding Source for the Combined Work, excluding any source code
|
||||||
|
for portions of the Combined Work that, considered in isolation, are
|
||||||
|
based on the Application, and not on the Linked Version.
|
||||||
|
|
||||||
|
The "Corresponding Application Code" for a Combined Work means the
|
||||||
|
object code and/or source code for the Application, including any data
|
||||||
|
and utility programs needed for reproducing the Combined Work from the
|
||||||
|
Application, but excluding the System Libraries of the Combined Work.
|
||||||
|
|
||||||
|
1. Exception to Section 3 of the GNU GPL.
|
||||||
|
|
||||||
|
You may convey a covered work under sections 3 and 4 of this License
|
||||||
|
without being bound by section 3 of the GNU GPL.
|
||||||
|
|
||||||
|
2. Conveying Modified Versions.
|
||||||
|
|
||||||
|
If you modify a copy of the Library, and, in your modifications, a
|
||||||
|
facility refers to a function or data to be supplied by an Application
|
||||||
|
that uses the facility (other than as an argument passed when the
|
||||||
|
facility is invoked), then you may convey a copy of the modified
|
||||||
|
version:
|
||||||
|
|
||||||
|
a) under this License, provided that you make a good faith effort to
|
||||||
|
ensure that, in the event an Application does not supply the
|
||||||
|
function or data, the facility still operates, and performs
|
||||||
|
whatever part of its purpose remains meaningful, or
|
||||||
|
|
||||||
|
b) under the GNU GPL, with none of the additional permissions of
|
||||||
|
this License applicable to that copy.
|
||||||
|
|
||||||
|
3. Object Code Incorporating Material from Library Header Files.
|
||||||
|
|
||||||
|
The object code form of an Application may incorporate material from
|
||||||
|
a header file that is part of the Library. You may convey such object
|
||||||
|
code under terms of your choice, provided that, if the incorporated
|
||||||
|
material is not limited to numerical parameters, data structure
|
||||||
|
layouts and accessors, or small macros, inline functions and templates
|
||||||
|
(ten or fewer lines in length), you do both of the following:
|
||||||
|
|
||||||
|
a) Give prominent notice with each copy of the object code that the
|
||||||
|
Library is used in it and that the Library and its use are
|
||||||
|
covered by this License.
|
||||||
|
|
||||||
|
b) Accompany the object code with a copy of the GNU GPL and this license
|
||||||
|
document.
|
||||||
|
|
||||||
|
4. Combined Works.
|
||||||
|
|
||||||
|
You may convey a Combined Work under terms of your choice that,
|
||||||
|
taken together, effectively do not restrict modification of the
|
||||||
|
portions of the Library contained in the Combined Work and reverse
|
||||||
|
engineering for debugging such modifications, if you also do each of
|
||||||
|
the following:
|
||||||
|
|
||||||
|
a) Give prominent notice with each copy of the Combined Work that
|
||||||
|
the Library is used in it and that the Library and its use are
|
||||||
|
covered by this License.
|
||||||
|
|
||||||
|
b) Accompany the Combined Work with a copy of the GNU GPL and this license
|
||||||
|
document.
|
||||||
|
|
||||||
|
c) For a Combined Work that displays copyright notices during
|
||||||
|
execution, include the copyright notice for the Library among
|
||||||
|
these notices, as well as a reference directing the user to the
|
||||||
|
copies of the GNU GPL and this license document.
|
||||||
|
|
||||||
|
d) Do one of the following:
|
||||||
|
|
||||||
|
0) Convey the Minimal Corresponding Source under the terms of this
|
||||||
|
License, and the Corresponding Application Code in a form
|
||||||
|
suitable for, and under terms that permit, the user to
|
||||||
|
recombine or relink the Application with a modified version of
|
||||||
|
the Linked Version to produce a modified Combined Work, in the
|
||||||
|
manner specified by section 6 of the GNU GPL for conveying
|
||||||
|
Corresponding Source.
|
||||||
|
|
||||||
|
1) Use a suitable shared library mechanism for linking with the
|
||||||
|
Library. A suitable mechanism is one that (a) uses at run time
|
||||||
|
a copy of the Library already present on the user's computer
|
||||||
|
system, and (b) will operate properly with a modified version
|
||||||
|
of the Library that is interface-compatible with the Linked
|
||||||
|
Version.
