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Add command line option parsing

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This commit is contained in:
Paul Schaub 2018-11-14 20:38:51 +01:00
parent 8420a54c97
commit e91fed4459
Signed by: vanitasvitae
GPG key ID: 62BEE9264BF17311
11 changed files with 501 additions and 0 deletions
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2
.gitignore vendored
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid* hs_err_pid*
.idea
.gradle

23
build.gradle Normal file
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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'
}

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gradle/wrapper/gradle-wrapper.properties vendored Normal file
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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

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gradlew vendored Executable file
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#!/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" "$@"

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@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

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requirements.md Normal file
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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)

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settings.gradle Normal file
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rootProject.name = 'imi.codes'

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src/main/java/de/vanitasvitae/imi/codes/Arguments.java Normal file
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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;
}
}

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src/main/java/de/vanitasvitae/imi/codes/InputValidator.java Normal file
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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);
}
}

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src/main/java/de/vanitasvitae/imi/codes/Main.java Normal file
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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 <paul.schaub@wwu.de>";
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);
}
}

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src/main/java/de/vanitasvitae/imi/codes/SampleType.java Normal file
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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;
}
}