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Revision 82 - Directory Listing
Modified Thu Apr 13 10:54:05 2006 UTC (11 years, 7 months ago) by duarte
Copied from: trunk revision 81
Creation of tools version 0.1:
Freezing tools rev81 to tag tools-0.1
I am planning to change completely some of the classes: DataDistribution and ClusterConnection. Will continue developing on trunk while we have this freeze so others can use programs as they are now.
Revision 81 - Directory Listing
Modified Wed Apr 12 15:27:05 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Changed the Connection fields to be MySQLConnection.
Thanks to this, simplify considerably a lot of the methods by using the MySQLConnection methods.
Got rid of method loadSQLDriver and URL final field
Revision 80 - Directory Listing
Modified Wed Apr 12 14:59:37 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Introduced better javadoc comments in constructors.
Revision 79 - Directory Listing
Modified Wed Apr 12 11:03:01 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Modified insertIdsToKeyMaster method. Now removing pk in table before inserting, then removing zeros and adding finally the pk back. At that point mysql should complain if there are duplicates
New methods to deal with key_master database actions. They belong in another class, but for the moment here.
- createNewKeyMasterTbl
- removePK
- addPK
- removeZeros
Revision 78 - Directory Listing
Modified Wed Apr 12 08:52:25 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of method createNewKeyMasterTbl
Didn't belong here but in DataDistribution (at least for now)

