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• bash - how to filter java exception info

  - by Michael Mao

  Hi all: We've got a multi-agent Java environment where different agent would most likely produce all sorts of exceptions thrown to stderr. Here is a sample taken from the huge exception log **java.security.AccessControlException: access denied (java.io.FilePermission ..\tournament\Driver\HotelRoomAnalyser.class read)** at java.security.AccessControlContext.checkPermission(Unknown Source) at java.security.AccessController.checkPermission(Unknown Source) at java.lang.SecurityManager.checkPermission(Unknown Source) at java.lang.SecurityManager.checkRead(Unknown Source) at java.io.File.length(Unknown Source) at emarket.client.EmarketSandbox$SandboxFileLoader.loadClassData(EmarketSandbox.java:218) at emarket.client.EmarketSandbox$SandboxFileLoader.loadClass(EmarketSandbox.java:199) at java.lang.ClassLoader.loadClass(Unknown Source) **java.security.AccessControlException: access denied (java.io.FilePermission ..\tournament\Driver\HotelRoomAnalyser.class read)** at java.security.AccessControlContext.checkPermission(Unknown Source) at java.security.AccessController.checkPermission(Unknown Source) at java.lang.SecurityManager.checkPermission(Unknown Source) at java.lang.SecurityManager.checkRead(Unknown Source) at java.io.File.length(Unknown Source) at emarket.client.EmarketSandbox$SandboxFileLoader.loadClassData(EmarketSandbox.java:218) at emarket.client.EmarketSandbox$SandboxFileLoader.loadClass(EmarketSandbox.java:199) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClassInternal(Unknown Source) at MySmarterAgent.hotelRoomBookings(MySmarterAgent.java:108) fortunately all top-tier exceptions are denoted by no leading spaces, as wrapped by ** above. My concern is to get all of the top-tier exception name (delimited by colon :), together with the first line below which contains something like at emarket.client.EmarketSandbox$SandboxFileLoader.loadClassData(EmarketSandbox.java:218) Basically, something with padded style, starts with "at" and ends with ".java:108" So this info can be forwarded to the owner of that error-prone agent and let him/her fix it. My code in ~/.bashrc is incompleted now : alias startmatch='java -jar "emarket.jar" ../tournament 100'; function geterrors() { startmatch 2>"$1"; a=0; while read line do if true; then a=$(($a+1)); echo $a; fi; done } What it does now is to redirect all stderr to a text file specified by the first argument passed in, and after that, parse that text file line by line, if certain conditions returns true, echo only that line. And I am stuck with what to do inside the loop. Any suggestion is much appreciates, any hint is welcomed.

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• Java split xml file

  - by CC

  Hi all, I'm working on a piece of code to split files. I want to split flat file (that's ok, it is working fine) and xml file. The idea is to split based of a number of files to split: I have a file, and I want to split it in x files (x is a parameters). I'm doing the split by taking the size of the file and spliting the size by the number of files to split. Then, mysolution was to use a BufferedReader and to use it like while ((n = reader.read(buffer, 0, buffer.length)) != -1) { { The main problem is that for the xml file I cannot just split it, but I have to split it based on a block delimited by a start xml tag and end xml tag: <start tag> bla bla xml stuff </end tag> So I cannot cut a block at the middle. So if when I'm at the half of a block, is the size of my new file is greater than my max, I will have to read until the end of the tag, and then, to start a next file. The problem is that I have all sort of cases, and is a bit difficult to search the end tag. - the block reads a text until the middle of the end tag - the block reads a text until the end of the end tag, and no more other caracter after - etc and in the same time to have a loop and read the next block. Some times the end of a block concatenated with the start of the next one, I have the end xml tag. I hope you get the idea. My question is, does anyone have some algorithm that does that more accurate and who i treating all special cases ? The idea is to split the file as quickly as possible. Thanks alot.

