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Posted to commits@airavata.apache.org by sc...@apache.org on 2015/08/24 21:28:51 UTC
[13/32] 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/scfb/SCFbParser.java
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diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbParser.java
new file mode 100644
index 0000000..ec055f9
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbParser.java
@@ -0,0 +1,580 @@
+/*
+*
+* 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.scfb;
+
+
+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 SCFbParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{
+
+ /** Default constructor. */
+ public SCFbParser() {super();}
+
+ /** Constructor which sets the default scanner. */
+ public SCFbParser(java_cup.runtime.Scanner s) {super(s);}
+
+ /**
+ * Constructor which uses a file reader.
+ */
+ public SCFbParser(final FileReader fileReader) {
+ super(new SCFbLexer(fileReader));
+ }
+
+
+ /** Production table. */
+ protected static final short _production_table[][] =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\016\000\002\015\002\000\002\003\006\000\002\002" +
+ "\004\000\002\016\002\000\002\004\006\000\002\017\002" +
+ "\000\002\020\002\000\002\021\002\000\002\022\002\000" +
+ "\002\023\002\000\002\024\002\000\002\025\002\000\002" +
+ "\026\002\000\002\014\043"});
+
+ /** 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\054\000\004\004\006\001\002\000\004\033\014\001" +
+ "\002\000\004\002\012\001\002\000\004\005\ufffe\001\002" +
+ "\000\004\005\010\001\002\000\004\050\011\001\002\000" +
+ "\004\033\ufffd\001\002\000\004\002\uffff\001\002\000\004" +
+ "\046\001\001\002\000\004\034\ufffc\001\002\000\004\034" +
+ "\016\001\002\000\004\044\017\001\002\000\004\051\020" +
+ "\001\002\000\004\040\ufffb\001\002\000\004\040\022\001" +
+ "\002\000\004\047\023\001\002\000\004\045\024\001\002" +
+ "\000\004\035\ufffa\001\002\000\004\035\026\001\002\000" +
+ "\004\044\027\001\002\000\004\051\030\001\002\000\004" +
+ "\037\ufff9\001\002\000\004\037\032\001\002\000\004\044" +
+ "\033\001\002\000\004\051\034\001\002\000\004\036\ufff8" +
+ "\001\002\000\004\036\036\001\002\000\004\044\037\001" +
+ "\002\000\004\051\040\001\002\000\004\041\ufff7\001\002" +
+ "\000\004\041\042\001\002\000\004\044\043\001\002\000" +
+ "\004\051\044\001\002\000\004\042\ufff6\001\002\000\004" +
+ "\042\046\001\002\000\004\044\047\001\002\000\004\051" +
+ "\050\001\002\000\004\043\ufff5\001\002\000\004\043\052" +
+ "\001\002\000\004\044\053\001\002\000\004\051\054\001" +
+ "\002\000\004\046\ufff4\001\002\000\004\046\056\001\002" +
+ "\000\004\002\000\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\054\000\006\003\004\004\003\001\001\000\004\014" +
+ "\012\001\001\000\002\001\001\000\004\016\006\001\001" +
+ "\000\002\001\001\000\002\001\001\000\002\001\001\000" +
+ "\002\001\001\000\004\015\054\001\001\000\004\017\014" +
+ "\001\001\000\002\001\001\000\002\001\001\000\002\001" +
+ "\001\000\004\020\020\001\001\000\002\001\001\000\002" +
+ "\001\001\000\002\001\001\000\004\021\024\001\001\000" +
+ "\002\001\001\000\002\001\001\000\002\001\001\000\004" +
+ "\022\030\001\001\000\002\001\001\000\002\001\001\000" +
+ "\002\001\001\000\004\023\034\001\001\000\002\001\001" +
+ "\000\002\001\001\000\002\001\001\000\004\024\040\001" +
+ "\001\000\002\001\001\000\002\001\001\000\002\001\001" +
+ "\000\004\025\044\001\001\000\002\001\001\000\002\001" +
+ "\001\000\002\001\001\000\004\026\050\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;
+
+ 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 {
+ parse();
+ HashMap<String,String> results= new HashMap<String,String>();
+ int eeCount=0;
+ int peCount=0;
+ int keCount=0;
+ int s2Count=0;
+ int minUSVTCount=0;
+ int convgCount=0;
+ int auCount=0;
+ int erhfCount=0;
+ int lenxCount=0;
+ for(int i=0;i<result.size();i++){
+ String singleString = result.get(i);
+ String[] temp= singleString.split(" ");
+ if(temp.length>1){
+ String keyString= temp[0];
+ String dataString=temp[1];
+ if(keyString.equalsIgnoreCase("EE")){
+ results.put("SCFbParser_EE_"+eeCount,dataString);
+ eeCount++;
+ }else if(keyString.equalsIgnoreCase("PE")){
+ results.put("SCFbParser_PE_"+peCount,dataString);
+ peCount++;
+ }else if(keyString.equalsIgnoreCase("KE")){
+ results.put("SCFbParser_KE_"+keCount,dataString);
+ keCount++;
+ }else if(keyString.equalsIgnoreCase("S2")) {
+ results.put("SCFbParser_S2_" + s2Count, dataString);
+ s2Count++;
+ }else if(keyString.equalsIgnoreCase("MINUSVT")) {