|
||||||
|
|
||||||
|
e) Provide Installation Information, but only if you would otherwise
|
||||||
|
be required to provide such information under section 6 of the
|
||||||
|
GNU GPL, and only to the extent that such information is
|
||||||
|
necessary to install and execute a modified version of the
|
||||||
|
Combined Work produced by recombining or relinking the
|
||||||
|
Application with a modified version of the Linked Version. (If
|
||||||
|
you use option 4d0, the Installation Information must accompany
|
||||||
|
the Minimal Corresponding Source and Corresponding Application
|
||||||
|
Code. If you use option 4d1, you must provide the Installation
|
||||||
|
Information in the manner specified by section 6 of the GNU GPL
|
||||||
|
for conveying Corresponding Source.)
|
||||||
|
|
||||||
|
5. Combined Libraries.
|
||||||
|
|
||||||
|
You may place library facilities that are a work based on the
|
||||||
|
Library side by side in a single library together with other library
|
||||||
|
facilities that are not Applications and are not covered by this
|
||||||
|
License, and convey such a combined library under terms of your
|
||||||
|
choice, if you do both of the following:
|
||||||
|
|
||||||
|
a) Accompany the combined library with a copy of the same work based
|
||||||
|
on the Library, uncombined with any other library facilities,
|
||||||
|
conveyed under the terms of this License.
|
||||||
|
|
||||||
|
b) Give prominent notice with the combined library that part of it
|
||||||
|
is a work based on the Library, and explaining where to find the
|
||||||
|
accompanying uncombined form of the same work.
|
||||||
|
|
||||||
|
6. Revised Versions of the GNU Lesser General Public License.
|
||||||
|
|
||||||
|
The Free Software Foundation may publish revised and/or new versions
|
||||||
|
of the GNU Lesser General Public License from time to time. Such new
|
||||||
|
versions will be similar in spirit to the present version, but may
|
||||||
|
differ in detail to address new problems or concerns.
|
||||||
|
|
||||||
|
Each version is given a distinguishing version number. If the
|
||||||
|
Library as you received it specifies that a certain numbered version
|
||||||
|
of the GNU Lesser General Public License "or any later version"
|
||||||
|
applies to it, you have the option of following the terms and
|
||||||
|
conditions either of that published version or of any later version
|
||||||
|
published by the Free Software Foundation. If the Library as you
|
||||||
|
received it does not specify a version number of the GNU Lesser
|
||||||
|
General Public License, you may choose any version of the GNU Lesser
|
||||||
|
General Public License ever published by the Free Software Foundation.
|
||||||
|
|
||||||
|
If the Library as you received it specifies that a proxy can decide
|
||||||
|
whether future versions of the GNU Lesser General Public License shall
|
||||||
|
apply, that proxy's public statement of acceptance of any version is
|
||||||
|
permanent authorization for you to choose that version for the
|
||||||
|
Library.
|
||||||
61
README.md
Normal file
61
README.md
Normal file
@@ -0,0 +1,61 @@
|
|||||||
|
# Onkostar Plugin "mv64e-onkostar-plugin-export"
|
||||||
|
|
||||||
|
Aufgabe dieses Plugins ist es, die Inhalte der DNPM-Formulare in die Datenstruktur des DNPM-Datenmodells 2.1 zu wandeln
|
||||||
|
und anhand festgelegter Regeln die Notwendigkeit zum Export zu prüfen und diesen durchzuführen.
|
||||||
|
|
||||||
|
Hierzu verwendet das Plugin das Projekt https://github.com/pcvolkmer/mv64e-onkostar-data.
|
||||||
|
|
||||||
|
## Einstellungen
|
||||||
|
|
||||||
|
Zum Betrieb dieses Plugins ist die Angabe der URL der Zielanwendung erforderlich.
|
||||||
|
|
||||||
|
Dies lässt sich initial durch folgende Datenbankanfrage anlegen, später dann in den allgemeinen Einstellungen von
|
||||||
|
Onkostar auch ändern.
|
||||||
|
|
||||||
|
```
|
||||||
|
INSERT INTO einstellung
|
||||||
|
(name, wert, kategorie, beschreibung)
|
||||||
|
VALUES(
|
||||||
|
'dnpmexport_url',
|
||||||
|
'http://localhost:9000/mtb/etl/patient-record',
|
||||||
|
'DNPM',
|
||||||
|
'DNPM-Export - URL'
|
||||||
|
);
|
||||||
|
|
||||||
|
INSERT INTO einstellung
|
||||||
|
(name, wert, kategorie, beschreibung)
|
||||||
|
VALUES(
|
||||||
|
'dnpmexport_prefix',
|
||||||
|
'TEST',
|
||||||
|
'DNPM',
|
||||||
|
'DNPM-Export - Prefix'
|
||||||
|
);
|
||||||
|
```
|
||||||
|
|
||||||
|
## Einordnung innerhalb einer DNPM-ETL-Strecke
|
||||||
|
|
||||||
|
Dieses Plugin erlaubt das Extrahieren (das "E" in ETL) der benötigten Informationen aus Onkostar und das Übertragen an
|
||||||
|
die weitere ETL-Strecke.