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• Extending ASP.NET role providers

  - by Quick Joe Smith

  Because the RoleProvider interface seems to treat roles as nothing more than simple strings, I'm wondering if there is any non-hacky way to apply an optional value for a role on a per-user basis. Our current login management system implements roles as key-value pairs, where the value part is optional and usually used to clarify or limit the permissions granted by a role. For example, a role 'editor' might contain a user 'barry', but for 'barry' it will have an optional value 'raptors', which the system would interpret to mean that Barry can only edit articles filed under the 'raptors' category. I have seen elsewhere a suggestion to simply create additional delimited roles, such as 'editor.raptors' or somesuch. That's not really going to be ideal because it would bloat the number of roles greatly, and I can tell it's going to be a very hard sell to replace our current implementation (which is also very less than ideal, but has the advantage of being custom made to work with our user database). I can tell already that the concatenation method mentioned above is going to involve a lot of tedious string-splitting and partial matching. Is there a better way?

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• How to write regex that searches for a dynamic amount of pairs?

  - by citronas

  Lets say a have a string such as this one: string txt = "Lore ipsum {{abc|prop1=\"asd\";prop2=\"bcd\";}} asd lore ipsum"; The information I want to extract "abc" and pairs like ("prop1","asd") , ("prop3", "bcd") where each pair used a ; as delimeter. Edit1: (based on MikeB's) code Ah, getting close. I found out how to parse the following: string txt = "Lore ipsum {{abc|prop1=\"asd\";prop2=\"http:///www.foo.com?foo=asd\";prop3=\"asd\";prop4=\"asd\";prop5=\"asd\";prop6=\"asd\";}} asd"; Regex r = new Regex("{{(?<single>([a-z0-9]*))\\|((?<pair>([a-z0-9]*=\"[a-z0-9.:/?=]*\";))*)}}", RegexOptions.Singleline | RegexOptions.IgnoreCase); Match m = r.Match(txt); if (m.Success) { Console.WriteLine(m.Groups["single"].Value); foreach (Capture cap in m.Groups["pair"].Captures) { Console.WriteLine(cap.Value); } } Question 1: How must I adjust the regex to say 'each value of a pair in delimited by \" only? I added chars like '.',';' etc, but I can't think of any char that I want to permit. The other way around would be much nicer. Question 2: How must I adjust this regex work with this thing here? string txt = "Lore ipsum {{abc|prop1=\"asd\";prop2=\"http:///www.foo.com?foo=asd\";prop3=\"asd\";prop4=\"asd\";prop5=\"asd\";prop6=\"asd\";}} asd lore ipsum {{aabc|prop1=\"asd\";prop2=\"http:///www.foo.com?foo=asd\";prop3=\"asd\";prop4=\"asd\";prop5=\"asd\";prop6=\"asd\";}}"; Therefore I'd probably try to get groups of {{...}} and use the other regex?

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• javascript normalize whitespace and other plain-text formatting routines

  - by dreftymac

  Background: The language is JavaScript. The goal is to find a library or pre-existing code to do low-level plain-text formatting. I can write it myself, but why re-invent the wheel. The issue is: it is tough to determine if a "wheel" is out there, since any search for JavaScript libraries pulls up an ocean of HTML-centric stuff. I am not interested in HTML necessarily, just text. Example: I need a JavaScript function that changes this: BEFORE: nisi ut aliquip | ex ea commodo consequat duis |aute irure dolor in esse cillum dolore | eu fugiat nulla pariatur |excepteur sint occa in culpa qui | officia deserunt mollit anim id |est laborum ... into this ... AFTER: nisi ut aliquip | ex ea commodo consequat duis | aute irure dolor in esse cillum dolore | eu fugiat nulla pariatur | excepteur sint occa in culpa qui | officia deserunt mollit anim id | est laborum Question: Does it exist, a JavaScript library that is non-html-web-development-centric that has functions for normalizing spaces in delimited plain text, justifying and spacing plain text? Rationale: Investigating JavaScript for use in a programmer's text editor.