+ results.put("SCFbParser_MINUSVT_" + minUSVTCount, dataString);
+ minUSVTCount++;
+ }else if(keyString.equalsIgnoreCase("CONVG")) {
+ results.put("SCFbParser_CONVG_" + convgCount, dataString);
+ convgCount++;
+ }else if(keyString.equalsIgnoreCase("AU")) {
+ results.put("SCFbParser_AU_" + auCount, dataString);
+ auCount++;
+ }else if(keyString.equalsIgnoreCase("ERHF")) {
+ results.put("SCFbParser_ERHF_" + erhfCount, dataString);
+ erhfCount++;
+ }else if(keyString.equalsIgnoreCase("LENX")) {
+ results.put("SCFbParser_LENX_" + lenxCount, dataString);
+ lenxCount++;
+ }
+
+
+ }
+
+ }
+ return results;
+ }
+
+ /** 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 2;}
+
+ /** <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 Final Results:";
+
+ public static JTable getTable() {
+ return table;
+ }
+
+ public static String getTableLabel() {
+ return tableLabel;
+ }
+
+ private final SCFbParser SCFbParser;
+
+ /** Constructor */
+ CUP$parser$actions(SCFbParser SCFbParser) {
+ this.SCFbParser = SCFbParser;
+ }
+
+ /** 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 13: // scffinal ::= SCFDONE NT$2 ERHF EQUALS FLOAT NT$3 AU INT DUMMY NT$4 CONVG EQUALS FLOAT NT$5 MINUSVT EQUALS FLOAT NT$6 S2 EQUALS FLOAT NT$7 KE EQUALS FLOAT NT$8 PE EQUALS FLOAT NT$9 EE EQUALS FLOAT
+ {
+ Object RESULT = null;
+ // propagate RESULT from NT$2
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-31)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-31)).value;
+ // propagate RESULT from NT$3
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-27)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-27)).value;
+ // propagate RESULT from NT$4
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-23)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-23)).value;
+ // propagate RESULT from NT$5
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-19)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-19)).value;
+ // propagate RESULT from NT$6
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-15)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-15)).value;
+ // propagate RESULT from NT$7
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-11)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-11)).value;
+ // propagate RESULT from NT$8
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-7)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-7)).value;
+ // propagate RESULT from NT$9
+ if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value != null )
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-3)).value;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-28)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-28)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-28)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-25)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-25)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-25)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-20)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-20)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-20)).value;
+ int mleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).left;
+ int mright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).right;
+ String m = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-16)).value;
+ int s2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).left;
+ int s2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).right;
+ String s2 = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-12)).value;
+ int keleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).left;
+ int keright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).right;
+ String ke = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-8)).value;
+ int peleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int peright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String pe = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int eeleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int eeright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String ee = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //____________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: EE "+ee);
+SCFbParser.addToResult("EE "+ee);
+//parseSCF.putField("EE", ee);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(10/*scffinal*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-32)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 12: // NT$9 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-24)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-24)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-24)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-21)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-21)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-21)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-16)).value;