|
||||||
|
|
||||||
|
## Ablauf des Exports
|
||||||
|
|
||||||
|
Beim Abschließen eines DNPM-Formulars wird für die Formulare (und damit auch Unterformulare)
|
||||||
|
|
||||||
|
* DNPM Klinik/Anamnese
|
||||||
|
* DNPM Therapieplan
|
||||||
|
* DNPM FollowUp *(aktuell nicht nicht umgesetzt)*
|
||||||
|
|
||||||
|
der Inhalt aller zugehörigen DNPM-Formulare für den Patienten und die Erkrankung, für den/die ein DNPM-Formular
|
||||||
|
abgeschlossen wurde, ermittelt und zusammengetragen.
|
||||||
|
|
||||||
|
Hierbei wird im Falle eines Formulars *DNPM Therapieplan* das entsprechende Formular *DNPM Klinik/Anamnese* ermittelt
|
||||||
|
und in Folge die zugehörigen Formulare ermittelt:
|
||||||
|
|
||||||
|
* **DNPM Klinik/Anamnese** => Ermittlung der Formulare *DNPM Therapieplan* die einen Formularverweis auf dieses Formular
|
||||||
|
eingetragen haben.
|
||||||
|
* **DNPM Therapieplan** => Ermittlung der Formulare *DNPM FollowUp* die einen Formularverweis auf dieses Formular
|
||||||
|
eingetragen haben.
|
||||||
|
Zudem werden die Formulare *OS.Tumorkonferenz* und *OS.Molekulargenetik* anhand der verwendeten Verweise ermittelt.
|
||||||
|
|
||||||
|
Die Übermittlung erfolgt ohne weiteres Zutun von Seiten des Anwenders und wird bereits durch das Abschließen eines
|
||||||
|
DNPM-Formulars ausgelöst.
|
||||||
55
build.gradle
Normal file
55
build.gradle
Normal file
@@ -0,0 +1,55 @@
|
|||||||
|
plugins {
|
||||||
|
id 'java-library'
|
||||||
|
}
|
||||||
|
|
||||||
|
group = 'dev.pcvolkmer.onco'
|
||||||
|
version = '0.1.0-SNAPSHOT'
|
||||||
|
description = 'OS Export-Plugin für das DNPM-Datenmodell 2.1'
|
||||||
|
|
||||||
|
java.sourceCompatibility = JavaVersion.VERSION_11
|
||||||
|
|
||||||
|
repositories {
|
||||||
|
mavenLocal()
|
||||||
|
mavenCentral()
|
||||||
|
}
|
||||||
|
|
||||||
|
configurations {
|
||||||
|
configureEach {
|
||||||
|
resolutionStrategy {
|
||||||
|
cacheChangingModulesFor(5, "minutes")
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ext {
|
||||||
|
onkostarVersion = '2.14.1'
|
||||||
|
springVersion = '4.3.8.RELEASE'
|
||||||
|
slf4jVersion = '1.7.2'
|
||||||
|
junitVersion = '5.12.1'
|
||||||
|
assertjVersion = '3.27.3'
|
||||||
|
mockitoVersion = '5.16.1'
|
||||||
|
}
|
||||||
|
|
||||||
|
dependencies {
|
||||||
|
implementation files("./libs/onkostar-api-${onkostarVersion}.jar")
|
||||||
|
|
||||||
|
implementation "org.springframework:spring-beans:${springVersion}"
|
||||||
|
implementation "org.springframework:spring-context:${springVersion}"
|
||||||
|
implementation "org.springframework:spring-jdbc:${springVersion}"
|
||||||
|
implementation "org.slf4j:slf4j-api:${slf4jVersion}"
|
||||||
|
|
||||||
|
implementation("dev.pcvolkmer.onco:mv64e-onkostar-data:0.1.0-SNAPSHOT") { changing = true }
|
||||||
|
|
||||||
|
testImplementation "org.springframework:spring-test:${springVersion}"
|
||||||
|
testImplementation "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
|
||||||
|
testImplementation "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
|
||||||
|
testImplementation "org.assertj:assertj-core:${assertjVersion}"
|
||||||
|
testImplementation "org.mockito:mockito-core:${mockitoVersion}"
|
||||||
|
testImplementation "org.mockito:mockito-junit-jupiter:${mockitoVersion}"
|
||||||
|
testImplementation "ca.uhn.hapi:hapi-structures-v26:2.3"
|
||||||
|
testImplementation "org.hibernate:hibernate-core:4.3.11.Final"
|
||||||
|
}
|
||||||
|
|
||||||
|
tasks.named('test') {
|
||||||
|
useJUnitPlatform()
|
||||||
|
}
|
||||||
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
Binary file not shown.
