http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Lexer.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Lexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Lexer.java new file mode 100644 index 0000000..e62dd46 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Lexer.java @@ -0,0 +1,886 @@ +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.B3PW91;/* The following code was generated by JFlex 1.4.3 on 9/7/14 9:49 PM */ + +import java_cup.runtime.Symbol; +import java_cup.sym; +import org.apache.airavata.datacat.parsers.gridchem.Settings; + +import java.io.IOException; + + +/** + * This class is a scanner generated by + * <a href="http://www.jflex.de/";>JFlex</a> 1.4.3 + * on 9/7/14 9:49 PM from the specification file + * <tt>B3PW91.flex</tt> + */ +public class B3PW91Lexer implements java_cup.runtime.Scanner { + + /** This character denotes the end of file */ + public static final int YYEOF = -1; + + /** initial size of the lookahead buffer */ + private static final int ZZ_BUFFERSIZE = 16384; + + /** lexical states */ + public static final int FLOATMP3 = 24; + public static final int ITER2 = 4; + public static final int FLOATMP2 = 22; + public static final int FLOATMP1 = 20; + public static final int MPOPT = 18; + public static final int INTMP = 28; + public static final int INTVALUE = 8; + public static final int IGNOREALL = 26; + public static final int ITER = 2; + public static final int YYINITIAL = 0; + public static final int MP2 = 16; + public static final int FLOAT2 = 14; + public static final int FLOAT1 = 12; + public static final int FLOATVALUE = 10; + public static final int ITER3 = 6; + + /** + * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l + * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l + * at the beginning of a line + * l is of the form l = 2*k, k a non negative integer + */ + private static final int ZZ_LEXSTATE[] = { + 0, 0, 1, 1, 2, 2, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, + 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 2, 2, 12, 12 + }; + + /** + * Translates characters to character classes + */ + private static final char [] ZZ_CMAP = { + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 14, 0, 0, 0, 0, 0, 0, 50, 29, 7, 0, 32, 0, 3, 4, 1, + 2, 37, 46, 48, 2, 2, 47, 2, 2, 36, 27, 0, 0, 6, 0, 0, + 0, 0, 31, 24, 26, 28, 25, 49, 33, 0, 0, 0, 0, 38, 8, 42, + 34, 0, 30, 23, 0, 51, 0, 35, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 39, 11, 41, 45, 12, 16, 0, 22, 20, 0, 0, 44, 10, 21, 15, + 19, 0, 13, 17, 18, 9, 0, 0, 40, 0, 43, 0, 5, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + + /** + * Translates DFA states to action switch labels. + */ + private static final int [] ZZ_ACTION = zzUnpackAction(); + + private static final String ZZ_ACTION_PACKED_0 = + "\15\0\6\1\1\2\23\1\1\3\1\1\36\0\1\4"+ + "\1\5\1\6\6\0\1\7\1\10\1\11\70\0\1\12"+ + "\32\0\1\13\5\0\1\14\16\0\1\15\1\16\2\0"+ + "\1\17\1\20\53\0\1\21\1\22\1\23\7\0\1\24"+ + "\1\25"; + + private static int [] zzUnpackAction() { + int [] result = new int[248]; + int offset = 0; + offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAction(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /** + * Translates a state to a row index in the transition table + */ + private static final int [] ZZ_ROWMAP = zzUnpackRowMap(); + + private static final String ZZ_ROWMAP_PACKED_0 = + "\0\0\0\64\0\150\0\234\0\320\0\u0104\0\u0138\0\u016c"+ + "\0\u01a0\0\u01d4\0\u0208\0\u023c\0\u0270\0\u02a4\0\u02d8\0\u030c"+ + "\0\u0340\0\u0374\0\u03a8\0\u03dc\0\u03dc\0\u0410\0\u0444\0\u0478"+ + "\0\u04ac\0\u04e0\0\u0514\0\u0548\0\u057c\0\u05b0\0\u05e4\0\u0618"+ + "\0\u064c\0\u0680\0\u06b4\0\u06e8\0\u071c\0\u0750\0\u0784\0\u07b8"+ + "\0\u07b8\0\u07ec\0\u0820\0\u0854\0\u0888\0\u08bc\0\u08f0\0\u0410"+ + "\0\u0924\0\u0478\0\u0958\0\u04e0\0\u098c\0\u09c0\0\u09f4\0\u0a28"+ + "\0\u0a5c\0\u0a90\0\u0ac4\0\u0680\0\u0af8\0\u06e8\0\u0b2c\0\u0750"+ + "\0\u0b60\0\u0b94\0\u0bc8\0\u0bfc\0\u0c30\0\u0c64\0\u0c98\0\u0924"+ + "\0\u0958\0\u098c\0\u0ccc\0\u0d00\0\u0d34\0\u0d68\0\u0d9c\0\u0dd0"+ + "\0\u0af8\0\u0b2c\0\u0b60\0\u0e04\0\u0e38\0\u0e6c\0\u0ea0\0\u0ed4"+ + "\0\u0f08\0\u0f3c\0\u0f70\0\u0fa4\0\u0fd8\0\u100c\0\u1040\0\u1074"+ + "\0\u10a8\0\u10dc\0\u1110\0\u1144\0\u1178\0\u11ac\0\u11e0\0\u1214"+ + "\0\u1248\0\u127c\0\u12b0\0\u12e4\0\u1318\0\u134c\0\u1380\0\u13b4"+ + "\0\u13e8\0\u141c\0\u1450\0\u1484\0\u14b8\0\u14ec\0\u1520\0\u1554"+ + "\0\u1588\0\u15bc\0\u15f0\0\u1624\0\u1658\0\u168c\0\u16c0\0\u16f4"+ + "\0\u1728\0\u175c\0\u1790\0\u17c4\0\u17f8\0\u182c\0\u1860\0\u1894"+ + "\0\u18c8\0\u18fc\0\u1930\0\u02a4\0\u1964\0\u1998\0\u19cc\0\u1a00"+ + "\0\u1a34\0\u1a68\0\u1a9c\0\u1ad0\0\u1b04\0\u1b38\0\u1b6c\0\u1ba0"+ + "\0\u1bd4\0\u1c08\0\u1c3c\0\u1c70\0\u1ca4\0\u1cd8\0\u1d0c\0\u1d40"+ + "\0\u1d74\0\u1da8\0\u1ddc\0\u1e10\0\u1e44\0\u1e78\0\u02a4\0\u1eac"+ + "\0\u1ee0\0\u1f14\0\u1f48\0\u1f7c\0\u02a4\0\u1fb0\0\u1fe4\0\u2018"+ + "\0\u204c\0\u2080\0\u20b4\0\u20e8\0\u211c\0\u2150\0\u2184\0\u21b8"+ + "\0\u21ec\0\u2220\0\u2254\0\u02a4\0\u02a4\0\u2288\0\u22bc\0\u02a4"+ + "\0\u02a4\0\u22f0\0\u2324\0\u2358\0\u238c\0\u23c0\0\u23f4\0\u2428"+ + "\0\u245c\0\u2490\0\u24c4\0\u24f8\0\u252c\0\u2560\0\u2594\0\u25c8"+ + "\0\u25fc\0\u2630\0\u2664\0\u2698\0\u26cc\0\u2700\0\u2734\0\u2768"+ + "\0\u279c\0\u27d0\0\u2804\0\u2838\0\u286c\0\u28a0\0\u28d4\0\u2908"+ + "\0\u293c\0\u2970\0\u29a4\0\u29d8\0\u2a0c\0\u2a40\0\u2a74\0\u2aa8"+ + "\0\u2adc\0\u2b10\0\u2b44\0\u2b78\0\u02a4\0\u02a4\0\u02a4\0\u2bac"+ + "\0\u2be0\0\u2c14\0\u2c48\0\u2c7c\0\u2cb0\0\u2ce4\0\u02a4\0\u02a4"; + + private static int [] zzUnpackRowMap() { + int [] result = new int[248]; + int offset = 0; + offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackRowMap(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int high = packed.charAt(i++) << 16; + result[j++] = high | packed.charAt(i++); + } + return j; + } + + /** + * The transition table of the DFA + */ + private static final int [] ZZ_TRANS = zzUnpackTrans(); + + private static final String ZZ_TRANS_PACKED_0 = + "\10\16\1\17\102\16\1\20\6\16\1\21\7\16\1\22"+ + "\3\16\1\23\77\16\1\24\1\25\1\16\1\25\32\16"+ + "\1\25\3\16\2\24\10\16\3\24\5\16\1\26\1\27"+ + "\1\16\1\27\32\16\1\27\3\16\2\26\10\16\3\26"+ + "\5\16\1\30\1\31\1\16\1\31\32\16\1\31\3\16"+ + "\2\30\10\16\3\30\5\16\1\32\1\33\1\16\1\33"+ + "\32\16\1\33\3\16\2\32\10\16\3\32\51\16\1\34"+ + "\44\16\1\35\4\16\1\36\1\16\1\37\7\16\1\40"+ + "\3\16\1\41\13\16\1\42\1\43\1\16\1\43\32\16"+ + "\1\43\3\16\2\42\10\16\3\42\5\16\1\44\1\45"+ + "\1\16\1\45\32\16\1\45\3\16\2\44\10\16\3\44"+ + "\5\16\1\46\1\47\1\16\1\47\32\16\1\47\3\16"+ + "\2\46\10\16\3\46\5\16\1\50\1\51\1\16\1\51"+ + "\32\16\1\51\3\16\2\50\10\16\3\50\3\16\75\0"+ + "\1\52\74\0\1\53\5\0\1\54\101\0\1\55\64\0"+ + "\1\56\37\0\1\57\42\0\1\24\41\0\2\24\10\0"+ + "\3\24\5\0\1\60\1\0\1\61\37\0\2\60\10\0"+ + "\3\60\5\0\1\60\41\0\2\60\10\0\3\60\5\0"+ + "\1\62\1\0\1\63\37\0\2\62\10\0\3\62\5\0"+ + "\1\62\41\0\2\62\10\0\3\62\5\0\1\64\1\0"+ + "\1\65\37\0\2\64\10\0\3\64\5\0\1\64\41\0"+ + "\2\64\10\0\3\64\45\0\1\66\43\0\1\67\124\0"+ + "\1\70\46\0\1\71\64\0\1\72\37\0\1\73\42\0"+ + "\1\74\1\0\1\75\37\0\2\74\10\0\3\74\5\0"+ + "\1\74\41\0\2\74\10\0\3\74\5\0\1\76\1\0"+ + "\1\77\37\0\2\76\10\0\3\76\5\0\1\76\41\0"+ + "\2\76\10\0\3\76\5\0\1\100\1\0\1\101\37\0"+ + "\2\100\10\0\3\100\5\0\1\100\41\0\2\100\10\0"+ + "\3\100\5\0\1\50\41\0\2\50\10\0\3\50\15\0"+ + "\1\102\65\0\1\103\100\0\1\104\61\0\1\105\104\0"+ + "\1\106\35\0\1\107\43\0\1\110\41\0\2\110\10\0"+ + "\3\110\5\0\1\111\41\0\2\111\10\0\3\111\5\0"+ + "\1\112\41\0\2\112\10\0\3\112\61\0\1\113\21\0"+ + "\1\114\115\0\1\115\44\0\1\116\104\0\1\117\35\0"+ + "\1\120\43\0\1\121\41\0\2\121\10\0\3\121\5\0"+ + "\1\122\41\0\2\122\10\0\3\122\5\0\1\123\41\0"+ + "\2\123\10\0\3\123\16\0\1\124\73\0\1\125\56\0"+ + "\1\126\63\0\1\127\71\0\1\130\63\0\1\131\40\0"+ + "\1\132\105\0\1\133\102\0\1\134\37\0\1\135\71\0"+ + "\1\136\63\0\1\137\53\0\1\140\65\0\1\141\77\0"+ + "\1\142\47\0\1\143\57\0\1\144\63\0\1\145\130\0"+ + "\1\146\22\0\1\147\123\0\1\150\23\0\1\151\57\0"+ + "\1\152\63\0\1\153\66\0\1\154\73\0\1\155\55\0"+ + "\1\156\62\0\1\157\56\0\1\160\76\0\1\161\42\0"+ + "\1\162\105\0\1\163\54\0\1\164\63\0\1\165\56\0"+ + "\1\166\76\0\1\167\55\0\1\170\56\0\1\171\77\0"+ + "\1\172\54\0\1\173\57\0\1\174\124\0\1\175\70\0"+ + "\1\176\14\0\1\177\60\0\1\200\73\0\1\201\57\0"+ + "\1\202\124\0\1\203\27\0\1\204\56\0\1\205\65\0"+ + "\1\206\65\0\1\207\63\0\1\210\114\0\1\211\61\0"+ + "\1\212\30\0\1\213\67\0\1\214\63\0\1\215\63\0"+ + "\1\216\114\0\1\217\34\0\1\220\56\0\1\221\103\0"+ + "\1\222\61\0\1\223\63\0\1\224\54\0\1\225\122\0"+ + "\1\226\15\0\1\227\101\0\1\230\63\0\1\231\54\0"+ + "\1\232\57\0\1\233\61\0\1\234\65\0\1\235\64\0"+ + "\1\236\63\0\1\237\70\0\1\240\74\0\1\241\42\0"+ + "\1\242\66\0\1\243\63\0\1\244\70\0\1\245\60\0"+ + "\1\246\57\0\1\247\64\0\1\250\62\0\1\251\63\0"+ + "\1\252\65\0\1\253\121\0\1\254\23\0\1\255\63\0"+ + "\1\256\63\0\1\257\65\0\1\260\66\0\1\261\75\0"+ + "\1\262\100\0\1\263\63\0\1\264\37\0\1\265\120\0"+ + "\1\266\52\0\1\267\63\0\1\270\37\0\1\271\52\0"+ + "\1\272\104\0\1\273\42\0\1\274\63\0\1\275\65\0"+ + "\1\276\54\0\1\277\70\0\1\300\63\0\1\301\65\0"+ + "\1\302\70\0\1\303\76\0\1\304\76\0\1\305\30\0"+ + "\1\306\116\0\1\307\33\0\1\310\101\0\1\311\43\0"+ + "\1\312\116\0\1\313\30\0\1\314\62\0\1\315\105\0"+ + "\1\316\35\0\1\317\74\0\1\320\52\0\1\321\75\0"+ + "\1\322\100\0\1\323\45\0\1\324\62\0\1\325\64\0"+ + "\1\326\65\0\1\327\67\0\1\330\106\0\1\331\15\0"+ + "\1\332\131\0\1\333\25\0\1\334\50\0\1\335\74\0"+ + "\1\336\105\0\1\337\41\0\1\340\71\0\1\341\103\0"+ + "\1\342\43\0\1\343\71\0\1\344\55\0\1\345\67\0"+ + "\1\346\100\0\1\347\34\0\1\350\100\0\1\351\46\0"+ + "\1\352\73\0\1\353\103\0\1\354\74\0\1\355\36\0"+ + "\1\356\110\0\1\357\27\0\1\360\107\0\1\361\34\0"+ + "\1\362\54\0\1\363\71\0\1\364\64\0\1\365\56\0"+ + "\1\366\60\0\1\367\102\0\1\370\36\0"; + + private static int [] zzUnpackTrans() { + int [] result = new int[11544]; + int offset = 0; + offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackTrans(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + value--; + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /* error codes */ + private static final int ZZ_UNKNOWN_ERROR = 0; + private static final int ZZ_NO_MATCH = 1; + private static final int ZZ_PUSHBACK_2BIG = 2; + + /* error messages for the codes above */ + private static final String ZZ_ERROR_MSG[] = { + "Unkown internal scanner error", + "Error: could not match input", + "Error: pushback value was too large" + }; + + /** + * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code> + */ + private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute(); + + private static final String ZZ_ATTRIBUTE_PACKED_0 = + "\15\0\1\11\33\1\36\0\3\1\6\0\3\1\70\0"+ + "\1\11\32\0\1\11\5\0\1\11\16\0\2\11\2\0"+ + "\2\11\53\0\3\11\7\0\2\11"; + + private static int [] zzUnpackAttribute() { + int [] result = new int[248]; + int offset = 0; + offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAttribute(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + /** the input device */ + private java.io.Reader zzReader; + + /** the current state of the DFA */ + private int zzState; + + /** the current lexical state */ + private int zzLexicalState = YYINITIAL; + + /** this buffer contains the current text to be matched and is + the source of the yytext() string */ + private char zzBuffer[] = new char[ZZ_BUFFERSIZE]; + + /** the textposition at the last accepting state */ + private int zzMarkedPos; + + /** the current text position in the buffer */ + private int zzCurrentPos; + + /** startRead marks the beginning of the yytext() string in the buffer */ + private int zzStartRead; + + /** endRead marks the last character in the buffer, that has been read + from input */ + private int zzEndRead; + + /** number of newlines encountered up to the start of the matched text */ + private int yyline; + + /** the number of characters up to the start of the matched text */ + private int yychar; + + /** + * the number of characters from the last newline up to the start of the + * matched text + */ + private int yycolumn; + + /** + * zzAtBOL == true <=> the scanner is currently at the beginning of a line + */ + private boolean zzAtBOL = true; + + /** zzAtEOF == true <=> the scanner is at the EOF */ + private boolean zzAtEOF; + + /** denotes if the user-EOF-code has already been executed */ + private boolean zzEOFDone; + + /* user code: */ + public static boolean DEBUG = false; + + + /** + * Creates a new scanner + * There is also a java.io.InputStream version of this constructor. + * + * @param in the java.io.Reader to read input from. + */ + public B3PW91Lexer(java.io.Reader in) { + this.zzReader = in; + } + + /** + * Creates a new scanner. + * There is also java.io.Reader version of this constructor. + * + * @param in the java.io.Inputstream to read input from. + */ + public B3PW91Lexer(java.io.InputStream in) { + this(new