+ int mleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).left;
+ int mright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).right;
+ String m = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-12)).value;
+ int s2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).left;
+ int s2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).right;
+ String s2 = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-8)).value;
+ int keleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int keright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String ke = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int peleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int peright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String pe = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //____________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: PE "+pe);
+SCFbParser.addToResult("PE "+pe);
+//parseSCF.putField("PE", pe);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(20/*NT$9*/, ((java_cup.runtime.Symbol)CUP$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 11: // NT$8 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-20)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-20)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-20)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-17)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-17)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-17)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-12)).value;
+ int mleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).left;
+ int mright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).right;
+ String m = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-8)).value;
+ int s2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int s2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String s2 = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int keleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int keright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String ke = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //____________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: KE "+ke);
+SCFbParser.addToResult("KE "+ke);
+//parseSCF.putField("KE", ke);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(19/*NT$8*/, ((java_cup.runtime.Symbol)CUP$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 10: // NT$7 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-16)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-16)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-13)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-13)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-13)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-8)).value;
+ int mleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int mright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String m = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int s2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int s2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String s2 = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //____________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: S2 "+s2);
+SCFbParser.addToResult("S2 "+s2);
+//parseSCF.putField("S2", s2);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(18/*NT$7*/, ((java_cup.runtime.Symbol)CUP$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 9: // NT$6 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-12)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-12)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-9)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-9)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-9)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int mleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int mright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String m = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //________________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: MINUSVT "+m);
+SCFbParser.addToResult("MINUSVT "+m);