7
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
7
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
@@ -0,0 +1,7 @@
|
|||||||
|
distributionBase=GRADLE_USER_HOME
|
||||||
|
distributionPath=wrapper/dists
|
||||||
|
distributionUrl=https\://services.gradle.org/distributions/gradle-8.10-bin.zip
|
||||||
|
networkTimeout=10000
|
||||||
|
validateDistributionUrl=true
|
||||||
|
zipStoreBase=GRADLE_USER_HOME
|
||||||
|
zipStorePath=wrapper/dists
|
||||||
252
gradlew
vendored
Executable file
252
gradlew
vendored
Executable file
@@ -0,0 +1,252 @@
|
|||||||
|
#!/bin/sh
|
||||||
|
|
||||||
|
#
|
||||||
|
# Copyright © 2015-2021 the original authors.
|
||||||
|
#
|
||||||
|
# Licensed 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
|
||||||
|
#
|
||||||
|
# https://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.
|
||||||
|
#
|
||||||
|
# SPDX-License-Identifier: Apache-2.0
|
||||||
|
#
|
||||||
|
|
||||||
|
##############################################################################
|
||||||
|
#
|
||||||
|
# Gradle start up script for POSIX generated by Gradle.
|
||||||
|
#
|
||||||
|
# Important for running:
|
||||||
|
#
|
||||||
|
# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
|
||||||
|
# noncompliant, but you have some other compliant shell such as ksh or
|
||||||
|
# bash, then to run this script, type that shell name before the whole
|
||||||
|
# command line, like:
|
||||||
|
#
|
||||||
|
# ksh Gradle
|
||||||
|
#
|
||||||
|
# Busybox and similar reduced shells will NOT work, because this script
|
||||||
|
# requires all of these POSIX shell features:
|
||||||
|
# * functions;
|
||||||
|
# * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
|
||||||
|
# «${var#prefix}», «${var%suffix}», and «$( cmd )»;
|
||||||
|
# * compound commands having a testable exit status, especially «case»;
|
||||||
|
# * various built-in commands including «command», «set», and «ulimit».
|
||||||
|
#
|
||||||
|
# Important for patching:
|
||||||
|
#
|
||||||
|
# (2) This script targets any POSIX shell, so it avoids extensions provided
|
||||||
|
# by Bash, Ksh, etc; in particular arrays are avoided.
|
||||||
|
#
|
||||||
|
# The "traditional" practice of packing multiple parameters into a
|
||||||
|
# space-separated string is a well documented source of bugs and security
|
||||||
|
# problems, so this is (mostly) avoided, by progressively accumulating
|
||||||
|
# options in "$@", and eventually passing that to Java.
|
||||||
|
#
|
||||||
|
# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
|
||||||
|
# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
|
||||||
|
# see the in-line comments for details.
|
||||||
|
#
|
||||||
|
# There are tweaks for specific operating systems such as AIX, CygWin,
|
||||||
|
# Darwin, MinGW, and NonStop.
|
||||||
|
#
|
||||||
|
# (3) This script is generated from the Groovy template
|
||||||
|
# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
|
||||||
|
# within the Gradle project.
|
||||||
|
#
|
||||||
|
# You can find Gradle at https://github.com/gradle/gradle/.
|
||||||
|
#
|
||||||
|
##############################################################################
|
||||||
|
|
||||||
|
# Attempt to set APP_HOME
|
||||||
|
|
||||||
|
# Resolve links: $0 may be a link
|
||||||
|
app_path=$0
|
||||||
|
|
||||||
|
# Need this for daisy-chained symlinks.
|
||||||
|
while
|
||||||
|
APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path
|
||||||
|
[ -h "$app_path" ]
|
||||||
|
do
|
||||||
|
ls=$( ls -ld "$app_path" )
|
||||||
|
link=${ls#*' -> '}
|
||||||
|
case $link in #(
|
||||||