java.io.InputStreamReader(in)); + } + + + /** + * Refills the input buffer. + * + * @return <code>false</code>, iff there was new input. + * + * @exception java.io.IOException if any I/O-Error occurs + */ + private boolean zzRefill() throws java.io.IOException { + + /* first: make room (if you can) */ + if (zzStartRead > 0) { + System.arraycopy(zzBuffer, zzStartRead, + zzBuffer, 0, + zzEndRead-zzStartRead); + + /* translate stored positions */ + zzEndRead-= zzStartRead; + zzCurrentPos-= zzStartRead; + zzMarkedPos-= zzStartRead; + zzStartRead = 0; + } + + /* is the buffer big enough? */ + if (zzCurrentPos >= zzBuffer.length) { + /* if not: blow it up */ + char newBuffer[] = new char[zzCurrentPos*2]; + System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length); + zzBuffer = newBuffer; + } + + /* finally: fill the buffer with new input */ + int numRead = zzReader.read(zzBuffer, zzEndRead, + zzBuffer.length-zzEndRead); + + if (numRead > 0) { + zzEndRead+= numRead; + return false; + } + // unlikely but not impossible: read 0 characters, but not at end of stream + if (numRead == 0) { + int c = zzReader.read(); + if (c == -1) { + return true; + } else { + zzBuffer[zzEndRead++] = (char) c; + return false; + } + } + + // numRead < 0 + return true; + } + + + /** + * Closes the input stream. + */ + public final void yyclose() throws java.io.IOException { + zzAtEOF = true; /* indicate end of file */ + zzEndRead = zzStartRead; /* invalidate buffer */ + + if (zzReader != null) + zzReader.close(); + } + + + /** + * Resets the scanner to read from a new input stream. + * Does not close the old reader. + * + * All internal variables are reset, the old input stream + * <b>cannot</b> be reused (internal buffer is discarded and lost). + * Lexical state is set to <tt>ZZ_INITIAL</tt>. + * + * @param reader the new input stream + */ + public final void yyreset(java.io.Reader reader) { + zzReader = reader; + zzAtBOL = true; + zzAtEOF = false; + zzEOFDone = false; + zzEndRead = zzStartRead = 0; + zzCurrentPos = zzMarkedPos = 0; + yyline = yychar = yycolumn = 0; + zzLexicalState = YYINITIAL; + } + + + /** + * Returns the current lexical state. + */ + public final int yystate() { + return zzLexicalState; + } + + + /** + * Enters a new lexical state + * + * @param newState the new lexical state + */ + public final void yybegin(int newState) { + zzLexicalState = newState; + } + + + /** + * Returns the text matched by the current regular expression. + */ + public final String yytext() { + return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead ); + } + + + /** + * Returns the character at position <tt>pos</tt> from the + * matched text. + * + * It is equivalent to yytext().charAt(pos), but faster + * + * @param pos the position of the character to fetch. + * A value from 0 to yylength()-1. + * + * @return the character at position pos + */ + public final char yycharat(int pos) { + return zzBuffer[zzStartRead+pos]; + } + + + /** + * Returns the length of the matched text region. + */ + public final int yylength() { + return zzMarkedPos-zzStartRead; + } + + + /** + * Reports an error that occured while scanning. + * + * In a wellformed scanner (no or only correct usage of + * yypushback(int) and a match-all fallback rule) this method + * will only be called with things that "Can't Possibly Happen". + * If this method is called, something is seriously wrong + * (e.g. a JFlex bug producing a faulty scanner etc.). + * + * Usual syntax/scanner level error handling should be done + * in error fallback rules. + * + * @param errorCode the code of the errormessage to display + */ + private void zzScanError(int errorCode) { + String message; + try { + message = ZZ_ERROR_MSG[errorCode]; + } + catch (ArrayIndexOutOfBoundsException e) { + message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR]; + } + + throw new Error(message); + } + + + /** + * Pushes the specified amount of characters back into the input stream. + * + * They will be read again by then next call of the scanning method + * + * @param number the number of characters to be read again. + * This number must not be greater than yylength()! + */ + public void yypushback(int number) { + if ( number > yylength() ) + zzScanError(ZZ_PUSHBACK_2BIG); + + zzMarkedPos -= number; + } + + + /** + * Contains user EOF-code, which will be executed exactly once, + * when the end of file is reached + */ + private void zzDoEOF() throws java.io.IOException { + if (!zzEOFDone) { + zzEOFDone = true; + yyclose(); + } + } + + + /** + * Resumes scanning until the next regular expression is matched, + * the end of input is encountered or an I/O-Error occurs. + * + * @return the next token + * @exception java.io.IOException if any I/O-Error occurs + */ + public Symbol next_token() throws IOException { + int zzInput; + int zzAction; + + // cached fields: + int zzCurrentPosL; + int zzMarkedPosL; + int zzEndReadL = zzEndRead; + char [] zzBufferL = zzBuffer; + char [] zzCMapL = ZZ_CMAP; + + int [] zzTransL = ZZ_TRANS; + int [] zzRowMapL = ZZ_ROWMAP; + int [] zzAttrL = ZZ_ATTRIBUTE; + + while (true) { + zzMarkedPosL = zzMarkedPos; + + zzAction = -1; + + zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL; + + zzState = ZZ_LEXSTATE[zzLexicalState]; + + + zzForAction: { + while (true) { + + if (zzCurrentPosL < zzEndReadL) + zzInput = zzBufferL[zzCurrentPosL++]; + else if (zzAtEOF) { + zzInput = YYEOF; + break zzForAction; + } + else { + // store back cached positions + zzCurrentPos = zzCurrentPosL; + zzMarkedPos = zzMarkedPosL; + boolean eof = zzRefill(); + // get translated positions and possibly new buffer + zzCurrentPosL = zzCurrentPos; + zzMarkedPosL = zzMarkedPos; + zzBufferL = zzBuffer; + zzEndReadL = zzEndRead; + if (eof) { + zzInput = YYEOF; + break zzForAction; + } + else { + zzInput = zzBufferL[zzCurrentPosL++]; + } + } + int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ]; + if (zzNext == -1) break zzForAction; + zzState = zzNext; + + int zzAttributes = zzAttrL[zzState]; + if ( (zzAttributes & 1) == 1 ) { + zzAction = zzState; + zzMarkedPosL = zzCurrentPosL; + if ( (zzAttributes & 8) == 8 ) break zzForAction; + } + + } + } + + // store back cached position + zzMarkedPos = zzMarkedPosL; + + switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) { + case 7: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: MP2 Found the energy"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(MPOPT); + return new