mirror of
https://github.com/dnpm-dip/mv64e-mtb-dto-java.git
synced 2025-07-01 10:12:55 +00:00
Initial commit
This commit is contained in:
39
.gitignore
vendored
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39
.gitignore
vendored
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|||||||
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.gradle
|
||||||
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build/
|
||||||
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!gradle/wrapper/gradle-wrapper.jar
|
||||||
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!**/src/main/**/build/
|
||||||
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!**/src/test/**/build/
|
||||||
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|
||||||
|
### IntelliJ IDEA ###
|
||||||
|
.idea/
|
||||||
|
*.iws
|
||||||
|
*.iml
|
||||||
|
*.ipr
|
||||||
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out/
|
||||||
|
!**/src/main/**/out/
|
||||||
|
!**/src/test/**/out/
|
||||||
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|
||||||
|
### Eclipse ###
|
||||||
|
.apt_generated
|
||||||
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.classpath
|
||||||
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.factorypath
|
||||||
|
.project
|
||||||
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.settings
|
||||||
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.springBeans
|
||||||
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.sts4-cache
|
||||||
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bin/
|
||||||
|
!**/src/main/**/bin/
|
||||||
|
!**/src/test/**/bin/
|
||||||
|
|
||||||
|
### NetBeans ###
|
||||||
|
/nbproject/private/
|
||||||
|
/nbbuild/
|
||||||
|
/dist/
|
||||||
|
/nbdist/
|
||||||
|
/.nb-gradle/
|
||||||
|
|
||||||
|
### VS Code ###
|
||||||
|
.vscode/
|
||||||
|
|
||||||
|
### Mac OS ###
|
||||||
|
.DS_Store
|
21
LICENSE.txt
Normal file
21
LICENSE.txt
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@ -0,0 +1,21 @@
|
|||||||
|
MIT License
|
||||||
|
|
||||||
|
Copyright (c) 2024 Paul-Christian Volkmer
|
||||||
|
|
||||||
|
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||||
|
of this software and associated documentation files (the "Software"), to deal
|
||||||
|
in the Software without restriction, including without limitation the rights
|
||||||
|
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
copies of the Software, and to permit persons to whom the Software is
|
||||||
|
furnished to do so, subject to the following conditions:
|
||||||
|
|
||||||
|
The above copyright notice and this permission notice shall be included in all
|
||||||
|
copies or substantial portions of the Software.
|
||||||
|
|
||||||
|
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||||
|
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||||
|
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||||
|
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||||
|
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||||
|
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||||
|
SOFTWARE.
|
11
README.md
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11
README.md
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@ -0,0 +1,11 @@
|
|||||||
|
# DNPM:DIP MTB Data-Transfer-Objects for Java
|
||||||
|
|
||||||
|
Serialization and deserialization of DNPM:DIP MTB DTOs for the Java programming language.
|
||||||
|
|
||||||
|
This library provides DNPM:DIP data model for use with "Modellvorhaben gem. §64e SGB V"
|
||||||
|
|
||||||
|
## Usage notices
|
||||||
|
|
||||||
|
Since this library is also intended to be used with Onkostar, the default Java version is limited to Java 11
|
||||||
|
and all date-time objects do not use JSR 310 types but `java.util.Date`.
|
||||||
|
|
21
build.gradle
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21
build.gradle
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|
|||||||
|
plugins {
|
||||||
|
id 'java-library'
|
||||||
|
}
|
||||||
|
|
||||||
|
group = 'dev.pcvolkmer.mv64e'
|
||||||
|
version = '0.1.0-SNAPSHOT'
|
||||||
|
|
||||||
|
repositories {
|
||||||
|
mavenCentral()
|
||||||
|
}
|
||||||
|
|
||||||
|
dependencies {
|
||||||
|
api 'com.fasterxml.jackson.core:jackson-databind:2.12.7.2'
|
||||||
|
|
||||||
|
testImplementation platform('org.junit:junit-bom:5.10.0')
|
||||||
|
testImplementation 'org.junit.jupiter:junit-jupiter'
|
||||||
|
}
|
||||||
|
|
||||||
|
test {
|
||||||
|
useJUnitPlatform()
|
||||||
|
}
|
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
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Binary file not shown.
6
gradle/wrapper/gradle-wrapper.properties
vendored
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6
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
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|
|||||||
|
#Tue Jul 09 16:02:43 CEST 2024
|
||||||
|
distributionBase=GRADLE_USER_HOME
|
||||||
|
distributionPath=wrapper/dists
|
||||||
|
distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-bin.zip
|
||||||
|
zipStoreBase=GRADLE_USER_HOME
|
||||||
|
zipStorePath=wrapper/dists
|
234
gradlew
vendored
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gradlew
vendored
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|
|||||||
|
#!/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.
|
||||||
|
#
|
||||||
|
|
||||||
|
##############################################################################
|
||||||
|
#
|
||||||
|
# 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/master/subprojects/plugins/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
|
||||||
|
|
||||||
|
APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
|
||||||
|
|
||||||
|
APP_NAME="Gradle"
|
||||||
|
APP_BASE_NAME=${0##*/}
|
||||||
|
|
||||||
|
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
|
||||||
|
DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
|
||||||
|
|
||||||
|
# Use the maximum available, or set MAX_FD != -1 to use that value.
|
||||||
|
MAX_FD=maximum
|
||||||
|
|
||||||
|
warn () {
|
||||||
|
echo "$*"
|
||||||
|
} >&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: $JAVA_HOME
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
else
|
||||||
|
JAVACMD=java
|
||||||
|
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
|
||||||
|
Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
location of your Java installation."
|
||||||
|
fi
|
||||||
|
|
||||||
|
# Increase the maximum file descriptors if we can.
|
||||||
|
if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
|
||||||
|
case $MAX_FD in #(
|
||||||
|
max*)
|
||||||
|
MAX_FD=$( ulimit -H -n ) ||
|
||||||
|
warn "Could not query maximum file descriptor limit"
|
||||||
|
esac
|
||||||
|
case $MAX_FD in #(
|
||||||
|
'' | soft) :;; #(
|
||||||
|
*)
|
||||||
|
ulimit -n "$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
|
||||||
|
|
||||||
|
# Collect all arguments for the java command;
|
||||||
|
# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
|
||||||
|
# shell script including quotes and variable substitutions, so put them in
|
||||||
|
# double quotes to make sure that they get re-expanded; and
|
||||||
|
# * put everything else in single quotes, so that it's not re-expanded.
|
||||||
|
|
||||||
|
set -- \
|
||||||
|
"-Dorg.gradle.appname=$APP_BASE_NAME" \
|
||||||
|
-classpath "$CLASSPATH" \
|
||||||
|
org.gradle.wrapper.GradleWrapperMain \
|
||||||
|
"$@"
|
||||||
|
|
||||||
|
# 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 "$JAVACMD" "$@"
|
89
gradlew.bat
vendored
Normal file
89
gradlew.bat
vendored
Normal file
@ -0,0 +1,89 @@
|
|||||||
|
@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
|
||||||
|
|
||||||
|
@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=.
|
||||||
|
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%" == "0" goto execute
|
||||||
|
|
||||||
|
echo.
|
||||||
|
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
|
||||||
|
echo.
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
echo location of your Java installation.
|
||||||
|
|
||||||
|
goto fail
|
||||||
|
|
||||||
|
:findJavaFromJavaHome
|
||||||
|
set JAVA_HOME=%JAVA_HOME:"=%
|
||||||
|
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
|
||||||
|
|
||||||
|
if exist "%JAVA_EXE%" goto execute
|
||||||
|
|
||||||
|
echo.
|
||||||
|
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
|
||||||
|
echo.
|
||||||
|
echo Please set the JAVA_HOME variable in your environment to match the
|
||||||
|
echo location of your Java installation.
|
||||||
|
|
||||||
|
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%"=="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!
|
||||||
|
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
|
||||||
|
exit /b 1
|
||||||
|
|
||||||
|
:mainEnd
|
||||||
|
if "%OS%"=="Windows_NT" endlocal
|
||||||
|
|
||||||
|
:omega
|
2
settings.gradle
Normal file
2
settings.gradle
Normal file
@ -0,0 +1,2 @@
|
|||||||
|
rootProject.name = 'mtb-dto'
|
||||||
|
|
34
src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java
Normal file
34
src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum AddendumCode {
|
||||||
|
IS, IV, R, Z;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case IS: return "is";
|
||||||
|
case IV: return "iv";
|
||||||
|
case R: return "R";
|
||||||
|
case Z: return "Z";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static AddendumCode forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "is":
|
||||||
|
return IS;
|
||||||
|
case "iv":
|
||||||
|
return IV;
|
||||||
|
case "R":
|
||||||
|
return R;
|
||||||
|
case "Z":
|
||||||
|
return Z;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize AddendumCode");
|
||||||
|
}
|
||||||
|
}
|
12
src/main/java/dev/pcvolkmer/mv64e/mtb/Address.java
Normal file
12
src/main/java/dev/pcvolkmer/mv64e/mtb/Address.java
Normal file
@ -0,0 +1,12 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Address {
|
||||||
|
private String municipalityCode;
|
||||||
|
|
||||||
|
@JsonProperty("municipalityCode")
|
||||||
|
public String getMunicipalityCode() { return municipalityCode; }
|
||||||
|
@JsonProperty("municipalityCode")
|
||||||
|
public void setMunicipalityCode(String value) { this.municipalityCode = value; }
|
||||||
|
}
|
94
src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java
Normal file
94
src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java
Normal file
@ -0,0 +1,94 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum Chromosome {
|
||||||
|
CHR1, CHR10, CHR11, CHR12, CHR13, CHR14, CHR15, CHR16, CHR17, CHR18, CHR19, CHR2, CHR20, CHR21, CHR22, CHR3, CHR4, CHR5, CHR6, CHR7, CHR8, CHR9, CHR_X, CHR_Y;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case CHR1: return "chr1";
|
||||||
|
case CHR10: return "chr10";
|
||||||
|
case CHR11: return "chr11";
|
||||||
|
case CHR12: return "chr12";
|
||||||
|
case CHR13: return "chr13";
|
||||||
|
case CHR14: return "chr14";
|
||||||
|
case CHR15: return "chr15";
|
||||||
|
case CHR16: return "chr16";
|
||||||
|
case CHR17: return "chr17";
|
||||||
|
case CHR18: return "chr18";
|
||||||
|
case CHR19: return "chr19";
|
||||||
|
case CHR2: return "chr2";
|
||||||
|
case CHR20: return "chr20";
|
||||||
|
case CHR21: return "chr21";
|
||||||
|
case CHR22: return "chr22";
|
||||||
|
case CHR3: return "chr3";
|
||||||
|
case CHR4: return "chr4";
|
||||||
|
case CHR5: return "chr5";
|
||||||
|
case CHR6: return "chr6";
|
||||||
|
case CHR7: return "chr7";
|
||||||
|
case CHR8: return "chr8";
|
||||||
|
case CHR9: return "chr9";
|
||||||
|
case CHR_X: return "chrX";
|
||||||
|
case CHR_Y: return "chrY";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static Chromosome forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "chr1":
|
||||||
|
return CHR1;
|
||||||
|
case "chr10":
|
||||||
|
return CHR10;
|
||||||
|
case "chr11":
|
||||||
|
return CHR11;
|
||||||
|
case "chr12":
|
||||||
|
return CHR12;
|
||||||
|
case "chr13":
|
||||||
|
return CHR13;
|
||||||
|
case "chr14":
|
||||||
|
return CHR14;
|
||||||
|
case "chr15":
|
||||||
|
return CHR15;
|
||||||
|
case "chr16":
|
||||||
|
return CHR16;
|
||||||
|
case "chr17":
|
||||||
|
return CHR17;
|
||||||
|
case "chr18":
|
||||||
|
return CHR18;
|
||||||
|
case "chr19":
|
||||||
|
return CHR19;
|
||||||
|
case "chr2":
|
||||||
|
return CHR2;
|
||||||
|
case "chr20":
|
||||||
|
return CHR20;
|
||||||
|
case "chr21":
|
||||||
|
return CHR21;
|
||||||
|
case "chr22":
|
||||||
|
return CHR22;
|
||||||
|
case "chr3":
|
||||||
|
return CHR3;
|
||||||
|
case "chr4":
|
||||||
|
return CHR4;
|
||||||
|
case "chr5":
|
||||||
|
return CHR5;
|
||||||
|
case "chr6":
|
||||||
|
return CHR6;
|
||||||
|
case "chr7":
|
||||||
|
return CHR7;
|
||||||
|
case "chr8":
|
||||||
|
return CHR8;
|
||||||
|
case "chr9":
|
||||||
|
return CHR9;
|
||||||
|
case "chrX":
|
||||||
|
return CHR_X;
|
||||||
|
case "chrY":
|
||||||
|
return CHR_Y;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize Chromosome");
|
||||||
|
}
|
||||||
|
}
|
33
src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java
