pcvolkmer/mv64e-mtb-dto-java
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Paul-Christian Volkmer
2024-07-09 16:36:24 +02:00
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.gitignore vendored Normal file
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.gradle
build/
!gradle/wrapper/gradle-wrapper.jar
!**/src/main/**/build/
!**/src/test/**/build/
### IntelliJ IDEA ###
.idea/
*.iws
*.iml
*.ipr
out/
!**/src/main/**/out/
!**/src/test/**/out/
### Eclipse ###
.apt_generated
.classpath
.factorypath
.project
.settings
.springBeans
.sts4-cache
bin/
!**/src/main/**/bin/
!**/src/test/**/bin/
### NetBeans ###
/nbproject/private/
/nbbuild/
/dist/
/nbdist/
/.nb-gradle/
### VS Code ###
.vscode/
### Mac OS ###
.DS_Store

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LICENSE.txt Normal file
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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.

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README.md Normal file
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# 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`.

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build.gradle Normal file
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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()
}

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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

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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 "$JAVACMD" "$@"

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@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

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rootProject.name = 'mtb-dto'

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src/main/java/dev/pcvolkmer/mv64e/mtb/AddendumCode.java Normal file
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Address.java Normal file
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Chromosome.java Normal file
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/Claim.java Normal file
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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; }
}

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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaim.java Normal file
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseClaimType.java Normal file
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/ClaimResponseStatus.java Normal file
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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");
}
}

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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");
}
}

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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/CnvType.java Normal file
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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
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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
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingClaimResponseStatus.java Normal file
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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
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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
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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; }
}

30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceAddendum.java Normal file
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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; }
}

30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingLevelOfEvidenceGrading.java Normal file
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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
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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; }
}

30
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTherapyStatusReason.java Normal file
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionLocalization.java Normal file
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenCollectionMethod.java Normal file
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/CodingTumorSpecimenType.java Normal file
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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
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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
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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
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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
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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;
}
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/CopyNumberNeutralLoH.java Normal file
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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
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner3Prime.java Normal file
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/DnaFusionFusionPartner5Prime.java Normal file
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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
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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
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/FluffyCode.java Normal file
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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
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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
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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");
}
}

31
src/main/java/dev/pcvolkmer/mv64e/mtb/GeneticCounselingRecommendation.java Normal file
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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
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/GuidelineTreatmentStatus.java Normal file
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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
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/HistologyReportSpecimen.java Normal file
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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
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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
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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
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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
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/MtbCarePlan.java Normal file
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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
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/MtbDiagnosisTumorSpread.java Normal file
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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
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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; }
}

62
src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationRecommendation.java Normal file
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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; }
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/MtbMedicationTherapy.java Normal file
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/ReferencePublication.java Normal file
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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; }
}

18
src/main/java/dev/pcvolkmer/mv64e/mtb/ReportedAffectedGene.java Normal file
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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
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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
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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; }
}

22
src/main/java/dev/pcvolkmer/mv64e/mtb/ResponseTherapyType.java Normal file
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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");
}
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner3Prime.java Normal file
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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; }
}

36
src/main/java/dev/pcvolkmer/mv64e/mtb/RnaFusionFusionPartner5Prime.java Normal file
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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
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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");
}
}

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src/main/java/dev/pcvolkmer/mv64e/mtb/RnaSeq.java Normal file
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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; }
}

37
src/main/java/dev/pcvolkmer/mv64e/mtb/StudyEnrollmentRecommendation.java Normal file
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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
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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
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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; }
}

34
src/main/java/dev/pcvolkmer/mv64e/mtb/TherapyRecommendationPriority.java Normal file
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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
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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
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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; }
}

24
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorCellContentMethod.java Normal file
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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
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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
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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; }
}

31
src/main/java/dev/pcvolkmer/mv64e/mtb/TumorSpecimenCollectionLocalization.java Normal file
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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");
}
}

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