+//parseSCF.putField("-V/T", m);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(17/*NT$6*/, ((java_cup.runtime.Symbol)CUP$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 8: // NT$5 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-8)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-8)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-5)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-5)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-5)).value;
+ int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String c = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //______________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: CONVG "+c);
+SCFbParser.addToResult("CONVG "+c);
+//parseSCF.putField("CONVG", c);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(16/*NT$5*/, ((java_cup.runtime.Symbol)CUP$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 7: // NT$4 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-4)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value;
+ //___________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: AU "+i);
+ SCFbParser.addToResult("AU "+i);
+//parseSCF.putField("AU", i);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(15/*NT$4*/, ((java_cup.runtime.Symbol)CUP$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: // NT$3 ::=
+ {
+ Object RESULT = null;
+ int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String e = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ //_____________________________________________________
+if (DEBUG) System.out.println("CUP:scfb: ERHF "+e);
+ SCFbParser.addToResult("ERHF "+e);
+//parseSCF.putField("E(RHF)", e);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(14/*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 5: // NT$2 ::=
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:scfb: scfdone ");
+ CUP$parser$result = new java_cup.runtime.Symbol(13/*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 4: // scfintro ::= FOUNDSCF NT$1 FOUNDLENX LENXINT
+ {
+ 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$top-2)).value;
+ int ileft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int iright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String i = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ if (DEBUG) System.out.println("CUP:scfb: LENX --> "+i);
+ SCFbParser.addToResult("LENX "+i);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$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 3: // NT$1 ::=
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:scfb: found SCF");
+ CUP$parser$result = new java_cup.runtime.Symbol(12/*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 2: // $START ::= startpt EOF
+ {
+ Object RESULT = null;
+ int start_valleft = ((java_cup.runtime.Symbol)CUP$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 1: // startpt ::= scfintro scffinal NT$0 LEAVE
+ {
+ 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$top-1)).value;
+ if (DEBUG) System.out.println("CUP:scfb: found LEAVE");
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$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 0: // NT$0 ::=
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:scfa: found scfintro scffinal");
+ table = new JTable();
+ // table = parseSCF.getTable();
+
+ CUP$parser$result = new java_cup.runtime.Symbol(11/*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;
+
+ /* . . . . . .*/
+ 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/scfb/SCFbSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbSym.java
new file mode 100644
index 0000000..ba1693f
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/scfb/SCFbSym.java
@@ -0,0 +1,71 @@
+/*
+*
+* 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.scfb;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Mon Sep 15 16:04:59 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class SCFbSym {
+ /* terminals */
+ public static final int TEE = 12;
+ public static final int EQUALS = 34;
+ public static final int PE = 32;
+ public static final int GTEF = 20;
+ public static final int INT = 37;
+ public static final int LEAVE = 36;
+ public static final int LTEF = 19;
+ public static final int SCFDONE = 25;
+ public static final int CONVG = 27;
+ public static final int DUMMY = 35;
+ public static final int IS = 15;
+ public static final int PASS = 5;
+ public static final int ERR = 21;
+ public static final int MAXDP = 23;
+ public static final int S2 = 28;
+ public static final int ATCYCLE = 10;
+ public static final int IE = 16;
+ public static final int EOF = 0;
+ public static final int COEFF = 11;
+ public static final int RMSDP = 22;
+ public static final int IDIAG = 6;
+ public static final int error = 1;
+ public static final int ERHF = 26;