Normal file
33
src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class Claim {
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private Patient patient;
|
||||||
|
private String therapy;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("therapy")
|
||||||
|
public String getTherapy() { return therapy; }
|
||||||
|
@JsonProperty("therapy")
|
||||||
|
public void setTherapy(String value) { this.therapy = value; }
|
||||||
|
}
|
45
src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java
Normal file
45
src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponse.java
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class ClaimResponse {
|
||||||
|
private ClaimResponseClaim claim;
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private Patient patient;
|
||||||
|
private ClaimResponseStatusReason reason;
|
||||||
|
private CodingClaimResponseStatus status;
|
||||||
|
|
||||||
|
@JsonProperty("claim")
|
||||||
|
public ClaimResponseClaim getClaim() { return claim; }
|
||||||
|
@JsonProperty("claim")
|
||||||
|
public void setClaim(ClaimResponseClaim value) { this.claim = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public ClaimResponseStatusReason getReason() { return reason; }
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public void setReason(ClaimResponseStatusReason value) { this.reason = value; }
|
||||||
|
|
||||||
|
@JsonProperty("status")
|
||||||
|
public CodingClaimResponseStatus getStatus() { return status; }
|
||||||
|
@JsonProperty("status")
|
||||||
|
public void setStatus(CodingClaimResponseStatus value) { this.status = value; }
|
||||||
|
}
|
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class ClaimResponseClaim {
|
||||||
|
private String id;
|
||||||
|
private ClaimResponseClaimType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public ClaimResponseClaimType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(ClaimResponseClaimType value) { this.type = value; }
|
||||||
|
}
|
@ -0,0 +1,22 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum ClaimResponseClaimType {
|
||||||
|
CLAIM;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case CLAIM: return "Claim";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static ClaimResponseClaimType forValue(String value) throws IOException {
|
||||||
|
if (value.equals("Claim")) return CLAIM;
|
||||||
|
throw new IOException("Cannot deserialize ClaimResponseClaimType");
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,31 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum ClaimResponseStatus {
|
||||||
|
ACCEPTED, REJECTED, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case ACCEPTED: return "accepted";
|
||||||
|
case REJECTED: return "rejected";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static ClaimResponseStatus forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "accepted":
|
||||||
|
return ACCEPTED;
|
||||||
|
case "rejected":
|
||||||
|
return REJECTED;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize ClaimResponseStatus");
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,46 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum ClaimResponseStatusReason {
|
||||||
|
APPROVAL_REVOCATION, FORMAL_REASONS, INCLUSION_IN_STUDY, INSUFFICIENT_EVIDENCE, OTHER, OTHER_THERAPY_RECOMMENDED, STANDARD_THERAPY_NOT_EXHAUSTED, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case APPROVAL_REVOCATION: return "approval-revocation";
|
||||||
|
case FORMAL_REASONS: return "formal-reasons";
|
||||||
|
case INCLUSION_IN_STUDY: return "inclusion-in-study";
|
||||||
|
case INSUFFICIENT_EVIDENCE: return "insufficient-evidence";
|
||||||
|
case OTHER: return "other";
|
||||||
|
case OTHER_THERAPY_RECOMMENDED: return "other-therapy-recommended";
|
||||||
|
case STANDARD_THERAPY_NOT_EXHAUSTED: return "standard-therapy-not-exhausted";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static ClaimResponseStatusReason forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "approval-revocation":
|
||||||
|
return APPROVAL_REVOCATION;
|
||||||
|
case "formal-reasons":
|
||||||
|
return FORMAL_REASONS;
|
||||||
|
case "inclusion-in-study":
|
||||||
|
return INCLUSION_IN_STUDY;
|
||||||
|
case "insufficient-evidence":
|
||||||
|
return INSUFFICIENT_EVIDENCE;
|
||||||
|
case "other":
|
||||||
|
return OTHER;
|
||||||
|
case "other-therapy-recommended":
|
||||||
|
return OTHER_THERAPY_RECOMMENDED;
|
||||||
|
case "standard-therapy-not-exhausted":
|
||||||
|
return STANDARD_THERAPY_NOT_EXHAUSTED;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize ClaimResponseStatusReason");
|
||||||
|
}
|
||||||
|
}
|
79
src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java
Normal file
79
src/main/java/dev/pcvolkmer/mv64e/mtb/Cnv.java
Normal file
@ -0,0 +1,79 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class Cnv {
|
||||||
|
private Chromosome chromosome;
|
||||||
|
private Double cnA;
|
||||||
|
private Double cnB;
|
||||||
|
private List<CopyNumberNeutralLoH> copyNumberNeutralLoH;
|
||||||
|
private EndRange endRange;
|
||||||
|
private String id;
|
||||||
|
private Double relativeCopyNumber;
|
||||||
|
private List<ReportedAffectedGene> reportedAffectedGenes;
|
||||||
|
private String reportedFocality;
|
||||||
|
private StartRange startRange;
|
||||||
|
private Long totalCopyNumber;
|
||||||
|
private CnvType type;
|
||||||
|
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public Chromosome getChromosome() { return chromosome; }
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public void setChromosome(Chromosome value) { this.chromosome = value; }
|
||||||
|
|
||||||
|
@JsonProperty("cnA")
|
||||||
|
public Double getCnA() { return cnA; }
|
||||||
|
@JsonProperty("cnA")
|
||||||
|
public void setCnA(Double value) { this.cnA = value; }
|
||||||
|
|
||||||
|
@JsonProperty("cnB")
|
||||||
|
public Double getCnB() { return cnB; }
|
||||||
|
@JsonProperty("cnB")
|
||||||
|
public void setCnB(Double value) { this.cnB = value; }
|
||||||
|
|
||||||
|
@JsonProperty("copyNumberNeutralLoH")
|
||||||
|
public List<CopyNumberNeutralLoH> getCopyNumberNeutralLoH() { return copyNumberNeutralLoH; }
|
||||||
|
@JsonProperty("copyNumberNeutralLoH")
|
||||||
|
public void setCopyNumberNeutralLoH(List<CopyNumberNeutralLoH> value) { this.copyNumberNeutralLoH = value; }
|
||||||
|
|
||||||
|
@JsonProperty("endRange")
|
||||||
|
public EndRange getEndRange() { return endRange; }
|
||||||
|
@JsonProperty("endRange")
|
||||||
|
public void setEndRange(EndRange value) { this.endRange = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("relativeCopyNumber")
|
||||||
|
public Double getRelativeCopyNumber() { return relativeCopyNumber; }
|
||||||
|
@JsonProperty("relativeCopyNumber")
|
||||||
|
public void setRelativeCopyNumber(Double value) { this.relativeCopyNumber = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reportedAffectedGenes")
|
||||||
|
public List<ReportedAffectedGene> getReportedAffectedGenes() { return reportedAffectedGenes; }
|
||||||
|
@JsonProperty("reportedAffectedGenes")
|
||||||
|
public void setReportedAffectedGenes(List<ReportedAffectedGene> value) { this.reportedAffectedGenes = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reportedFocality")
|
||||||
|
public String getReportedFocality() { return reportedFocality; }
|
||||||
|
@JsonProperty("reportedFocality")
|
||||||
|
public void setReportedFocality(String value) { this.reportedFocality = value; }
|
||||||
|
|
||||||
|
@JsonProperty("startRange")
|
||||||
|
public StartRange getStartRange() { return startRange; }
|
||||||
|
@JsonProperty("startRange")
|
||||||
|
public void setStartRange(StartRange value) { this.startRange = value; }
|
||||||
|
|
||||||
|
@JsonProperty("totalCopyNumber")
|
||||||
|
public Long getTotalCopyNumber() { return totalCopyNumber; }
|
||||||
|
@JsonProperty("totalCopyNumber")
|
||||||
|
public void setTotalCopyNumber(Long value) { this.totalCopyNumber = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public CnvType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(CnvType value) { this.type = value; }
|
||||||
|
}
|
31
src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java
Normal file
31
src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java
Normal file
@ -0,0 +1,31 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum CnvType {
|
||||||
|
HIGH_LEVEL_GAIN, LOSS, LOW_LEVEL_GAIN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case HIGH_LEVEL_GAIN: return "high-level-gain";
|
||||||
|
case LOSS: return "loss";
|
||||||
|
case LOW_LEVEL_GAIN: return "low-level-gain";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static CnvType forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "high-level-gain":
|
||||||
|
return HIGH_LEVEL_GAIN;
|
||||||
|
case "loss":
|
||||||
|
return LOSS;
|
||||||
|
case "low-level-gain":
|
||||||
|
return LOW_LEVEL_GAIN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize CNVType");
|
||||||
|
}
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/Code.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Code {
|
||||||
|
private String code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public String getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(String value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/Coding.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/Coding.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Coding {
|
||||||
|
private String code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public String getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(String value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingClaimResponseStatus {
|
||||||
|
private ClaimResponseStatus code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public ClaimResponseStatus getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(ClaimResponseStatus value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingEcog.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingEcog {
|
||||||
|
private PurpleCode code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public PurpleCode getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(PurpleCode value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingGender.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingGender {
|
||||||
|
private Gender code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public Gender getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(Gender value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingLevelOfEvidenceAddendum {
|
||||||
|
private AddendumCode code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public AddendumCode getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(AddendumCode value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingLevelOfEvidenceGrading {
|
||||||
|
private GradingCode code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public GradingCode getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(GradingCode value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingRecist.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingRecist {
|
||||||
|
private FluffyCode code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public FluffyCode getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(FluffyCode value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingTherapyStatusReason {
|
||||||
|
private NotDoneReasonCode code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
private String version;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public NotDoneReasonCode getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(NotDoneReasonCode value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("version")
|
||||||
|
public String getVersion() { return version; }
|
||||||
|
@JsonProperty("version")
|
||||||
|
public void setVersion(String value) { this.version = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingTumorSpecimenCollectionLocalization {
|
||||||
|
private TumorSpecimenCollectionLocalization code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public TumorSpecimenCollectionLocalization getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(TumorSpecimenCollectionLocalization value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingTumorSpecimenCollectionMethod {
|
||||||
|
private TumorSpecimenCollectionMethod code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public TumorSpecimenCollectionMethod getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(TumorSpecimenCollectionMethod value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CodingTumorSpecimenType {
|
||||||
|
private TumorSpecimenType code;
|
||||||
|
private String display;
|
||||||
|
private String system;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public TumorSpecimenType getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(TumorSpecimenType value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("display")
|
||||||
|
public String getDisplay() { return display; }
|
||||||
|
@JsonProperty("display")
|
||||||
|
