diff --git a/dictionaryweights/.gitignore b/dictionaryweights/.gitignore new file mode 100644 index 0000000..549e00a --- /dev/null +++ b/dictionaryweights/.gitignore @@ -0,0 +1,33 @@ +HELP.md +target/ +!.mvn/wrapper/maven-wrapper.jar +!**/src/main/**/target/ +!**/src/test/**/target/ + +### STS ### +.apt_generated +.classpath +.factorypath +.project +.settings +.springBeans +.sts4-cache + +### IntelliJ IDEA ### +.idea +*.iws +*.iml +*.ipr + +### NetBeans ### +/nbproject/private/ +/nbbuild/ +/dist/ +/nbdist/ +/.nb-gradle/ +build/ +!**/src/main/**/build/ +!**/src/test/**/build/ + +### VS Code ### +.vscode/ diff --git a/dictionaryweights/Dockerfile b/dictionaryweights/Dockerfile new file mode 100644 index 0000000..5bab457 --- /dev/null +++ b/dictionaryweights/Dockerfile @@ -0,0 +1,16 @@ +FROM maven:3.9-eclipse-temurin-22-alpine AS build + +COPY pom.xml . + +RUN mvn -B dependency:go-offline + +COPY src src + +RUN mvn -B package -DskipTests + +FROM amazoncorretto:22-alpine + +# Copy jar and access token from maven build +COPY --from=build target/dictionaryweights-*.jar /dictionaryweights.jar + +ENTRYPOINT java -jar /dictionaryweights.jar \ No newline at end of file diff --git a/dictionaryweights/mvnw b/dictionaryweights/mvnw new file mode 100755 index 0000000..d7c358e --- /dev/null +++ b/dictionaryweights/mvnw @@ -0,0 +1,259 @@ +#!/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 +# +# 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. +# ---------------------------------------------------------------------------- + +# ---------------------------------------------------------------------------- +# Apache Maven Wrapper startup batch script, version 3.3.2 +# +# Optional ENV vars +# ----------------- +# JAVA_HOME - location of a JDK home dir, required when download maven via java source +# MVNW_REPOURL - repo url base for downloading maven distribution +# MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven +# MVNW_VERBOSE - true: enable verbose log; debug: trace the mvnw script; others: silence the output +# ---------------------------------------------------------------------------- + +set -euf +[ "${MVNW_VERBOSE-}" != debug ] || set -x + +# OS specific support. +native_path() { printf %s\\n "$1"; } +case "$(uname)" in +CYGWIN* | MINGW*) + [ -z "${JAVA_HOME-}" ] || JAVA_HOME="$(cygpath --unix "$JAVA_HOME")" + native_path() { cygpath --path --windows "$1"; } + ;; +esac + +# set JAVACMD and JAVACCMD +set_java_home() { + # For Cygwin and MinGW, ensure paths are in Unix format before anything is touched + if [ -n "${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" + JAVACCMD="$JAVA_HOME/jre/sh/javac" + else + JAVACMD="$JAVA_HOME/bin/java" + JAVACCMD="$JAVA_HOME/bin/javac" + + if [ ! -x "$JAVACMD" ] || [ ! -x "$JAVACCMD" ]; then + echo "The JAVA_HOME environment variable is not defined correctly, so mvnw cannot run." >&2 + echo "JAVA_HOME is set to \"$JAVA_HOME\", but \"\$JAVA_HOME/bin/java\" or \"\$JAVA_HOME/bin/javac\" does not exist." >&2 + return 1 + fi + fi + else + JAVACMD="$( + 'set' +e + 'unset' -f command 2>/dev/null + 'command' -v java + )" || : + JAVACCMD="$( + 'set' +e + 'unset' -f command 2>/dev/null + 'command' -v javac + )" || : + + if [ ! -x "${JAVACMD-}" ] || [ ! -x "${JAVACCMD-}" ]; then + echo "The java/javac command does not exist in PATH nor is JAVA_HOME set, so mvnw cannot run." >&2 + return 1 + fi + fi +} + +# hash string like Java String::hashCode +hash_string() { + str="${1:-}" h=0 + while [ -n "$str" ]; do + char="${str%"${str#?}"}" + h=$(((h * 31 + $(LC_CTYPE=C printf %d "'$char")) % 4294967296)) + str="${str#?