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  • scipy.io typeerror:buffer too small for requested array

    - by kartiku
    I have a problem in python. I'm using scipy, where i use scipy.io to load a .mat file. The .mat file was created using MATLAB. listOfFiles = os.listdir(loadpathTrain) for f in listOfFiles: fullPath = loadpathTrain + '/' + f mat_contents = sio.loadmat(fullPath) print fullPath Here's the error: Traceback (most recent call last): File "tryRankNet.py", line 1112, in demo() File "tryRankNet.py", line 645, in demo mat_contents = sio.loadmat(fullPath) File "/usr/lib/python2.6/dist-packages/scipy/io/matlab/mio.py", line 111, in loadmat matfile_dict = MR.get_variables() File "/usr/lib/python2.6/dist-packages/scipy/io/matlab/miobase.py", line 356, in get_variables getter = self.matrix_getter_factory() File "/usr/lib/python2.6/dist-packages/scipy/io/matlab/mio5.py", line 602, in matrix_getter_factory return self._array_reader.matrix_getter_factory() File "/usr/lib/python2.6/dist-packages/scipy/io/matlab/mio5.py", line 274, in matrix_getter_factory tag = self.read_dtype(self.dtypes['tag_full']) File "/usr/lib/python2.6/dist-packages/scipy/io/matlab/miobase.py", line 171, in read_dtype order='F') TypeError: buffer is too small for requested array The whole thing is in a loop, and I checked the size of the file where it gives the error by loading it interactively in IDLE. The size is (9,521), which is not at all huge. I tried to find if I'm supposed to clear the buffer after each iteration of the loop, but I could not find anything. Any help would be appreciated. Thanks.

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  • Python TypeError: an integer is required

    - by kartiku
    import scipy,array def try_read_file(): def line_reader(lines): for l in lines: i = l.find('#') if i != -1: l = l[:i] l = l.strip() if l: yield l def column_counter(): inputer = (line.split() for line in line_reader(file('/home/kartik/Downloads/yahoo_dataset/set1.train.txt'.strip()))) loopexit = 0 for line in inputer: feature_tokens = (token.split(':') for token in line[6:]) feature_ids = array.array('I') for t in feature_tokens: feature_ids.append(int (t[0])) tmpLength = feature_ids[-1] print feature_ids loopexit = loopexit + 1 if loopexit > 0: break return tmpLength def line_counter(): inputer = (line.split() for line in line_reader(file('/home/kartik/Downloads/yahoo_dataset/set1.train.txt'.strip()))) noOfRows = 0 for line in inputer: noOfRows = noOfRows + 1 return noOfRows inputer = (line.split() for line in line_reader(file('/home/kartik/Downloads/yahoo_dataset/set1.train.txt'.strip()))) feature_id_list = [] feature_value_list = [] relevance_list = [] noOfRows = line_counter() noOfCols = column_counter() print noOfRows print noOfCols # line 52 #Create the feature array feature_array = scipy.zeros((noOfRows,noOfCols), float) rowCounter = 1; for line in inputer: feature_tokens = (token.split(':') for token in line[6:]) feature_ids = array.array('I') feature_values = array.array('f') for t in feature_tokens: feature_ids.append(int(t[0])) if (t[0]!=colCounter): feature_array[rowCounter,colCounter] = 0 else: feature_array[rowCounter,colCounter] = t[1] feature_values.append(float(t[1])) colCounter = colCounter + 1; label = float(line[0]) assert(line[1].startswith('qid:')) query_id = int(line[1][4:]) feature_id_list.append(feature_ids) feature_value_list.append(feature_values) relevance_list.append(label) rowCounter = rowCounter + 1; return feature_array Error: Traceback (most recent call last): File "<pyshell#97>", line 1, in <module> try_read_file() File "/home/kartik/Python/prelim_read.py", line 52, in try_read_file print noOfCols TypeError: an integer is required What is the problem, i couldn't figure it out? I tried to debug it, but it doesnt really go inside those methods. It gives me an address in place of those variables.