public void setDisplay(String value) { this.display = value; }
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public String getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(String value) { this.system = value; }
|
||||||
|
}
|
27
src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java
Normal file
27
src/main/java/dev/pcvolkmer/mv64e/mtb/Collection.java
Normal file
@ -0,0 +1,27 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class Collection {
|
||||||
|
private Date date;
|
||||||
|
private CodingTumorSpecimenCollectionLocalization localization;
|
||||||
|
private CodingTumorSpecimenCollectionMethod method;
|
||||||
|
|
||||||
|
@JsonProperty("date")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getDate() { return date; }
|
||||||
|
@JsonProperty("date")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setDate(Date value) { this.date = value; }
|
||||||
|
|
||||||
|
@JsonProperty("localization")
|
||||||
|
public CodingTumorSpecimenCollectionLocalization getLocalization() { return localization; }
|
||||||
|
@JsonProperty("localization")
|
||||||
|
public void setLocalization(CodingTumorSpecimenCollectionLocalization value) { this.localization = value; }
|
||||||
|
|
||||||
|
@JsonProperty("method")
|
||||||
|
public CodingTumorSpecimenCollectionMethod getMethod() { return method; }
|
||||||
|
@JsonProperty("method")
|
||||||
|
public void setMethod(CodingTumorSpecimenCollectionMethod value) { this.method = value; }
|
||||||
|
}
|
24
src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java
Normal file
24
src/main/java/dev/pcvolkmer/mv64e/mtb/Consent.java
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Consent {
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private ConsentStatus status;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("status")
|
||||||
|
public ConsentStatus getStatus() { return status; }
|
||||||
|
@JsonProperty("status")
|
||||||
|
public void setStatus(ConsentStatus value) { this.status = value; }
|
||||||
|
}
|
24
src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java
Normal file
24
src/main/java/dev/pcvolkmer/mv64e/mtb/ConsentStatus.java
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum ConsentStatus {
|
||||||
|
ACTIVE, REJECTED;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case ACTIVE: return "active";
|
||||||
|
case REJECTED: return "rejected";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static ConsentStatus forValue(String value) throws IOException {
|
||||||
|
if (value.equals("active")) return ACTIVE;
|
||||||
|
if (value.equals("rejected")) return REJECTED;
|
||||||
|
throw new IOException("Cannot deserialize ConsentStatus");
|
||||||
|
}
|
||||||
|
}
|
107
src/main/java/dev/pcvolkmer/mv64e/mtb/Converter.java
Normal file
107
src/main/java/dev/pcvolkmer/mv64e/mtb/Converter.java
Normal file
@ -0,0 +1,107 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.core.JsonParser;
|
||||||
|
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||||
|
import com.fasterxml.jackson.databind.*;
|
||||||
|
import com.fasterxml.jackson.databind.module.SimpleModule;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.text.SimpleDateFormat;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class Converter {
|
||||||
|
// Date-time helpers
|
||||||
|
|
||||||
|
private static final String[] DATE_TIME_FORMATS = {
|
||||||
|
"yyyy-MM-dd'T'HH:mm:ss.SX",
|
||||||
|
"yyyy-MM-dd'T'HH:mm:ss.S",
|
||||||
|
"yyyy-MM-dd'T'HH:mm:ssX",
|
||||||
|
"yyyy-MM-dd'T'HH:mm:ss",
|
||||||
|
"yyyy-MM-dd HH:mm:ss.SX",
|
||||||
|
"yyyy-MM-dd HH:mm:ss.S",
|
||||||
|
"yyyy-MM-dd HH:mm:ssX",
|
||||||
|
"yyyy-MM-dd HH:mm:ss",
|
||||||
|
"HH:mm:ss.SZ",
|
||||||
|
"HH:mm:ss.S",
|
||||||
|
"HH:mm:ssZ",
|
||||||
|
"HH:mm:ss",
|
||||||
|
"yyyy-MM-dd",
|
||||||
|
};
|
||||||
|
|
||||||
|
public static Date parseAllDateTimeString(String str) {
|
||||||
|
for (String format : DATE_TIME_FORMATS) {
|
||||||
|
try {
|
||||||
|
return new SimpleDateFormat(format).parse(str);
|
||||||
|
} catch (Exception ex) {
|
||||||
|
// Ignored
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String serializeDateTime(Date datetime) {
|
||||||
|
return new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ssZ").format(datetime);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String serializeDate(Date datetime) {
|
||||||
|
return new SimpleDateFormat("yyyy-MM-dd").format(datetime);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String serializeTime(Date datetime) {
|
||||||
|
return new SimpleDateFormat("hh:mm:ssZ").format(datetime);
|
||||||
|
}
|
||||||
|
// Serialize/deserialize helpers
|
||||||
|
|
||||||
|
public static Mtb fromJsonString(String json) throws IOException {
|
||||||
|
return getObjectReader().readValue(json);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String toJsonString(Mtb obj) throws JsonProcessingException {
|
||||||
|
return getObjectWriter().writeValueAsString(obj);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static ObjectReader reader;
|
||||||
|
private static ObjectWriter writer;
|
||||||
|
|
||||||
|
private static void instantiateMapper() {
|
||||||
|
ObjectMapper mapper = new ObjectMapper();
|
||||||
|
mapper.findAndRegisterModules();
|
||||||
|
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||||
|
mapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
|
||||||
|
SimpleModule module = new SimpleModule();
|
||||||
|
module.addDeserializer(Date.class, new JsonDeserializer<>() {
|
||||||
|
@Override
|
||||||
|
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
|
||||||
|
String value = jsonParser.getText();
|
||||||
|
return Converter.parseAllDateTimeString(value);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
module.addDeserializer(Date.class, new JsonDeserializer<>() {
|
||||||
|
@Override
|
||||||
|
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
|
||||||
|
String value = jsonParser.getText();
|
||||||
|
return Converter.parseAllDateTimeString(value);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
module.addDeserializer(Date.class, new JsonDeserializer<>() {
|
||||||
|
@Override
|
||||||
|
public Date deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException {
|
||||||
|
String value = jsonParser.getText();
|
||||||
|
return Converter.parseAllDateTimeString(value);
|
||||||
|
}
|
||||||
|
});
|
||||||
|
mapper.registerModule(module);
|
||||||
|
reader = mapper.readerFor(Mtb.class);
|
||||||
|
writer = mapper.writerFor(Mtb.class);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static ObjectReader getObjectReader() {
|
||||||
|
if (reader == null) instantiateMapper();
|
||||||
|
return reader;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static ObjectWriter getObjectWriter() {
|
||||||
|
if (writer == null) instantiateMapper();
|
||||||
|
return writer;
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class CopyNumberNeutralLoH {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusion.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class DnaFusion {
|
||||||
|
private DnaFusionFusionPartner3Prime fusionPartner3Prime;
|
||||||
|
private DnaFusionFusionPartner5Prime fusionPartner5Prime;
|
||||||
|
private String id;
|
||||||
|
private long reportedNumReads;
|
||||||
|
|
||||||
|
@JsonProperty("fusionPartner3prime")
|
||||||
|
public DnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; }
|
||||||
|
@JsonProperty("fusionPartner3prime")
|
||||||
|
public void setFusionPartner3Prime(DnaFusionFusionPartner3Prime value) { this.fusionPartner3Prime = value; }
|
||||||
|
|
||||||
|
@JsonProperty("fusionPartner5prime")
|
||||||
|
public DnaFusionFusionPartner5Prime getFusionPartner5Prime() { return fusionPartner5Prime; }
|
||||||
|
@JsonProperty("fusionPartner5prime")
|
||||||
|
public void setFusionPartner5Prime(DnaFusionFusionPartner5Prime value) { this.fusionPartner5Prime = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reportedNumReads")
|
||||||
|
public long getReportedNumReads() { return reportedNumReads; }
|
||||||
|
@JsonProperty("reportedNumReads")
|
||||||
|
public void setReportedNumReads(long value) { this.reportedNumReads = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class DnaFusionFusionPartner3Prime {
|
||||||
|
private Chromosome chromosome;
|
||||||
|
private PurpleGene gene;
|
||||||
|
private double position;
|
||||||
|
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public Chromosome getChromosome() { return chromosome; }
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public void setChromosome(Chromosome value) { this.chromosome = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public PurpleGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(PurpleGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("position")
|
||||||
|
public double getPosition() { return position; }
|
||||||
|
@JsonProperty("position")
|
||||||
|
public void setPosition(double value) { this.position = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class DnaFusionFusionPartner5Prime {
|
||||||
|
private Chromosome chromosome;
|
||||||
|
private FluffyGene gene;
|
||||||
|
private double position;
|
||||||
|
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public Chromosome getChromosome() { return chromosome; }
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public void setChromosome(Chromosome value) { this.chromosome = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public FluffyGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(FluffyGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("position")
|
||||||
|
public double getPosition() { return position; }
|
||||||
|
@JsonProperty("position")
|
||||||
|
public void setPosition(double value) { this.position = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/EndRange.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/EndRange.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class EndRange {
|
||||||
|
private Double end;
|
||||||
|
private double start;
|
||||||
|
|
||||||
|
@JsonProperty("end")
|
||||||
|
public Double getEnd() { return end; }
|
||||||
|
@JsonProperty("end")
|
||||||
|
public void setEnd(Double value) { this.end = value; }
|
||||||
|
|
||||||
|
@JsonProperty("start")
|
||||||
|
public double getStart() { return start; }
|
||||||
|
@JsonProperty("start")
|
||||||
|
public void setStart(double value) { this.start = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/ExtId.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class ExtId {
|
||||||
|
private SystemEnum system;
|
||||||
|
private String value;
|
||||||
|
|
||||||
|
@JsonProperty("system")
|
||||||
|
public SystemEnum getSystem() { return system; }
|
||||||
|
@JsonProperty("system")
|
||||||
|
public void setSystem(SystemEnum value) { this.system = value; }
|
||||||
|
|
||||||
|
@JsonProperty("value")
|
||||||
|
public String getValue() { return value; }
|
||||||
|
@JsonProperty("value")
|
||||||
|
public void setValue(String value) { this.value = value; }
|
||||||
|
}
|
43
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyCode.java
Normal file
43
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyCode.java
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum FluffyCode {
|
||||||
|
CR, MR, NA, NYA, PD, PR, SD;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case CR: return "CR";
|
||||||
|
case MR: return "MR";
|
||||||
|
case NA: return "NA";
|
||||||
|
case NYA: return "NYA";
|
||||||
|
case PD: return "PD";
|
||||||
|
case PR: return "PR";
|
||||||
|
case SD: return "SD";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static FluffyCode forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "CR":
|
||||||
|
return CR;
|
||||||
|
case "MR":
|
||||||
|
return MR;
|
||||||
|
case "NA":
|
||||||
|
return NA;
|
||||||
|
case "NYA":
|
||||||
|
return NYA;
|
||||||
|
case "PD":
|
||||||
|
return PD;
|
||||||
|
case "PR":
|
||||||
|
return PR;
|
||||||
|
case "SD":
|
||||||
|
return SD;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize FluffyCode");
|
||||||
|
}
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class FluffyGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
34
src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java
Normal file
34
src/main/java/dev/pcvolkmer/mv64e/mtb/Gender.java
Normal file
@ -0,0 +1,34 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum Gender {
|
||||||
|
FEMALE, MALE, OTHER, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case FEMALE: return "female";
|
||||||
|
case MALE: return "male";
|
||||||
|
case OTHER: return "other";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static Gender forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "female":
|
||||||
|
return FEMALE;
|
||||||
|
case "male":
|
||||||
|
return MALE;
|
||||||
|
case "other":
|
||||||
|
return OTHER;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize Gender");
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,31 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class GeneticCounselingRecommendation {