Revision 77 - Directory Listing
Modified Wed Apr 12 08:26:36 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Bug in new method createNewKeyMasterTbl
The query for inserting the new record in dbs_keys was totally wrong
Wrote something more correct and simpler!
Revision 76 - Directory Listing
Modified Tue Apr 11 16:00:26 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Minor change, in getHostId4Ifx one of the error messages was being written to out, now to err
Revision 75 - Directory Listing
Modified Tue Apr 11 14:33:39 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
In latest commit method insertIdsToKeyMaster wasn't yet complying with the new way of dealing with key
Now modified insertIdsToKeyMaster accordingly. Now we create a ClusterConnection object to call the createNewKeyMasterTable method.
Revision 74 - Directory Listing
Modified Tue Apr 11 14:27:17 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
New method createNewKeyMasterTbl
To create a new keyMaster table in the key_master database for a certain table
Will also insert a new record in dbs_keys for the new table.
If a record for it already existed it will print an error and continue as the error is harmless.
Revision 73 - Directory Listing
Modified Tue Apr 11 10:42:54 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of keyColumn
Now key is directly the keyColumn name, e.g. key is asu_id not asu
This makes things less confusing and simpler.
We've done this following last commit of DataDistribution to also change the ways we deal with key/keyColumn.
Note that now the checkKeyCounts and checkDifferingKeys are using to get the keyTable name a ClusterConnection object and the new ClusterConnection method getTableOnNode
Revision 72 - Directory Listing
Modified Tue Apr 11 10:29:39 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
2 important changes:
Fixed important bug on the constructor that gets the key passed (the bug was there since a lot of revisions ago and always passed since that constructor was not used in other classes)
Got rid of keyColumn, was useless. Now key is directly the keyColumn name which is more logical and makes everything simpler
- changed all calls to keyColumn to key
- got rid of keyColumn field and setKeyColumn
- changed completely the methods setKeyTable to get the table name from the dbs_keys on key_master db
- introduced new method getTableOnNode. Gets the name of the table where splitted data is stored for this db and key
Revision 71 - Directory Listing
Modified Mon Apr 10 16:01:01 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
New method getIdSetsFromNodes, equivalent to splitIdsIntoSets but rather a posteriori, when tables are already distributed in cluster's nodes
Modified method getAllIds4KeyAndTable, now taking host as parameter too, more general
Changed the comments a lot for all those 3 methods. There are many catches to be taken in account, the comments explain them quite well
Revision 70 - Directory Listing
Modified Fri Apr 7 14:49:02 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
KEYMASTERDB had value for testing, change that back.
Revision 69 - Directory Listing
Modified Fri Apr 7 14:44:08 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method insertIdsToKeyMaster
Added call to the new insertIdsToKeyMaster in splitTableToCluster method
Revision 68 - Directory Listing
Modified Fri Apr 7 13:26:05 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added another clusterExecuteQuery method to take a HashMap of queries rather than only one.
To be used in cases where the queries to be sent to nodes are different for each node (like in load/dump methods of this class)
Right now strictly serial must paralelize it as with the other clusterExecuteQuery
Revision 67 - Directory Listing
Modified Fri Apr 7 12:59:18 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Modified methods getAllIdxAndClients and getAllIdxFromMaster.
They return now:
- getAllIdxAndClients: an int[]
- getAllIdxFromMaster: a HashMap<Integer,String>
Got rid of having ResultSets returned which is very messy and dangerous.
Revision 66 - Directory Listing
Modified Fri Apr 7 09:31:08 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Made MASTER final static variable also public. It is in use by other classes.
Revision 65 - Directory Listing
Modified Fri Apr 7 09:26:03 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Initial commit of DataDistribution.java into aglappe repository
Copied from repository scripts-jose rev 69
If want to have a look at previous history must do it from repository scripts-jose, there was no way of copying with history between different repositories
Revision 64 - Directory Listing
Modified Thu Apr 6 14:47:09 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method getCreateIndex4Table
Revision 63 - Directory Listing
Modified Thu Apr 6 12:18:18 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Fixed bug in getAllIndexes4Table, the SELECT needed a DISTINCT
Revision 62 - Directory Listing
Modified Thu Apr 6 12:15:37 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Got rid of method dbExists. Was useless and not working.
Revision 61 - Directory Listing
Modified Thu Apr 6 10:07:22 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method setSqlMode, to set sql_mode server variable
Revision 60 - Directory Listing
Modified Thu Apr 6 09:24:28 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added method dbExists to check whether database exists in server, used in constructor that passes a dbName
Moved all the private methods to the beginning of methods section
Revision 59 - Directory Listing
Modified Thu Apr 6 08:24:15 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Changed comments in constructors
Changed in method readConnectionFile:
- variable to count mandatory parameters to paramCount
- number of mandatory parameters now 4, dbname is also mandatory
Revision 58 - Directory Listing
Modified Wed Apr 5 08:45:23 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Now executeSQL method throws exception instead of catching it. Thought it was better than the calling class deals with these exceptions.
Revision 57 - Directory Listing
Modified Wed Apr 5 07:38:32 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added getConnectionObject
Added printDbSizeInfo and 2 getRange methods from utils4DB
Made private the loadMySQLDriver and readConnectionFile methods