|
/*) app_path=$link ;; #(
|
||||||
|
*) app_path=$APP_HOME$link ;;
|
||||||
|
esac
|
||||||
|
done
|
||||||
|
|
||||||
|
# This is normally unused
|
||||||
|
# shellcheck disable=SC2034
|
||||||
|
APP_BASE_NAME=${0##*/}
|
||||||
|
# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
|
||||||
|
APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
|
||||||
|
' "$PWD" ) || exit
|
||||||
|
|
||||||
|
# Use the maximum available, or set MAX_FD != -1 to use that value.
|
||||||
|
MAX_FD=maximum
|
||||||
|
|
||||||
|
warn () {
|
||||||
|
echo "$*"
|
||||||
|
} >&2
|
||||||
|
|
||||||
|
die () {
|
||||||
|
echo
|
||||||
|
echo "$*"
|
||||||
|
echo
|
||||||
|
exit 1
|
||||||
|
} >&2
|
||||||
|
|
||||||
|
# OS specific support (must be 'true' or 'false').
|
||||||
|
cygwin=false
|
||||||
|
msys=false
|
||||||
|
darwin=false
|
||||||
|
nonstop=false
|
||||||
|
case "$( uname )" in #(
|
||||||
|
CYGWIN* ) cygwin=true ;; #(
|
||||||
|
Darwin* ) darwin=true ;; #(
|
||||||
|
MSYS* | MINGW* ) msys=true ;; #(
|
||||||
|
NONSTOP* ) nonstop=true ;;
|
||||||
|
esac
|
||||||
|
|
||||||
|
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
|
||||||
|
|
||||||
|
|
||||||
|
# Determine the Java command to use to start the JVM.
|
||||||
|
if [ -n "$JAVA_HOME" ] ; then
|
||||||
|
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
|
||||||
|
# IBM's JDK on AIX uses strange locations for the executables
|
||||||
|
JAVACMD=$JAVA_HOME/jre/sh/java
|
||||||
|
else
|
||||||
|
JAVACMD=$JAVA_HOME/bin/java
|
||||||
|
fi
|
||||||
|
if [ ! -x "$JAVACMD" ] ; then
|
||||||
|
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
JAVACMD=java
|
||||||
|
if ! command -v java >/dev/null 2>&1
|
||||||
|
then
|
||||||
|
die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Increase the maximum file descriptors if we can.
|
||||||
|
if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
|
||||||
|
case $MAX_FD in #(
|
||||||
|
max*)
|
||||||
|
# In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
|
||||||
|
# shellcheck disable=SC2039,SC3045
|
||||||
|
MAX_FD=$( ulimit -H -n ) ||
|
||||||
|
warn "Could not query maximum file descriptor limit"
|
||||||
|
esac
|
||||||
|
case $MAX_FD in #(
|
||||||
|
'' | soft) :;; #(
|
||||||
|
*)
|
||||||
|
# In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
|
||||||
|
# shellcheck disable=SC2039,SC3045
|
||||||
|
ulimit -n "$MAX_FD" ||
|
||||||
|
warn "Could not set maximum file descriptor limit to $MAX_FD"
|
||||||
|
esac
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Collect all arguments for the java command, stacking in reverse order:
|
||||||
|
# * args from the command line
|
||||||
|
# * the main class name
|
||||||
|
# * -classpath
|
||||||
|
# * -D...appname settings
|
||||||
|
# * --module-path (only if needed)
|
||||||
|
# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
|
||||||
|
|
||||||
|
# For Cygwin or MSYS, switch paths to Windows format before running java
|
||||||
|
if "$cygwin" || "$msys" ; then
|
||||||
|
APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
|
||||||
|
CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
|
||||||
|
|
||||||
|
JAVACMD=$( cygpath --unix "$JAVACMD" )
|
||||||
|
|
||||||
|
# Now convert the arguments - kludge to limit ourselves to /bin/sh
|
||||||
|
for arg do
|
||||||
|
if
|
||||||
|
case $arg in #(
|
||||||
|
-*) false ;; # don't mess with options #(
|
||||||
|
/?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath
|
||||||
|
[ -e "$t" ] ;; #(
|
||||||
|
*) false ;;
|
||||||
|
esac
|
||||||
|
then
|
||||||
|
arg=$( cygpath --path --ignore --mixed "$arg" )