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private Patient patient;
|
||||||
|
private String reason;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public String getReason() { return reason; }
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public void setReason(String value) { this.reason = value; }
|
||||||
|
}
|
49
src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java
Normal file
49
src/main/java/dev/pcvolkmer/mv64e/mtb/GradingCode.java
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum GradingCode {
|
||||||
|
M1_A, M1_B, M1_C, M2_A, M2_B, M2_C, M3, M4, UNDEFINED;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case M1_A: return "m1A";
|
||||||
|
case M1_B: return "m1B";
|
||||||
|
case M1_C: return "m1C";
|
||||||
|
case M2_A: return "m2A";
|
||||||
|
case M2_B: return "m2B";
|
||||||
|
case M2_C: return "m2C";
|
||||||
|
case M3: return "m3";
|
||||||
|
case M4: return "m4";
|
||||||
|
case UNDEFINED: return "undefined";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static GradingCode forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "m1A":
|
||||||
|
return M1_A;
|
||||||
|
case "m1B":
|
||||||
|
return M1_B;
|
||||||
|
case "m1C":
|
||||||
|
return M1_C;
|
||||||
|
case "m2A":
|
||||||
|
return M2_A;
|
||||||
|
case "m2B":
|
||||||
|
return M2_B;
|
||||||
|
case "m2C":
|
||||||
|
return M2_C;
|
||||||
|
case "m3":
|
||||||
|
return M3;
|
||||||
|
case "m4":
|
||||||
|
return M4;
|
||||||
|
case "undefined":
|
||||||
|
return UNDEFINED;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize GradingCode");
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,37 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum GuidelineTreatmentStatus {
|
||||||
|
EXHAUSTED, IMPOSSIBLE, NON_EXHAUSTED, NO_GUIDELINES_AVAILABLE, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case EXHAUSTED: return "exhausted";
|
||||||
|
case IMPOSSIBLE: return "impossible";
|
||||||
|
case NON_EXHAUSTED: return "non-exhausted";
|
||||||
|
case NO_GUIDELINES_AVAILABLE: return "no-guidelines-available";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static GuidelineTreatmentStatus forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "exhausted":
|
||||||
|
return EXHAUSTED;
|
||||||
|
case "impossible":
|
||||||
|
return IMPOSSIBLE;
|
||||||
|
case "non-exhausted":
|
||||||
|
return NON_EXHAUSTED;
|
||||||
|
case "no-guidelines-available":
|
||||||
|
return NO_GUIDELINES_AVAILABLE;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize GuidelineTreatmentStatus");
|
||||||
|
}
|
||||||
|
}
|
45
src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java
Normal file
45
src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReport.java
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class HistologyReport {
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private Patient patient;
|
||||||
|
private HistologyReportSpecimen specimen;
|
||||||
|
private TumorCellContent tumorCellContent;
|
||||||
|
private TumorMorphology tumorMorphology;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public HistologyReportSpecimen getSpecimen() { return specimen; }
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public void setSpecimen(HistologyReportSpecimen value) { this.specimen = value; }
|
||||||
|
|
||||||
|
@JsonProperty("tumorCellContent")
|
||||||
|
public TumorCellContent getTumorCellContent() { return tumorCellContent; }
|
||||||
|
@JsonProperty("tumorCellContent")
|
||||||
|
public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
|
||||||
|
|
||||||
|
@JsonProperty("tumorMorphology")
|
||||||
|
public TumorMorphology getTumorMorphology() { return tumorMorphology; }
|
||||||
|
@JsonProperty("tumorMorphology")
|
||||||
|
public void setTumorMorphology(TumorMorphology value) { this.tumorMorphology = value; }
|
||||||
|
}
|
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class HistologyReportSpecimen {
|
||||||
|
private String id;
|
||||||
|
private SpecimenType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public SpecimenType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(SpecimenType value) { this.type = value; }
|
||||||
|
}
|
25
src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java
Normal file
25
src/main/java/dev/pcvolkmer/mv64e/mtb/LevelOfEvidence.java
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class LevelOfEvidence {
|
||||||
|
private List<CodingLevelOfEvidenceAddendum> addendums;
|
||||||
|
private CodingLevelOfEvidenceGrading grading;
|
||||||
|
private List<ReferencePublication> publications;
|
||||||
|
|
||||||
|
@JsonProperty("addendums")
|
||||||
|
public List<CodingLevelOfEvidenceAddendum> getAddendums() { return addendums; }
|
||||||
|
@JsonProperty("addendums")
|
||||||
|
public void setAddendums(List<CodingLevelOfEvidenceAddendum> value) { this.addendums = value; }
|
||||||
|
|
||||||
|
@JsonProperty("grading")
|
||||||
|
public CodingLevelOfEvidenceGrading getGrading() { return grading; }
|
||||||
|
@JsonProperty("grading")
|
||||||
|
public void setGrading(CodingLevelOfEvidenceGrading value) { this.grading = value; }
|
||||||
|
|
||||||
|
@JsonProperty("publications")
|
||||||
|
public List<ReferencePublication> getPublications() { return publications; }
|
||||||
|
@JsonProperty("publications")
|
||||||
|
public void setPublications(List<ReferencePublication> value) { this.publications = value; }
|
||||||
|
}
|
36
src/main/java/dev/pcvolkmer/mv64e/mtb/Metadatum.java
Normal file
36
src/main/java/dev/pcvolkmer/mv64e/mtb/Metadatum.java
Normal file
@ -0,0 +1,36 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Metadatum {
|
||||||
|
private String kitManufacturer;
|
||||||
|
private String kitType;
|
||||||
|
private String pipeline;
|
||||||
|
private String referenceGenome;
|
||||||
|
private String sequencer;
|
||||||
|
|
||||||
|
@JsonProperty("kitManufacturer")
|
||||||
|
public String getKitManufacturer() { return kitManufacturer; }
|
||||||
|
@JsonProperty("kitManufacturer")
|
||||||
|
public void setKitManufacturer(String value) { this.kitManufacturer = value; }
|
||||||
|
|
||||||
|
@JsonProperty("kitType")
|
||||||
|
public String getKitType() { return kitType; }
|
||||||
|
@JsonProperty("kitType")
|
||||||
|
public void setKitType(String value) { this.kitType = value; }
|
||||||
|
|
||||||
|
@JsonProperty("pipeline")
|
||||||
|
public String getPipeline() { return pipeline; }
|
||||||
|
@JsonProperty("pipeline")
|
||||||
|
public void setPipeline(String value) { this.pipeline = value; }
|
||||||
|
|
||||||
|
@JsonProperty("referenceGenome")
|
||||||
|
public String getReferenceGenome() { return referenceGenome; }
|
||||||
|
@JsonProperty("referenceGenome")
|
||||||
|
public void setReferenceGenome(String value) { this.referenceGenome = value; }
|
||||||
|
|
||||||
|
@JsonProperty("sequencer")
|
||||||
|
public String getSequencer() { return sequencer; }
|
||||||
|
@JsonProperty("sequencer")
|
||||||
|
public void setSequencer(String value) { this.sequencer = value; }
|
||||||
|
}
|
13
src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java
Normal file
13
src/main/java/dev/pcvolkmer/mv64e/mtb/MolecularTherapy.java
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class MolecularTherapy {
|
||||||
|
private List<MtbMedicationTherapy> history;
|
||||||
|
|
||||||
|
@JsonProperty("history")
|
||||||
|
public List<MtbMedicationTherapy> getHistory() { return history; }
|
||||||
|
@JsonProperty("history")
|
||||||
|
public void setHistory(List<MtbMedicationTherapy> value) { this.history = value; }
|
||||||
|
}
|
115
src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java
Normal file
115
src/main/java/dev/pcvolkmer/mv64e/mtb/Mtb.java
Normal file
@ -0,0 +1,115 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class Mtb {
|
||||||
|
private List<MtbCarePlan> carePlans;
|
||||||
|
private List<ClaimResponse> claimResponses;
|
||||||
|
private List<Claim> claims;
|
||||||
|
private Consent consent;
|
||||||
|
private List<MtbDiagnosis> diagnoses;
|
||||||
|
private List<PerformanceStatus> ecogStatus;
|
||||||
|
private MtbEpisode episode;
|
||||||
|
private List<GeneticCounselingRecommendation> geneticCounsellingRequests;
|
||||||
|
private List<HistologyReport> histologyReports;
|
||||||
|
private List<MtbMedicationTherapy> lastGuidelineTherapies;
|
||||||
|
private List<MolecularTherapy> molecularTherapies;
|
||||||
|
private List<SomaticNgsReport> ngsReports;
|
||||||
|
private MtbPatient patient;
|
||||||
|
private List<MtbMedicationTherapy> previousGuidelineTherapies;
|
||||||
|
private List<MtbMedicationRecommendation> recommendations;
|
||||||
|
private List<Response> responses;
|
||||||
|
private List<TumorSpecimen> specimens;
|
||||||
|
private List<StudyEnrollmentRecommendation> studyInclusionRequests;
|
||||||
|
|
||||||
|
@JsonProperty("carePlans")
|
||||||
|
public List<MtbCarePlan> getCarePlans() { return carePlans; }
|
||||||
|
@JsonProperty("carePlans")
|
||||||
|
public void setCarePlans(List<MtbCarePlan> value) { this.carePlans = value; }
|
||||||
|
|
||||||
|
@JsonProperty("claimResponses")
|
||||||
|
public List<ClaimResponse> getClaimResponses() { return claimResponses; }
|
||||||
|
@JsonProperty("claimResponses")
|
||||||
|
public void setClaimResponses(List<ClaimResponse> value) { this.claimResponses = value; }
|
||||||
|
|
||||||
|
@JsonProperty("claims")
|
||||||
|
public List<Claim> getClaims() { return claims; }
|
||||||
|
@JsonProperty("claims")
|
||||||
|
public void setClaims(List<Claim> value) { this.claims = value; }
|
||||||
|
|
||||||
|
@JsonProperty("consent")
|
||||||
|
public Consent getConsent() { return consent; }
|
||||||
|
@JsonProperty("consent")
|
||||||
|
public void setConsent(Consent value) { this.consent = value; }
|
||||||
|
|
||||||
|
@JsonProperty("diagnoses")
|
||||||
|
public List<MtbDiagnosis> getDiagnoses() { return diagnoses; }
|
||||||
|
@JsonProperty("diagnoses")
|
||||||
|
public void setDiagnoses(List<MtbDiagnosis> value) { this.diagnoses = value; }
|
||||||
|
|
||||||
|
@JsonProperty("ecogStatus")
|
||||||
|
public List<PerformanceStatus> getEcogStatus() { return ecogStatus; }
|
||||||
|
@JsonProperty("ecogStatus")
|
||||||
|
public void setEcogStatus(List<PerformanceStatus> value) { this.ecogStatus = value; }
|
||||||
|
|
||||||
|
@JsonProperty("episode")
|
||||||
|
public MtbEpisode getEpisode() { return episode; }
|
||||||
|
@JsonProperty("episode")
|
||||||
|
public void setEpisode(MtbEpisode value) { this.episode = value; }
|
||||||
|
|
||||||
|
@JsonProperty("geneticCounsellingRequests")
|
||||||
|
public List<GeneticCounselingRecommendation> getGeneticCounsellingRequests() { return geneticCounsellingRequests; }
|
||||||
|
@JsonProperty("geneticCounsellingRequests")
|
||||||
|
public void setGeneticCounsellingRequests(List<GeneticCounselingRecommendation> value) { this.geneticCounsellingRequests = value; }
|
||||||
|
|
||||||
|
@JsonProperty("histologyReports")
|
||||||
|
public List<HistologyReport> getHistologyReports() { return histologyReports; }
|
||||||
|
@JsonProperty("histologyReports")
|
||||||
|
public void setHistologyReports(List<HistologyReport> value) { this.histologyReports = value; }
|
||||||
|
|
||||||
|
@JsonProperty("lastGuidelineTherapies")
|
||||||
|
public List<MtbMedicationTherapy> getLastGuidelineTherapies() { return lastGuidelineTherapies; }
|
||||||
|
@JsonProperty("lastGuidelineTherapies")
|
||||||
|
public void setLastGuidelineTherapies(List<MtbMedicationTherapy> value) { this.lastGuidelineTherapies = value; }
|
||||||
|
|
||||||
|
@JsonProperty("molecularTherapies")
|
||||||
|
public List<MolecularTherapy> getMolecularTherapies() { return molecularTherapies; }
|
||||||
|
@JsonProperty("molecularTherapies")
|
||||||
|
public void setMolecularTherapies(List<MolecularTherapy> value) { this.molecularTherapies = value; }
|
||||||
|
|
||||||
|
@JsonProperty("ngsReports")
|
||||||
|
public List<SomaticNgsReport> getNgsReports() { return ngsReports; }
|
||||||
|
@JsonProperty("ngsReports")
|
||||||
|
public void setNgsReports(List<SomaticNgsReport> value) { this.ngsReports = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public MtbPatient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(MtbPatient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("previousGuidelineTherapies")
|
||||||
|
public List<MtbMedicationTherapy> getPreviousGuidelineTherapies() { return previousGuidelineTherapies; }
|
||||||
|
@JsonProperty("previousGuidelineTherapies")
|
||||||
|
public void setPreviousGuidelineTherapies(List<MtbMedicationTherapy> value) { this.previousGuidelineTherapies = value; }
|
||||||
|
|
||||||
|
@JsonProperty("recommendations")
|
||||||
|
public List<MtbMedicationRecommendation> getRecommendations() { return recommendations; }
|
||||||
|
@JsonProperty("recommendations")
|
||||||
|
public void setRecommendations(List<MtbMedicationRecommendation> value) { this.recommendations = value; }
|
||||||
|
|
||||||
|
@JsonProperty("responses")
|
||||||
|
public List<Response> getResponses() { return responses; }
|
||||||
|
@JsonProperty("responses")
|
||||||
|