Revision 56 - Directory Listing
Modified Tue Apr 4 17:27:58 2006 UTC (11 years, 7 months ago) by filippis
Original Path: trunk
execUpdateQuery method added and code in comments was removed
Revision 55 - Directory Listing
Modified Tue Apr 4 15:27:49 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Initial commit.
Class to create a connection to mysql db with basic functionality.
Cann take parameters for connection as argument in constructor or from connection file (passing the filename to the constructor)
Using code from both DBConnection (henning) and mySQLConnect (ioannis)
Revision 54 - Directory Listing
Modified Wed Mar 29 14:26:03 2006 UTC (11 years, 7 months ago) by stehr
Original Path: trunk
initial import
Revision 53 - Directory Listing
Modified Wed Mar 29 13:01:40 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Fixed a bug with setKeyDb method, was not actually working:
 as well as setting the MASTERDB string needed to change connection to master database to point to new db!
From now on take care if setKeyDb is used in another class. It will open another master connection, thus master connection won't be always the same during the run of the program
Revision 52 - Directory Listing
Modified Wed Mar 29 12:49:13 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Changed error message printed in getHostId4Idx
Revision 51 - Directory Listing
Modified Wed Mar 29 12:29:56 2006 UTC (11 years, 7 months ago) by duarte
Original Path: trunk
Added setKeyDb method, to be used in testing, i.e. with this method we can change from another class the default MASTERDB database.
Revision 50 - Directory Listing
Modified Tue Mar 28 15:05:31 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
More examples added and the current ones modified according to Graph2Pml changes
Revision 49 - Directory Listing
Modified Tue Mar 28 15:04:24 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
More flexibility in coloring, popDefaults/setDefaults methods plus comments
Revision 48 - Directory Listing
Modified Tue Mar 28 15:03:32 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Refresh method added plus refresh added before saving image
Revision 47 - Directory Listing
Modified Mon Mar 27 21:01:06 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Added cgo functionality/examples in Graph2Pml and testGraph2Pml
Revision 46 - Directory Listing
Modified Mon Mar 27 20:59:42 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
PyMol class: adding refresh in saveImage methods
Revision 45 - Directory Listing
Modified Mon Mar 27 16:32:22 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Graph2Pymol class now functional
testGraph2Pymol class now functional with comments also
PyMol class:python strings methods and removeList, concatList, refresh methods added
Machine class: indentation
Revision 44 - Directory Listing
Modified Wed Mar 22 17:14:01 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
In PyMol class, objectNameQuotes class variable is replaced by the method parameter called variable. Graph2Pml is modified accrodingly.
Revision 43 - Directory Listing
Modified Wed Mar 22 09:30:40 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added executeSql method
Revision 42 - Directory Listing
Modified Tue Mar 21 19:13:20 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding Graph2Pml and testGraph2Pml classes (non functional code!)
Revision 41 - Directory Listing
Modified Tue Mar 21 18:41:48 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
getRange methods now return double array instead of Float array. Previous code is into comments.
Revision 40 - Directory Listing
Modified Tue Mar 21 18:21:00 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding Msdsd2Pdb and PyMol classes
Revision 39 - Directory Listing
Modified Tue Mar 21 17:21:54 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding comments
Revision 38 - Directory Listing
Modified Mon Mar 20 11:37:12 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added getAllIdxAndClients method:
gets all ids and client_names for a certain key
Revision 37 - Directory Listing
Modified Fri Mar 17 11:22:19 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Some changes in error messages to be more clear.
Revision 36 - Directory Listing
Modified Fri Mar 17 11:03:15 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Now using constructor without key and createStatement with key, since createStatement without key is not allowed anymore (is now private)
Revision 35 - Directory Listing
Modified Fri Mar 17 11:00:33 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Clean up a bit and added some more comments
Revision 34 - Directory Listing
Modified Fri Mar 17 10:48:03 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Refactor some method names to be more consistent.
Changed some fields to be final (and uppercase them)
Added comments for the most importat methods
Made the createStatment(idx) method private, this should only be used internally. Would be dangerous to use it from anothe class.
Revision 33 - Directory Listing
Modified Wed Mar 15 11:58:24 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Changed all error printing in catches to STDERR instead of STDOUT
Revision 32 - Directory Listing
Modified Tue Mar 14 09:45:57 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
New exec method taking only a String argument wasn't working. Fixed the bug.
Revision 31 - Directory Listing
Modified Tue Mar 14 07:40:32 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added exec method to take only a string as argument.
Revision 30 - Directory Listing
Modified Fri Mar 10 15:19:32 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
introduced generics, so class will compile in Java 5, not sure though whether the functionality is the same as before, will need more testing
Revision 29 - Directory Listing
Modified Fri Mar 10 10:57:12 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
changed server port to standard
Revision 28 - Directory Listing
Modified Fri Mar 10 10:56:22 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
prevent overlong commands from being sent to the server
Revision 27 - Directory Listing
Modified Thu Mar 9 17:12:43 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
initial import
Revision 26 - Directory Listing
Modified Thu Mar 9 15:55:56 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
fixed bug for very long command strings (> 255 characters)
Revision 25 - Directory Listing
Modified Thu Mar 9 10:11:16 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk

Revision 24 - Directory Listing
Modified Thu Mar 9 10:08:44 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
moved executables (classes with main function) to root directory
Revision 23 - Directory Listing
Modified Wed Mar 8 15:25:45 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Fixed important bug:
- now closing nCon connection before opening a new one in the setHost method.
- this is important. Before lots of connection were left opened after having used the ClusterConnection object
Revision 22 - Directory Listing
Modified Tue Mar 7 13:22:37 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Fixed bug in getIdxSet method. Wasn't reading properly the index_matrix table into the array. Was starting from columnn 1 which actually is the serial column. Now starting from column 2.
Revision 21 - Directory Listing
Modified Tue Mar 7 11:50:37 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
New method int[][] getIdxSet. 
- Returns a 2-dimensional array with all indices for a certain key.
- Each column j corresponds to client_id j+1
- Each row i is a set of idx values for each of the client_ids. If there is no idx for a certain client_id then the value is 0.

Revision 20 - Directory Listing
Modified Mon Mar 6 15:19:40 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
updated commentary
Revision 19 - Directory Listing
Modified Mon Mar 6 15:15:57 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
deleted, file was a copy of makenbhtable.java, original file was lost
Revision 18 - Directory Listing
Modified Mon Mar 6 15:03:46 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
initial import

Revision 17 - Directory Listing
Modified Mon Mar 6 09:20:16 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Grouped all the setIdxColumn and setMasterTable into setKey.
Also rationalised a bit the constructors by calling one from the other.
Revision 16 - Directory Listing
Modified Mon Mar 6 08:32:55 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Added package tools.
Revision 15 - Directory Listing
Modified Mon Mar 6 08:25:22 2006 UTC (11 years, 8 months ago) by duarte
Original Path: trunk
Initial commit of the ClusterConnection class + small test class to test it out.

Revision 14 - Directory Listing
Modified Mon Mar 6 08:05:31 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
removed ununsed imports and variables
Revision 13 - Directory Listing
Modified Fri Mar 3 15:15:31 2006 UTC (11 years, 8 months ago) by filippis
Original Path: trunk
Adding SystemCmd class
Revision 12 - Directory Listing
Modified Thu Mar 2 17:21:28 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
removed some debug code

Revision 11 - Directory Listing
Modified Thu Mar 2 15:42:09 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
Corrected some bad mistake

Revision 10 - Directory Listing
Modified Thu Mar 2 11:42:06 2006 UTC (11 years, 8 months ago) by stehr
Original Path: trunk
Initial commit of the remote-pymol-from-java stuff

Revision 9 - Directory Listing
Modified Tue Feb 14 11:00:40 2006 UTC (11 years, 9 months ago) by filippis
Original Path: trunk
Adding R class
Revision 8 - Directory Listing
Modified Mon Jan 23 09:20:44 2006 UTC (11 years, 10 months ago) by duarte
Original Path: trunk
Deleted old tools.trunk files
Revision 7 - Directory Listing
Modified Mon Jan 23 09:19:47 2006 UTC (11 years, 10 months ago) by duarte
Original Path: trunk
Moved everything to subdir tools, so that we keep the tools name for the package. Also changed the package name in the files to tools. To work with it please check out only file:///.../svn/tools/trunk/tools
Revision 6 - Directory Listing
Modified Wed Jan 18 19:07:41 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Adding getDbSizeInfo method into utils4DB program
Revision 5 - Directory Listing
Modified Wed Jan 18 18:52:48 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Adding files utils*
Revision 4 - Directory Listing
Modified Wed Jan 18 18:49:01 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Package tools changed to tools.trunk because code could not compile!
Revision 3 - Directory Listing
Modified Wed Jan 18 18:23:39 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
The name of the report table can be passed as argument now (default value is report as previous)
Revision 2 - Directory Listing
Modified Wed Jan 18 18:10:10 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Comments in system.out.println & Dealing with no password cases
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (11 years, 10 months ago) by filippis
Original Path: trunk
Initial import of tools