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• java BufferedReader specific length returns NUL characters

  - by Bastien

  I have a TCP socket client receiving messages (data) from a server. messages are of the type length (2 bytes) + data (length bytes), delimited by STX & ETX characters. I'm using a bufferedReader to retrieve the two first bytes, decode the length, then read again from the same bufferedReader the appropriate length and put the result in a char array. most of the time, I have no problem, but SOMETIMES (1 out of thousands of messages received), when attempting to read (length) bytes from the reader, I get only part of it, the rest of my array being filled with "NUL" characters. I imagine it's because the buffer has not yet been filled. char[] bufLen = new char[2]; _bufferedReader.read(bufLen); int len = decodeLength(bufLen); char[] _rawMsg = new char[len]; _bufferedReader.read(_rawMsg); return _rawMsg; I solved the problem in several iterative ways: first I tested the last char of my array: if it wasn't ETX I would read chars from the bufferedReader one by one until I would reach ETX, then start over my regular routine. the consequence is that I would basically DROP one message. then, in order to still retrieve that message, I would find the first occurence of the NUL char in my "truncated" message, read & store additional characters one at a time until I reached ETX, and append them to my "truncated" messages, confirming length is ok. it works also, but I'm really thinking there's something I could do better, like checking if the total number of characters I need are available in the buffer before reading it, but can't find the right way to do it... any idea / pointer ? thanks !

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• Read alphanumeric characters from csv file in C#

  - by Prasad

  I am using the following code to read my csv file: public DataTable ParseCSV(string path) { if (!File.Exists(path)) return null; string full = Path.GetFullPath(path); string file = Path.GetFileName(full); string dir = Path.GetDirectoryName(full); //create the "database" connection string string connString = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=\"" + dir + "\\\";" + "Extended Properties=\"text;HDR=Yes;FMT=Delimited;IMEX=1\""; //create the database query string query = "SELECT * FROM " + file; //create a DataTable to hold the query results DataTable dTable = new DataTable(); //create an OleDbDataAdapter to execute the query OleDbDataAdapter dAdapter = new OleDbDataAdapter(query, connString); //fill the DataTable dAdapter.Fill(dTable); dAdapter.Dispose(); return dTable; } But the above doesn't reads the alphanumeric value from the csv file. it reads only i either numeric or alpha. Whats the fix i need to make to read the alphanumeric values? Please suggest.

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• Python and csv help

  - by user353064

  I'm trying to create this script that will check the computer host name then search a master list for the value to return a corresponding value in the csv file. Then open another file and do a find an replace. I know this should be easy but haven't done so much in python before. Here is what I have so far... masterlist.txt (tab delimited) Name UID Bob-Smith.local bobs Carmen-Jackson.local carmenj David-Kathman.local davidk Jenn-Roberts.local jennr Here is the script that I have created thus far #GET CLIENT HOST NAME import socket host = socket.gethostname() print host #IMPORT MASTER DATA import csv, sys filename = "masterlist.txt" reader = csv.reader(open(filename, "rU")) #PRINT MASTER DATA for row in reader: print row #SEARCH ON HOSTNAME AND RETURN UID #REPLACE VALUE IN FILE WITH UID #import fileinput #for line in fileinput.FileInput("filetoreplace",inplace=1): # line = line.replace("replacethistext","UID") # print line Right now, it's just set to print the master list. I'm not sure if the list needs to be parsed and placed into a dictionary or what. I really need to figure out how to search the first field for the hostname and then return the field in the second column. Thanks in advance for your help, Aaron

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• Inserting null fields with dbi:Pg