public void setResponses(List<Response> value) { this.responses = value; }
|
||||||
|
|
||||||
|
@JsonProperty("specimens")
|
||||||
|
public List<TumorSpecimen> getSpecimens() { return specimens; }
|
||||||
|
@JsonProperty("specimens")
|
||||||
|
public void setSpecimens(List<TumorSpecimen> value) { this.specimens = value; }
|
||||||
|
|
||||||
|
@JsonProperty("studyInclusionRequests")
|
||||||
|
public List<StudyEnrollmentRecommendation> getStudyInclusionRequests() { return studyInclusionRequests; }
|
||||||
|
@JsonProperty("studyInclusionRequests")
|
||||||
|
public void setStudyInclusionRequests(List<StudyEnrollmentRecommendation> value) { this.studyInclusionRequests = value; }
|
||||||
|
}
|
62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java
Normal file
62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java
Normal file
@ -0,0 +1,62 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class MtbCarePlan {
|
||||||
|
private String description;
|
||||||
|
private String diagnosis;
|
||||||
|
private String geneticCounsellingRequest;
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private NoTargetFinding noTargetFinding;
|
||||||
|
private Patient patient;
|
||||||
|
private List<String> recommendations;
|
||||||
|
private List<String> studyInclusionRequests;
|
||||||
|
|
||||||
|
@JsonProperty("description")
|
||||||
|
public String getDescription() { return description; }
|
||||||
|
@JsonProperty("description")
|
||||||
|
public void setDescription(String value) { this.description = value; }
|
||||||
|
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public String getDiagnosis() { return diagnosis; }
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public void setDiagnosis(String value) { this.diagnosis = value; }
|
||||||
|
|
||||||
|
@JsonProperty("geneticCounsellingRequest")
|
||||||
|
public String getGeneticCounsellingRequest() { return geneticCounsellingRequest; }
|
||||||
|
@JsonProperty("geneticCounsellingRequest")
|
||||||
|
public void setGeneticCounsellingRequest(String value) { this.geneticCounsellingRequest = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("noTargetFinding")
|
||||||
|
public NoTargetFinding getNoTargetFinding() { return noTargetFinding; }
|
||||||
|
@JsonProperty("noTargetFinding")
|
||||||
|
public void setNoTargetFinding(NoTargetFinding value) { this.noTargetFinding = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("recommendations")
|
||||||
|
public List<String> getRecommendations() { return recommendations; }
|
||||||
|
@JsonProperty("recommendations")
|
||||||
|
public void setRecommendations(List<String> value) { this.recommendations = value; }
|
||||||
|
|
||||||
|
@JsonProperty("studyInclusionRequests")
|
||||||
|
public List<String> getStudyInclusionRequests() { return studyInclusionRequests; }
|
||||||
|
@JsonProperty("studyInclusionRequests")
|
||||||
|
public void setStudyInclusionRequests(List<String> value) { this.studyInclusionRequests = value; }
|
||||||
|
}
|
62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java
Normal file
62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosis.java
Normal file
@ -0,0 +1,62 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class MtbDiagnosis {
|
||||||
|
private Coding code;
|
||||||
|
private Coding guidelineTreatmentStatus;
|
||||||
|
private List<String> histologyResults;
|
||||||
|
private Coding icdO3T;
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private Date recordedOn;
|
||||||
|
private List<StatusHistory> statusHistory;
|
||||||
|
private Coding whoGrade;
|
||||||
|
|
||||||
|
@JsonProperty("code")
|
||||||
|
public Coding getCode() { return code; }
|
||||||
|
@JsonProperty("code")
|
||||||
|
public void setCode(Coding value) { this.code = value; }
|
||||||
|
|
||||||
|
@JsonProperty("guidelineTreatmentStatus")
|
||||||
|
public Coding getGuidelineTreatmentStatus() { return guidelineTreatmentStatus; }
|
||||||
|
@JsonProperty("guidelineTreatmentStatus")
|
||||||
|
public void setGuidelineTreatmentStatus(Coding value) { this.guidelineTreatmentStatus = value; }
|
||||||
|
|
||||||
|
@JsonProperty("histologyResults")
|
||||||
|
public List<String> getHistologyResults() { return histologyResults; }
|
||||||
|
@JsonProperty("histologyResults")
|
||||||
|
public void setHistologyResults(List<String> value) { this.histologyResults = value; }
|
||||||
|
|
||||||
|
@JsonProperty("icdO3T")
|
||||||
|
public Coding getIcdO3T() { return icdO3T; }
|
||||||
|
@JsonProperty("icdO3T")
|
||||||
|
public void setIcdO3T(Coding value) { this.icdO3T = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("recordedOn")
|
||||||
|
public Date getRecordedOn() { return recordedOn; }
|
||||||
|
@JsonProperty("recordedOn")
|
||||||
|
public void setRecordedOn(Date value) { this.recordedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("statusHistory")
|
||||||
|
public List<StatusHistory> getStatusHistory() { return statusHistory; }
|
||||||
|
@JsonProperty("statusHistory")
|
||||||
|
public void setStatusHistory(List<StatusHistory> value) { this.statusHistory = value; }
|
||||||
|
|
||||||
|
@JsonProperty("whoGrade")
|
||||||
|
public Coding getWhoGrade() { return whoGrade; }
|
||||||
|
@JsonProperty("whoGrade")
|
||||||
|
public void setWhoGrade(Coding value) { this.whoGrade = value; }
|
||||||
|
}
|
@ -0,0 +1,34 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum MtbDiagnosisTumorSpread {
|
||||||
|
LOCAL, METASTASIZED, TUMOR_FREE, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case LOCAL: return "local";
|
||||||
|
case METASTASIZED: return "metastasized";
|
||||||
|
case TUMOR_FREE: return "tumor-free";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static MtbDiagnosisTumorSpread forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "local":
|
||||||
|
return LOCAL;
|
||||||
|
case "metastasized":
|
||||||
|
return METASTASIZED;
|
||||||
|
case "tumor-free":
|
||||||
|
return TUMOR_FREE;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize MTBDiagnosisTumorSpread");
|
||||||
|
}
|
||||||
|
}
|
24
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java
Normal file
24
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbEpisode.java
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class MtbEpisode {
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private PeriodLocalDate period;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("period")
|
||||||
|
public PeriodLocalDate getPeriod() { return period; }
|
||||||
|
@JsonProperty("period")
|
||||||
|
public void setPeriod(PeriodLocalDate value) { this.period = value; }
|
||||||
|
}
|
@ -0,0 +1,62 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class MtbMedicationRecommendation {
|
||||||
|
private String diagnosis;
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private LevelOfEvidence levelOfEvidence;
|
||||||
|
private List<Coding> medication;
|
||||||
|
private String ngsReport;
|
||||||
|
private Patient patient;
|
||||||
|
private TherapyRecommendationPriority priority;
|
||||||
|
private List<String> supportingVariants;
|
||||||
|
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public String getDiagnosis() { return diagnosis; }
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public void setDiagnosis(String value) { this.diagnosis = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("levelOfEvidence")
|
||||||
|
public LevelOfEvidence getLevelOfEvidence() { return levelOfEvidence; }
|
||||||
|
@JsonProperty("levelOfEvidence")
|
||||||
|
public void setLevelOfEvidence(LevelOfEvidence value) { this.levelOfEvidence = value; }
|
||||||
|
|
||||||
|
@JsonProperty("medication")
|
||||||
|
public List<Coding> getMedication() { return medication; }
|
||||||
|
@JsonProperty("medication")
|
||||||
|
public void setMedication(List<Coding> value) { this.medication = value; }
|
||||||
|
|
||||||
|
@JsonProperty("ngsReport")
|
||||||
|
public String getNgsReport() { return ngsReport; }
|
||||||
|
@JsonProperty("ngsReport")
|
||||||
|
public void setNgsReport(String value) { this.ngsReport = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("priority")
|
||||||
|
public TherapyRecommendationPriority getPriority() { return priority; }
|
||||||
|
@JsonProperty("priority")
|
||||||
|
public void setPriority(TherapyRecommendationPriority value) { this.priority = value; }
|
||||||
|
|
||||||
|
@JsonProperty("supportingVariants")
|
||||||
|
public List<String> getSupportingVariants() { return supportingVariants; }
|
||||||
|
@JsonProperty("supportingVariants")
|
||||||
|
public void setSupportingVariants(List<String> value) { this.supportingVariants = value; }
|
||||||
|
}
|
@ -0,0 +1,80 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class MtbMedicationTherapy {
|
||||||
|
private String basedOn;
|
||||||
|
private String diagnosis;
|
||||||
|
private String id;
|
||||||
|
private List<Coding> medication;
|
||||||
|
private CodingTherapyStatusReason notDoneReason;
|
||||||
|
private String note;
|
||||||
|
private Patient patient;
|
||||||
|
private PeriodLocalDate period;
|
||||||
|
private CodingTherapyStatusReason reasonStopped;
|
||||||
|
private Date recordedOn;
|
||||||
|
private TherapyStatus status;
|
||||||
|
private Long therapyLine;
|
||||||
|
|
||||||
|
@JsonProperty("basedOn")
|
||||||
|
public String getBasedOn() { return basedOn; }
|
||||||
|
@JsonProperty("basedOn")
|
||||||
|
public void setBasedOn(String value) { this.basedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public String getDiagnosis() { return diagnosis; }
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public void setDiagnosis(String value) { this.diagnosis = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("medication")
|
||||||
|
public List<Coding> getMedication() { return medication; }
|
||||||
|
@JsonProperty("medication")
|
||||||
|
public void setMedication(List<Coding> value) { this.medication = value; }
|
||||||
|
|
||||||
|
@JsonProperty("notDoneReason")
|
||||||
|
public CodingTherapyStatusReason getNotDoneReason() { return notDoneReason; }
|
||||||
|
@JsonProperty("notDoneReason")
|
||||||
|
public void setNotDoneReason(CodingTherapyStatusReason value) { this.notDoneReason = value; }
|
||||||
|
|
||||||
|
@JsonProperty("note")
|
||||||
|
public String getNote() { return note; }
|
||||||
|
@JsonProperty("note")
|
||||||
|
public void setNote(String value) { this.note = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("period")
|
||||||
|
public PeriodLocalDate getPeriod() { return period; }
|
||||||
|
@JsonProperty("period")
|
||||||
|
public void setPeriod(PeriodLocalDate value) { this.period = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reasonStopped")
|
||||||
|
public CodingTherapyStatusReason getReasonStopped() { return reasonStopped; }
|
||||||
|
@JsonProperty("reasonStopped")
|
||||||
|
public void setReasonStopped(CodingTherapyStatusReason value) { this.reasonStopped = value; }
|
||||||
|
|
||||||
|
@JsonProperty("recordedOn")
|
||||||
|
public Date getRecordedOn() { return recordedOn; }
|
||||||
|
@JsonProperty("recordedOn")
|
||||||
|
public void setRecordedOn(Date value) { this.recordedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("status")
|
||||||
|
public TherapyStatus getStatus() { return status; }
|
||||||
|
@JsonProperty("status")
|
||||||
|
public void setStatus(TherapyStatus value) { this.status = value; }
|
||||||
|
|
||||||
|
@JsonProperty("therapyLine")
|
||||||
|
public Long getTherapyLine() { return therapyLine; }
|
||||||
|
@JsonProperty("therapyLine")
|
||||||
|
public void setTherapyLine(Long value) { this.therapyLine = value; }
|
||||||
|
}
|
45
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java
Normal file
45
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbPatient.java
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class MtbPatient {
|
||||||
|
private Address address;
|
||||||
|
private Date birthDate;
|
||||||
|
private Date dateOfDeath;
|
||||||
|
private CodingGender gender;
|
||||||
|
private String id;
|
||||||
|
private String insurance;
|
||||||
|
|
||||||
|
@JsonProperty("address")
|
||||||
|
public Address getAddress() { return address; }
|
||||||
|
@JsonProperty("address")
|
||||||
|
public void setAddress(Address value) { this.address = value; }
|
||||||
|
|
||||||
|
@JsonProperty("birthDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getBirthDate() { return birthDate; }
|
||||||
|
@JsonProperty("birthDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setBirthDate(Date value) { this.birthDate = value; }
|
||||||
|
|
||||||
|
@JsonProperty("dateOfDeath")
|
||||||
|
public Date getDateOfDeath() { return dateOfDeath; }
|
||||||
|
@JsonProperty("dateOfDeath")
|
||||||
|
public void setDateOfDeath(Date value) { this.dateOfDeath = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gender")
|
||||||
|
public CodingGender getGender() { return gender; }
|
||||||
|
@JsonProperty("gender")
|
||||||
|
public void setGender(CodingGender value) { this.gender = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("insurance")
|
||||||
|
