restructuring directories

build.gradle

+apply plugin: 'java-library'
+apply plugin: 'maven'
+apply plugin: 'antlr'
+
+apply plugin: 'idea'
+apply plugin: 'eclipse'
+
+group = 'net.catdata'
+version = '0.9-SNAPSHOT-maven'
+
+description = "Categorical Data IDE"
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+tasks.withType(JavaCompile) {
+	options.encoding = 'UTF-8'
+}
+
+configurations.all {
+}
+
+generateGrammarSource {
+    maxHeapSize = "64m"
+    // arguments << "-lib" << "src/main/antlr/catdata/aql/grammer"
+    arguments << "-visitor" << "-listener"
+    arguments << "-long-messages"
+}
+
+repositories {
+     maven { url "https://nexus.isis.vanderbilt.edu/repository/maven-releases" }
+     maven { url "https://nexus.isis.vanderbilt.edu/repository/maven-snapshots" }
+     maven { url "http://repo.maven.apache.org/maven2" }
+}
+
+dependencies {
+    compile group: 'net.sourceforge.collections', name: 'collections-generic', version:'4.01'
+    compile group: 'org.apache.commons', name: 'commons-csv', version:'1.5'
+    compile group: 'org.apache.commons', name: 'commons-exec', version:'1.3'
+    compile group: 'org.apache.commons', name: 'commons-lang3', version:'3.7'
+    compile group: 'com.h2database', name: 'h2', version:'1.4.196'
+    compile group: 'org.glassfish', name: 'javax.json', version:'1.1.2'
+    compile group: 'jgraph', name: 'jgraph', version:'5.12.3.2'
+    compile group: 'org.jparsec', name: 'jparsec', version:'3.0'
+    compile group: 'net.sf.jung', name: 'jung-algorithms', version:'2.1.1'
+    compile group: 'net.sf.jung', name: 'jung-api', version:'2.1.1'
+    compile group: 'net.sf.jung', name: 'jung-graph-impl', version:'2.1.1'
+    compile group: 'net.sf.jung', name: 'jung-visualization', version:'2.1.1'
+    compile group: 'org.antlr', name: 'antlr4', version:'4.7'
+    compile group: 'com.opencsv', name: 'opencsv', version:'4.1'
+    compile group: 'com.fifesoft', name: 'autocomplete', version:'2.6.1'
+    compile group: 'com.fifesoft', name: 'rstaui', version:'2.6.1'
+    compile group: 'com.fifesoft', name: 'rsyntaxtextarea', version:'2.6.1'
+    compile group: 'es.nitaur.markdown', name: 'txtmark', version:'0.16'
+    antlr group: 'org.antlr', name: 'antlr4', version: '4.7'
+    testCompile group: 'junit', name: 'junit', version:'4.12'
+}

buildSrc/src/main/groovy/org/babeloff/ReleaseVersionTask.groovy

+package org.babeloff
+
+class ReleaseVersionTask {
+}

buildSrc/src/main/groovy/org/babeloff/SnapshotVersionTask.groovy

+package org.babeloff
+
+import org.gradle.api.DefaultTask
+import org.gradle.api.tasks.Input
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.TaskAction
+
+class ReleaseVersionTask extends DefaultTask {
+    @Input Boolean release
+    @OutputFile File destFile
+
+    ReleaseVersionTask() {
+        group = 'versioning'
+        description = 'Makes project a release version.'
+    }
+
+    @TaskAction
+    void start() {
+        project.version.release = true
+        ant.propertyfile(file: destFile) {
+            entry(key: 'release', type: 'string', operation: '=', value: 'true')
+        }
+    }
+}

gradle/grammar.gradle

+
+generateGrammarSource {
+    maxHeapSize = "64m"
+    arguments += ["-visitor", "-listener", "-long-messages",
+                  "-package", "catdata.aql.grammar",
+                  "-grammar", "AqlParser.g4"]
+}
\ No newline at end of file

gradle/version.properties

+#Fri, 07 Sep 2018 15:15:28 -0500
+
+year=2018
+month=9
+day=10
+release=false

gradle/wrapper/gradle-wrapper.properties

+#Wed Sep 05 08:42:09 CDT 2018
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.9-all.zip

gradlew

+#!/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" "$@"