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  • BULK INSERT problem in mysql

    - by kartiku
    Hi, I get an error with the following sql command for bulk insert....any help would be appreciated. BULK INSERT libra.faculty FROM 'd\:faculty.csv' WITH ( FIELDTERMINATOR = ',', ROWTERMINATOR = '\n' ); Here's the error message ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'BULK INSERT libra.faculty FROM 'd:\faculty.csv' WITH ( FIELDTERMINATOR = ',', RO' at line 1

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  • select for update problem in jdbc

    - by kartiku
    I'm having a problem with select for update in jdbc. The table i'm trying to update is the smalldb table, i'm having problems-- i'm using select for update which does a lock on the selected row the update statement is -- String updateQ = "UPDATE libra.smalldb SET hIx = ? WHERE name = ?"; the select statement is -- rs = stmt1.executeQuery("SELECT hIx FROM libra.smalldb for update"); rs0 = stmt2.executeQuery("SELECT name,aff FROM libra.smalldb"); the second statement is because i need those fields as well. Here is the complete code -- import java.sql.*; import java.util.ArrayList; import java.util.Collections; public class Jdbcexample1 { /** * @param args */ public static void main(String[] args) { Connection con = null; try { Class.forName("com.mysql.jdbc.Driver").newInstance(); con = DriverManager.getConnection("jdbc:mysql:///test", "root", "*****"); //String url = "jdbc:msql://200.210.220.1:1114/Demo"; //Connection conn = DriverManager.getConnection(url,"",""); Statement stmt1 = con.createStatement(); Statement stmt2 = con.createStatement(); Statement stmt3 = con.createStatement(); Statement stmt4 = con.createStatement(); ResultSet rs0; ResultSet rs; ResultSet rs1; ResultSet rs2; String name; String hIx; int hIxInt; StringBuffer sb = new StringBuffer(); String affiliationSmall; ArrayList<String> affiliation = new ArrayList<String>(); ArrayList<Float> matchValues = new ArrayList<Float>(); ArrayList<Integer> hixValues = new ArrayList<Integer>(); ArrayList<Integer> idValues = new ArrayList<Integer>(); boolean moreFlag = false; String queryString; int tmpIdx; String name1; //get the hix at that index where the similarity is maximum int tmpHidx = 0; int tmpHix = 0; int id = 0; int count; int tmpidIdx = 0; //rs = stmt.executeQuery("SELECT id FROM libra.researchint WHERE id = 910887"); // Get name, affiliation , hIx from smalldb //rs = stmt1.executeQuery("SELECT name,aff,hIx FROM libra.smalldb"); // String cursorName = "OUR_CURSOR"; // stmt1.setCursorName(cursorName); //rs = stmt1.executeQuery("SELECT name,aff,hIx FROM libra.smalldb for update"); rs = stmt1.executeQuery("SELECT hIx FROM libra.smalldb for update"); rs0 = stmt2.executeQuery("SELECT name,aff FROM libra.smalldb"); while ( rs.next() && rs0.next() ) { //String lastName = rs.getString("id"); hIx = rs.getString("hIx"); hIxInt = Integer.parseInt(hIx); //if hIx if (hIxInt==-1) continue; //name = rs.getString("name"); name = rs0.getString("name"); name1 = new String(name); System.out.println(name); //affiliationSmall = rs.getString("aff"); affiliationSmall = rs0.getString("aff"); //name = "\"" +name+ "\""; // Get matching names from large faculty table //String queryString = "SELECT id,name,hIx FROM libra.faculty WHERE name = " +name; //name = does not work names are similar but not same (in faculty and // smalldb) String query = "SELECT id,name,hIx FROM libra.faculty WHERE name like ?"; //String query = "SELECT id,name,hIx FROM libra.faculty for update of hIx WHERE name like ?"; PreparedStatement prepStmt = con.prepareStatement(query); String[] nameArr = name.split(" "); StringBuffer tmpSb = new StringBuffer(); for(int idx = 0;idx<nameArr.length;idx++) { tmpSb.append(nameArr[idx] + "%"); } name = tmpSb.toString(); prepStmt.setString(1, name); rs1 = prepStmt.executeQuery(); //Try to get matching names from faculty big db //Execute the query on faculty table //rs1 = stmt2.executeQuery(queryString); if(rs1.isClosed()) continue; count = 0; matchValues.clear(); affiliation.clear(); while(rs1.next()) { //name = rs1.getString("name"); id = Integer.parseInt(rs1.getString("id")); //idValues.add(id); tmpHix = Integer.parseInt(rs1.getString("hIx")); queryString = "SELECT aff FROM libra.affiliation WHERE id = "+id; rs2 = stmt3.executeQuery(queryString); //affiliation = rs1.getString("aff"); sb.delete(0, sb.length()); while (rs2.next()) { //Concatenate it to the