public String getInsurance() { return insurance; }
|
||||||
|
@JsonProperty("insurance")
|
||||||
|
public void setInsurance(String value) { this.insurance = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/NgsReportSpecimen.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class NgsReportSpecimen {
|
||||||
|
private String id;
|
||||||
|
private SpecimenType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public SpecimenType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(SpecimenType value) { this.type = value; }
|
||||||
|
}
|
25
src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java
Normal file
25
src/main/java/dev/pcvolkmer/mv64e/mtb/NoTargetFinding.java
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class NoTargetFinding {
|
||||||
|
private String diagnosis;
|
||||||
|
private Date issuedOn;
|
||||||
|
private Patient patient;
|
||||||
|
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public String getDiagnosis() { return diagnosis; }
|
||||||
|
@JsonProperty("diagnosis")
|
||||||
|
public void setDiagnosis(String value) { this.diagnosis = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
}
|
73
src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java
Normal file
73
src/main/java/dev/pcvolkmer/mv64e/mtb/NotDoneReasonCode.java
Normal file
@ -0,0 +1,73 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum NotDoneReasonCode {
|
||||||
|
CHRONIC_REMISSION, CONTINUED_EXTERNALLY, DETERIORATION, LOST_TO_FU, MEDICAL_REASON, NO_INDICATION, OTHER, OTHER_THERAPY_CHOSEN, PATIENT_DEATH, PATIENT_REFUSAL, PATIENT_WISH, PAYMENT_ENDED, PAYMENT_PENDING, PAYMENT_REFUSED, PROGRESSION, TOXICITY, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case CHRONIC_REMISSION: return "chronic-remission";
|
||||||
|
case CONTINUED_EXTERNALLY: return "continued-externally";
|
||||||
|
case DETERIORATION: return "deterioration";
|
||||||
|
case LOST_TO_FU: return "lost-to-fu";
|
||||||
|
case MEDICAL_REASON: return "medical-reason";
|
||||||
|
case NO_INDICATION: return "no-indication";
|
||||||
|
case OTHER: return "other";
|
||||||
|
case OTHER_THERAPY_CHOSEN: return "other-therapy-chosen";
|
||||||
|
case PATIENT_DEATH: return "patient-death";
|
||||||
|
case PATIENT_REFUSAL: return "patient-refusal";
|
||||||
|
case PATIENT_WISH: return "patient-wish";
|
||||||
|
case PAYMENT_ENDED: return "payment-ended";
|
||||||
|
case PAYMENT_PENDING: return "payment-pending";
|
||||||
|
case PAYMENT_REFUSED: return "payment-refused";
|
||||||
|
case PROGRESSION: return "progression";
|
||||||
|
case TOXICITY: return "toxicity";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static NotDoneReasonCode forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "chronic-remission":
|
||||||
|
return CHRONIC_REMISSION;
|
||||||
|
case "continued-externally":
|
||||||
|
return CONTINUED_EXTERNALLY;
|
||||||
|
case "deterioration":
|
||||||
|
return DETERIORATION;
|
||||||
|
case "lost-to-fu":
|
||||||
|
return LOST_TO_FU;
|
||||||
|
case "medical-reason":
|
||||||
|
return MEDICAL_REASON;
|
||||||
|
case "no-indication":
|
||||||
|
return NO_INDICATION;
|
||||||
|
case "other":
|
||||||
|
return OTHER;
|
||||||
|
case "other-therapy-chosen":
|
||||||
|
return OTHER_THERAPY_CHOSEN;
|
||||||
|
case "patient-death":
|
||||||
|
return PATIENT_DEATH;
|
||||||
|
case "patient-refusal":
|
||||||
|
return PATIENT_REFUSAL;
|
||||||
|
case "patient-wish":
|
||||||
|
return PATIENT_WISH;
|
||||||
|
case "payment-ended":
|
||||||
|
return PAYMENT_ENDED;
|
||||||
|
case "payment-pending":
|
||||||
|
return PAYMENT_PENDING;
|
||||||
|
case "payment-refused":
|
||||||
|
return PAYMENT_REFUSED;
|
||||||
|
case "progression":
|
||||||
|
return PROGRESSION;
|
||||||
|
case "toxicity":
|
||||||
|
return TOXICITY;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize NotDoneReasonCode");
|
||||||
|
}
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/Patient.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Patient {
|
||||||
|
private String id;
|
||||||
|
private PatientType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public PatientType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(PatientType value) { this.type = value; }
|
||||||
|
}
|
22
src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java
Normal file
22
src/main/java/dev/pcvolkmer/mv64e/mtb/PatientType.java
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum PatientType {
|
||||||
|
PATIENT;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case PATIENT: return "Patient";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static PatientType forValue(String value) throws IOException {
|
||||||
|
if (value.equals("Patient")) return PATIENT;
|
||||||
|
throw new IOException("Cannot deserialize PatientType");
|
||||||
|
}
|
||||||
|
}
|
33
src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java
Normal file
33
src/main/java/dev/pcvolkmer/mv64e/mtb/PerformanceStatus.java
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class PerformanceStatus {
|
||||||
|
private Date effectiveDate;
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private CodingEcog value;
|
||||||
|
|
||||||
|
@JsonProperty("effectiveDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getEffectiveDate() { return effectiveDate; }
|
||||||
|
@JsonProperty("effectiveDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setEffectiveDate(Date value) { this.effectiveDate = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("value")
|
||||||
|
public CodingEcog getValue() { return value; }
|
||||||
|
@JsonProperty("value")
|
||||||
|
public void setValue(CodingEcog value) { this.value = value; }
|
||||||
|
}
|
21
src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java
Normal file
21
src/main/java/dev/pcvolkmer/mv64e/mtb/PeriodLocalDate.java
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class PeriodLocalDate {
|
||||||
|
private Date end;
|
||||||
|
private Date start;
|
||||||
|
|
||||||
|
@JsonProperty("end")
|
||||||
|
public Date getEnd() { return end; }
|
||||||
|
@JsonProperty("end")
|
||||||
|
public void setEnd(Date value) { this.end = value; }
|
||||||
|
|
||||||
|
@JsonProperty("start")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getStart() { return start; }
|
||||||
|
@JsonProperty("start")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setStart(Date value) { this.start = value; }
|
||||||
|
}
|
37
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleCode.java
Normal file
37
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleCode.java
Normal file
@ -0,0 +1,37 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum PurpleCode {
|
||||||
|
THE_0, THE_1, THE_2, THE_3, THE_4;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case THE_0: return "0";
|
||||||
|
case THE_1: return "1";
|
||||||
|
case THE_2: return "2";
|
||||||
|
case THE_3: return "3";
|
||||||
|
case THE_4: return "4";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static PurpleCode forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "0":
|
||||||
|
return THE_0;
|
||||||
|
case "1":
|
||||||
|
return THE_1;
|
||||||
|
case "2":
|
||||||
|
return THE_2;
|
||||||
|
case "3":
|
||||||
|
return THE_3;
|
||||||
|
case "4":
|
||||||
|
return THE_4;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize PurpleCode");
|
||||||
|
}
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/PurpleGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class PurpleGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
42
src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java
Normal file
42
src/main/java/dev/pcvolkmer/mv64e/mtb/RNAFusion.java
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class RNAFusion {
|
||||||
|
private String cosmicId;
|
||||||
|
private String effect;
|
||||||
|
private RnaFusionFusionPartner3Prime fusionPartner3Prime;
|
||||||
|
private RnaFusionFusionPartner5Prime fusionPartner5Prime;
|
||||||
|
private String id;
|
||||||
|
private long reportedNumReads;
|
||||||
|
|
||||||
|
@JsonProperty("cosmicId")
|
||||||
|
public String getCosmicId() { return cosmicId; }
|
||||||
|
@JsonProperty("cosmicId")
|
||||||
|
public void setCosmicId(String value) { this.cosmicId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("effect")
|
||||||
|
public String getEffect() { return effect; }
|
||||||
|
@JsonProperty("effect")
|
||||||
|
public void setEffect(String value) { this.effect = value; }
|
||||||
|
|
||||||
|
@JsonProperty("fusionPartner3prime")
|
||||||
|
public RnaFusionFusionPartner3Prime getFusionPartner3Prime() { return fusionPartner3Prime; }
|
||||||
|
@JsonProperty("fusionPartner3prime")
|
||||||
|
public void setFusionPartner3Prime(RnaFusionFusionPartner3Prime value) { this.fusionPartner3Prime = value; }
|
||||||
|
|
||||||
|
@JsonProperty("fusionPartner5prime")
|
||||||
|
public RnaFusionFusionPartner5Prime getFusionPartner5Prime() { return fusionPartner5Prime; }
|
||||||
|
@JsonProperty("fusionPartner5prime")
|
||||||
|
public void setFusionPartner5Prime(RnaFusionFusionPartner5Prime value) { this.fusionPartner5Prime = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reportedNumReads")
|
||||||
|
public long getReportedNumReads() { return reportedNumReads; }
|
||||||
|
@JsonProperty("reportedNumReads")
|
||||||
|
public void setReportedNumReads(long value) { this.reportedNumReads = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class ReferencePublication {
|
||||||
|
private ExtId extId;
|
||||||
|
private String type;
|
||||||
|
private String uri;
|
||||||
|
|
||||||
|
@JsonProperty("extId")
|
||||||
|
public ExtId getExtId() { return extId; }
|
||||||
|
@JsonProperty("extId")
|
||||||
|
public void setExtId(ExtId value) { this.extId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public String getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(String value) { this.type = value; }
|
||||||
|
|
||||||
|
@JsonProperty("uri")
|
||||||
|
public String getUri() { return uri; }
|
||||||
|
@JsonProperty("uri")
|
||||||
|
public void setUri(String value) { this.uri = value; }
|
||||||
|
}
|
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class ReportedAffectedGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
39
src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java
Normal file
39
src/main/java/dev/pcvolkmer/mv64e/mtb/Response.java
Normal file
@ -0,0 +1,39 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class Response {
|
||||||
|
private Date effectiveDate;
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private ResponseTherapy therapy;
|
||||||
|
private CodingRecist value;
|
||||||
|
|
||||||
|
@JsonProperty("effectiveDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getEffectiveDate() { return effectiveDate; }
|
||||||
|
@JsonProperty("effectiveDate")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setEffectiveDate(Date value) { this.effectiveDate = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("therapy")
|
||||||
|
public ResponseTherapy getTherapy() { return therapy; }
|
||||||
|
@JsonProperty("therapy")
|
||||||
|
public void setTherapy(ResponseTherapy value) { this.therapy = value; }
|
||||||
|
|
||||||
|
@JsonProperty("value")
|
||||||
|
public CodingRecist getValue() { return value; }
|
||||||
|
@JsonProperty("value")
|
||||||
|
public void setValue(CodingRecist value) { this.value = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapy.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class ResponseTherapy {
|
||||||
|
private String id;
|
||||||
|
private ResponseTherapyType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public ResponseTherapyType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(ResponseTherapyType value) { this.type = value; }
|
||||||
|
}
|
@ -0,0 +1,22 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum ResponseTherapyType {
|
||||||
|
MTB_MEDICATION_THERAPY;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case MTB_MEDICATION_THERAPY: return "MTBMedicationTherapy";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static ResponseTherapyType forValue(String value) throws IOException {
|
||||||
|
if (value.equals("MTBMedicationTherapy")) return MTB_MEDICATION_THERAPY;
|
||||||
|
throw new IOException("Cannot deserialize ResponseTherapyType");
|
||||||
|
}
|
||||||
|
}
|
@ -0,0 +1,36 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class RnaFusionFusionPartner3Prime {
|
||||||
|
private String exon;
|
||||||
|
private TentacledGene gene;
|
||||||
|
private double position;
|
||||||
|
private RnaFusionStrand strand;
|
||||||
|
private String transcriptId;
|
||||||
|
|
||||||
|
@JsonProperty("exon")
|
||||||
|
public String getExon() { return exon; }
|
||||||
|
@JsonProperty("exon")
|
||||||
|
public void setExon(String value) { this.exon = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public TentacledGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(TentacledGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("position")
|
||||||
|
public double getPosition() { return position; }
|
||||||
|
@JsonProperty("position")
|
||||||