|
||||||
|
fi
|
||||||
|
# Roll the args list around exactly as many times as the number of
|
||||||
|
# args, so each arg winds up back in the position where it started, but
|
||||||
|
# possibly modified.
|
||||||
|
#
|
||||||
|
# NB: a `for` loop captures its iteration list before it begins, so
|
||||||
|
# changing the positional parameters here affects neither the number of
|
||||||
|
# iterations, nor the values presented in `arg`.
|
||||||
|
shift # remove old arg
|
||||||
|
set -- "$@" "$arg" # push replacement arg
|
||||||
|
done
|
||||||
|
fi
|
||||||
|
|
||||||
|
|
||||||
|
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
|
||||||
|
|
||||||
|
# Collect all arguments for the java command:
|
||||||
|
# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
|
||||||
|
# and any embedded shellness will be escaped.
|
||||||
|
# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
|
||||||
|
# treated as '${Hostname}' itself on the command line.
|
||||||
|
|
||||||
|
set -- \
|
||||||
|
"-Dorg.gradle.appname=$APP_BASE_NAME" \
|
||||||
|
-classpath "$CLASSPATH" \
|
||||||
|
org.gradle.wrapper.GradleWrapperMain \
|
||||||
|
"$@"
|
||||||
|
|
||||||
|
# Stop when "xargs" is not available.
|
||||||
|
if ! command -v xargs >/dev/null 2>&1
|
||||||
|
then
|
||||||
|
die "xargs is not available"
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Use "xargs" to parse quoted args.
|
||||||
|
#
|
||||||
|
# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
|
||||||
|
#
|
||||||
|
# In Bash we could simply go:
|
||||||
|
#
|
||||||
|
# readarray ARGS < <( xargs -n1 <<<"$var" ) &&
|
||||||
|
# set -- "${ARGS[@]}" "$@"
|
||||||
|
#
|
||||||
|
# but POSIX shell has neither arrays nor command substitution, so instead we
|
||||||
|
# post-process each arg (as a line of input to sed) to backslash-escape any
|
||||||
|
# character that might be a shell metacharacter, then use eval to reverse
|
||||||
|
# that process (while maintaining the separation between arguments), and wrap
|
||||||
|
# the whole thing up as a single "set" statement.
|
||||||
|
#
|
||||||
|
# This will of course break if any of these variables contains a newline or
|
||||||
|
# an unmatched quote.
|
||||||
|
#
|
||||||
|
|
||||||
|
eval "set -- $(
|
||||||
|
printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
|
||||||
|
xargs -n1 |
|
||||||
|
sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
|
||||||
|
tr '\n' ' '
|
||||||
|
)" '"$@"'
|
||||||
|
|
||||||
|
exec "$JAVACMD" "$@"
|
||||||
94
gradlew.bat
vendored
Normal file
94
gradlew.bat
vendored
Normal file
@@ -0,0 +1,94 @@
|
|||||||
|
@rem
|
||||||
|
@rem Copyright 2015 the original author or authors.
|
||||||
|
@rem
|
||||||
|
@rem Licensed under the Apache License, Version 2.0 (the "License");
|
||||||
|
@rem you may not use this file except in compliance with the License.
|
||||||
|
@rem You may obtain a copy of the License at
|
||||||
|
@rem
|
||||||
|
@rem https://www.apache.org/licenses/LICENSE-2.0
|
||||||
|
@rem
|
||||||
|
@rem Unless required by applicable law or agreed to in writing, software
|
||||||
|
@rem distributed under the License is distributed on an "AS IS" BASIS,
|
||||||
|
@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||||
|
@rem See the License for the specific language governing permissions and
|
||||||
|
@rem limitations under the License.
|
||||||
|
@rem
|
||||||
|
@rem SPDX-License-Identifier: Apache-2.0
|
||||||
|
@rem
|
||||||
|
|
||||||
|
@if "%DEBUG%"=="" @echo off
|
||||||
|
@rem ##########################################################################
|
||||||
|
@rem
|
||||||
|
@rem Gradle startup script for Windows
|
||||||
|
@rem
|
||||||
|
@rem ##########################################################################
|
||||||
|
|
||||||
|
@rem Set local scope for the variables with windows NT shell
|
||||||
|
if "%OS%"=="Windows_NT" setlocal
|
||||||
|
|
||||||
|
set DIRNAME=%~dp0
|
||||||
|
if "%DIRNAME%"=="" set DIRNAME=.
|
||||||
|
@rem This is normally unused
|
||||||
|
set APP_BASE_NAME=%~n0
|
||||||
|
set APP_HOME=%DIRNAME%
|
||||||
|
|
||||||
|
@rem Resolve any "." and ".." in APP_HOME to make it shorter.