}" + done + printf %x\\n $h +} + +verbose() { :; } +[ "${MVNW_VERBOSE-}" != true ] || verbose() { printf %s\\n "${1-}"; } + +die() { + printf %s\\n "$1" >&2 + exit 1 +} + +trim() { + # MWRAPPER-139: + # Trims trailing and leading whitespace, carriage returns, tabs, and linefeeds. + # Needed for removing poorly interpreted newline sequences when running in more + # exotic environments such as mingw bash on Windows. + printf "%s" "${1}" | tr -d '[:space:]' +} + +# parse distributionUrl and optional distributionSha256Sum, requires .mvn/wrapper/maven-wrapper.properties +while IFS="=" read -r key value; do + case "${key-}" in + distributionUrl) distributionUrl=$(trim "${value-}") ;; + distributionSha256Sum) distributionSha256Sum=$(trim "${value-}") ;; + esac +done <"${0%/*}/.mvn/wrapper/maven-wrapper.properties" +[ -n "${distributionUrl-}" ] || die "cannot read distributionUrl property in ${0%/*}/.mvn/wrapper/maven-wrapper.properties" + +case "${distributionUrl##*/}" in +maven-mvnd-*bin.*) + MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ + case "${PROCESSOR_ARCHITECTURE-}${PROCESSOR_ARCHITEW6432-}:$(uname -a)" in + *AMD64:CYGWIN* | *AMD64:MINGW*) distributionPlatform=windows-amd64 ;; + :Darwin*x86_64) distributionPlatform=darwin-amd64 ;; + :Darwin*arm64) distributionPlatform=darwin-aarch64 ;; + :Linux*x86_64*) distributionPlatform=linux-amd64 ;; + *) + echo "Cannot detect native platform for mvnd on $(uname)-$(uname -m), use pure java version" >&2 + distributionPlatform=linux-amd64 + ;; + esac + distributionUrl="${distributionUrl%-bin.*}-$distributionPlatform.zip" + ;; +maven-mvnd-*) MVN_CMD=mvnd.sh _MVNW_REPO_PATTERN=/maven/mvnd/ ;; +*) MVN_CMD="mvn${0##*/mvnw}" _MVNW_REPO_PATTERN=/org/apache/maven/ ;; +esac + +# apply MVNW_REPOURL and calculate MAVEN_HOME +# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-,maven-mvnd--}/ +[ -z "${MVNW_REPOURL-}" ] || distributionUrl="$MVNW_REPOURL$_MVNW_REPO_PATTERN${distributionUrl#*"$_MVNW_REPO_PATTERN"}" +distributionUrlName="${distributionUrl##*/}" +distributionUrlNameMain="${distributionUrlName%.*}" +distributionUrlNameMain="${distributionUrlNameMain%-bin}" +MAVEN_USER_HOME="${MAVEN_USER_HOME:-${HOME}/.m2}" +MAVEN_HOME="${MAVEN_USER_HOME}/wrapper/dists/${distributionUrlNameMain-}/$(hash_string "$distributionUrl")" + +exec_maven() { + unset MVNW_VERBOSE MVNW_USERNAME MVNW_PASSWORD MVNW_REPOURL || : + exec "$MAVEN_HOME/bin/$MVN_CMD" "$@" || die "cannot exec $MAVEN_HOME/bin/$MVN_CMD" +} + +if [ -d "$MAVEN_HOME" ]; then + verbose "found existing MAVEN_HOME at $MAVEN_HOME" + exec_maven "$@" +fi + +case "${distributionUrl-}" in +*?-bin.zip | *?maven-mvnd-?*-?*.zip) ;; +*) die "distributionUrl is not valid, must match *-bin.zip or maven-mvnd-*.zip, but found '${distributionUrl-}'" ;; +esac + +# prepare tmp dir +if TMP_DOWNLOAD_DIR="$(mktemp -d)" && [ -d "$TMP_DOWNLOAD_DIR" ]; then + clean() { rm -rf -- "$TMP_DOWNLOAD_DIR"; } + trap clean HUP INT TERM EXIT +else + die "cannot create temp dir" +fi + +mkdir -p -- "${MAVEN_HOME%/*}" + +# Download and Install Apache Maven +verbose "Couldn't find MAVEN_HOME, downloading and installing it ..." +verbose "Downloading from: $distributionUrl" +verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName" + +# select .zip or .tar.gz +if ! command -v unzip >/dev/null; then + distributionUrl="${distributionUrl%.zip}.tar.gz" + distributionUrlName="${distributionUrl##*/}" +fi + +# verbose opt +__MVNW_QUIET_WGET=--quiet __MVNW_QUIET_CURL=--silent __MVNW_QUIET_UNZIP=-q __MVNW_QUIET_TAR='' +[ "${MVNW_VERBOSE-}" != true ] || __MVNW_QUIET_WGET='' __MVNW_QUIET_CURL='' __MVNW_QUIET_UNZIP='' __MVNW_QUIET_TAR=v + +# normalize http auth +case "${MVNW_PASSWORD:+has-password}" in +'') MVNW_USERNAME='' MVNW_PASSWORD='' ;; +has-password) [ -n "${MVNW_USERNAME-}" ] || MVNW_USERNAME='' MVNW_PASSWORD='' ;; +esac + +if [ -z "${MVNW_USERNAME-}" ] && command -v wget >/dev/null; then + verbose "Found wget ... using wget" + wget ${__MVNW_QUIET_WGET:+"$__MVNW_QUIET_WGET"} "$distributionUrl" -O "$TMP_DOWNLOAD_DIR/$distributionUrlName" || die "wget: Failed to fetch $distributionUrl" +elif [ -z "${MVNW_USERNAME-}" ] && command -v curl >/dev/null; then + verbose "Found curl ... using curl" + curl ${__MVNW_QUIET_CURL:+"$__MVNW_QUIET_CURL"} -f -L -o "$TMP_DOWNLOAD_DIR/$distributionUrlName" "$distributionUrl" || die "curl: Failed to fetch $distributionUrl" +elif set_java_home; then + verbose "Falling back to use Java to download" + javaSource="$TMP_DOWNLOAD_DIR/Downloader.java" + targetZip="$TMP_DOWNLOAD_DIR/$distributionUrlName" + cat >"$javaSource" <<-END + public class Downloader extends java.net.Authenticator + { + protected java.net.PasswordAuthentication getPasswordAuthentication() + { + return new java.net.PasswordAuthentication( System.getenv( "MVNW_USERNAME" ), System.getenv( "MVNW_PASSWORD" ).toCharArray() ); + } + public static void main( String[] args ) throws Exception + { + setDefault( new Downloader() ); + java.nio.file.Files.copy( java.net.URI.create( args[0] ).toURL().openStream(), java.nio.file.Paths.get( args[1] ).toAbsolutePath().normalize() ); + } + } + END + # For Cygwin/MinGW, switch paths to Windows format before running javac and java + verbose " - Compiling Downloader.java ..." + "$(native_path "$JAVACCMD")" "$(native_path "$javaSource")" || die "Failed to compile Downloader.java" + verbose " - Running Downloader.java ..." + "$(native_path "$JAVACMD")" -cp "$(native_path "$TMP_DOWNLOAD_DIR")" Downloader "$distributionUrl" "$(native_path "$targetZip")" +fi + +# If specified, validate the SHA-256 sum of the Maven distribution zip file +if [ -n "${distributionSha256Sum-}" ]; then + distributionSha256Result=false + if [ "$MVN_CMD" = mvnd.sh ]; then + echo "Checksum validation is not supported for maven-mvnd." >&2 + echo "Please disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2 + exit 1 + elif command -v sha256sum >/dev/null; then + if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | sha256sum -c >/dev/null 2>&1; then + distributionSha256Result=true + fi + elif command -v shasum >/dev/null; then + if echo "$distributionSha256Sum $TMP_DOWNLOAD_DIR/$distributionUrlName" | shasum -a 256 -c >/dev/null 2>&1; then + distributionSha256Result=true + fi + else + echo "Checksum validation was requested but neither 'sha256sum' or 'shasum' are available." >&2 + echo "Please install either command, or disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." >&2 + exit 1 + fi + if [ $distributionSha256Result = false ]; then + echo "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised." >&2 + echo "If you updated your Maven version, you need to update the specified distributionSha256Sum property." >&2 + exit 1 + fi +fi + +# unzip and move +if command -v unzip >/dev/null; then + unzip ${__MVNW_QUIET_UNZIP:+"$__MVNW_QUIET_UNZIP"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -d "$TMP_DOWNLOAD_DIR" || die "failed to unzip" +else + tar xzf${__MVNW_QUIET_TAR:+"$__MVNW_QUIET_TAR"} "$TMP_DOWNLOAD_DIR/$distributionUrlName" -C "$TMP_DOWNLOAD_DIR" || die "failed to untar" +fi +printf %s\\n "$distributionUrl" >"$TMP_DOWNLOAD_DIR/$distributionUrlNameMain/mvnw.url" +mv -- "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" "$MAVEN_HOME" || [ -d "$MAVEN_HOME" ] || die "fail to move MAVEN_HOME" + +clean || : +exec_maven "$@" diff --git a/dictionaryweights/mvnw.cmd b/dictionaryweights/mvnw.cmd new file mode 100644 index 0000000..6f779cf --- /dev/null +++ b/dictionaryweights/mvnw.cmd @@ -0,0 +1,149 @@ +<# : batch portion +@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 