|
public void setPosition(double value) { this.position = value; }
|
||||||
|
|
||||||
|
@JsonProperty("strand")
|
||||||
|
public RnaFusionStrand getStrand() { return strand; }
|
||||||
|
@JsonProperty("strand")
|
||||||
|
public void setStrand(RnaFusionStrand value) { this.strand = value; }
|
||||||
|
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public String getTranscriptId() { return transcriptId; }
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public void setTranscriptId(String value) { this.transcriptId = value; }
|
||||||
|
}
|
@ -0,0 +1,36 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class RnaFusionFusionPartner5Prime {
|
||||||
|
private String exon;
|
||||||
|
private StickyGene gene;
|
||||||
|
private double position;
|
||||||
|
private RnaFusionStrand strand;
|
||||||
|
private String transcriptId;
|
||||||
|
|
||||||
|
@JsonProperty("exon")
|
||||||
|
public String getExon() { return exon; }
|
||||||
|
@JsonProperty("exon")
|
||||||
|
public void setExon(String value) { this.exon = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public StickyGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(StickyGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("position")
|
||||||
|
public double getPosition() { return position; }
|
||||||
|
@JsonProperty("position")
|
||||||
|
public void setPosition(double value) { this.position = value; }
|
||||||
|
|
||||||
|
@JsonProperty("strand")
|
||||||
|
public RnaFusionStrand getStrand() { return strand; }
|
||||||
|
@JsonProperty("strand")
|
||||||
|
public void setStrand(RnaFusionStrand value) { this.strand = value; }
|
||||||
|
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public String getTranscriptId() { return transcriptId; }
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public void setTranscriptId(String value) { this.transcriptId = value; }
|
||||||
|
}
|
24
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java
Normal file
24
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionStrand.java
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum RnaFusionStrand {
|
||||||
|
EMPTY, RNA_FUSION_STRAND;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case EMPTY: return "+";
|
||||||
|
case RNA_FUSION_STRAND: return "-";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static RnaFusionStrand forValue(String value) throws IOException {
|
||||||
|
if (value.equals("+")) return EMPTY;
|
||||||
|
if (value.equals("-")) return RNA_FUSION_STRAND;
|
||||||
|
throw new IOException("Cannot deserialize RNAFusionStrand");
|
||||||
|
}
|
||||||
|
}
|
72
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java
Normal file
72
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java
Normal file
@ -0,0 +1,72 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class RnaSeq {
|
||||||
|
private Long cohortRanking;
|
||||||
|
private String ensemblId;
|
||||||
|
private String entrezId;
|
||||||
|
private double fragmentsPerKilobaseMillion;
|
||||||
|
private boolean fromNgs;
|
||||||
|
private RnaSeqGene gene;
|
||||||
|
private String id;
|
||||||
|
private long librarySize;
|
||||||
|
private long rawCounts;
|
||||||
|
private boolean tissueCorrectedExpression;
|
||||||
|
private String transcriptId;
|
||||||
|
|
||||||
|
@JsonProperty("cohortRanking")
|
||||||
|
public Long getCohortRanking() { return cohortRanking; }
|
||||||
|
@JsonProperty("cohortRanking")
|
||||||
|
public void setCohortRanking(Long value) { this.cohortRanking = value; }
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("entrezId")
|
||||||
|
public String getEntrezId() { return entrezId; }
|
||||||
|
@JsonProperty("entrezId")
|
||||||
|
public void setEntrezId(String value) { this.entrezId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("fragmentsPerKilobaseMillion")
|
||||||
|
public double getFragmentsPerKilobaseMillion() { return fragmentsPerKilobaseMillion; }
|
||||||
|
@JsonProperty("fragmentsPerKilobaseMillion")
|
||||||
|
public void setFragmentsPerKilobaseMillion(double value) { this.fragmentsPerKilobaseMillion = value; }
|
||||||
|
|
||||||
|
@JsonProperty("fromNGS")
|
||||||
|
public boolean getFromNgs() { return fromNgs; }
|
||||||
|
@JsonProperty("fromNGS")
|
||||||
|
public void setFromNgs(boolean value) { this.fromNgs = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public RnaSeqGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(RnaSeqGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("librarySize")
|
||||||
|
public long getLibrarySize() { return librarySize; }
|
||||||
|
@JsonProperty("librarySize")
|
||||||
|
public void setLibrarySize(long value) { this.librarySize = value; }
|
||||||
|
|
||||||
|
@JsonProperty("rawCounts")
|
||||||
|
public long getRawCounts() { return rawCounts; }
|
||||||
|
@JsonProperty("rawCounts")
|
||||||
|
public void setRawCounts(long value) { this.rawCounts = value; }
|
||||||
|
|
||||||
|
@JsonProperty("tissueCorrectedExpression")
|
||||||
|
public boolean getTissueCorrectedExpression() { return tissueCorrectedExpression; }
|
||||||
|
@JsonProperty("tissueCorrectedExpression")
|
||||||
|
public void setTissueCorrectedExpression(boolean value) { this.tissueCorrectedExpression = value; }
|
||||||
|
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public String getTranscriptId() { return transcriptId; }
|
||||||
|
@JsonProperty("transcriptId")
|
||||||
|
public void setTranscriptId(String value) { this.transcriptId = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeqGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class RnaSeqGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/SimpleVariantGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class SimpleVariantGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
84
src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java
Normal file
84
src/main/java/dev/pcvolkmer/mv64e/mtb/Snv.java
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Snv {
|
||||||
|
private double allelicFrequency;
|
||||||
|
private String altAllele;
|
||||||
|
private Coding aminoAcidChange;
|
||||||
|
private Chromosome chromosome;
|
||||||
|
private String cosmicId;
|
||||||
|
private String dbSnpId;
|
||||||
|
private Coding dnaChange;
|
||||||
|
private SimpleVariantGene gene;
|
||||||
|
private String id;
|
||||||
|
private Coding interpretation;
|
||||||
|
private long readDepth;
|
||||||
|
private String refAllele;
|
||||||
|
private StartEnd startEnd;
|
||||||
|
|
||||||
|
@JsonProperty("allelicFrequency")
|
||||||
|
public double getAllelicFrequency() { return allelicFrequency; }
|
||||||
|
@JsonProperty("allelicFrequency")
|
||||||
|
public void setAllelicFrequency(double value) { this.allelicFrequency = value; }
|
||||||
|
|
||||||
|
@JsonProperty("altAllele")
|
||||||
|
public String getAltAllele() { return altAllele; }
|
||||||
|
@JsonProperty("altAllele")
|
||||||
|
public void setAltAllele(String value) { this.altAllele = value; }
|
||||||
|
|
||||||
|
@JsonProperty("aminoAcidChange")
|
||||||
|
public Coding getAminoAcidChange() { return aminoAcidChange; }
|
||||||
|
@JsonProperty("aminoAcidChange")
|
||||||
|
public void setAminoAcidChange(Coding value) { this.aminoAcidChange = value; }
|
||||||
|
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public Chromosome getChromosome() { return chromosome; }
|
||||||
|
@JsonProperty("chromosome")
|
||||||
|
public void setChromosome(Chromosome value) { this.chromosome = value; }
|
||||||
|
|
||||||
|
@JsonProperty("cosmicId")
|
||||||
|
public String getCosmicId() { return cosmicId; }
|
||||||
|
@JsonProperty("cosmicId")
|
||||||
|
public void setCosmicId(String value) { this.cosmicId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("dbSNPId")
|
||||||
|
public String getDbSnpId() { return dbSnpId; }
|
||||||
|
@JsonProperty("dbSNPId")
|
||||||
|
public void setDbSnpId(String value) { this.dbSnpId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("dnaChange")
|
||||||
|
public Coding getDnaChange() { return dnaChange; }
|
||||||
|
@JsonProperty("dnaChange")
|
||||||
|
public void setDnaChange(Coding value) { this.dnaChange = value; }
|
||||||
|
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public SimpleVariantGene getGene() { return gene; }
|
||||||
|
@JsonProperty("gene")
|
||||||
|
public void setGene(SimpleVariantGene value) { this.gene = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("interpretation")
|
||||||
|
public Coding getInterpretation() { return interpretation; }
|
||||||
|
@JsonProperty("interpretation")
|
||||||
|
public void setInterpretation(Coding value) { this.interpretation = value; }
|
||||||
|
|
||||||
|
@JsonProperty("readDepth")
|
||||||
|
public long getReadDepth() { return readDepth; }
|
||||||
|
@JsonProperty("readDepth")
|
||||||
|
public void setReadDepth(long value) { this.readDepth = value; }
|
||||||
|
|
||||||
|
@JsonProperty("refAllele")
|
||||||
|
public String getRefAllele() { return refAllele; }
|
||||||
|
@JsonProperty("refAllele")
|
||||||
|
public void setRefAllele(String value) { this.refAllele = value; }
|
||||||
|
|
||||||
|
@JsonProperty("startEnd")
|
||||||
|
public StartEnd getStartEnd() { return startEnd; }
|
||||||
|
@JsonProperty("startEnd")
|
||||||
|
public void setStartEnd(StartEnd value) { this.startEnd = value; }
|
||||||
|
}
|
98
src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java
Normal file
98
src/main/java/dev/pcvolkmer/mv64e/mtb/SomaticNgsReport.java
Normal file
@ -0,0 +1,98 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
import java.util.List;
|
||||||
|
|
||||||
|
public class SomaticNgsReport {
|
||||||
|
private Double brcaness;
|
||||||
|
private List<Cnv> copyNumberVariants;
|
||||||
|
private List<DnaFusion> dnaFusions;
|
||||||
|
private String id;
|
||||||
|
private Date issueDate;
|
||||||
|
private List<Metadatum> metadata;
|
||||||
|
private Double msi;
|
||||||
|
private Patient patient;
|
||||||
|
private List<RNAFusion> rnaFusions;
|
||||||
|
private List<RnaSeq> rnaSeqs;
|
||||||
|
private Coding sequencingType;
|
||||||
|
private List<Snv> simpleVariants;
|
||||||
|
private NgsReportSpecimen specimen;
|
||||||
|
private Double tmb;
|
||||||
|
private TumorCellContent tumorCellContent;
|
||||||
|
|
||||||
|
@JsonProperty("brcaness")
|
||||||
|
public Double getBrcaness() { return brcaness; }
|
||||||
|
@JsonProperty("brcaness")
|
||||||
|
public void setBrcaness(Double value) { this.brcaness = value; }
|
||||||
|
|
||||||
|
@JsonProperty("copyNumberVariants")
|
||||||
|
public List<Cnv> getCopyNumberVariants() { return copyNumberVariants; }
|
||||||
|
@JsonProperty("copyNumberVariants")
|
||||||
|
public void setCopyNumberVariants(List<Cnv> value) { this.copyNumberVariants = value; }
|
||||||
|
|
||||||
|
@JsonProperty("dnaFusions")
|
||||||
|
public List<DnaFusion> getDnaFusions() { return dnaFusions; }
|
||||||
|
@JsonProperty("dnaFusions")
|
||||||
|
public void setDnaFusions(List<DnaFusion> value) { this.dnaFusions = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issueDate")
|
||||||
|
public Date getIssueDate() { return issueDate; }
|
||||||
|
@JsonProperty("issueDate")
|
||||||
|
public void setIssueDate(Date value) { this.issueDate = value; }
|
||||||
|
|
||||||
|
@JsonProperty("metadata")
|
||||||
|
public List<Metadatum> getMetadata() { return metadata; }
|
||||||
|
@JsonProperty("metadata")
|
||||||
|
public void setMetadata(List<Metadatum> value) { this.metadata = value; }
|
||||||
|
|
||||||
|
@JsonProperty("msi")
|
||||||
|
public Double getMsi() { return msi; }
|
||||||
|
@JsonProperty("msi")
|
||||||
|
public void setMsi(Double value) { this.msi = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("rnaFusions")
|
||||||
|
public List<RNAFusion> getRnaFusions() { return rnaFusions; }
|
||||||
|
@JsonProperty("rnaFusions")
|
||||||
|
public void setRnaFusions(List<RNAFusion> value) { this.rnaFusions = value; }
|
||||||
|
|
||||||
|
@JsonProperty("rnaSeqs")
|
||||||
|
public List<RnaSeq> getRnaSeqs() { return rnaSeqs; }
|
||||||
|
@JsonProperty("rnaSeqs")
|
||||||
|
public void setRnaSeqs(List<RnaSeq> value) { this.rnaSeqs = value; }
|
||||||
|
|
||||||
|
@JsonProperty("sequencingType")
|
||||||
|
public Coding getSequencingType() { return sequencingType; }
|
||||||
|
@JsonProperty("sequencingType")
|
||||||
|
public void setSequencingType(Coding value) { this.sequencingType = value; }
|
||||||
|
|
||||||
|
@JsonProperty("simpleVariants")
|
||||||
|
public List<Snv> getSimpleVariants() { return simpleVariants; }
|
||||||
|
@JsonProperty("simpleVariants")
|
||||||
|
public void setSimpleVariants(List<Snv> value) { this.simpleVariants = value; }
|
||||||
|
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public NgsReportSpecimen getSpecimen() { return specimen; }
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public void setSpecimen(NgsReportSpecimen value) { this.specimen = value; }
|
||||||
|
|
||||||
|
@JsonProperty("tmb")
|
||||||
|
public Double getTmb() { return tmb; }
|
||||||
|
@JsonProperty("tmb")
|
||||||
|
public void setTmb(Double value) { this.tmb = value; }