+ public static final int NO09 = 17;
+ public static final int FOUNDLENX = 3;
+ public static final int COLON = 24;
+ public static final int GAP = 13;
+ public static final int DELTAE = 8;
+ public static final int NK = 14;
+ public static final int EE = 33;
+ public static final int DIIS = 9;
+ public static final int LENXINT = 38;
+ public static final int FLOAT = 39;
+ public static final int KE = 31;
+ public static final int MINUSVT = 29;
+ public static final int NV01 = 18;
+ public static final int AU = 30;
+ public static final int FOUNDSCF = 2;
+ public static final int CYCLE = 4;
+ public static final int ENERGY = 7;
+}
+
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/AccessLevels.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/AccessLevels.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/AccessLevels.java
new file mode 100644
index 0000000..f08cb5d
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/AccessLevels.java
@@ -0,0 +1,28 @@
+/*
+*
+* 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.util;
+
+public class AccessLevels {
+ public static final String PRIVATE = "private";
+ public static final String GROUP = "group";
+ public static final String COMMUNITY = "community";
+ public static final String GLOBAL = "global";
+}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Constants.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Constants.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Constants.java
new file mode 100644
index 0000000..2f0fc0a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Constants.java
@@ -0,0 +1,39 @@
+/*
+*
+* 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.util;
+
+public class Constants {
+ public static final String PARSER_SEQUENCE = "PARSER_SEQUENCE";
+
+ public static final String ARCHIVING_NODE = "ARCHIVING_NODE";
+
+ public static final String APPLICATION_NAME = "APPLICATION_NAME";
+
+ public static final String USERNAME = "USERNAME";
+
+ public static final String AGENT_USERNAME = "AGENT_USERNAME";
+
+ public static final String AGENT_PASSWORD = "AGENT_PASSWORD";
+
+ public static final String TMP_DIR = "TMP_DIR";
+
+ public static final String SAMPLE_OUTPUT = "SAMPLE_OUTPUT";
+}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Fields.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Fields.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Fields.java
new file mode 100644
index 0000000..01d93f7
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/Fields.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.util;
+
+public class Fields {
+ public static final String INCHI = "inchi";
+ public static final String INCHI_KEY = "inchi_key";
+}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/GridChemProperties.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/GridChemProperties.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/GridChemProperties.java
new file mode 100644
index 0000000..6d2b29f
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/util/GridChemProperties.java
@@ -0,0 +1,77 @@
+/*
+*
+* 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.util;
+
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
+
+import java.io.*;
+
+public class GridChemProperties {
+ public static final String GRIDCHEM_PARSERS_PROPERTIES = "../conf/gridchem.properties";
+ public static final String DEFAULT_GRIDCHEM_PARSERS_PROPERTIES = "gridchem.properties";
+
+ private static GridChemProperties instance;
+
+ private final Logger logger = LogManager.getLogger(GridChemProperties.class);
+ private java.util.Properties properties = null;
+
+ private GridChemProperties() {
+ try {
+ InputStream fileInput;
+ if (new File(GRIDCHEM_PARSERS_PROPERTIES).exists()) {
+ fileInput = new FileInputStream(GRIDCHEM_PARSERS_PROPERTIES);
+ } else {
+ fileInput = ClassLoader.getSystemResource(DEFAULT_GRIDCHEM_PARSERS_PROPERTIES).openStream();
+ }
+ java.util.Properties properties = new java.util.Properties();
+ properties.load(fileInput);
+ fileInput.close();
+ this.properties = properties;
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public static GridChemProperties getInstance() {
+ if (instance == null) {
+ instance = new GridChemProperties();
+ }
+ return instance;
+ }
+
+ public String[] getParserSequence() {
+ String parsers = getProperty(Constants.PARSER_SEQUENCE, "");
+ String[] parserArray = parsers.split(",");
+ return parserArray;
+ }
+ public String getProperty(String key, String defaultVal) {
+ String val = this.properties.getProperty(key);
+
+ if (val.isEmpty() || val == "") {
+ return defaultVal;
+ } else {