|
||||||
|
for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
|
||||||
|
|
||||||
|
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
|
||||||
|
|
||||||
|
@rem Find java.exe
|
||||||
|
if defined JAVA_HOME goto findJavaFromJavaHome
|
||||||
|
|
||||||
|
set JAVA_EXE=java.exe
|
||||||
|
%JAVA_EXE% -version >NUL 2>&1
|
||||||
|
if %ERRORLEVEL% equ 0 goto execute
|
||||||
|
|
||||||
|
echo. 1>&2
|
||||||
|
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
|
||||||
|
echo. 1>&2
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
|
||||||
|
echo location of your Java installation. 1>&2
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:findJavaFromJavaHome
|
||||||
|
set JAVA_HOME=%JAVA_HOME:"=%
|
||||||
|
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
|
||||||
|
|
||||||
|
if exist "%JAVA_EXE%" goto execute
|
||||||
|
|
||||||
|
echo. 1>&2
|
||||||
|
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
|
||||||
|
echo. 1>&2
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the 1>&2
|
||||||
|
echo location of your Java installation. 1>&2
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:execute
|
||||||
|
@rem Setup the command line
|
||||||
|
|
||||||
|
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
|
||||||
|
|
||||||
|
|
||||||
|
@rem Execute Gradle
|
||||||
|
"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
|
||||||
|
|
||||||
|
:end
|
||||||
|
@rem End local scope for the variables with windows NT shell
|
||||||
|
if %ERRORLEVEL% equ 0 goto mainEnd
|
||||||
|
|
||||||
|
:fail
|
||||||
|
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
|
||||||
|
rem the _cmd.exe /c_ return code!
|
||||||
|
set EXIT_CODE=%ERRORLEVEL%
|
||||||
|
if %EXIT_CODE% equ 0 set EXIT_CODE=1
|
||||||
|
if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
|
||||||
|
exit /b %EXIT_CODE%
|
||||||
|
|
||||||
|
:mainEnd
|
||||||
|
if "%OS%"=="Windows_NT" endlocal
|
||||||
|
|
||||||
|
:omega
|
||||||
1
libs/.gitkeep
Normal file
1
libs/.gitkeep
Normal file
@@ -0,0 +1 @@
|
|||||||
|
Place onkostar-api.jar here
|
||||||
1
settings.gradle
Normal file
1
settings.gradle
Normal file
@@ -0,0 +1 @@
|
|||||||
|
rootProject.name = 'mv64e-onkostar-export'
|
||||||
106
src/main/java/dev/pcvolkmer/onco/dnpmexport/ExportAnalyzer.java
Normal file
106
src/main/java/dev/pcvolkmer/onco/dnpmexport/ExportAnalyzer.java
Normal file
@@ -0,0 +1,106 @@
|
|||||||
|
package dev.pcvolkmer.onco.dnpmexport;
|
||||||
|
|
||||||
|
import de.itc.onkostar.api.Disease;
|
||||||
|
import de.itc.onkostar.api.IOnkostarApi;
|
||||||
|
import de.itc.onkostar.api.Procedure;
|
||||||
|
import de.itc.onkostar.api.analysis.AnalyzerRequirement;
|
||||||
|
import de.itc.onkostar.api.analysis.IProcedureAnalyzer;
|
||||||
|
import de.itc.onkostar.api.analysis.OnkostarPluginType;
|
||||||
|
import dev.pcvolkmer.onco.datamapper.mapper.MtbDataMapper;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
import org.springframework.stereotype.Component;
|
||||||
|
|
||||||
|
import javax.sql.DataSource;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Analyzer to start export if DNPM Klinik/Anamnese or DNPM Therapieplan form gets locked
|
||||||
|
*
|
||||||
|
* @author Paul-Christian Volkmer
|
||||||
|
* @since 0.1
|
||||||
|
*/
|
||||||
|
@Component
|
||||||
|
public class ExportAnalyzer implements IProcedureAnalyzer {
|
||||||
|
|
||||||
|
private static final Logger logger = LoggerFactory.getLogger(ExportAnalyzer.class);
|
||||||
|
|
||||||
|
private final IOnkostarApi onkostarApi;
|
||||||
|
private final MtbDataMapper mtbDataMapper;
|
||||||
|
|
||||||
|
public ExportAnalyzer(final IOnkostarApi onkostarApi, final DataSource dataSource) {
|
||||||
|
this.onkostarApi = onkostarApi;
|
||||||
|
// Reuse default Onkostar DataSource for MtbDataMapper
|
||||||
|
this.mtbDataMapper = MtbDataMapper.create(dataSource);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public OnkostarPluginType getType() {
|
||||||
|
return OnkostarPluginType.ANALYZER;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getVersion() {
|
||||||
|