|
||||||
|
|
||||||
|
@JsonProperty("tumorCellContent")
|
||||||
|
public TumorCellContent getTumorCellContent() { return tumorCellContent; }
|
||||||
|
@JsonProperty("tumorCellContent")
|
||||||
|
public void setTumorCellContent(TumorCellContent value) { this.tumorCellContent = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/Specimen.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class Specimen {
|
||||||
|
private String id;
|
||||||
|
private SpecimenType type;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public SpecimenType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(SpecimenType value) { this.type = value; }
|
||||||
|
}
|
22
src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java
Normal file
22
src/main/java/dev/pcvolkmer/mv64e/mtb/SpecimenType.java
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum SpecimenType {
|
||||||
|
TUMOR_SPECIMEN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case TUMOR_SPECIMEN: return "TumorSpecimen";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static SpecimenType forValue(String value) throws IOException {
|
||||||
|
if (value.equals("TumorSpecimen")) return TUMOR_SPECIMEN;
|
||||||
|
throw new IOException("Cannot deserialize SpecimenType");
|
||||||
|
}
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartEnd.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class StartEnd {
|
||||||
|
private Double end;
|
||||||
|
private double start;
|
||||||
|
|
||||||
|
@JsonProperty("end")
|
||||||
|
public Double getEnd() { return end; }
|
||||||
|
@JsonProperty("end")
|
||||||
|
public void setEnd(Double value) { this.end = value; }
|
||||||
|
|
||||||
|
@JsonProperty("start")
|
||||||
|
public double getStart() { return start; }
|
||||||
|
@JsonProperty("start")
|
||||||
|
public void setStart(double value) { this.start = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartRange.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StartRange.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class StartRange {
|
||||||
|
private Double end;
|
||||||
|
private double start;
|
||||||
|
|
||||||
|
@JsonProperty("end")
|
||||||
|
public Double getEnd() { return end; }
|
||||||
|
@JsonProperty("end")
|
||||||
|
public void setEnd(Double value) { this.end = value; }
|
||||||
|
|
||||||
|
@JsonProperty("start")
|
||||||
|
public double getStart() { return start; }
|
||||||
|
@JsonProperty("start")
|
||||||
|
public void setStart(double value) { this.start = value; }
|
||||||
|
}
|
21
src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java
Normal file
21
src/main/java/dev/pcvolkmer/mv64e/mtb/StatusHistory.java
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class StatusHistory {
|
||||||
|
private Date date;
|
||||||
|
private MtbDiagnosisTumorSpread status;
|
||||||
|
|
||||||
|
@JsonProperty("date")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public Date getDate() { return date; }
|
||||||
|
@JsonProperty("date")
|
||||||
|
@JsonFormat(pattern = "yyyy-MM-dd")
|
||||||
|
public void setDate(Date value) { this.date = value; }
|
||||||
|
|
||||||
|
@JsonProperty("status")
|
||||||
|
public MtbDiagnosisTumorSpread getStatus() { return status; }
|
||||||
|
@JsonProperty("status")
|
||||||
|
public void setStatus(MtbDiagnosisTumorSpread value) { this.status = value; }
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/StickyGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class StickyGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
@ -0,0 +1,37 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
import java.util.Date;
|
||||||
|
|
||||||
|
public class StudyEnrollmentRecommendation {
|
||||||
|
private String id;
|
||||||
|
private Date issuedOn;
|
||||||
|
private String nctNumber;
|
||||||
|
private Patient patient;
|
||||||
|
private String reason;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public Date getIssuedOn() { return issuedOn; }
|
||||||
|
@JsonProperty("issuedOn")
|
||||||
|
public void setIssuedOn(Date value) { this.issuedOn = value; }
|
||||||
|
|
||||||
|
@JsonProperty("nctNumber")
|
||||||
|
public String getNctNumber() { return nctNumber; }
|
||||||
|
@JsonProperty("nctNumber")
|
||||||
|
public void setNctNumber(String value) { this.nctNumber = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public String getReason() { return reason; }
|
||||||
|
@JsonProperty("reason")
|
||||||
|
public void setReason(String value) { this.reason = value; }
|
||||||
|
}
|
22
src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java
Normal file
22
src/main/java/dev/pcvolkmer/mv64e/mtb/SystemEnum.java
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum SystemEnum {
|
||||||
|
HTTPS_PUBMED_NCBI_NLM_NIH_GOV;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case HTTPS_PUBMED_NCBI_NLM_NIH_GOV: return "https://pubmed.ncbi.nlm.nih.gov/";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static SystemEnum forValue(String value) throws IOException {
|
||||||
|
if (value.equals("https://pubmed.ncbi.nlm.nih.gov/")) return HTTPS_PUBMED_NCBI_NLM_NIH_GOV;
|
||||||
|
throw new IOException("Cannot deserialize SystemEnum");
|
||||||
|
}
|
||||||
|
}
|
18
src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java
Normal file
18
src/main/java/dev/pcvolkmer/mv64e/mtb/TentacledGene.java
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class TentacledGene {
|
||||||
|
private String ensemblId;
|
||||||
|
private String hgncId;
|
||||||
|
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public String getEnsemblId() { return ensemblId; }
|
||||||
|
@JsonProperty("ensemblId")
|
||||||
|
public void setEnsemblId(String value) { this.ensemblId = value; }
|
||||||
|
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public String getHgncId() { return hgncId; }
|
||||||
|
@JsonProperty("hgncId")
|
||||||
|
public void setHgncId(String value) { this.hgncId = value; }
|
||||||
|
}
|
@ -0,0 +1,34 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum TherapyRecommendationPriority {
|
||||||
|
PRIORITY_1, PRIORITY_2, PRIORITY_3, PRIORITY_4;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case PRIORITY_1: return "1";
|
||||||
|
case PRIORITY_2: return "2";
|
||||||
|
case PRIORITY_3: return "3";
|
||||||
|
case PRIORITY_4: return "4";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static TherapyRecommendationPriority forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "1":
|
||||||
|
return PRIORITY_1;
|
||||||
|
case "2":
|
||||||
|
return PRIORITY_2;
|
||||||
|
case "3":
|
||||||
|
return PRIORITY_3;
|
||||||
|
case "4":
|
||||||
|
return PRIORITY_4;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize TherapyRecommendationPriority");
|
||||||
|
}
|
||||||
|
}
|
37
src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java
Normal file
37
src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyStatus.java
Normal file
@ -0,0 +1,37 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum TherapyStatus {
|
||||||
|
COMPLETED, NOT_DONE, ON_GOING, STOPPED, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case COMPLETED: return "completed";
|
||||||
|
case NOT_DONE: return "not-done";
|
||||||
|
case ON_GOING: return "on-going";
|
||||||
|
case STOPPED: return "stopped";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static TherapyStatus forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "completed":
|
||||||
|
return COMPLETED;
|
||||||
|
case "not-done":
|
||||||
|
return NOT_DONE;
|
||||||
|
case "on-going":
|
||||||
|
return ON_GOING;
|
||||||
|
case "stopped":
|
||||||
|
return STOPPED;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize TherapyStatus");
|
||||||
|
}
|
||||||
|
}
|
30
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java
Normal file
30
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContent.java
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class TumorCellContent {
|
||||||
|
private String id;
|
||||||
|
private TumorCellContentMethod method;
|
||||||
|
private String specimen;
|
||||||
|
private double value;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("method")
|
||||||
|
public TumorCellContentMethod getMethod() { return method; }
|
||||||
|
@JsonProperty("method")
|
||||||
|
public void setMethod(TumorCellContentMethod value) { this.method = value; }
|
||||||
|
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public String getSpecimen() { return specimen; }
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public void setSpecimen(String value) { this.specimen = value; }
|
||||||
|
|
||||||
|
@JsonProperty("value")
|
||||||
|
public double getValue() { return value; }
|
||||||
|
@JsonProperty("value")
|
||||||
|
public void setValue(double value) { this.value = value; }
|
||||||
|
}
|
@ -0,0 +1,24 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum TumorCellContentMethod {
|
||||||
|
BIOINFORMATIC, HISTOLOGIC;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case BIOINFORMATIC: return "bioinformatic";
|
||||||
|
case HISTOLOGIC: return "histologic";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static TumorCellContentMethod forValue(String value) throws IOException {
|
||||||
|
if (value.equals("bioinformatic")) return BIOINFORMATIC;
|
||||||
|
if (value.equals("histologic")) return HISTOLOGIC;
|
||||||
|
throw new IOException("Cannot deserialize TumorCellContentMethod");
|
||||||
|
}
|
||||||
|
}
|
36
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java
Normal file
36
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorMorphology.java
Normal file
@ -0,0 +1,36 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class TumorMorphology {
|
||||||
|
private String id;
|
||||||
|
private String note;
|
||||||
|
private Patient patient;
|
||||||
|
private String specimen;
|
||||||
|
private Coding value;
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("note")
|
||||||
|
public String getNote() { return note; }
|
||||||
|
@JsonProperty("note")
|
||||||
|
public void setNote(String value) { this.note = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public String getSpecimen() { return specimen; }
|
||||||
|
@JsonProperty("specimen")
|
||||||
|
public void setSpecimen(String value) { this.specimen = value; }
|
||||||
|
|
||||||
|
@JsonProperty("value")
|
||||||
|
public Coding getValue() { return value; }
|
||||||
|
@JsonProperty("value")
|
||||||
|
public void setValue(Coding value) { this.value = value; }
|
||||||
|
}
|
36
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java
Normal file
36
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimen.java
Normal file
@ -0,0 +1,36 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public class TumorSpecimen {
|
||||||
|
private Collection collection;
|
||||||
|
private Coding icd10;
|
||||||
|
private String id;
|
||||||
|
private Patient patient;
|
||||||
|
private CodingTumorSpecimenType type;
|
||||||
|
|
||||||
|
@JsonProperty("collection")
|
||||||
|
public Collection getCollection() { return collection; }
|
||||||
|
@JsonProperty("collection")
|
||||||
|
public void setCollection(Collection value) { this.collection = value; }
|
||||||
|
|
||||||
|
@JsonProperty("icd10")
|
||||||
|
public Coding getIcd10() { return icd10; }
|
||||||
|
@JsonProperty("icd10")
|
||||||
|
public void setIcd10(Coding value) { this.icd10 = value; }
|
||||||
|
|
||||||
|
@JsonProperty("id")
|
||||||
|
public String getId() { return id; }
|
||||||
|
@JsonProperty("id")
|
||||||
|
public void setId(String value) { this.id = value; }
|
||||||
|
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public Patient getPatient() { return patient; }
|
||||||
|
@JsonProperty("patient")
|
||||||
|
public void setPatient(Patient value) { this.patient = value; }
|
||||||
|
|
||||||
|
@JsonProperty("type")
|
||||||
|
public CodingTumorSpecimenType getType() { return type; }
|
||||||
|
@JsonProperty("type")
|
||||||
|
public void setType(CodingTumorSpecimenType value) { this.type = value; }
|
||||||
|
}
|
@ -0,0 +1,31 @@
|
|||||||
|
package dev.pcvolkmer.mv64e.mtb;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import com.fasterxml.jackson.annotation.*;
|
||||||
|
|
||||||
|
public enum TumorSpecimenCollectionLocalization {
|
||||||
|
METASTASIS, PRIMARY_TUMOR, UNKNOWN;
|
||||||
|
|
||||||
|
@JsonValue
|
||||||
|
public String toValue() {
|
||||||
|
switch (this) {
|
||||||
|
case METASTASIS: return "metastasis";
|
||||||
|
case PRIMARY_TUMOR: return "primary-tumor";
|
||||||
|
case UNKNOWN: return "unknown";
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
@JsonCreator
|
||||||
|
public static TumorSpecimenCollectionLocalization forValue(String value) throws IOException {
|
||||||
|
switch (value) {
|
||||||
|
case "metastasis":
|
||||||
|
return METASTASIS;
|
||||||
|
case "primary-tumor":
|
||||||
|
return PRIMARY_TUMOR;
|
||||||
|
case "unknown":
|
||||||
|
return UNKNOWN;
|
||||||
|
}
|
||||||
|
throw new IOException("Cannot deserialize TumorSpecimenCollectionLocalization");
|
||||||
|
}
|
||||||
|
}
|
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user