Symbol(B3PW91Sym.MPENERGY, new Float(yytext())); + } + case 22: break; + case 16: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found Maximum Force"); + yybegin(FLOATMP2); + return new Symbol(B3PW91Sym.MPMax); + } + case 23: break; + case 11: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the Step number"); + yybegin(INTVALUE); + return new Symbol(B3PW91Sym.NSearch1); + } + case 24: break; + case 4: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the energy in FLOATVALUE"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER); + return new Symbol(B3PW91Sym.ENERGY1, new Float(yytext())); + } + case 25: break; + case 6: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the RMS force"); +if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER); + return new Symbol(B3PW91Sym.RGRAD1, new Float(yytext())); + } + case 26: break; + case 17: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: SCFDONE1, Optimization completed"); + yybegin(MP2); + return new Symbol(B3PW91Sym.SCFDONE1); + } + case 27: break; + case 2: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin (ITER); + return new Symbol(B3PW91Sym.ITERATION1, new Integer(yytext())); + } + case 28: break; + case 8: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: MP2 Found the maximum force"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(MPOPT); + return new Symbol(B3PW91Sym.MPMGRAD, new Float(yytext())); + } + case 29: break; + case 19: + { yybegin(IGNOREALL); + return new Symbol(B3PW91Sym.MPDONE); + } + case 30: break; + case 9: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: MP2 Found the RMS force"); +if (Settings.DEBUG) System.out.println(yytext()); + yybegin(MPOPT); + return new Symbol(B3PW91Sym.MPRGRAD, new Float(yytext())); + } + case 31: break; + case 13: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found RMS Force"); + yybegin(FLOAT2); + return new Symbol(B3PW91Sym.RmsGrad1); + } + case 32: break; + case 5: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the maximum force"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER); + return new Symbol(B3PW91Sym.MGRAD1, new Float(yytext())); + } + case 33: break; + case 14: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found Maximum Force"); + yybegin(FLOAT1); + return new Symbol(B3PW91Sym.MaxGrad1); + } + case 34: break; + case 10: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found MP2 energy"); + yybegin(FLOATMP1); + return new Symbol(B3PW91Sym.MPEnerg); + } + case 35: break; + case 21: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found Number of steps"); + yybegin(ITER); + return new Symbol(B3PW91Sym.FOUNDITER1); + } + case 36: break; + case 12: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the Step number for MP"); + yybegin(INTMP); + return new Symbol(B3PW91Sym.NMP); + } + case 37: break; + case 20: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found the energy in ITER"); + yybegin(FLOATVALUE); + return new Symbol(B3PW91Sym.Energ1); + } + case 38: break; + case 18: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found MP2(Full)"); + yybegin(MPOPT); + return new Symbol(B3PW91Sym.MPStart); + } + case 39: break; + case 15: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: Found RMS Force"); + yybegin(FLOATMP3); + return new Symbol(B3PW91Sym.MPRms); + } + case 40: break; + case 3: + { if (Settings.DEBUG) System.out.println("B3PW91Flex: MP2 Found iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin (MPOPT); + return new Symbol(B3PW91Sym.MPITER, new Integer(yytext())); + } + case 41: break; + case 1: + { + } + case 42: break; + default: + if (zzInput == YYEOF && zzStartRead == zzCurrentPos) { + zzAtEOF = true; + zzDoEOF(); + { return new Symbol(B3PW91Sym.EOF); } + } + else { + zzScanError(ZZ_NO_MATCH); + } + } + } + } + + /** + * Converts an int token code into the name of the + * token by reflection on the cup symbol class/interface sym + * + * This code was contributed by Karl Meissner <[email protected]> + */ + private String getTokenName(int token) { + try { + java.lang.reflect.Field [] classFields = sym.class.getFields(); + for (int i = 0; i < classFields.length; i++) { + if (classFields[i].getInt(null) == token) { + return classFields[i].getName(); + } + } + } catch (Exception e) { + e.printStackTrace(System.err); + } + + return "UNKNOWN TOKEN"; + } + + /** + * Same as next_token but also prints the token to standard out + * for debugging. + * + * This code was contributed by Karl Meissner <[email protected]> + */ + public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException { + java_cup.runtime.Symbol s = next_token(); + System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--"); + return s; + } + + /** + * Runs the scanner on input files. + * + * This is a standalone scanner, it will print any unmatched + * text to System.out unchanged. + * + * @param argv the command line, contains the filenames to run + * the scanner on. + */ + public static void main(String argv[]) { + if (argv.length == 0) { + System.out.println("Usage : java B3PW91Lexer <inputfile>"); + } + else { + for (int i = 0; i < argv.length; i++) { + B3PW91Lexer scanner = null; + try { + scanner = new B3PW91Lexer( new java.io.FileReader(argv[i]) ); + while ( !scanner.zzAtEOF ) scanner.next_token(); + } + catch (java.io.FileNotFoundException e) { + System.out.println("File not found : \""+argv[i]+"\""); + } + catch (java.io.IOException e) { + System.out.println("IO error scanning file \""+argv[i]+"\""); + System.out.println(e); + } + catch (Exception e) { + System.out.println("Unexpected exception:"); + e.printStackTrace(); + } + } + } + } + + +}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Parser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Parser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Parser.java new file mode 100644 index 0000000..cf3f2a1 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Parser.java @@ -0,0 +1,544 @@ +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.B3PW91; + +import java_cup.runtime.lr_parser; +import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser; + +import javax.swing.