+ return val;
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramLexer.java
new file mode 100644
index 0000000..10d93b7
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramLexer.java
@@ -0,0 +1,642 @@
+package org.apache.airavata.datacat.parsers.gridchem.whichProgram;/* The following code was generated by JFlex 1.4.3 on 11/12/14 6:52 PM */
+
+
+/*
+*
+* 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.
+*
+*/
+import java_cup.runtime.Symbol;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+/**
+ * This class is a scanner generated by
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 11/12/14 6:52 PM from the specification file
+ * <tt>whichProgram.flex</tt>
+ */
+public class WhichProgramLexer 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 IGNOREALL = 6;
+ public static final int GETREVISION = 2;
+ public static final int YYINITIAL = 0;
+ public static final int GETVERSION = 4;
+
+ /**
+ * 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, 3, 3
+ };
+
+ /**
+ * 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,
+ 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12, 0, 1, 0,
+ 10, 2, 2, 11, 2, 2, 2, 2, 2, 2, 0, 0, 0, 22, 0, 0,
+ 0, 13, 1, 1, 1, 15, 1, 3, 1, 19, 1, 1, 26, 14, 21, 20,
+ 23, 1, 18, 16, 25, 1, 17, 1, 1, 24, 1, 0, 0, 0, 0, 0,
+ 0, 4, 1, 1, 1, 1, 1, 1, 1, 7, 1, 1, 1, 1, 8, 1,
+ 1, 1, 1, 6, 1, 5, 1, 1, 1, 1, 1, 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, 0, 0
+ };
+
+ /**
+ * Translates DFA states to action switch labels.
+ */
+ private static final int [] ZZ_ACTION = zzUnpackAction();
+
+ private static final String ZZ_ACTION_PACKED_0 =
+ "\4\0\3\1\1\2\1\1\13\0\1\3\25\0\1\4"+
+ "\10\0\1\5\5\0\1\6";
+
+ private static int [] zzUnpackAction() {
+ int [] result = new int[58];
+ 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\33\0\66\0\121\0\154\0\207\0\242\0\275"+
+ "\0\330\0\363\0\u010e\0\u0129\0\u0144\0\u015f\0\u017a\0\u0195"+
+ "\0\u01b0\0\u01cb\0\u01e6\0\u0201\0\154\0\u021c\0\u0237\0\u0252"+
+ "\0\u026d\0\u0288\0\u02a3\0\u02be\0\u02d9\0\u02f4\0\u030f\0\u032a"+
+ "\0\u0345\0\u0360\0\u037b\0\u0396\0\u03b1\0\u03cc\0\u03e7\0\u0402"+
+ "\0\u041d\0\u0438\0\154\0\u0453\0\u046e\0\u0489\0\u04a4\0\u04bf"+
+ "\0\u04da\0\u04f5\0\u0510\0\154\0\u052b\0\u0546\0\u0561\0\u057c"+
+ "\0\u0597\0\154";
+
+ private static int [] zzUnpackRowMap() {
+ int [] result = new int[58];
+ 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 =
+ "\3\5\1\6\23\5\1\7\4\5\10\10\1\5\2\10"+
+ "\1\5\11\10\1\5\4\10\2\5\1\11\7\5\2\11"+
+ "\52\5\37\0\1\12\10\0\1\13\37\0\1\14\11\0"+
+ "\10\10\1\0\2\10\1\0\11\10\1\0\4\10\2\0"+
+ "\1\15\7\0\2\15\24\0\1\16\43\0\1\17\40\0"+
+ "\1\20\10\0\1\21\7\0\2\21\25\0\1\22\43\0"+
+ "\1\23\16\0\1\24\31\0\1\25\7\0\2\25\25\0"+
+ "\1\26\44\0\1\27\34\0\1\30\17\0\1\31\43\0"+
+ "\1\32\27\0\1\33\21\0\1\34\37\0\1\35\37\0"+
+ "\1\36\24\0\1\37\43\0\1\40\22\0\1\41\32\0"+
+ "\1\42\40\0\1\43\33\0\1\44\24\0\1\45\42\0"+
+ "\1\46\40\0\1\47\15\0\1\50\37\0\1\51\32\0"+
+ "\1\52\26\0\1\53\41\0\1\54\40\0\1\55\25\0"+
+ "\1\56\25\0\1\57\40\0\1\60\23\0\1\61\25\0"+
+ "\1\62\32\0\1\63\47\0\1\64\22\0\1\65\40\0"+
+ "\1\66\40\0\1\67\27\0\1\70\25\0\1\71\34\0"+
+ "\1\72\6\0";
+
+ private static int [] zzUnpackTrans() {
+ int [] result = new int[1458];
+ 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 =
+ "\4\0\1\11\4\1\13\0\1\11\25\0\1\11\10\0"+
+ "\1\11\5\0\1\11";
+
+ private static int [] zzUnpackAttribute() {
+ int [] result = new int[58];
+ 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;
+ public static String format;
+
+
+ /**
+ * 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 WhichProgramLexer(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 WhichProgramLexer(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;
+ }
+
+
+ /**
+ * 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 int yylex() throws java.io.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 2:
+ { if (Settings.DEBUG) System.out.println(yytext());
+ yybegin(IGNOREALL);
+ }
+ case 7: break;
+ case 3:
+ { if (Settings.DEBUG) System.out.println(yytext());
+ yybegin(IGNOREALL);
+ }
+ case 8: break;
+ case 4:
+ { if (Settings.DEBUG) System.out.println(yytext());
+ WhichProgramLexer.format = "Gauss03";
+ }
+ case 9: break;
+ case 6:
+ { System.out.println(yytext());
+ WhichProgramLexer.format = "Molpro";
+ yybegin(IGNOREALL);
+ }
+ case 10: break;
+ case 5:
+ { if (Settings.DEBUG) System.out.println(yytext());
+ WhichProgramLexer.format = "GAMESS";
+ yybegin(GETVERSION);
+ }
+ case 11: break;
+ case 1:
+ {
+ }
+ case 12: break;
+ default:
