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[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/chado ChadoAdapter.java, 1.42, 1.43
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From: Jonathan C. <jcr...@us...> - 2006-07-13 12:12:39
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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv7478 Modified Files: ChadoAdapter.java Log Message: Removed another swath of commented-out code, in this case the old non-XML configuration file parsing routine. I've left a couple of smaller commented-out sections untouched until I figure out for sure that they're no longer relevant (and are unlikely to become so again in the near future.) I've also added a few extra debug statements to the writeback calls. Index: ChadoAdapter.java =================================================================== RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/chado/ChadoAdapter.java,v retrieving revision 1.42 retrieving revision 1.43 diff -C2 -d -r1.42 -r1.43 *** ChadoAdapter.java 9 Jun 2006 17:23:23 -0000 1.42 --- ChadoAdapter.java 13 Jul 2006 12:12:36 -0000 1.43 *************** *** 1,26 **** package apollo.dataadapter.chado; - //import java.io.File; - //import java.io.IOException; import java.util.ArrayList; - //import java.util.HashMap; import java.util.List; - //import java.util.Map; import java.util.Properties; - //import java.util.StringTokenizer; import java.util.Vector; - //import javax.xml.parsers.DocumentBuilder; - //import javax.xml.parsers.DocumentBuilderFactory; - //import javax.xml.parsers.ParserConfigurationException; - import org.bdgp.io.DataAdapterUI; import org.bdgp.io.IOOperation; import org.bdgp.util.ProgressEvent; - //import org.w3c.dom.Document; - //import org.w3c.dom.Element; - //import org.w3c.dom.Node; - //import org.w3c.dom.NodeList; - //import org.xml.sax.SAXException; import apollo.config.Config; --- 1,12 ---- *************** *** 38,41 **** --- 24,28 ---- import apollo.datamodel.DbXref; import apollo.datamodel.SequenceI; + import apollo.editor.TransactionManager; /** *************** *** 109,118 **** public static String USERNAME = "USERNAME"; public static String PASSWORD = "PASSWORD"; - //public static String SEQUENCE_TYPE = "SEQUENCE_TYPE"; - //public static String INPUT_ID = "SEQUENCE_ID"; - //public static String ORGANISM_LIKE = "ORGANISM_LIKE"; - //public static String STYLE = "STYLE"; - //public static String START = "START"; - //public static String END = "END"; /** --- 96,99 ---- *************** *** 120,125 **** */ protected Properties stateInfo = new Properties(); - // More information than simple texts in stateInfo. So use object directly - //private ChadoInstance chadoInstance; /** --- 101,104 ---- *************** *** 137,142 **** /** if true print debugging statements */ ! //protected boolean DEBUG = true; ! protected static boolean DEBUG; // ----------------------------------------------------------------------- --- 116,120 ---- /** if true print debugging statements */ ! protected static boolean DEBUG = false; // ----------------------------------------------------------------------- *************** *** 271,275 **** // Commit transactions only // Make sure Transaction instances coalesced ! curation.getTransactionManager().coalesce(); //JDBCTransactionWriter processor = new JDBCTransactionWriter(url, dbUser, dbPwd); JDBCTransactionWriter processor = new JDBCTransactionWriter(getActiveDatabase()); --- 249,255 ---- // Commit transactions only // Make sure Transaction instances coalesced ! TransactionManager tm = curation.getTransactionManager(); ! if (DEBUG) System.out.println("Coalescing transactions with " + tm); ! tm.coalesce(); //JDBCTransactionWriter processor = new JDBCTransactionWriter(url, dbUser, dbPwd); JDBCTransactionWriter processor = new JDBCTransactionWriter(getActiveDatabase()); *************** *** 289,292 **** --- 269,273 ---- } + if (DEBUG) System.out.println("Setting JDBCTransactionWriter transformer to " + transformer + " chromosome to " + curation.getChromosome()); processor.setTransformer(transformer); processor.setMapID(curation.getChromosome()); *************** *** 303,308 **** --- 284,291 ---- // } try { + if (DEBUG) System.out.println("Committing transactions"); processor.commitTransactions(curation.getTransactionManager()); // All transactions should be emptied after a successful writing to the db. + if (DEBUG) System.out.println("Emptying transactions"); curation.getTransactionManager().emptyTransactions(); } *************** *** 502,506 **** } - // List getLocationTopLevelSeqIds(ChadoDatabase selectedDb,String seqType) // throws ApolloAdapterException { --- 485,488 ---- *************** *** 516,651 **** } } - - - /* Each line of the configuration file (that is not a blank line or - * part of a comment) is expected to look like this:<br> - * <br> - * <pre> - * "Chado Cryptococcus database" "apollo.dataadapter.chado.jdbc.SybaseChadoAdapter" "jdbc:sybase:Tds:dbserver.yourcompany.com:2025" "cryptdb" "Cryptococcus%" - * </pre> - * <br> - * The fields do not have to be quoted unless they contain whitespace. The fields are whitespace - * -delimited and should be interpreted as follows: - * <ol> - * <li>A human-readable descriptor that uniquely identifies a single chado database</li> - * <li>The name of a subclass of apollo.dataadapter.chado.jdbc.JdbcChadoAdapter (or