*; +import java.io.FileReader; +import java.util.ArrayList; +import java.util.HashMap; + +public class B3PW91Parser extends java_cup.runtime.lr_parser implements GridChemQueueParser { + + /** Default constructor. */ + public B3PW91Parser() {super();} + + /** Constructor which sets the default scanner. */ + public B3PW91Parser(java_cup.runtime.Scanner s) {super(s);} + + /** + * Constructor which uses a file reader. + */ + public B3PW91Parser(final FileReader fileReader) { + super(new B3PW91Lexer(fileReader)); + } + + /** Production table. */ + protected static final short _production_table[][] = + lr_parser.unpackFromStrings(new String[]{ + "\000\025\000\002\003\007\000\002\002\004\000\002\004" + + "\003\000\002\005\004\000\002\005\003\000\002\021\002" + + "\000\002\006\006\000\002\022\002\000\002\007\007\000" + + "\002\010\004\000\002\011\004\000\002\012\004\000\002" + + "\013\003\000\002\014\004\000\002\014\003\000\002\023" + + "\002\000\002\016\006\000\002\024\002\000\002\015\007" + + "\000\002\017\004\000\002\020\004"}); + + /** Access to production table. */ + public short[][] production_table() {return _production_table;} + + /** Parse-action table. */ + protected static final short[][] _action_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\052\000\004\004\005\001\002\000\004\007\012\001" + + "\002\000\004\007\uffff\001\002\000\004\002\007\001\002" + + "\000\004\002\000\001\002\000\006\005\027\007\012\001" + + "\002\000\006\005\ufffd\007\ufffd\001\002\000\004\022\013" + + "\001\002\000\004\006\ufffc\001\002\000\004\006\016\001" + + "\002\000\006\005\ufffb\007\ufffb\001\002\000\004\020\017" + + "\001\002\000\004\010\ufffa\001\002\000\004\010\022\001" + + "\002\000\004\011\024\001\002\000\004\023\023\001\002" + + "\000\004\011\ufff8\001\002\000\004\024\026\001\002\000" + + "\006\005\ufff9\007\ufff9\001\002\000\006\005\ufff7\007\ufff7" + + "\001\002\000\004\012\031\001\002\000\006\005\ufffe\007" + + "\ufffe\001\002\000\004\014\ufff5\001\002\000\004\017\054" + + "\001\002\000\004\014\035\001\002\000\006\014\035\017" + + "\ufff6\001\002\000\004\025\037\001\002\000\006\014\ufff3" + + "\017\ufff3\001\002\000\004\013\ufff2\001\002\000\004\013" + + "\041\001\002\000\004\021\043\001\002\000\006\014\ufff1" + + "\017\ufff1\001\002\000\004\015\ufff0\001\002\000\004\015" + + "\046\001\002\000\004\016\051\001\002\000\004\026\047" + + "\001\002\000\004\016\uffee\001\002\000\006\014\uffef\017" + + "\uffef\001\002\000\004\027\052\001\002\000\006\014\uffed" + + "\017\uffed\001\002\000\006\014\ufff4\017\ufff4\001\002\000" + + "\004\002\001\001\002"}); + + /** Access to parse-action table. */ + public short[][] action_table() {return _action_table;} + + /** <code>reduce_goto</code> table. */ + protected static final short[][] _reduce_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\052\000\006\003\005\004\003\001\001\000\006\005" + + "\007\006\010\001\001\000\002\001\001\000\002\001\001" + + "\000\002\001\001\000\004\006\027\001\001\000\002\001" + + "\001\000\002\001\001\000\004\021\013\001\001\000\004" + + "\007\014\001\001\000\002\001\001\000\002\001\001\000" + + "\004\022\017\001\001\000\004\010\020\001\001\000\004" + + "\011\024\001\001\000\002\001\001\000\002\001\001\000" + + "\002\001\001\000\002\001\001\000\002\001\001\000\006" + + "\012\031\013\032\001\001\000\002\001\001\000\002\001" + + "\001\000\002\001\001\000\006\014\033\016\035\001\001" + + "\000\004\016\052\001\001\000\002\001\001\000\002\001" + + "\001\000\004\023\037\001\001\000\004\015\041\001\001" + + "\000\002\001\001\000\002\001\001\000\004\024\043\001" + + "\001\000\004\017\044\001\001\000\004\020\047\001\001" + + "\000\002\001\001\000\002\001\001\000\002\001\001\000" + + "\002\001\001\000\002\001\001\000\002\001\001\000\002" + + "\001\001"}); + + /** Access to <code>reduce_goto</code> table. */ + public short[][] reduce_table() {return _reduce_table;} + + /** Instance of action encapsulation class. */ + protected CUP$parser$actions action_obj; + + //Each string is of the format + //rmsForce, maximum force, iteration and energy + private ArrayList<String> result = new ArrayList<String>(); + private String tempStr = ""; + + + public ArrayList<String> getResult() { + return result; + } + + public void addToResult(String value) { + result.add(value); + } + + public String getTempStr() { + return tempStr; + } + + public void setTempStr(String s) { + this.tempStr = s; + } + + /*Adding the parsed data to the hash map */ + @Override + public HashMap<String, String> getParsedData() throws Exception { + HashMap<String,String> resultsMap= new HashMap<String,String>(); + parse(); + int mpRMSForceCount=0; + int mpMaximumForce=0; + int mpIteration=0; + int energyCount=0; + int rmsForceCount=0; + int maximumForceCount=0; + int iterationCount=0; + for (int i=0; i<resultsMap.size();i++){ + String singleString= resultsMap.get(i); + String[] temp= singleString.split(" "); + if(temp.length>1){ + String keyString= temp[0]; + String dataString= temp[1]; + if(keyString.equalsIgnoreCase("MPRMSForce")){ + resultsMap.put("B3PW91Parser_MP_RMS_Force_"+mpRMSForceCount,dataString); + mpRMSForceCount++; + }else if(keyString.equalsIgnoreCase("MPMaximumForce")){ + resultsMap.put("B3PW91Parser_MP_Maximum_Force_"+mpMaximumForce,dataString); + mpMaximumForce++; + }else if(keyString.equalsIgnoreCase("MPITERATION")){ + resultsMap.put("B3PW91Parser_MP_ITERATION_"+mpIteration,dataString); + mpIteration++; + }else if(keyString.equalsIgnoreCase("ENERGY")){ + resultsMap.put("B3PW91Parser_ENERGY_"+energyCount,dataString); + energyCount++; + }else if (keyString.equalsIgnoreCase("RMSForce")){ + resultsMap.put("B3PW91Parser_RMS_Force_"+rmsForceCount,dataString); + rmsForceCount++; + }else if (keyString.equalsIgnoreCase("MaximumForce")){ + resultsMap.put("B3PW91Parser_Maximum_Force_"+maximumForceCount,dataString); + maximumForceCount++; + }else if (keyString.equalsIgnoreCase("ITERATION")){ + resultsMap.put("B3PW91Parser_ITERATION_"+iterationCount,dataString); + iterationCount++; + } + } + } + return null; + } + + + /** Action encapsulation object initializer. */ + protected void init_actions() + { + action_obj = new CUP$parser$actions(this); + } + + /** Invoke a user supplied parse action. */ + public java_cup.runtime.Symbol do_action( + int act_num, + java_cup.runtime.lr_parser parser, + java.util.Stack stack, + int top) + throws java.lang.Exception + { + /* call code in generated class */ + return action_obj.CUP$parser$do_action(act_num, parser, stack, top); + } + + /** Indicates start state. */ + public int start_state() {return 0;} + /** Indicates start production. */ + public int start_production() {return 1;} + + /** <code>EOF</code> Symbol index. */ + public int EOF_sym() {return 0;} + + /** <code>error</code> Symbol index. */ + public int error_sym() {return 1;} + + +} + +/** Cup generated class to encapsulate user supplied action code.