gradlew.bat

+@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

pom.xml

@@ -106,8 +106,8 @@
                         </manifest>
                     </archive>
                     <descriptors>
-                      <descriptor>src/assembly/bin.xml</descriptor>
-                      <descriptor>src/assembly/jar-with-deps.xml</descriptor>
+                      <descriptor>src/main/java/assembly/bin.xml</descriptor>
+                      <descriptor>src/main/java/assembly/jar-with-deps.xml</descriptor>
                     </descriptors>
                 </configuration>
                 <executions>
@@ -142,6 +142,23 @@
               </executions>
             </plugin>
             -->
+            <plugin>
+                <groupId>org.antlr</groupId>
+                <artifactId>antlr4-maven-plugin</artifactId>
+                <version>4.7.1</version>
+                <executions>
+                    <execution>
+                        <id>antlr</id>
+                        <goals>
+                            <goal>antlr4</goal>
+                        </goals>
+                        <configuration>
+                            <listener>true</listener>
+                            <visitor>true</visitor>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>

settings.gradle

+rootProject.name = 'fql'

src/main/antlr/.gitignore

+*.class
+

src/main/antlr/README.md

+
+The antlr4 files are build by running the 
+boot promote 
+
+from catdata/aql/grammar
+
+Once the java files have been built eclipse needs to 
+know about them.
+The easiest way is to make a symbolic link.
+
+ln -s ../../../gen/catdata/aql/grammar/ ./src/catdata/aql/grammar
+
+This will confuse maven though so the link needs to be removed before running 
+
+mvn package
+

