From 2298cc6baa7035ad33ff4aaa3889dcbeeba7a4b3 Mon Sep 17 00:00:00 2001 From: Shahim Essaid Date: Mon, 4 Dec 2023 09:47:08 -0800 Subject: [PATCH] Adding base model entities to implement Element, Extension, and StringElement. --- .../.mvn/wrapper/maven-wrapper.properties | 18 ++ hapipheno-core/bin/generate-model.sh | 25 ++ hapipheno-core/mvnw | 287 ++++++++++++++++++ hapipheno-core/mvnw.cmd | 187 ++++++++++++ .../phenoex/model/Coding.java | 34 ++- .../model/PhenomicsExchangePacket.java | 13 +- .../phenoex/model/Phenotype.java | 13 +- .../phenoex/model/base/Element.java | 49 +++ .../phenoex/model/base/Extension.java | 67 ++++ .../phenoex/model/base/StringElement.java | 37 +++ .../phenoex/model/model.modeldsl | 24 +- .../phenoex/PhenomicsTests.java | 4 +- 12 files changed, 750 insertions(+), 8 deletions(-) create mode 100644 hapipheno-core/.mvn/wrapper/maven-wrapper.properties create mode 100755 hapipheno-core/bin/generate-model.sh create mode 100755 hapipheno-core/mvnw create mode 100644 hapipheno-core/mvnw.cmd create mode 100644 hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Element.java create mode 100644 hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Extension.java create mode 100644 hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/StringElement.java diff --git a/hapipheno-core/.mvn/wrapper/maven-wrapper.properties b/hapipheno-core/.mvn/wrapper/maven-wrapper.properties new file mode 100644 index 0000000..2f9352f --- /dev/null +++ b/hapipheno-core/.mvn/wrapper/maven-wrapper.properties @@ -0,0 +1,18 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you 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. +distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.6/apache-maven-3.9.6-bin.zip +wrapperUrl=https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.2.0/maven-wrapper-3.2.0.jar diff --git a/hapipheno-core/bin/generate-model.sh b/hapipheno-core/bin/generate-model.sh new file mode 100755 index 0000000..cd47239 --- /dev/null +++ b/hapipheno-core/bin/generate-model.sh @@ -0,0 +1,25 @@ +#!/usr/bin/env bash +#set -x +set -e +set -u +set -o pipefail +set -o noclobber + +# https://www.gnu.org/software/bash/manual/html_node/The-Shopt-Builtin.html +shopt -s nullglob + +# stack overflow #59895 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do + DIR="$(cd -P "$(dirname "$SOURCE")" && pwd)" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" +done +DIR="$(cd -P "$(dirname "$SOURCE")" && pwd)" + +cd "$DIR"/.. + +./mvnw -U exec:java \ + -Dexec.mainClass=com.essaid.model.dsl.Main \ + -Dexec.args="--dsl-source src/main/java/org/monarchinitiative/phenoex/model/model.modeldsl --out-dir src-gen/main/java" + diff --git a/hapipheno-core/mvnw b/hapipheno-core/mvnw new file mode 100755 index 0000000..b7f0646 --- /dev/null +++ b/hapipheno-core/mvnw @@ -0,0 +1,287 @@ +#!/bin/sh +# ---------------------------------------------------------------------------- +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. +# ---------------------------------------------------------------------------- + +# ---------------------------------------------------------------------------- +# Apache Maven Wrapper startup batch script, version 3.1.1 +# +# Required ENV vars: +# ------------------ +# JAVA_HOME - location of a JDK home dir +# +# Optional ENV vars +# ----------------- +# MAVEN_OPTS - parameters passed to the Java VM when running Maven +# e.g. to debug Maven itself, use +# set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000 +# MAVEN_SKIP_RC - flag to disable loading of mavenrc files +# ---------------------------------------------------------------------------- + +if [ -z "$MAVEN_SKIP_RC" ] ; then + + if [ -f /usr/local/etc/mavenrc ] ; then + . /usr/local/etc/mavenrc + fi + + if [ -f /etc/mavenrc ] ; then + . /etc/mavenrc + fi + + if [ -f "$HOME/.mavenrc" ] ; then + . "$HOME/.mavenrc" + fi + +fi + +# OS specific support. $var _must_ be set to either true or false. +cygwin=false; +darwin=false; +mingw=false +case "`uname`" in + CYGWIN*) cygwin=true ;; + MINGW*) mingw=true;; + Darwin*) darwin=true + # Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home + # See https://developer.apple.com/library/mac/qa/qa1170/_index.html + if [ -z "$JAVA_HOME" ]; then + if [ -x "/usr/libexec/java_home" ]; then + JAVA_HOME="`/usr/libexec/java_home`"; export JAVA_HOME + else + JAVA_HOME="/Library/Java/Home"; export JAVA_HOME + fi + fi + ;; +esac + +if [ -z "$JAVA_HOME" ] ; then + if [ -r /etc/gentoo-release ] ; then + JAVA_HOME=`java-config --jre-home` + fi +fi + +# For Cygwin, ensure paths are in UNIX format before anything is touched +if $cygwin ; then + [ -n "$JAVA_HOME" ] && + JAVA_HOME=`cygpath --unix "$JAVA_HOME"` + [ -n "$CLASSPATH" ] && + CLASSPATH=`cygpath --path --unix "$CLASSPATH"` +fi + +# For Mingw, ensure paths are in UNIX format before anything is touched +if $mingw ; then + [ -n "$JAVA_HOME" ] && + JAVA_HOME="`(cd "$JAVA_HOME"; pwd)`" +fi + +if [ -z "$JAVA_HOME" ]; then + javaExecutable="`which javac`" + if [ -n "$javaExecutable" ] && ! [ "`expr \"$javaExecutable\" : '\([^ ]*\)'`" = "no" ]; then + # readlink(1) is not available as standard on Solaris 10. + readLink=`which readlink` + if [ ! `expr "$readLink" : '\([^ ]*\)'` = "no" ]; then + if $darwin ; then + javaHome="`dirname \"$javaExecutable\"`" + javaExecutable="`cd \"$javaHome\" && pwd -P`/javac" + else + javaExecutable="`readlink -f \"$javaExecutable\"`" + fi + javaHome="`dirname \"$javaExecutable\"`" + javaHome=`expr "$javaHome" : '\(.*\)/bin'` + JAVA_HOME="$javaHome" + export JAVA_HOME + fi + fi +fi + +if [ -z "$JAVACMD" ] ; then + 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 + else + JAVACMD="`\\unset -f command; \\command -v java`" + fi +fi + +if [ ! -x "$JAVACMD" ] ; then + echo "Error: JAVA_HOME is not defined correctly." >&2 + echo " We cannot execute $JAVACMD" >&2 + exit 1 +fi + +if [ -z "$JAVA_HOME" ] ; then + echo "Warning: JAVA_HOME environment variable is not set." +fi + +# traverses directory structure from process work directory to filesystem root +# first directory with .mvn subdirectory is considered project base directory +find_maven_basedir() { + if [ -z "$1" ] + then + echo "Path not specified to find_maven_basedir" + return 1 + fi + + basedir="$1" + wdir="$1" + while [ "$wdir" != '/' ] ; do + if [ -d "$wdir"/.mvn ] ; then + basedir=$wdir + break + fi + # workaround for JBEAP-8937 (on Solaris 10/Sparc) + if [ -d "${wdir}" ]; then + wdir=`cd "$wdir/.."; pwd` + fi + # end of workaround + done + printf '%s' "$(cd "$basedir"; pwd)" +} + +# concatenates all lines of a file +concat_lines() { + if [ -f "$1" ]; then + echo "$(tr -s '\n' ' ' < "$1")" + fi +} + +BASE_DIR=$(find_maven_basedir "$(dirname $0)") +if [ -z "$BASE_DIR" ]; then + exit 1; +fi + +MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}; export MAVEN_PROJECTBASEDIR +if [ "$MVNW_VERBOSE" = true ]; then + echo $MAVEN_PROJECTBASEDIR +fi + +########################################################################################## +# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central +# This allows using the maven wrapper in projects that prohibit checking in binary data. +########################################################################################## +if [ -r "$BASE_DIR/.mvn/wrapper/maven-wrapper.jar" ]; then + if [ "$MVNW_VERBOSE" = true ]; then + echo "Found .mvn/wrapper/maven-wrapper.jar" + fi +else + if [ "$MVNW_VERBOSE" = true ]; then + echo "Couldn't find .mvn/wrapper/maven-wrapper.jar, downloading it ..." + fi + if [ -n "$MVNW_REPOURL" ]; then + wrapperUrl="$MVNW_REPOURL/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar" + else + wrapperUrl="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar" + fi + while IFS="=" read key value; do + case "$key" in (wrapperUrl) wrapperUrl="$value"; break ;; + esac + done < "$BASE_DIR/.mvn/wrapper/maven-wrapper.properties" + if [ "$MVNW_VERBOSE" = true ]; then + echo "Downloading from: $wrapperUrl" + fi + wrapperJarPath="$BASE_DIR/.mvn/wrapper/maven-wrapper.jar" + if $cygwin; then + wrapperJarPath=`cygpath --path --windows "$wrapperJarPath"` + fi + + if command -v wget > /dev/null; then + QUIET="--quiet" + if [ "$MVNW_VERBOSE" = true ]; then + echo "Found wget ... using wget" + QUIET="" + fi + if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then + wget $QUIET "$wrapperUrl" -O "$wrapperJarPath" + else + wget $QUIET --http-user="$MVNW_USERNAME" --http-password="$MVNW_PASSWORD" "$wrapperUrl" -O "$wrapperJarPath" + fi + [ $? -eq 0 ] || rm -f "$wrapperJarPath" + elif command -v curl > /dev/null; then + QUIET="--silent" + if [ "$MVNW_VERBOSE" = true ]; then + echo "Found curl ... using curl" + QUIET="" + fi + if [ -z "$MVNW_USERNAME" ] || [ -z "$MVNW_PASSWORD" ]; then + curl $QUIET -o "$wrapperJarPath" "$wrapperUrl" -f -L + else + curl $QUIET --user "$MVNW_USERNAME:$MVNW_PASSWORD" -o "$wrapperJarPath" "$wrapperUrl" -f -L + fi + [ $? -eq 0 ] || rm -f "$wrapperJarPath" + else + if [ "$MVNW_VERBOSE" = true ]; then + echo "Falling back to using Java to download" + fi + javaSource="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.java" + javaClass="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class" + # For Cygwin, switch paths to Windows format before running javac + if $cygwin; then + javaSource=`cygpath --path --windows "$javaSource"` + javaClass=`cygpath --path --windows "$javaClass"` + fi + if [ -e "$javaSource" ]; then + if [ ! -e "$javaClass" ]; then + if [ "$MVNW_VERBOSE" = true ]; then + echo " - Compiling MavenWrapperDownloader.java ..." + fi + # Compiling the Java class + ("$JAVA_HOME/bin/javac" "$javaSource") + fi + if [ -e "$javaClass" ]; then + # Running the downloader + if [ "$MVNW_VERBOSE" = true ]; then + echo " - Running MavenWrapperDownloader.java ..." + fi + ("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$MAVEN_PROJECTBASEDIR") + fi + fi + fi +fi +########################################################################################## +# End of extension +########################################################################################## + +MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS" + +# For Cygwin, switch paths to Windows format before running java +if $cygwin; then + [ -n "$JAVA_HOME" ] && + JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"` + [ -n "$CLASSPATH" ] && + CLASSPATH=`cygpath --path --windows "$CLASSPATH"` + [ -n "$MAVEN_PROJECTBASEDIR" ] && + MAVEN_PROJECTBASEDIR=`cygpath --path --windows "$MAVEN_PROJECTBASEDIR"` +fi + +# Provide a "standardized" way to retrieve the CLI args that will +# work with both Windows and non-Windows executions. +MAVEN_CMD_LINE_ARGS="$MAVEN_CONFIG $@" +export MAVEN_CMD_LINE_ARGS + +WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain + +exec "$JAVACMD" \ + $MAVEN_OPTS \ + $MAVEN_DEBUG_OPTS \ + -classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \ + "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \ + ${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@" diff --git a/hapipheno-core/mvnw.cmd b/hapipheno-core/mvnw.cmd new file mode 100644 index 0000000..474c9d6 --- /dev/null +++ b/hapipheno-core/mvnw.cmd @@ -0,0 +1,187 @@ +@REM ---------------------------------------------------------------------------- +@REM Licensed to the Apache Software Foundation (ASF) under one +@REM or more contributor license agreements. See the NOTICE file +@REM distributed with this work for additional information +@REM regarding copyright ownership. The ASF licenses this file +@REM to you under the Apache License, Version 2.0 (the +@REM "License"); you may not use this file except in compliance +@REM with the License. You may obtain a copy of the License at +@REM +@REM http://www.apache.org/licenses/LICENSE-2.0 +@REM +@REM Unless required by applicable law or agreed to in writing, +@REM software distributed under the License is distributed on an +@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +@REM KIND, either express or implied. See the License for the +@REM specific language governing permissions and limitations +@REM under the License. +@REM ---------------------------------------------------------------------------- + +@REM ---------------------------------------------------------------------------- +@REM Apache Maven Wrapper startup batch script, version 3.1.1 +@REM +@REM Required ENV vars: +@REM JAVA_HOME - location of a JDK home dir +@REM +@REM Optional ENV vars +@REM MAVEN_BATCH_ECHO - set to 'on' to enable the echoing of the batch commands +@REM MAVEN_BATCH_PAUSE - set to 'on' to wait for a keystroke before ending +@REM MAVEN_OPTS - parameters passed to the Java VM when running Maven +@REM e.g. to debug Maven itself, use +@REM set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000 +@REM MAVEN_SKIP_RC - flag to disable loading of mavenrc files +@REM ---------------------------------------------------------------------------- + +@REM Begin all REM lines with '@' in case MAVEN_BATCH_ECHO is 'on' +@echo off +@REM set title of command window +title %0 +@REM enable echoing by setting MAVEN_BATCH_ECHO to 'on' +@if "%MAVEN_BATCH_ECHO%" == "on" echo %MAVEN_BATCH_ECHO% + +@REM set %HOME% to equivalent of $HOME +if "%HOME%" == "" (set "HOME=%HOMEDRIVE%%HOMEPATH%") + +@REM Execute a user defined script before this one +if not "%MAVEN_SKIP_RC%" == "" goto skipRcPre +@REM check for pre script, once with legacy .bat ending and once with .cmd ending +if exist "%USERPROFILE%\mavenrc_pre.bat" call "%USERPROFILE%\mavenrc_pre.bat" %* +if exist "%USERPROFILE%\mavenrc_pre.cmd" call "%USERPROFILE%\mavenrc_pre.cmd" %* +:skipRcPre + +@setlocal + +set ERROR_CODE=0 + +@REM To isolate internal variables from possible post scripts, we use another setlocal +@setlocal + +@REM ==== START VALIDATION ==== +if not "%JAVA_HOME%" == "" goto OkJHome + +echo. +echo Error: JAVA_HOME not found in your environment. >&2 +echo Please set the JAVA_HOME variable in your environment to match the >&2 +echo location of your Java installation. >&2 +echo. +goto error + +:OkJHome +if exist "%JAVA_HOME%\bin\java.exe" goto init + +echo. +echo Error: JAVA_HOME is set to an invalid directory. >&2 +echo JAVA_HOME = "%JAVA_HOME%" >&2 +echo Please set the JAVA_HOME variable in your environment to match the >&2 +echo location of your Java installation. >&2 +echo. +goto error + +@REM ==== END VALIDATION ==== + +:init + +@REM Find the project base dir, i.e. the directory that contains the folder ".mvn". +@REM Fallback to current working directory if not found. + +set MAVEN_PROJECTBASEDIR=%MAVEN_BASEDIR% +IF NOT "%MAVEN_PROJECTBASEDIR%"=="" goto endDetectBaseDir + +set EXEC_DIR=%CD% +set WDIR=%EXEC_DIR% +:findBaseDir +IF EXIST "%WDIR%"\.mvn goto baseDirFound +cd .. +IF "%WDIR%"=="%CD%" goto baseDirNotFound +set WDIR=%CD% +goto findBaseDir + +:baseDirFound +set MAVEN_PROJECTBASEDIR=%WDIR% +cd "%EXEC_DIR%" +goto endDetectBaseDir + +:baseDirNotFound +set MAVEN_PROJECTBASEDIR=%EXEC_DIR% +cd "%EXEC_DIR%" + +:endDetectBaseDir + +IF NOT EXIST "%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config" goto endReadAdditionalConfig + +@setlocal EnableExtensions EnableDelayedExpansion +for /F "usebackq delims=" %%a in ("%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config") do set JVM_CONFIG_MAVEN_PROPS=!JVM_CONFIG_MAVEN_PROPS! %%a +@endlocal & set JVM_CONFIG_MAVEN_PROPS=%JVM_CONFIG_MAVEN_PROPS% + +:endReadAdditionalConfig + +SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe" +set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar" +set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain + +set WRAPPER_URL="https://repo.maven.apache.org/maven2/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar" + +FOR /F "usebackq tokens=1,2 delims==" %%A IN ("%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties") DO ( + IF "%%A"=="wrapperUrl" SET WRAPPER_URL=%%B +) + +@REM Extension to allow automatically downloading the maven-wrapper.jar from Maven-central +@REM This allows using the maven wrapper in projects that prohibit checking in binary data. +if exist %WRAPPER_JAR% ( + if "%MVNW_VERBOSE%" == "true" ( + echo Found %WRAPPER_JAR% + ) +) else ( + if not "%MVNW_REPOURL%" == "" ( + SET WRAPPER_URL="%MVNW_REPOURL%/org/apache/maven/wrapper/maven-wrapper/3.1.1/maven-wrapper-3.1.1.jar" + ) + if "%MVNW_VERBOSE%" == "true" ( + echo Couldn't find %WRAPPER_JAR%, downloading it ... + echo Downloading from: %WRAPPER_URL% + ) + + powershell -Command "&{"^ + "$webclient = new-object System.Net.WebClient;"^ + "if (-not ([string]::IsNullOrEmpty('%MVNW_USERNAME%') -and [string]::IsNullOrEmpty('%MVNW_PASSWORD%'))) {"^ + "$webclient.Credentials = new-object System.Net.NetworkCredential('%MVNW_USERNAME%', '%MVNW_PASSWORD%');"^ + "}"^ + "[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12; $webclient.DownloadFile('%WRAPPER_URL%', '%WRAPPER_JAR%')"^ + "}" + if "%MVNW_VERBOSE%" == "true" ( + echo Finished downloading %WRAPPER_JAR% + ) +) +@REM End of extension + +@REM Provide a "standardized" way to retrieve the CLI args that will +@REM work with both Windows and non-Windows executions. +set MAVEN_CMD_LINE_ARGS=%* + +%MAVEN_JAVA_EXE% ^ + %JVM_CONFIG_MAVEN_PROPS% ^ + %MAVEN_OPTS% ^ + %MAVEN_DEBUG_OPTS% ^ + -classpath %WRAPPER_JAR% ^ + "-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" ^ + %WRAPPER_LAUNCHER% %MAVEN_CONFIG% %* +if ERRORLEVEL 1 goto error +goto end + +:error +set ERROR_CODE=1 + +:end +@endlocal & set ERROR_CODE=%ERROR_CODE% + +if not "%MAVEN_SKIP_RC%"=="" goto skipRcPost +@REM check for post script, once with legacy .bat ending and once with .cmd ending +if exist "%USERPROFILE%\mavenrc_post.bat" call "%USERPROFILE%\mavenrc_post.bat" +if exist "%USERPROFILE%\mavenrc_post.cmd" call "%USERPROFILE%\mavenrc_post.cmd" +:skipRcPost + +@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on' +if "%MAVEN_BATCH_PAUSE%"=="on" pause + +if "%MAVEN_TERMINATE_CMD%"=="on" exit %ERROR_CODE% + +cmd /C exit /B %ERROR_CODE% diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Coding.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Coding.java index aa8973f..7ccb9a6 100644 --- a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Coding.java +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Coding.java @@ -1,10 +1,12 @@ package org.monarchinitiative.phenoex.model; +import org.monarchinitiative.phenoex.model.base.Element; + /** * Coding */ @SuppressWarnings("all") -public interface Coding { +public interface Coding extends Element { /** * The code. */ @@ -15,6 +17,16 @@ public interface Coding { */ void setCode(final String code); + /** + * The code. + */ + String getOrDefaultCode(final String defaultValue); + + /** + * The code. + */ + String getOrSetCode(final String setValue); + /** * The code. */ @@ -35,6 +47,16 @@ public interface Coding { */ void setDisplay(final String display); + /** + * The display + */ + String getOrDefaultDisplay(final String defaultValue); + + /** + * The display + */ + String getOrSetDisplay(final String setValue); + /** * The display */ @@ -55,6 +77,16 @@ public interface Coding { */ void setSystem(final String system); + /** + * The system + */ + String getOrDefaultSystem(final String defaultValue); + + /** + * The system + */ + String getOrSetSystem(final String setValue); + /** * The system */ diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/PhenomicsExchangePacket.