  - by User1

  I have a Perl script inserting data into Postgres according to a pipe delimited text file. Sometimes, a field is null (as expected). However, Perl makes this field into an empty string and the Postgres insert statement fails. Here's a snippet of code: use DBI; #Connect to the database. $dbh=DBI-connect('dbi:Pg:dbname=mydb','mydb','mydb',{AutoCommit=1,RaiseError=1,PrintError=1}); #Prepare an insert. $sth=$dbh-prepare("INSERT INTO mytable (field0,field1) SELECT ?,?"); while (<){ #Remove the whitespace chomp; #Parse the fields. @field=split(/\|/,$_); print "$_\n"; #Do the insert. $sth-execute($field[0],$field[1]); } And if the input is: a|1 b| c|3 EDIT: Use this input instead. a|1|x b||x c|3|x It will fail at b|. DBD::Pg::st execute failed: ERROR: invalid input syntax for integer: "" I just want it to insert a null on field1 instead. Any ideas? EDIT: I simplified the input at the last minute. The old input actually made it work for some reason. So now I changed the input to something that will make the program fail. Also note that field1 is a nullable integer datatype.

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• Normalize whitespace and other plain-text formatting routines

  - by dreftymac

  Background: The language is JavaScript. The goal is to find a library or pre-existing code to do low-level plain-text formatting. I can write it myself, but why re-invent the wheel. The issue is: it is tough to determine if a "wheel" is out there, since any search for JavaScript libraries pulls up an ocean of HTML-centric stuff. I am not interested in HTML necessarily, just text. Example: I need a JavaScript function that changes this: BEFORE: nisi ut aliquip | ex ea commodo consequat duis |aute irure dolor in esse cillum dolore | eu fugiat nulla pariatur |excepteur sint occa in culpa qui | officia deserunt mollit anim id |est laborum ... into this ... AFTER: nisi ut aliquip | ex ea commodo consequat duis | aute irure dolor in esse cillum dolore | eu fugiat nulla pariatur | excepteur sint occa in culpa qui | officia deserunt mollit anim id | est laborum Question: Does it exist, a JavaScript library that is non-html-web-development-centric that has functions for normalizing spaces in delimited plain text, justifying and spacing plain text? Rationale: Investigating JavaScript for use in a programmer's text editor.

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• Convert rank-per-candidate format to OpenSTV BLT format

  - by kibibu

  I recently gathered, using a questionnaire, a set of opinions on the importance of various software components. Figuring that some form of Condorcet voting method would be the best way to obtain an overall rank, I opted to use OpenSTV to analyze it. My data is in tabular format, space delimited, and looks more or less like: A B C D E F G # Candidates 5 2 4 3 7 6 1 # First ballot. G is ranked first, and E is ranked 7th 4 2 6 5 1 7 3 # Second ballot etc In this format, the number indicates the rank and the sequence order indicates the candidate. Each "candidate" has a rank (required) from 1 to 7, where a 1 means most important and a 7 means least important. No duplicates are allowed. This format struck me as the most natural way to represent the output, being a direct representation of the ballot format. The OpenSTV/BLT format uses a different method of representing the same info, conceptually as follows: G B D C A F E # Again, G is ranked first and E is ranked 7th E B G A D C F # etc The actual numeric file format uses the (1-based) index of the candidate, rather than the label, and so is more like: 7 2 4 3 1 6 5 # Same ballots as before. 5 2 7 1 4 3 6 # A -> 1, G -> 7 In this format, the number indicates the candidate, and the sequence order indicates the rank. The actual, real, BLT format also includes a leading weight and a following zero to indicate the end of each ballot, which I don't care too much about for this. My question is, what is the most elegant way to convert from the first format to the (numeric) second?