that class itself)</li> - * <li>A JDBC connection URL for the server on which the database resides</li> - * <li>The name of the database/schema; the interpretation of this field may be DBMS-specific</li> - * <li>A string to be used in a 'like' query to restrict which sequences are presented to the user (optional)</li> - * </ol> */ - // // JC: since apollo.gui.Config does not provide generic routines for parsing - // // configuration files, some of the code found below was copied verbatim from there. - // - // Vector databases = new Vector(); - // String configFileName = apollo.util.IOUtil.findFile("conf/chado-adapter.cfg"); - // - // if (configFileName == null) { - // configFileName = apollo.util.IOUtil.findFile("chado-adapter.cfg"); - // } - // - // if (configFileName == null) { - // System.err.println(this.getClass() + ": warning - unable to find chado-adapter.cfg"); - // } else { - // File configFile = new File(configFileName); - // try { - // StreamTokenizer tokenizer = new StreamTokenizer(new BufferedReader(new FileReader(configFile))); - // tokenizer.eolIsSignificant(true); - // tokenizer.slashStarComments(true); - // boolean done = false; - // int tokType = 0; - // Vector fields = new Vector(); - // - // while (!done) { - // int lineno = tokenizer.lineno(); - // - // // EOF - // if ((tokType = tokenizer.nextToken()) == StreamTokenizer.TT_EOF) { - // done = true; - // } - // // Another token - // else if (tokType != StreamTokenizer.TT_EOL) { - // fields.addElement(tokenizer.sval); - // } - // // End of line - // else { - // if (fields.size() == 0) { - // // This is OK; can happen on a comment or blank line - // } - // else if (fields.size() > 5) { - // System.err.println(this.getClass() + ": warning - unable to parse line " + lineno + " of " + configFileName + - // " with " + fields.size() + " fields"); - // } else { - // String name = (String)(fields.elementAt(0)); - // String className = (String)(fields.elementAt(1)); - // String url = (String)(fields.elementAt(2)); - // String dbName = (String)(fields.elementAt(3)); - // String login = (fields.size() >= 5) - // ? (String)(fields.elementAt(4)) : null; - // // The "like" argument is optional - // String organismLike = (fields.size() >= 6) - // ? (String)fields.elementAt(4) : null; - // ChadoDatabase cd = new ChadoDatabase(name, className, url, dbName, - // login, organismLike); - // databases.addElement(cd); - // } - // fields.removeAllElements(); - // } - // } - // - // } catch (Exception e) { - // System.err.println(this.getClass() + ": warning - parssing error " + configFileName+e); - // } - // } - // - // ChadoDatabase result[] = new ChadoDatabase[databases.size()]; - // databases.copyInto(result); - // return result; - // /** - // * Factory method that returns an instance of JdbcChadoAdapter, or one of its subclasses; - // * which subclass is used is determined by the GUI. The data adapter configuration file read - // * by <code>readConfigFile</code> allows the GUI to present the user with a list of available - // * Chado databases, each of which will have an associated JdbcChadoAdapter subclass. - // * - // * @return A JdbcChadoAdapter instance capable of communicating with the Chado database - // * instance currently selected by the user in the GUI. - // */ - // protected JdbcChadoAdapter getJdbcChadoAdapter() throws DataAdapterException { - - // // Properties needed to connect to Chado database; these are set by ChadoAdapterGUI - // // via <code>setStateInformation()</code>. - // // dont need to do this through properties - we have the lovely ChadoDB class - // // that provides all this - refactor? though stateInfo is the pattern vivek setup - // ChadoDatabase chadoDB = getActiveDatabase(); - // String driverClass = this.stateInfo.getProperty(DRIVER_CLASS); - // String jdbcUrl = this.stateInfo.getProperty(JDBC_URL); - // String chadoDb = this.stateInfo.getProperty(CHADO_DB); - // String username = this.stateInfo.getProperty(USERNAME); - // String password = this.stateInfo.getProperty(PASSWORD); - // String organismLike = this.stateInfo.getProperty(ORGANISM_LIKE); - // // driverClass specifies which subclass of apollo.dataadapter.chado.jdbc.JdbcChadoAdapter - // // should be used to communicate with this particular type of Chado database - // Class dc = null; - // try { - // dc = Class.forName(driverClass); - // } catch (ClassNotFoundException cnfe) { - // throw new DataAdapterException("Unable to find Chado driver class " + driverClass); - // } - - // // Attempt to instantiate an object of the appropriate class; by convention any subclass - // // of JdbcChadoAdapter will have a JavaBean-style 0-argument constructor. - // try { - // JdbcChadoAdapter chadoAdapter = (JdbcChadoAdapter) (dc.newInstance()); - // // Pass some essential connection information along to the adapter object. - // chadoAdapter.init(jdbcUrl, chadoDb, username, password, DEBUG, organismLike); - // // this is too late for DatabaseToStyle to take effect - needs to happen before new style - // // is set (in clearOldData) - // //setDatabase(chadoDb); // now done in ChadoAdapterGUI.doOperation - // chadoAdapter.setChadoInstance(chadoInstance); - // return chadoAdapter; - // } - // catch (Exception e) { - // System.err.println("ChadoAdapter.getJdbcChadoAdapter(): " + e); - // e.printStackTrace(); - // } - // return null; - // } --- 498,499 ---- |