*/ +class CUP$parser$actions { + + + //__________________________________ + public static boolean DEBUG = true; + private static JTable table; + private static final String tableLabel = "SCF Intermediate Results:"; +// private static String cycle = "0"; + + + public static JTable getTable() { + return table; + } + + public static String getTableLabel() { + return tableLabel; + } + +// } + + private final B3PW91Parser parser; + + /** Constructor */ + CUP$parser$actions(B3PW91Parser parser) { + this.parser = parser; + } + + /** Method with the actual generated action code. */ + public final java_cup.runtime.Symbol CUP$parser$do_action( + int CUP$parser$act_num, + java_cup.runtime.lr_parser CUP$parser$parser, + java.util.Stack CUP$parser$stack, + int CUP$parser$top) + throws java.lang.Exception + { + /* Symbol object for return from actions */ + java_cup.runtime.Symbol CUP$parser$result; + + /* select the action based on the action number */ + switch (CUP$parser$act_num) + { + /*. . . . . . . . . . . . . . . . . . . .*/ + case 20: // force2 ::= MPRms MPRGRAD + { + Object RESULT = null; + int mprgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int mprgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float mprg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:g1: MP RMS Force "+mprg); + parser.addToResult("MPRMSForce "+mprg); + + + + + CUP$parser$result = new java_cup.runtime.Symbol(14/*force2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 19: // force1 ::= MPMax MPMGRAD + { + Object RESULT = null; + int mpmgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int mpmgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float mpmg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:g1: MP Maximum Force "+mpmg); + parser.addToResult("MPMaximumForce "+mpmg); + + CUP$parser$result = new java_cup.runtime.Symbol(13/*force1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 18: // mpcycle ::= NMP MPITER NT$3 force1 force2 + { + Object RESULT = null; + // propagate RESULT from NT$3 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value; + int itleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left; + int itright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).right; + Integer it = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(11/*mpcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 17: // NT$3 ::= + { + Object RESULT = null; + int itleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int itright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Integer it = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:g1: MP ITERATION "+it); + parser.addToResult("MPITERATION "+it); + + + + CUP$parser$result = new java_cup.runtime.Symbol(18/*NT$3*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 16: // mpcycle1 ::= MPEnerg MPENERGY NT$2 mpcycle + { + Object RESULT = null; + // propagate RESULT from NT$2 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + int mpenleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left; + int mpenright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).right; + Float mpen = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(12/*mpcycle1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 15: // NT$2 ::= + { + Object RESULT = null; + int mpenleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int mpenright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float mpen = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:g1: ENERGY "+mpen); + parser.addToResult("ENERGY "+mpen); + + CUP$parser$result = new java_cup.runtime.Symbol(17/*NT$2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 14: // mppat ::= mpcycle1 + { + Object RESULT = null; + + CUP$parser$result = new java_cup.runtime.Symbol(10/*mppat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 13: // mppat ::= mppat mpcycle1 + { + Object RESULT = null; + + if (DEBUG) System.out.println("CUP:g1: in mppat"); + + CUP$parser$result = new java_cup.runtime.Symbol(10/*mppat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 12: // mpintro ::= MPStart + { + Object RESULT = null; + + if (DEBUG) System.out.println("CUP:g1: MPSTart "); + + CUP$parser$result = new java_cup.runtime.Symbol(9/*mpintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 11: // mp2 ::= mpintro mppat + { + Object RESULT = null; + + if (DEBUG) System.out.println("CUP:g1: in mp2 mpintro mppat"); + + CUP$parser$result = new java_cup.runtime.Symbol(8/*mp2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 10: // grad2 ::= RmsGrad1 RGRAD1 + { + Object RESULT = null; + int rgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int rgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float rg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gopt: RMS Force "+rg); + parser.addToResult("RMSForce "+rg); + + CUP$parser$result = new java_cup.runtime.Symbol(7/*grad2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 9: // grad1 ::= MaxGrad1 MGRAD1 + { + Object RESULT = null; + int mgleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int mgright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float mg = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gopt: Maximum Force "+mg); + parser.addToResult("MaximumForce "+mg); + + CUP$parser$result = new java_cup.runtime.Symbol(6/*grad1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 8: // cycle ::= NSearch1 ITERATION1 NT$1 grad1 grad2 + { + Object RESULT = null; + // propagate RESULT from NT$1 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(5/*cycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 7: // NT$1 ::= + { + Object RESULT = null; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gopt: ITERATION "+c); + parser.addToResult("ITERATION "+c); + + CUP$parser$result = new java_cup.runtime.Symbol(16/*NT$1*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 6: // scfcycle ::= Energ1 ENERGY1 NT$0 cycle + { + Object RESULT = null; + // propagate RESULT from NT$0 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left; + int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).right; + Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-2)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 5: // NT$0 ::= + { + Object RESULT = null; + int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gopt: ENERGY "+e); + parser.addToResult("ENERGY "+e); + + CUP$parser$result = new java_cup.runtime.Symbol(15/*NT$0*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 4: // scfpat ::= scfcycle + { + Object RESULT = null; + + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 3: // scfpat ::= scfpat scfcycle + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gopt: in scfpat"); + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 2: // scfintro ::= FOUNDITER1 + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gopt: found the start of Iteration"); + CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 1: // $START ::= startpt EOF + { + Object RESULT = null; + int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left; + int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right; + Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + RESULT = start_val; + CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + /* ACCEPT */ + CUP$parser$parser.done_parsing(); + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 0: // startpt ::= scfintro scfpat SCFDONE1 mp2 MPDONE + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gopt: end of parse tree "); + + CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /* . . . . . .*/ + default: + throw new Exception( + "Invalid action number found in internal parse table"); + + } + } +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Sym.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Sym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Sym.java new file mode 100644 index 0000000..b146ce2 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/B3PW91/B3PW91Sym.java @@ -0,0 +1,53 @@ +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.B3PW91; +//---------------------------------------------------- +// The following code was generated by CUP v0.10k +// Sun Sep 07 21:49:39 IST 2014 +//---------------------------------------------------- + +/** CUP generated class containing symbol constants. */ +public class B3PW91Sym { + /* terminals */ + public static final int ENERGY1 = 16; + public static final int MPMGRAD = 20; + public static final int MGRAD1 = 17; + public static final int MaxGrad1 = 6; + public static final int NSearch1 = 4; + public static final int MPRGRAD = 21; + public static final int MPRms = 12; + public static final int RmsGrad1 = 7; + public static final int MPMax = 11; + public static final int MPDONE = 13; + public static final int EOF = 0; + public static final int MPENERGY = 19; + public static final int ITERATION1 = 14; + public static final int NMP = 9; + public static final int MPEnerg = 10; + public static final int error = 1; + public static final int MPITER = 15; + public static final int MPStart = 8; + public static final int FOUNDITER1 = 2; + public static final int Energ1 = 5; + public static final int SCFDONE1 = 3; + public static final int RGRAD1 = 18; +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemDemoParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemDemoParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemDemoParser.java new file mode 100644 index 0000000..a92846d --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemDemoParser.java @@ -0,0 +1,81 @@ +/* + * + * 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. + * +*/ +package org.apache.airavata.datacat.parsers.gridchem; + +import org.apache.airavata.datacat.models.OutputMetadataDTO; +import org.apache.airavata.datacat.models.OutputMonitorMessage; +import org.apache.airavata.datacat.parsers.DefaultParser; +import org.apache.airavata.datacat.parsers.IParser; +import org.apache.airavata.datacat.parsers.gridchem.inchi.InChI; +import org.apache.airavata.datacat.parsers.gridchem.inchi.InChIGenerator; +import org.apache.airavata.datacat.parsers.gridchem.util.Constants; +import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties; +import org.apache.commons.io.FileUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.File; +import java.io.FilenameFilter; +import java.io.IOException; +import java.util.HashMap; +import java.util.UUID; + +public class GridChemDemoParser extends DefaultParser implements IParser{ + private final static Logger logger = LoggerFactory.getLogger(GridChemDemoParser.class); + + @Override + public OutputMetadataDTO parse(OutputMonitorMessage outputMonitorMessage) { + OutputMetadataDTO outputMetadataDTO = super.parse(outputMonitorMessage); + HashMap<String, String> customMetadata = new HashMap<>(); + + String[] outPutFiles = (new File(outputMonitorMessage.getOutputPath())).list(new FilenameFilter() { + public boolean accept(File dir, String filename) { + return filename.endsWith(".out"); + } + }); + if (outPutFiles != null && outPutFiles.length > 0) { + String outFilePath = outputMonitorMessage.getOutputPath() + File.separator + outPutFiles[0]; + String uniqueID = UUID.randomUUID().toString(); + File source = new File(outFilePath); + File dest = new File(GridChemProperties.getInstance().getProperty( + Constants.TMP_DIR, "") + "/" + uniqueID + ".out"); + try { + FileUtils.copyFile(source, dest); + try { + InChIGenerator inChIGenerator = new InChIGenerator(uniqueID); + InChI inChI = inChIGenerator.getInChI(); + customMetadata.put("inChi", inChI.getInchi()); + customMetadata.put("inChiKey", inChI.getInchiKey()); + } catch (Exception ex) { + logger.error( + "Parser Failure in " + outputMetadataDTO.getOutputPath() + "/" + outputMetadataDTO.getExperimentName() + + " in InChi Generators" + ); + } + } catch (IOException ex) { + logger.error("Cannot copy temp file to the tmp directory"); + } + } + outputMetadataDTO.setCustomMetaData(customMetadata); + + return outputMetadataDTO; + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemParser.java new file mode 100644 index 0000000..8307407 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemParser.java @@ -0,0 +1,173 @@ + +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem; + +import org.apache.airavata.datacat.models.OutputMetadataDTO; +import org.apache.airavata.datacat.models.OutputMonitorMessage; +import org.apache.airavata.datacat.parsers.IParser; +import org.apache.airavata.datacat.parsers.gridchem.inchi.InChI; +import org.apache.airavata.datacat.parsers.gridchem.inchi.InChIGenerator; +import org.apache.airavata.datacat.parsers.gridchem.util.Constants; +import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties; +import org.apache.commons.io.FileUtils; +import org.apache.log4j.LogManager; +import