diff --git a/.gitignore b/.gitignore index d3ffd6b..2e03ad7 100644 --- a/.gitignore +++ b/.gitignore @@ -22,3 +22,5 @@ # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml hs_err_pid* +.idea +.gradle diff --git a/build.gradle b/build.gradle new file mode 100644 index 0000000..b8d807d --- /dev/null +++ b/build.gradle @@ -0,0 +1,23 @@ +plugins { + id 'java' +} + +group 'de.vanitasvitae' +version '1.0-SNAPSHOT' + +sourceCompatibility = 1.8 + +repositories { + mavenCentral() + // Apache Repository for Commons CLI + maven { url "https://repository.apache.org/content/groups/snapshots/" } +} + +dependencies { + // Apache Commons CLI for parsing command line arguments + compile 'commons-cli:commons-cli:1.5-SNAPSHOT' + + + // Testing + testCompile group: 'junit', name: 'junit', version: '4.12' +} \ No newline at end of file diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000..d2c45a4 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,5 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-4.8-bin.zip +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 0000000..cccdd3d --- /dev/null +++ b/gradlew @@ -0,0 +1,172 @@ +#!/usr/bin/env sh + +############################################################################## +## +## Gradle start up script for UN*X +## +############################################################################## + +# Attempt to set APP_HOME +# Resolve links: $0 may be a link +PRG="$0" +# Need this for relative symlinks. +while [ -h "$PRG" ] ; do + ls=`ls -ld "$PRG"` + link=`expr "$ls" : '.*-> \(.*\)$'` + if expr "$link" : '/.*' > /dev/null; then + PRG="$link" + else + PRG=`dirname "$PRG"`"/$link" + fi +done +SAVED="`pwd`" +cd "`dirname \"$PRG\"`/" >/dev/null +APP_HOME="`pwd -P`" +cd "$SAVED" >/dev/null + +APP_NAME="Gradle" +APP_BASE_NAME=`basename "$0"` + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS="" + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD="maximum" + +warn () { + echo "$*" +} + +die () { + echo + echo "$*" + echo + exit 1 +} + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "`uname`" in + CYGWIN* ) + cygwin=true + ;; + Darwin* ) + darwin=true + ;; + MINGW* ) + msys=true + ;; + NONSTOP* ) + nonstop=true + ;; +esac + +CLASSPATH=$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" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then + MAX_FD_LIMIT=`ulimit -H -n` + if [ $? -eq 0 ] ; then + if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then + MAX_FD="$MAX_FD_LIMIT" + fi + ulimit -n $MAX_FD + if [ $? -ne 0 ] ; then + warn "Could not set maximum file descriptor limit: $MAX_FD" + fi + else + warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" + fi +fi + +# For Darwin, add options to specify how the application appears in the dock +if $darwin; then + GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" +fi + +# For Cygwin, switch paths to Windows format before running java +if $cygwin ; then + APP_HOME=`cygpath --path --mixed "$APP_HOME"` + CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` + JAVACMD=`cygpath --unix "$JAVACMD"` + + # We build the pattern for arguments to be converted via cygpath + ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` + SEP="" + for dir in $ROOTDIRSRAW ; do + ROOTDIRS="$ROOTDIRS$SEP$dir" + SEP="|" + done + OURCYGPATTERN="(^($ROOTDIRS))" + # Add a user-defined pattern to the cygpath arguments + if [ "$GRADLE_CYGPATTERN" != "" ] ; then + OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" + fi + # Now convert the arguments - kludge to limit ourselves to /bin/sh + i=0 + for arg in "$@" ; do + CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` + CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option + + if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition + eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` + else + eval `echo args$i`="\"$arg\"" + fi + i=$((i+1)) + done + case $i in + (0) set -- ;; + (1) set -- "$args0" ;; + (2) set -- "$args0" "$args1" ;; + (3) set -- "$args0" "$args1" "$args2" ;; + (4) set -- "$args0" "$args1" "$args2" "$args3" ;; + (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; + (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; + (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; + (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; + (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; + esac +fi + +# Escape application args +save () { + for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done + echo " " +} +APP_ARGS=$(save "$@") + +# Collect all arguments for the java command, following the shell quoting and substitution rules +eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" + +# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong +if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then + cd "$(dirname "$0")" +fi + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 0000000..e95643d --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,84 @@ +@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 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= + +@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 init + +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 init + +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 + +:init +@rem Get command-line arguments, handling Windows variants + +if not "%OS%" == "Windows_NT" goto win9xME_args + +:win9xME_args +@rem Slurp the command line arguments. +set CMD_LINE_ARGS= +set _SKIP=2 + +:win9xME_args_slurp +if "x%~1" == "x" goto execute + +set CMD_LINE_ARGS=%* + +: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 %CMD_LINE_ARGS% + +: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 diff --git a/requirements.md b/requirements.md new file mode 100644 index 0000000..031f399 --- /dev/null +++ b/requirements.md @@ -0,0 +1,42 @@ +Aufgabe: + +Erzeugen eines 8 stelligen Codes zum Bekleben von Tubes einer Biobank. + +· Die Codes sollen die Zeichen a-z,A-Z,0-9 unterstützen. + +· Hierbei sollen die ersten 3 Stellen die Studiennummer kodieren, + +· die nächste Stelle den Probentyp + +· und die letzten 4 Stellen die Probennummer hochgezählt. + + + +Eingabe: + +Angabe einer Studiennummer, eines Probentyps und einer gewünschten Anzahl. + + + +Ausgabe: + +Eine HTML-Darstellung der Etiketten. (Eine Tabelle reicht hier aus.) + + + +Technische Voraussetzungen: + +· Das Programm soll in Java sein. Wir verwenden Spring und programmieren Web-Applikationen, dies ist für diese + Aufgabe aber nicht erforderlich. Eine Jar-Datei mit README (Bedienungsanleitung) reicht. + +· Die Ausgabe kann eine HTML-Datei sein, die manuell geöffnet werden kann. + +· Die Eingabe kann über die Kommandozeile erfolgen, oder über eine simple GUI. + +· Es sollen 2 Studiennummern und 2 Probentypen vordefiniert werden (Hardcoded). Die Eingabe einer nicht + definierten Studie/Typ soll sinnvoll behandelt werden. + + · Es wäre schön, wenn sich das Programm die aktuelle Nummer zu einer Studie/Typ merken würde und bei einem + neuen Start weiterzählt. + +· Der Code sollte gut dokumentiert sein (auf Englisch) \ No newline at end of file diff --git a/settings.gradle b/settings.gradle new file mode 100644 index 0000000..7ee4c61 --- /dev/null +++ b/settings.gradle @@ -0,0 +1,2 @@ +rootProject.name = 'imi.codes' + diff --git a/src/main/java/de/vanitasvitae/imi/codes/Arguments.java b/src/main/java/de/vanitasvitae/imi/codes/Arguments.java new file mode 100644 index 0000000..9f0b250 --- /dev/null +++ b/src/main/java/de/vanitasvitae/imi/codes/Arguments.java @@ -0,0 +1,56 @@ +package de.vanitasvitae.imi.codes; + +import org.apache.commons.cli.Option; +import org.apache.commons.cli.Options; + +public class Arguments { + + static final Option STUDY_NUMBER = Option.builder("s") + .longOpt("study") + .desc("Three-letter code of the associated study") + .required() + .hasArg() + .argName("SNR") + .build(); + + static final Option SAMPLE_TYPE = Option.builder("t") + .longOpt("type") + .desc("Type of the sample (b = blood, u = urine)") + .required(true) + .hasArg() + .argName("sample type") + .build(); + + static final Option OUTPUT_DESTINATION = Option.builder("o") + .longOpt("OUTPUT_DESTINATION") + .desc("Filename for the generated html output") + .hasArg() + .argName("file name") + .build(); + + static final Option EXTERNAL_BROWSER = Option.builder("b") + .longOpt("EXTERNAL_BROWSER") + .desc("Open the generated HTML output in a an external browser") + .build(); + + static final Option HELP = Option.builder("h") + .longOpt("help") + .desc("Print this help