https://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 3.3.2 +@REM +@REM Optional ENV vars +@REM MVNW_REPOURL - repo url base for downloading maven distribution +@REM MVNW_USERNAME/MVNW_PASSWORD - user and password for downloading maven +@REM MVNW_VERBOSE - true: enable verbose log; others: silence the output +@REM ---------------------------------------------------------------------------- + +@IF "%__MVNW_ARG0_NAME__%"=="" (SET __MVNW_ARG0_NAME__=%~nx0) +@SET __MVNW_CMD__= +@SET __MVNW_ERROR__= +@SET __MVNW_PSMODULEP_SAVE=%PSModulePath% +@SET PSModulePath= +@FOR /F "usebackq tokens=1* delims==" %%A IN (`powershell -noprofile "& {$scriptDir='%~dp0'; $script='%__MVNW_ARG0_NAME__%'; icm -ScriptBlock ([Scriptblock]::Create((Get-Content -Raw '%~f0'))) -NoNewScope}"`) DO @( + IF "%%A"=="MVN_CMD" (set __MVNW_CMD__=%%B) ELSE IF "%%B"=="" (echo %%A) ELSE (echo %%A=%%B) +) +@SET PSModulePath=%__MVNW_PSMODULEP_SAVE% +@SET __MVNW_PSMODULEP_SAVE= +@SET __MVNW_ARG0_NAME__= +@SET MVNW_USERNAME= +@SET MVNW_PASSWORD= +@IF NOT "%__MVNW_CMD__%"=="" (%__MVNW_CMD__% %*) +@echo Cannot start maven from wrapper >&2 && exit /b 1 +@GOTO :EOF +: end batch / begin powershell #> + +$ErrorActionPreference = "Stop" +if ($env:MVNW_VERBOSE -eq "true") { + $VerbosePreference = "Continue" +} + +# calculate distributionUrl, requires .mvn/wrapper/maven-wrapper.properties +$distributionUrl = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionUrl +if (!$distributionUrl) { + Write-Error "cannot read distributionUrl property in $scriptDir/.mvn/wrapper/maven-wrapper.properties" +} + +switch -wildcard -casesensitive ( $($distributionUrl -replace '^.*/','') ) { + "maven-mvnd-*" { + $USE_MVND = $true + $distributionUrl = $distributionUrl -replace '-bin\.[^.]*$',"-windows-amd64.zip" + $MVN_CMD = "mvnd.cmd" + break + } + default { + $USE_MVND = $false + $MVN_CMD = $script -replace '^mvnw','mvn' + break + } +} + +# apply MVNW_REPOURL and calculate MAVEN_HOME +# maven home pattern: ~/.m2/wrapper/dists/{apache-maven-,maven-mvnd--}/ +if ($env:MVNW_REPOURL) { + $MVNW_REPO_PATTERN = if ($USE_MVND) { "/org/apache/maven/" } else { "/maven/mvnd/" } + $distributionUrl = "$env:MVNW_REPOURL$MVNW_REPO_PATTERN$($distributionUrl -replace '^.*'+$MVNW_REPO_PATTERN,'')" +} +$distributionUrlName = $distributionUrl -replace '^.*/','' +$distributionUrlNameMain = $distributionUrlName -replace '\.[^.]*$','' -replace '-bin$','' +$MAVEN_HOME_PARENT = "$HOME/.m2/wrapper/dists/$distributionUrlNameMain" +if ($env:MAVEN_USER_HOME) { + $MAVEN_HOME_PARENT = "$env:MAVEN_USER_HOME/wrapper/dists/$distributionUrlNameMain" +} +$MAVEN_HOME_NAME = ([System.Security.Cryptography.MD5]::Create().ComputeHash([byte[]][char[]]$distributionUrl) | ForEach-Object {$_.ToString("x2")}) -join '' +$MAVEN_HOME = "$MAVEN_HOME_PARENT/$MAVEN_HOME_NAME" + +if (Test-Path -Path "$MAVEN_HOME" -PathType Container) { + Write-Verbose "found existing MAVEN_HOME at $MAVEN_HOME" + Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD" + exit $? +} + +if (! $distributionUrlNameMain -or ($distributionUrlName -eq $distributionUrlNameMain)) { + Write-Error "distributionUrl is not valid, must end with *-bin.zip, but found $distributionUrl" +} + +# prepare tmp dir +$TMP_DOWNLOAD_DIR_HOLDER = New-TemporaryFile +$TMP_DOWNLOAD_DIR = New-Item -Itemtype Directory -Path "$TMP_DOWNLOAD_DIR_HOLDER.dir" +$TMP_DOWNLOAD_DIR_HOLDER.Delete() | Out-Null +trap { + if ($TMP_DOWNLOAD_DIR.Exists) { + try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null } + catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" } + } +} + +New-Item -Itemtype Directory -Path "$MAVEN_HOME_PARENT" -Force | Out-Null + +# Download and Install Apache Maven +Write-Verbose "Couldn't find MAVEN_HOME, downloading