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/PhenomicsExchangePacket.java index fcddc56..8023b8e 100644 --- a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/PhenomicsExchangePacket.java +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/PhenomicsExchangePacket.java @@ -1,12 +1,13 @@ package org.monarchinitiative.phenoex.model; import java.util.List; +import org.monarchinitiative.phenoex.model.base.Element; /** * PhenomicsExchangePacket */ @SuppressWarnings("all") -public interface PhenomicsExchangePacket { +public interface PhenomicsExchangePacket extends Element { /** * The Phenotypes */ @@ -17,6 +18,16 @@ public interface PhenomicsExchangePacket { */ void setPhenotypes(final List phenotypes); + /** + * The Phenotypes + */ + List getOrDefaultPhenotypes(final List defaultValue); + + /** + * The Phenotypes + */ + List getOrSetPhenotypes(final List setValue); + /** * The Phenotypes */ diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Phenotype.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Phenotype.java index 76cedf3..14932cd 100644 --- a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Phenotype.java +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/Phenotype.java @@ -1,12 +1,13 @@ package org.monarchinitiative.phenoex.model; import java.util.List; +import org.monarchinitiative.phenoex.model.base.Element; /** * Phenotype */ @SuppressWarnings("all") -public interface Phenotype { +public interface Phenotype extends Element { /** * JavaDoc for: codings */ @@ -17,6 +18,16 @@ public interface Phenotype { */ void setCodings(final List codings); + /** + * JavaDoc for: codings + */ + List getOrDefaultCodings(final List defaultValue); + + /** + * JavaDoc for: codings + */ + List getOrSetCodings(final List setValue); + /** * JavaDoc for: codings */ diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Element.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Element.java new file mode 100644 index 0000000..7f482a0 --- /dev/null +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Element.java @@ -0,0 +1,49 @@ +package org.monarchinitiative.phenoex.model.base; + +import java.util.List; + +/** + * Entity Element + */ +@SuppressWarnings("all") +public interface Element { + /** + * JavaDoc for: extensions + */ + List getExtensions(); + + /** + * JavaDoc for: extensions + */ + void setExtensions(final List extensions); + + /** + * JavaDoc for: extensions + */ + List getOrDefaultExtensions(final List defaultValue); + + /** + * JavaDoc for: extensions + */ + List getOrSetExtensions(final List setValue); + + /** + * JavaDoc for: extensions + */ + List cgetExtensions(); + + /** + * JavaDoc for: extensions + */ + Element csetExtensions(final List extensions); + + /** + * JavaDoc for: extensions + */ + Element addExtensions(final Extension extensions); + + /** + * JavaDoc for: extensions + */ + Extension addExtensions(); +} diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Extension.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Extension.java new file mode 100644 index 0000000..2411178 --- /dev/null +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/Extension.java @@ -0,0 +1,67 @@ +package org.monarchinitiative.phenoex.model.base; + +/** + * Entity Extension + */ +@SuppressWarnings("all") +public interface Extension extends Element { + /** + * JavaDoc for: key + */ + String getKey(); + + /** + * JavaDoc for: key + */ + void setKey(final String key); + + /** + * JavaDoc for: key + */ + String getOrDefaultKey(final String defaultValue); + + /** + * JavaDoc for: key + */ + String getOrSetKey(final String setValue); + + /** + * JavaDoc for: key + */ + String cgetKey(); + + /** + * JavaDoc for: key + */ + Extension csetKey(final String key); + + /** + * JavaDoc for: valueString + */ + String