org.apache.log4j.Logger; + +import java.io.File; +import java.io.FileReader; +import java.io.FilenameFilter; +import java.io.IOException; +import java.lang.reflect.Constructor; +import java.lang.reflect.InvocationTargetException; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Date; +import java.util.HashMap; +import java.util.Map; +import java.util.UUID; + +public class GridChemParser implements IParser { + + private final Logger logger = LogManager.getLogger(GridChemParser.class); + private String[] gridChemQueueParserses; + + public GridChemParser() { + } + + public OutputMetadataDTO parse(OutputMonitorMessage outputMonitorMessage) { + gridChemQueueParserses = GridChemProperties.getInstance().getParserSequence(); + logger.info("Loaded the GridChem Parser Sequence ..."); + + logger.info("Started passing new file monitor message..."); + + OutputMetadataDTO outputMetadataDTO = new OutputMetadataDTO(); + + //For Solr requirement date is in the format of yyyy-MM-ddTHH:mm:ssZ + DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); + Date now = new Date(); + String date = dateFormat.format(now).split(" ")[0] + "T" + dateFormat.format(now).split(" ")[1] + "Z"; + + //setting the basic file meta-data + outputMetadataDTO.setCreatedDate(date); + outputMetadataDTO.setHost(computingResourceName()); + outputMetadataDTO.setExperimentName(outputMonitorMessage.getExperimentName()); + outputMetadataDTO.setExperimentId(outputMonitorMessage.getExperimentID()); + outputMetadataDTO.setOutputPath(outputMonitorMessage.getOutputPath()); + outputMetadataDTO.setApplicationName(applicationName()); + outputMetadataDTO.setOwnerId(getOwnerId()); + + String[] outPutFiles = (new File(outputMonitorMessage.getOutputPath())).list(new FilenameFilter() { + public boolean accept(File dir, String filename) { + return filename.endsWith(".out"); + } + }); + + Map<String, String> results = new HashMap<String, String>(); + + if (outPutFiles != null && outPutFiles.length > 0) { + + // have a copy of the file in a temp location + //FIXME: is this really necessary? + String outFilePath = outputMonitorMessage.getOutputPath() + File.separator + outPutFiles[0]; + String uniqueID = UUID.randomUUID().toString(); + File source = new File(outFilePath); + File dest = new File(GridChemProperties.getInstance().getProperty( + Constants.TMP_DIR, "") + "/" + uniqueID + ".out"); + try{ + FileUtils.copyFile(source, dest); + try { + + InChIGenerator inChIGenerator = new InChIGenerator(uniqueID); + InChI inChI = inChIGenerator.getInChI(); + results.put("InChi", inChI.getInchi()); + results.put("InChiKey", inChI.getInchiKey()); + + //running the parser queue serially + Map<String, String> parserResult; + for (int j = 0; j < gridChemQueueParserses.length; j++) { + try { + long time = System.currentTimeMillis(); + //copying the file to the memory + //FIXME make this file shared rather than re-reading it. + FileReader fileReader = new FileReader(dest); + parserResult = loadAndParse(gridChemQueueParserses[j], fileReader); + results.putAll(parserResult); + } catch (Exception ex) { + logger.error( + "Parser Failure in " + outputMetadataDTO.getOutputPath() + "/" + outputMetadataDTO.getOutputPath() + + " in " + gridChemQueueParserses[j] + ); + } + } + } catch (Exception ex) { + logger.error( + "Parser Failure in " + outputMetadataDTO.getOutputPath() + "/" + outputMetadataDTO.getExperimentName() + + " in InChi Generators" + ); + } + }catch (IOException ex){ + logger.error("Cannot copy temp file to the tmp directory"); + } + //adding the custom parsed data to the fileMetaDataObject + outputMetadataDTO.setCustomMetaData(results); + return outputMetadataDTO; + } + logger.info("No output file corresponding to the file monitor message location"); + return null; + } + + private HashMap<String, String> loadAndParse(String classname, final FileReader reader) throws Exception { + ClassLoader classLoader = ClassLoader.getSystemClassLoader(); + Class parser = null; + try { + //todo: handle unparsed documents and log and ignore + parser = classLoader.loadClass(classname); + Constructor parserConstructor = parser.getConstructor(FileReader.class); + GridChemQueueParser queueParser = (GridChemQueueParser) parserConstructor.newInstance(reader); + HashMap<String, String> parsedData = queueParser.getParsedData(); + return parsedData; + } catch (ClassNotFoundException e) { + logger.error("Could not load the class ..." + e.getMessage()); + } catch (NoSuchMethodException e) { + logger.error("Could not load the constructor ... " + e.getMessage()); + } catch (InvocationTargetException e) { + logger.error("Could not load the Class ... " + e.getMessage()); + } catch (InstantiationException e) { + logger.error("Could not load the Class ... " + e.getMessage()); + } catch (IllegalAccessException e) { + logger.error("Could not load the Class ... " + e.getMessage()); + } + return null; + } + + public String computingResourceName() { + return GridChemProperties.getInstance().getProperty(Constants.ARCHIVING_NODE, ""); + } + + public String applicationName() { + return GridChemProperties.getInstance().getProperty(Constants.APPLICATION_NAME, ""); + } + + public String getOwnerId() { + return GridChemProperties.getInstance().getProperty(Constants.USERNAME, ""); + } +} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemQueueParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemQueueParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemQueueParser.java new file mode 100644 index 0000000..75974c7 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/GridChemQueueParser.java @@ -0,0 +1,30 @@ +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem; + +import java.util.HashMap; + +// Interface for individual parsers of the cup flex files +public interface GridChemQueueParser { + //parses the data using a file reader and returns a hash map of outputs + public HashMap<String, String> getParsedData() throws Exception; + +} http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/Settings.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/Settings.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/Settings.java new file mode 100644 index 0000000..00b357f --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/Settings.java @@ -0,0 +1,26 @@ +/* +* +* 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. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem; + + +public class Settings { + public static final boolean DEBUG = true; +}
