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Posted to commits@airavata.apache.org by sc...@apache.org on 2015/08/24 21:29:03 UTC
[25/32] airavata-sandbox git commit: adding datacat system
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
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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 <me...@yahoo.com>
+ */
+ 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 <me...@yahoo.com>
+ */
+ 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
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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;
+}