return "0.1.0";
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getName() {
|
||||||
|
return "DNPM-Export-Plugin";
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getDescription() {
|
||||||
|
return "OS Export-Plugin für das DNPM-Datenmodell 2.1";
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isSynchronous() {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public AnalyzerRequirement getRequirement() {
|
||||||
|
return AnalyzerRequirement.PROCEDURE;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isRelevantForDeletedProcedure() {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean isRelevantForAnalyzer(final Procedure procedure, final Disease disease) {
|
||||||
|
return null != procedure
|
||||||
|
&& ("DNPM Klinik/Anamnese".equals(procedure.getFormName()) || "DNPM Therapieplan".equals(procedure.getFormName()));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void analyze(final Procedure procedure, final Disease disease) {
|
||||||
|
logger.info("Starting export for procedure {}", procedure.getId());
|
||||||
|
|
||||||
|
try {
|
||||||
|
String caseId = "";
|
||||||
|
switch (procedure.getFormName()) {
|
||||||
|
case "DNPM Klinik/Anamnese":
|
||||||
|
caseId = procedure.getValue("FallnummrMV").getString();
|
||||||
|
break;
|
||||||
|
case "DNPM Therapieplan":
|
||||||
|
var kpaProcedure = onkostarApi.getProcedure(
|
||||||
|
procedure.getValue("ref_dnpm_klinikanamnese").getInt()
|
||||||
|
);
|
||||||
|
caseId = kpaProcedure.getValue("FallnummrMV").getString();
|
||||||
|
break;
|
||||||
|
default:
|
||||||
|
logger.info("Cannot handle procedure form {}", procedure.getFormName());
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
var mtb = mtbDataMapper.getByCaseId(caseId);
|
||||||
|
|
||||||
|
// TODO: Send MTB data to remote application
|
||||||
|
} catch (Exception e) {
|
||||||
|
logger.error("Could export mtb data for procedure {}", procedure.getId(), e);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
10
src/main/resources/de/itc/onkostar/library/moduleContext.xml
Normal file
10
src/main/resources/de/itc/onkostar/library/moduleContext.xml
Normal file
@@ -0,0 +1,10 @@
|
|||||||
|
<?xml version="1.0" encoding="UTF-8"?>
|
||||||
|
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||||
|
xmlns:context="http://www.springframework.org/schema/context"
|
||||||
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||||
|
xsi:schemaLocation="
|
||||||
|
http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-3.1.xsd
|
||||||
|
http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.1.xsd">
|
||||||
|
|
||||||
|
<context:component-scan base-package="dev.pcvolkmer.onco.dnpmexport" />
|
||||||
|
</beans>
|
||||||
1
src/main/resources/onkostar-config.properties
Normal file
1
src/main/resources/onkostar-config.properties
Normal file
@@ -0,0 +1 @@
|
|||||||
|
onkostar-api=2.14.1
|
||||||
@@ -0,0 +1,34 @@
|
|||||||
|
package dev.pcvolkmer.onco.dnpmexport;
|
||||||
|
|
||||||
|
import de.itc.onkostar.api.IOnkostarApi;
|
||||||
|
import org.junit.jupiter.api.BeforeEach;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
import org.junit.jupiter.api.extension.ExtendWith;
|
||||||
|
import org.mockito.Mock;
|
||||||
|
import org.mockito.junit.jupiter.MockitoExtension;
|
||||||
|
|
||||||
|
import javax.sql.DataSource;
|
||||||
|
|
||||||
|
@ExtendWith(MockitoExtension.class)
|
||||||
|
class ExportAnalyzerTest {
|
||||||
|
|
||||||
|
private IOnkostarApi onkostarApi;
|
||||||
|
private DataSource dataSource;
|
||||||
|
|
||||||
|
private ExportAnalyzer analyzer;
|
||||||
|
|
||||||
|
@BeforeEach
|
||||||
|
void setup(
|
||||||
|
@Mock IOnkostarApi onkostarApi,
|
||||||
|
@Mock DataSource dataSource
|
||||||
|
) {
|
||||||
|
this.onkostarApi = onkostarApi;
|
||||||
|
this.dataSource = dataSource;
|
||||||
|
this.analyzer = new ExportAnalyzer(onkostarApi, dataSource);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testShouldTestSomeAnalyzerImplementation() {
|
||||||
|
// Implement your first test
|
||||||
|
}
|
||||||
|
}
|
||||||
Reference in New Issue
Block a user