text") + .build(); + /** + * Assemble and return the available command line options. + * + * @return command line options. + */ + public static Options getCommandLineOptions() { + Options options = new Options(); + + options.addOption(STUDY_NUMBER); + options.addOption(SAMPLE_TYPE); + options.addOption(OUTPUT_DESTINATION); + options.addOption(EXTERNAL_BROWSER); + options.addOption(HELP); + + return options; + } +} diff --git a/src/main/java/de/vanitasvitae/imi/codes/InputValidator.java b/src/main/java/de/vanitasvitae/imi/codes/InputValidator.java new file mode 100644 index 0000000..892c8f7 --- /dev/null +++ b/src/main/java/de/vanitasvitae/imi/codes/InputValidator.java @@ -0,0 +1,47 @@ +package de.vanitasvitae.imi.codes; + +import java.util.regex.Pattern; + +public class InputValidator { + + // Allowed characters + private static final String ALPHABET = "[a-zA-Z0-9]"; + + /* + REGEX pattern for study numbers. Allowed are all 3-letter numbers from the alphabet [a-zA-Z0-9]. + */ + private static final Pattern STUDY_NUMBER_MATCHER = Pattern.compile(ALPHABET+"{3}"); + + /* + REGEX pattern for sample numbers. Allowed are four-letter numbers from the alphabet [a-zA-Z0-9]. + */ + private static final Pattern SAMPLE_NUMBER_MATCHER = Pattern.compile(ALPHABET+"{4}"); + + /** + * Validate a given study number. Valid study numbers are 3-letter codes from the alphabet [a-zA-Z0-9]. + * + * @param in input String + * @return unmodified input String if it matches. + * @throws IllegalArgumentException if the input String doesn't match the regex. + */ + public static String validateStudyNumber(String in) { + if (!STUDY_NUMBER_MATCHER.matcher(in).matches()) { + throw new IllegalArgumentException("Study number does not match REGEX."); + } + + return in; + } + + /** + * Validate a given sample type. Valid types are found in {@link SampleType}.# + * + * @param in input String + * @return parsed {@link SampleType}. + * + * @throws IllegalArgumentException if the given String doesn't match a {@link SampleType}. + * @throws NullPointerException in case the given String is {@code null}. + */ + public static SampleType validateSampleType(String in) { + return SampleType.valueOf(in); + } +} diff --git a/src/main/java/de/vanitasvitae/imi/codes/Main.java b/src/main/java/de/vanitasvitae/imi/codes/Main.java new file mode 100644 index 0000000..25d1998 --- /dev/null +++ b/src/main/java/de/vanitasvitae/imi/codes/Main.java @@ -0,0 +1,48 @@ +package de.vanitasvitae.imi.codes; + +import org.apache.commons.cli.CommandLine; +import org.apache.commons.cli.CommandLineParser; +import org.apache.commons.cli.DefaultParser; +import org.apache.commons.cli.HelpFormatter; +import org.apache.commons.cli.Options; +import org.apache.commons.cli.ParseException; + +public class Main { + + private static final String NAME_JAR = "imicodes"; + private static final String HELP_HEADER = "Generate ID codes for sample tubes."; + private static final String HELP_FOOTER = "\nAuthor: Paul Schaub "; + + public static void main(String[] args) { + + Options options = Arguments.getCommandLineOptions(); + CommandLineParser parser = new DefaultParser(); + + CommandLine arguments; + try { + arguments = parser.parse(options, args); + } catch (ParseException e) { + System.out.println(e.getMessage()); + printHelp(options); + return; + } + + if (arguments.hasOption(Arguments.HELP)) { + printHelp(options); + return; + } + } + + /** + * Print a descriptive help text to the console. + * + * @param options {@link Options} for which we want to print a help text. + */ + private static void printHelp(Options options) { + HelpFormatter formatter = new HelpFormatter(); + + formatter.printHelp(NAME_JAR, HELP_HEADER, options, HELP_FOOTER, true); + } + + +} diff --git a/src/main/java/de/vanitasvitae/imi/codes/SampleType.java b/src/main/java/de/vanitasvitae/imi/codes/SampleType.java new file mode 100644 index 0000000..621aeea --- /dev/null +++ b/src/main/java/de/vanitasvitae/imi/codes/SampleType.java @@ -0,0 +1,20 @@ +package de.vanitasvitae.imi.codes; + +public enum SampleType { + + b("Blood"), + u("Urine"), + ; + + // Members of the enum + + private final String name; + + SampleType(String name) { + this.name = name; + } + + public String getName() { + return name; + } +}