src/main/antlr/catdata/aql/grammar/AqlLexerRules.g4

+/**
+ *	A lexical grammar for Aql
+ */
+lexer grammar AqlLexerRules;
+
+options
+   {
+     // superClass = 'LexerAdaptor' ;
+   }
+
+// Common set of fragments
+import LexBasic;
+
+channels {
+  HIDDEN_CHANNEL,
+  WHITESPACE_CHANNEL,
+  BLOCK_COMMENT_CHANNEL,
+  LINE_COMMENT_CHANNEL,
+  DOC_COMMENT_CHANNEL
+}
+
+// ======================================================
+// Lexer specification
+//
+// -------------------------
+// Comments
+
+DOC_COMMENT
+   : DocComment  -> channel  (DOC_COMMENT_CHANNEL)
+   ;
+
+
+BLOCK_COMMENT
+   : BlockComment -> channel (BLOCK_COMMENT_CHANNEL)
+   ;
+
+
+BLOCK_COMMMENT
+  : BlockComment -> channel(HIDDEN_CHANNEL)
+  ;
+
+LINE_COMMENT
+  : LineComment   -> channel(HIDDEN_CHANNEL)
+  ;
+
+// -------------------------
+// Integer
+//
+
+INTEGER
+   : DecimalNumeral
+   ;
+
+NUMBER
+    // 1.35, 1.35E-9, 0.3, -4.5
+    :   '-'? DecimalNumeral Dot DecimalNumeral Exponent?
+    // 1e10 -3e4
+    |   '-'? DecimalNumeral Exponent
+    // -3, 45
+    |   '-'? DecimalNumeral
+    ;
+
+// -------------------------
+// Literal string
+//
+// Aql makes no distinction between a single character
+// literal and a multi-character string.
+// All literals are single quote delimited and
+// may contain unicode escape sequences of the form \uxxxx, where x
+// is a valid hexadecimal number (per Unicode standard).
+
+STRING_LITERAL
+   : SQuoteLiteral
+   ;
+
+UNTERMINATED_STRING_LITERAL
+   : USQuoteLiteral
+   ;
+
+CHAR : CharLiteral ;
+STRING :  DQuoteLiteral ;
+MULTI_STRING : DQuote MultiLine DQuote ;
+
+// -------------------------
+// Keywords
+//
+// Keywords may not be used as labels for rules or in any other context where
+// they would be ambiguous with the keyword vs some other identifier.
+// Some blocks are handled idiomatically
+// as island grammars in dedicated lexical modes.
+
+HTML
+   : 'html' Ws* LDocQuote  -> pushMode (Html)
+   ;
+
+
+MARKDOWN
+   : 'md' Ws* LDocQuote -> pushMode (MarkDown)
+   ;
+
+OPTIONS
+   : 'options' // -> pushMode (Options)
+   ;
+
+
+LITERAL : 'literal' ;
+IMPORTS : 'imports' ;
+FORALL : 'forall' ;
+WHERE : 'where' ;
+EXISTS : 'exists' ;
+UNIQUE : 'unique' ;
+
+GRAPH : 'graph' ;
+NODES : 'nodes' ;
+EDGES : 'edges' ;
+
+INSTANCE : 'instance' ;
+EMPTY : 'empty' ;
+SRC : 'src' ;
+DST : 'dst' ;
+DISTINCT : 'distinct' ;
+EVAL : 'eval' ;
+COEVAL : 'coeval' ;
+DELTA : 'delta' ;
+SIGMA : 'sigma' ;
+COPRODUCT_SIGMA : 'coproduct_sigma' ;
+COPRODUCT : 'coproduct' ;
+UNION : 'union' ;
+COPRODUCT_UNRESTRICTED: 'coproduct_unrestricted' ;
+COEQUALIZE : 'coequalize' ;
+COLIMIT : 'colimit' ;
+IMPORT_JDBC : 'import_jdbc' ;
+QUOTIENT_JDBC : 'quotient_jdbc' ;
+QUOTIENT_CSV : 'quotient_csv' ;
+IMPORT_JDBC_ALL : 'import_jdbc_all' ;
+IMPORT_CSV : 'import_csv' ;
+STATIC_TYPING : 'static_typing' ;
+QUOTIENT : 'quotient' ;
+CHASE : 'chase' ;
+RANDOM : 'random' ;
+GENERATORS : 'generators' ;
+EQUATIONS : 'equations' ;
+MULTI_EQUATIONS : 'multi_equations' ;
+RANDOM_SEED : 'random_seed' ;
+ANONYMIZE : 'anonymize' ;
+FROZEN : 'frozen' ;
+PI : 'pi' ;
+
+MAPPING : 'mapping' ;
+IDENTITY : 'identity' ;
+ENTITY : 'entity' ;
+ENTITIES : 'entities' ;
+FOREIGN_KEYS : 'foreign_keys' ;
+ATTRIBUTES : 'attributes' ;
+LAMBDA : 'lambda' ;
+
+IMPORT_JOINED : 'import_joined' ;
+MAP_NULLS_ARBITRARILY_UNSAFE :  'map_nulls_arbitrarily_unsafe' ;
+INTERPRET_AS_ALGEGRA :  'interpret_as_algebra' ;
+PREPEND_ENTITY_ON_IDS : 'prepend_entity_on_ids' ;
+NUM_THREADS :  'num_threads' ;
+TIMEOUT :  'timeout' ;
+REQUIRE_CONSISTENCY :  'require_consistency' ;
+SCHEMA_ONLY :  'schema_only' ;
+ALLOW_JAVA_EQS_UNSAFE :  'allow_java_eqs_unsafe' ;
+DONT_VALIDATE_UNSAFE :  'dont_validate_unsafe' ;
+ALWAYS_RELOAD :  'always_reload' ;
+CSV_FIELD_DELIM_CHAR :  'csv_field_delim_char' ;
+CSV_ESCAPE_CHAR :  'csv_escape_char' ;
+CSV_QUOTE_CHAR :  'csv_quote_char' ;
+CSV_FILE_EXTENSION :  'csv_file_extension' ;
+CSV_GENERATE_IDS :  'csv_generate_ids' ;
+ID_COLUMN_NAME :  'id_column_name' ;
+VARCHAR_LENGTH :  'varchar_length' ;
+START_IDS_AT :  'start_ids_at' ;
+IMPORT_AS_THEORY :  'import_as_theory' ;
+JDBC_DEFAULT_CLASS :  'jdbc_default_class' ;
+JDBC_DEFAULT_STRING :  'jdbc_default_string' ;
+DONT_VERIFY_FOR_UNSAFE :  'dont_verify_is_appropriate_for_prover_unsafe' ;
+PROVER :  'prover' ;
+PROGRAM_ALLOW_NONTERM_UNSAFE :  'program_allow_nontermination_unsafe' ;
+COMPLETION_PRECEDENCE :  'completion_precedence' ;
+COMPLETION_SORT :  'completion_sort' ;
+COMPLETION_COMPOSE :  'completion_compose' ;
+COMPLETION_FILTER_SUBSUMED :  'completion_filter_subsumed' ;
+COMPLETION_SYNTACTIC_AC :  'completion_syntactic_ac' ;
+QUERY_COMPOSE_USE_INCOMPLETE : 'query_compose_use_incomplete' ;
+
+GUI_MAX_TABLE_SIZE : 'gui_max_table_size' ;
+GUI_MAX_GRAPH_SIZE : 'gui_max_graph_size' ;