getValueString(); + + /** + * JavaDoc for: valueString + */ + void setValueString(final String valueString); + + /** + * JavaDoc for: valueString + */ + String getOrDefaultValueString(final String defaultValue); + + /** + * JavaDoc for: valueString + */ + String getOrSetValueString(final String setValue); + + /** + * JavaDoc for: valueString + */ + String cgetValueString(); + + /** + * JavaDoc for: valueString + */ + Extension csetValueString(final String valueString); +} diff --git a/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/StringElement.java b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/StringElement.java new file mode 100644 index 0000000..7381723 --- /dev/null +++ b/hapipheno-core/src-gen/main/java/org/monarchinitiative/phenoex/model/base/StringElement.java @@ -0,0 +1,37 @@ +package org.monarchinitiative.phenoex.model.base; + +/** + * Entity StringElement + */ +@SuppressWarnings("all") +public interface StringElement extends Element { + /** + * JavaDoc for: value + */ + String getValue(); + + /** + * JavaDoc for: value + */ + void setValue(final String value); + + /** + * JavaDoc for: value + */ + String getOrDefaultValue(final String defaultValue); + + /** + * JavaDoc for: value + */ + String getOrSetValue(final String setValue); + + /** + * JavaDoc for: value + */ + String cgetValue(); + + /** + * JavaDoc for: value + */ + StringElement csetValue(final String value); +} diff --git a/hapipheno-core/src/main/java/org/monarchinitiative/phenoex/model/model.modeldsl b/hapipheno-core/src/main/java/org/monarchinitiative/phenoex/model/model.modeldsl index aff5120..09e0c19 100644 --- a/hapipheno-core/src/main/java/org/monarchinitiative/phenoex/model/model.modeldsl +++ b/hapipheno-core/src/main/java/org/monarchinitiative/phenoex/model/model.modeldsl @@ -1,16 +1,18 @@ import java.util.List; +import org.monarchinitiative.phenoex.model.base.Element; + package org.monarchinitiative.phenoex.model { /* PhenomicsExchangePacket */ - entity PhenomicsExchangePacket { + entity PhenomicsExchangePacket extends Element { /* The Phenotypes */ phenotypes: List } /* Coding */ - entity Coding { + entity Coding extends Element { /* The code. */ code: String @@ -22,8 +24,24 @@ package org.monarchinitiative.phenoex.model { } /* Phenotype */ - entity Phenotype { + entity Phenotype extends Element { codings: List } } + +package org.monarchinitiative.phenoex.model.base { + + entity Element { + extensions: List + } + + entity Extension extends Element { + key: String + valueString: String + } + + entity StringElement extends Element { + value: String + } +} diff --git a/hapipheno-core/src/test/java/org/monarchinitiative/phenoex/PhenomicsTests.java b/hapipheno-core/src/test/java/org/monarchinitiative/phenoex/PhenomicsTests.java index 5083ca8..7361b76 100644 --- a/hapipheno-core/src/test/java/org/monarchinitiative/phenoex/PhenomicsTests.java +++ b/hapipheno-core/src/test/java/org/monarchinitiative/phenoex/PhenomicsTests.java @@ -50,7 +50,7 @@ void convertV2PhenopacketFileToR4Bundle() throws IOException { } // Set up the interface model and the converter (visitor) - EntityManager entityManager = Configs.getDefaultMapEntityManager(); + EntityManager entityManager = Configs.createDefaultMapEntityManager(); V2ToModel v2ToModel = new V2ToModel(entityManager); v2ToModel.getPrefixMap().put("HP", "http://HP"); PhenomicsExchangePacket phenomicsPacket = v2ToModel.visit(phenopacket); @@ -68,7 +68,7 @@ void convertV2PhenopacketFileToR4Bundle() throws IOException { void createPhenotype() throws IOException { // Set up the interface model and the converter (visitor) - EntityManager entityManager = Configs.getDefaultMapEntityManager(); + EntityManager entityManager = Configs.createDefaultMapEntityManager(); // V2ToModel v2ToModel = new V2ToModel(entityManager); // v2ToModel.getPrefixMap().put("HP", "http://HP");