and installing it ..." +Write-Verbose "Downloading from: $distributionUrl" +Write-Verbose "Downloading to: $TMP_DOWNLOAD_DIR/$distributionUrlName" + +$webclient = New-Object System.Net.WebClient +if ($env:MVNW_USERNAME -and $env:MVNW_PASSWORD) { + $webclient.Credentials = New-Object System.Net.NetworkCredential($env:MVNW_USERNAME, $env:MVNW_PASSWORD) +} +[Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12 +$webclient.DownloadFile($distributionUrl, "$TMP_DOWNLOAD_DIR/$distributionUrlName") | Out-Null + +# If specified, validate the SHA-256 sum of the Maven distribution zip file +$distributionSha256Sum = (Get-Content -Raw "$scriptDir/.mvn/wrapper/maven-wrapper.properties" | ConvertFrom-StringData).distributionSha256Sum +if ($distributionSha256Sum) { + if ($USE_MVND) { + Write-Error "Checksum validation is not supported for maven-mvnd. `nPlease disable validation by removing 'distributionSha256Sum' from your maven-wrapper.properties." + } + Import-Module $PSHOME\Modules\Microsoft.PowerShell.Utility -Function Get-FileHash + if ((Get-FileHash "$TMP_DOWNLOAD_DIR/$distributionUrlName" -Algorithm SHA256).Hash.ToLower() -ne $distributionSha256Sum) { + Write-Error "Error: Failed to validate Maven distribution SHA-256, your Maven distribution might be compromised. If you updated your Maven version, you need to update the specified distributionSha256Sum property." + } +} + +# unzip and move +Expand-Archive "$TMP_DOWNLOAD_DIR/$distributionUrlName" -DestinationPath "$TMP_DOWNLOAD_DIR" | Out-Null +Rename-Item -Path "$TMP_DOWNLOAD_DIR/$distributionUrlNameMain" -NewName $MAVEN_HOME_NAME | Out-Null +try { + Move-Item -Path "$TMP_DOWNLOAD_DIR/$MAVEN_HOME_NAME" -Destination $MAVEN_HOME_PARENT | Out-Null +} catch { + if (! (Test-Path -Path "$MAVEN_HOME" -PathType Container)) { + Write-Error "fail to move MAVEN_HOME" + } +} finally { + try { Remove-Item $TMP_DOWNLOAD_DIR -Recurse -Force | Out-Null } + catch { Write-Warning "Cannot remove $TMP_DOWNLOAD_DIR" } +} + +Write-Output "MVN_CMD=$MAVEN_HOME/bin/$MVN_CMD" diff --git a/dictionaryweights/pom.xml b/dictionaryweights/pom.xml new file mode 100644 index 0000000..9bc2280 --- /dev/null +++ b/dictionaryweights/pom.xml @@ -0,0 +1,75 @@ + + + 4.0.0 + + org.springframework.boot + spring-boot-starter-parent + 3.3.2 + + + edu.harvard.dbmi.avillach + dictionaryweights + 0.0.1-SNAPSHOT + dictionaryweights + Creates weights + + + + + + + + + + + + + + + 21 + + + + org.springframework.boot + spring-boot-starter-jdbc + + + + org.postgresql + postgresql + runtime + + + + org.springframework.boot + spring-boot-starter-test + test + + + org.springframework.boot + spring-boot-testcontainers + test + + + org.testcontainers + junit-jupiter + test + + + org.testcontainers + postgresql + test + + + + + + + org.springframework.boot + spring-boot-maven-plugin + + + + + diff --git a/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java new file mode 100644 index 0000000..1b7d1f8 --- /dev/null +++ b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplication.java @@ -0,0 +1,65 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.beans.factory.annotation.Value; +import org.springframework.boot.CommandLineRunner; +import org.springframework.boot.SpringApplication; +import org.springframework.boot.autoconfigure.SpringBootApplication; +import org.springframework.context.annotation.Bean; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.List; + +@SpringBootApplication +public class DictionaryWeightsApplication { + + private static final Logger LOG = LoggerFactory.getLogger(DictionaryWeightsApplication.class); + + @Autowired + WeightingParser parser; + + @Autowired + WeightUpdateCreator updateCreator; + + @Autowired + WeightUpdateApplier