+ if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+ zzAtEOF = true;
+ return YYEOF;
+ }
+ else {
+ zzScanError(ZZ_NO_MATCH);
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 WhichProgram <inputfile>");
+ }
+ else {
+ for (int i = 0; i < argv.length; i++) {
+ WhichProgramLexer scanner = null;
+ try {
+ scanner = new WhichProgramLexer( new java.io.FileReader(argv[i]) );
+ while ( !scanner.zzAtEOF ) scanner.yylex();
+ }
+ 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();
+ }
+ }
+ }
+ }
+
+
+ @Override
+ public Symbol next_token() throws Exception {
+ return null;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramParser.java
new file mode 100644
index 0000000..a929b4a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramParser.java
@@ -0,0 +1,306 @@
+/*
+*
+* 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.whichProgram;
+
+import java_cup.runtime.lr_parser;
+
+import javax.swing.*;
+
+
+public class WhichProgramParser extends java_cup.runtime.lr_parser {
+
+ /** Default constructor. */
+ public WhichProgramParser() {super();}
+
+ /** Constructor which sets the default scanner. */
+ public WhichProgramParser(java_cup.runtime.Scanner s) {super(s);}
+
+ /** Production table. */
+ protected static final short _production_table[][] =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\013\000\002\003\005\000\002\002\004\000\002\004" +
+ "\003\000\002\005\004\000\002\005\003\000\002\012\002" +
+ "\000\002\006\006\000\002\013\002\000\002\007\007\000" +
+ "\002\010\004\000\002\011\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\026\000\004\004\005\001\002\000\004\007\011\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\011\001" +
+ "\002\000\004\013\013\001\002\000\006\005\ufffd\007\ufffd" +
+ "\001\002\000\004\006\ufffc\001\002\000\004\006\015\001" +
+ "\002\000\004\012\017\001\002\000\006\005\ufffb\007\ufffb" +
+ "\001\002\000\004\010\ufffa\001\002\000\004\010\021\001" +
+ "\002\000\004\014\026\001\002\000\004\011\024\001\002" +
+ "\000\006\005\ufff9\007\ufff9\001\002\000\004\015\025\001" +
+ "\002\000\006\005\ufff7\007\ufff7\001\002\000\004\011\ufff8" +
+ "\001\002\000\004\002\001\001\002\000\006\005\ufffe\007" +
+ "\ufffe\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\026\000\006\003\005\004\003\001\001\000\006\005" +
+ "\007\006\011\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\012\013\001\001\000\004" +
+ "\007\015\001\001\000\002\001\001\000\002\001\001\000" +
+ "\004\013\017\001\001\000\004\010\021\001\001\000\002" +
+ "\001\001\000\004\011\022\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$actions action_obj;
+
+ /** Action encapsulation object initializer. */
+ protected void init_actions()
+ {
+ action_obj = new CUP$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$actions {
+
+
+ //__________________________________
+ public static boolean DEBUG = true;
+ private static JTable table;
+ private static final String tableLabel = "SCF Intermediate Results:";
+// private static String cycle = "0";
+
+
+ public static JTable getTable() {
+ return table;
+ }
+
+ public static String getTableLabel() {
+ return tableLabel;
+ }
+
+// }
+
+ private final WhichProgramParser parser;
+
+ /** Constructor */
+ CUP$parser$actions(WhichProgramParser WhichProgramParser) {
+ this.parser = WhichProgramParser;
+ }
+
+ /** Method with the actual generated action code. */
+ public final java_cup.runtime.Symbol CUP$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$act_num)
+ {
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 10: // grad2 ::= RmsGrad RGRAD
+ {
+ Object RESULT = null;
+ int rgleft = ((java_cup.runtime.Symbol)CUP$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$top-0)).value;
+ //___________________________________________________________________
+ if (DEBUG) System.out.println("CUP:gopt: RMS Force "+rg);
+
+ CUP$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$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 9: // grad1 ::= MaxGrad MGRAD
+ {
+ Object RESULT = null;
+ int mgleft = ((java_cup.runtime.Symbol)CUP$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$top-0)).value;
+ //___________________________________________________________________
+ if (DEBUG) System.out.println("CUP:gopt: Maximum Force "+mg);
+
+ CUP$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 ::= NSearch ITERATION 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$top-0)).value;
+ //___________________________________________________________________