same string using a stringbuffer sb.append(rs2.getString("aff")); //affiliation.add(rs2.getString("aff")); } affiliation.add(sb.toString()); count++; // if(count1) // { // moreFlag = true; // //Call fuzzy match function, store the distance values and select the // //affiliation that has the minimum distance from affiliationSmall // // //problem is here, affiliation.get Index: 2, Size: 2 // // matchValues.add(fuzzyMatch(affiliationSmall,affiliation.get(count))); // hixValues.add(tmpHix); // idValues.add(id); // } }//end of while rs1 -> faculty rs1.close(); int idx = 0; if(count>1) { moreFlag = true; //Call fuzzy match function, store the distance values and select the //affiliation that has the minimum distance from affiliationSmall //problem is here, affiliation.get Index: 2, Size: 2 matchValues.add(fuzzyMatch(affiliationSmall,affiliation.get(idx))); hixValues.add(tmpHix); idValues.add(id); idx++; } if(moreFlag) { Object obj = Collections.max(matchValues); float maxVal = Float.parseFloat(obj.toString()); //int tmpIdx = matchValues.indexOf(new Float(maxVal)); //get the index at which similarity between affiliation strings is maximum, //as returned by fuzzyMatch //int tmpIdx = matchValues.indexOf(maxVal); tmpIdx = matchValues.indexOf(maxVal); //get the hix at that index where the similarity is maximum //int tmpHidx = hixValues.get(tmpIdx); tmpHidx = hixValues.get(tmpIdx); tmpidIdx = idValues.get(tmpIdx); //update the smalldb table String updateQ = "UPDATE libra.smalldb SET hIx = ? WHERE name = ?"; //String updateQ = "UPDATE libra.smalldb SET hIx = ? WHERE current of "+cursorName; //PreparedStatement prepStmt1 = con.prepareStatement("UPDATE libra.smalldb SET hIx = ? WHERE current of "+cursorName); PreparedStatement prepStmt1 = con.prepareStatement(updateQ); //PreparedStatement prepStmt1 = con.prepareStatement(updateQ); prepStmt1.setString(2, name1); prepStmt1.setString(1, Integer.toString(tmpHidx)); prepStmt1.executeUpdate(updateQ); //prepStmt1.execute(); //stmt4.executeUpdate(updateQ); }//end of if //For matching names get the affiliation based on id from affiliation table //con.close(); //System.out.println(lastName); System.out.println(name); }//end of while rs -> smalldb rs.close(); // String updateQ = "UPDATE libra.smalldb1 SET hIx = "+Integer.toString(tmpHidx)+ "WHERE id = "+Integer.toString(tmpidIdx); // stmt4.executeUpdate(updateQ); con.close(); } catch (Exception e) { System.err.println("Got an exception! "); System.err.println(e.getMessage()); e.printStackTrace(); } } public static float fuzzyMatch(String affiliationSmall, String affiliation) { //float distance = 0; String[] temp = null; temp = affiliationSmall.split(" "); int index; //int index1 = affiliation.indexOf(affiliationSmall); int matchCount = 0; for (int idx = 0;idx<temp.length; idx++) { index = affiliation.indexOf(temp[idx]); if (index!=-1) { matchCount++; } } float tmpFloat = matchCount/temp.length; //int[] aff1= new int[affiliation1.length()]; //int[] aff2 = new int[affiliation2.length()]; return tmpFloat; } } i think it is because of the second select statement (rs0) Here is the error- Got an exception! You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '?' at line 1 com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '?' at line 1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.Util.getInstance(Util.java:384) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1054) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3562) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3494) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1960) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2114) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2690) at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1648) at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1567) at Jdbcexample1.main(Jdbcexample1.java:184)

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  • os.walk in python not running with cmd line parameter passed as path

    - by kartiku
    Hello, I needed to find the number of files in a folder on the system. This is what i used: file_count = sum((len(f) for _, _, f in os.walk('path'))) This works fine when we specify the path as a string in quotes, but when I enter a variable name that holds the path, type(file_count) is a generator object, and hence cannot be used as an integer. How to solve this and why does this happen?

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