updateApplier; + + @Value("${weights.filename}") + private String weightingFileName; + + + public static void main(String[] args) throws IOException { + SpringApplication.run(DictionaryWeightsApplication.class, args); + } + + @Bean + public CommandLineRunner commandLineRunner() { + return ignored -> { + LOG.info("Starting weighting..."); + File file = new File(weightingFileName); + if (!file.exists() || file.isDirectory()) { + LOG.error("File not found {}", weightingFileName); + System.exit(1); + } + + LOG.info("Found weighting file. Parsing weights..."); + List rawWeights = Files.readAllLines(file.toPath()); + List weightings = parser.parseWeights(rawWeights); + LOG.info("Found {} weights", weightings.size()); + if (weightings.isEmpty()) { + LOG.warn("Since no weightings were parsed, exiting."); + System.exit(1); + } + + String update = updateCreator.createUpdate(weightings); + updateApplier.applyUpdate(update); + LOG.info("Done. Exiting"); + System.exit(0); + }; + } + +} diff --git a/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java new file mode 100644 index 0000000..0b2409d --- /dev/null +++ b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/Weight.java @@ -0,0 +1,4 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +public record Weight(String key, int weight) { +} diff --git a/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java new file mode 100644 index 0000000..841ced4 --- /dev/null +++ b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateApplier.java @@ -0,0 +1,21 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.jdbc.core.JdbcTemplate; +import org.springframework.stereotype.Service; + +@Service +public class WeightUpdateApplier { + + private static final Logger LOG = LoggerFactory.getLogger(WeightUpdateApplier.class); + + @Autowired + JdbcTemplate template; + + public void applyUpdate(String query) { + LOG.info("Applying query to DB"); + template.update(query); + } +} diff --git a/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java new file mode 100644 index 0000000..1de1d56 --- /dev/null +++ b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreator.java @@ -0,0 +1,55 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.util.List; +import java.util.stream.Collectors; +import java.util.stream.IntStream; +import java.util.stream.Stream; + +@Service +public class WeightUpdateCreator { + + + private static final Logger LOG = LoggerFactory.getLogger(WeightUpdateCreator.class); + + public String createUpdate(List weights) { + LOG.info("Turning {} weights into a big concat query", weights.size()); + String searchableFields = weights.stream() + .flatMap(this::expand) + .collect(Collectors.joining(", ' ',\n ")); + return """ + UPDATE concept_node + SET SEARCHABLE_FIELDS = to_tsvector(data_table.search_str) + FROM + ( + SELECT + concat( + %s + ) AS search_str, + concept_node.concept_node_id AS search_key + FROM + concept_node + LEFT JOIN + ( + SELECT + concept_node.concept_node_id AS id, string_agg(value, ' ') AS values + FROM + concept_node + join concept_node_meta on concept_node.concept_node_id = concept_node_meta.concept_node_id + GROUP BY + concept_node.concept_node_id + ) AS concept_node_meta_str ON concept_node_meta_str.id = concept_node.concept_node_id + LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_id + ) AS data_table + WHERE concept_node.concept_node_id = data_table.search_key; + """.formatted(searchableFields); + } + + private Stream expand(Weight weight) { + return IntStream.range(0, weight.weight()).boxed() + .map(i -> weight.key()); + } +} diff --git a/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java new file mode 100644 index 0000000..b6a5197 --- /dev/null +++ b/dictionaryweights/src/main/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightingParser.java @@ -0,0 +1,43 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.stereotype.Service; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.List; +import java.util.Optional; +import java.util.stream.Stream; + +@Service +public class WeightingParser { + private static final Logger LOG = LoggerFactory.getLogger(WeightingParser.class); + + public List parseWeights(List weights) { + return weights.stream() + .flatMap(this::parseWeight) + .toList(); + + } + + private Stream parseWeight(String line) { + String[] split = line.split(","); + if (split.length != 2) { + LOG.warn("Failed to parse line {}, expected two column TSV", line); + return Stream.empty(); + } + + int weight; + try { + weight = Integer.parseInt(split[1]); + } catch (NumberFormatException ignored) { + LOG.warn("Failed to parse line {} because {} is not an int", line, split[1]); + return Stream.empty(); + } + + return Stream.of(new Weight(split[0], weight)); + } + +} diff --git a/dictionaryweights/src/main/resources/application.properties b/dictionaryweights/src/main/resources/application.properties new file mode 100644 index 0000000..f58d101 --- /dev/null +++ b/dictionaryweights/src/main/resources/application.properties @@ -0,0 +1,9 @@ +spring.application.name=dictionaryweights +spring.main.web-application-type=none + +spring.datasource.url=jdbc:postgresql://${POSTGRES_HOST}:5432/${POSTGRES_DB}?currentSchema=dict +spring.datasource.username=${POSTGRES_USER} +spring.datasource.password=${POSTGRES_PASSWORD} +spring.datasource.driver-class-name=org.postgresql.Driver + +weights.filename=/weights.csv \ No newline at end of file diff --git a/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java b/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java new file mode 100644 index 0000000..5ea332f --- /dev/null +++ b/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/DictionaryWeightsApplicationTests.java @@ -0,0 +1,13 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.junit.jupiter.api.Test; +import org.springframework.boot.test.context.SpringBootTest; + +@SpringBootTest +class DictionaryWeightsApplicationTests { + + @Test + void contextLoads() { + } + +} diff --git a/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java b/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java new file mode 100644 index 0000000..12c2bec --- /dev/null +++ b/dictionaryweights/src/test/java/edu/harvard/dbmi/avillach/dictionaryweights/WeightUpdateCreatorTest.java @@ -0,0 +1,50 @@ +package edu.harvard.dbmi.avillach.dictionaryweights; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; + +import java.util.List; + +@SpringBootTest +class WeightUpdateCreatorTest { + @Autowired + WeightUpdateCreator subject; + + @Test + void shouldCreateQueryForWeights() { + List weights = List.of(new Weight("TABLE_A.COLUMN", 2), new Weight("TABLE_B.COLUMN", 1)); + + String actual = subject.createUpdate(weights); + String expected = """ + UPDATE concept_node + SET SEARCHABLE_FIELDS = data_table.search_str + FROM + ( + SELECT + concat( + TABLE_A.COLUMN, ' ', + TABLE_A.COLUMN, ' ', + TABLE_B.COLUMN + ) AS search_str, + concept_node.concept_node_id AS search_key + FROM + concept_node + LEFT JOIN + ( + SELECT + concept_node.concept_node_id AS id, string_agg(value, ' ') AS values + FROM + concept_node + join concept_node_meta on concept_node.concept_node_id = concept_node_meta.concept_node_id + GROUP BY + concept_node.concept_node_id + ) AS inner_q ON inner_q.id = concept_node.concept_node_id + ) AS data_table + WHERE concept_node.concept_node_id = data_table.search_key; + """; + + Assertions.assertEquals(expected.trim(), actual.trim()); + } +} \ No newline at end of file