+ if (DEBUG) System.out.println("CUP:gopt: ITERATION "+c);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(9/*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 ::= Energ ENERGY 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$top-0)).value;
+ //___________________________________________________________________
+ if (DEBUG) System.out.println("CUP:gopt: ENERGY "+e);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(8/*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$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 2: // scfintro ::= FOUNDITER
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:gopt: found the start of Iteration");
+ CUP$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 SCFDONE
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:gopt: end of parse tree ");
+ table = new JTable();
+
+// table = parseSCF.getTable();
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).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/whichProgram/WhichProgramSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramSym.java
new file mode 100644
index 0000000..01fce30
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/whichProgram/WhichProgramSym.java
@@ -0,0 +1,43 @@
+/*
+*
+* 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.whichProgram;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Wed Nov 12 18:52:46 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class WhichProgramSym {
+ /* terminals */
+ public static final int MGRAD = 10;
+ public static final int RmsGrad = 7;
+ public static final int Energ = 5;
+ public static final int MaxGrad = 6;
+ public static final int ENERGY = 9;
+ public static final int EOF = 0;
+ public static final int ITERATION = 8;
+ public static final int NSearch = 4;
+ public static final int RGRAD = 11;
+ public static final int error = 1;
+ public static final int SCFDONE = 3;
+ public static final int FOUNDITER = 2;
+}
+
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/resources/gridchem.properties
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/resources/gridchem.properties b/datacat/parsers/src/main/resources/gridchem.properties
new file mode 100644
index 0000000..859d6db
--- /dev/null
+++ b/datacat/parsers/src/main/resources/gridchem.properties
@@ -0,0 +1,16 @@
+TMP_DIR=/home/supun/datacat/tmp
+
+SAMPLE_OUTPUT=/home/supun/datacat/data_root/2H2OOHNCmin.com.out/2H2OOHNCmin.com.out
+
+ARCHIVING_NODE=localhost
+
+APPLICATION_NAME=gaussian 9
+
+USERNAME=sudhakar
+
+AGENT_USERNAME=datacat_agent
+
+AGENT_PASSWORD=agent_password
+
+#specify the parser sequence using commas ( ',' )
+PARSER_SEQUENCE= org.apache.airavata.datacat.parsers.gridchem.gopt.GoptParser
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/resources/regexParser.properties
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/resources/regexParser.properties b/datacat/parsers/src/main/resources/regexParser.properties
new file mode 100644
index 0000000..3464bf5
--- /dev/null
+++ b/datacat/parsers/src/main/resources/regexParser.properties
@@ -0,0 +1,9 @@
+#here you can specify which details to extract by
+#<key_value>=<regex>
+#ex: RMS FORCE=RMS\s+Force\s+(\d*\.?\d*)
+
+RMS_Force = RMS\s+Force\s+(\d*\.?\d*)
+Maximum_Force = Maximum\s+Force\s+(\d*\.?\d*)
+Maximum_Displacement = Maximum\s+Displacement\s+(\d*\.?\d*)
+RMS_Displacement = RMS\s+Displacement\s+(\d*\.?\d*)
+Energy = Predicted\s+change\s+in\s+Energy=(.*)
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/test/java/org/apche/airavata/datacat/parsers/gridchem/AbstractGridChemParserTest.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/test/java/org/apche/airavata/datacat/parsers/gridchem/AbstractGridChemParserTest.java b/datacat/parsers/src/test/java/org/apche/airavata/datacat/parsers/gridchem/AbstractGridChemParserTest.java
new file mode 100644
index 0000000..8ea3aaf
--- /dev/null
+++ b/datacat/parsers/src/test/java/org/apche/airavata/datacat/parsers/gridchem/AbstractGridChemParserTest.java
@@ -0,0 +1,39 @@
+/*
+*
+* 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.apche.airavata.datacat.parsers.gridchem;
+
+import org.apache.airavata.datacat.parsers.gridchem.util.Constants;
+import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties;
+import org.apache.log4j.Logger;
+import org.junit.Before;
+
+import java.util.Properties;
+
+public abstract class AbstractGridChemParserTest {
+ protected Properties testProperties;
+ protected String TEST_OUTPUT;
+ private Logger logger = Logger.getLogger(AbstractGridChemParserTest.class);
+
+ @Before
+ public void setUp() {
+ TEST_OUTPUT = GridChemProperties.getInstance().getProperty(Constants.SAMPLE_OUTPUT,"");
+ }
+}
\ No newline at end of file