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• Navigating to nodes using xpath in flat structure

  - by James Berry

  I have an xml file in a flat structure. We do not control the format of this xml file, just have to deal with it. I've renamed the fields because they are highly domain specific and don't really make any difference to the problem. <attribute name="Title">Book A</attribute> <attribute name="Code">1</attribute> <attribute name="Author"> <value>James Berry</value> <value>John Smith</value> </attribute> <attribute name="Title">Book B</attribute> <attribute name="Code">2</attribute> <attribute name="Title">Book C</attribute> <attribute name="Code">3</attribute> <attribute name="Author"> <value>James Berry</value> </attribute> Key things to note: the file is not particularly hierarchical. Books are delimited by an occurance of an attribute element with name='Title'. But the name='Author' attribute node is optional. Is there a simple xpath statement I can use to find the authors of book 'n'? It is easy to identify the title of book 'n', but the authors value is optional. And you can't just take the following author because in the case of book 2, this would give the author for book 3. I have written a state machine to parse this as a series of elements, but I can't help thinking there would have been a way to directly get the results that I want.

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• Dependency Injection and decoupling of software layers

  - by cs31415

  I am trying to implement Dependency Injection to make my app tester friendly. I have a rather basic doubt. Data layer uses SqlConnection object to connect to a SQL server database. SqlConnection object is a dependency for data access layer. In accordance with the laws of dependency injection, we must not new() dependent objects, but rather accept them through constructor arguments. Not wanting to upset the DI gods, I dutifully create a constructor in my DAL that takes in SqlConnection. Business layer calls DAL. Business layer must therefore, pass in SqlConnection. Presentation layer calls Business layer. Hence it too, must pass in SqlConnection to business layer. This is great for class isolation and testability. But didn't we just couple the UI and Business layers to a specific implementation of the data layer which happens to use a relational database? Why do the Presentation and Business layers need to know that the underlying data store is SQL? What if the app needs to support multiple data sources other than SQL server (such as XML files, Comma delimited files etc.) Furthermore, what if I add another object upon which my data layer is dependent on (say, a second database). Now, I have to modify the upper layers to pass in this new object. How can I avoid this merry-go-round and reap all the benefits of DI without the pain?

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• Reading a large file into Perl array of arrays and manipulating the output for different purposes

  - by Brian D.

  Hello, I am relatively new to Perl and have only used it for converting small files into different formats and feeding data between programs. Now, I need to step it up a little. I have a file of DNA data that is 5,905 lines long, with 32 fields per line. The fields are not delimited by anything and vary in length within the line, but each field is the same size on all 5905 lines. I need each line fed into a separate array from the file, and each field within the line stored as its own variable. I am having no problems storing one line, but I am having difficulties storing each line successively through the entire file. This is how I separate the first line of the full array into individual variables: my $SampleID = substr("@HorseArray", 0, 7); my $PopulationID = substr("@HorseArray", 9, 4); my $Allele1A = substr("@HorseArray", 14, 3); my $Allele1B = substr("@HorseArray", 17, 3); my $Allele2A = substr("@HorseArray", 21, 3); my $Allele2B = substr("@HorseArray", 24, 3); ...etc. My issues are: 1) I need to store each of the 5905 lines as a separate array. 2) I need to be able to reference each line based on the sample ID, or a group of lines based on population ID and sort them. I can sort and manipulate the data fine once it is defined in variables, I am just having trouble constructing a multidimensional array with each of these fields so I can reference each line at will. Any help or direction is much appreciated. I've poured over the Q&A sections on here, but have not found the answer to my questions yet. Thanks!! -Brian

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• t-sql most efficient row to column? for xml path, pivot

  - by ajberry

  create table _orders ( OrderId int identity(1,1) primary key nonclustered ,CustomerId int ) create table _details ( DetailId int identity(1,1) primary key nonclustered ,OrderId int ,ProductId int ) insert into _orders (CustomerId) select 1 union select 2 union select 3 insert into _details (OrderId,ProductId) select 1,100 union select 1,158 union select 1,234 union select 2,125 union select 3,105 union select 3,101 union select 3,212 union select 3,250 -- select orderid ,REPLACE(( SELECT ' ' + CAST(ProductId as varchar) FROM _details d WHERE d.OrderId = o.OrderId ORDER BY d.OrderId,d.DetailId FOR XML PATH('') ),'&#x20;','') as Products from _orders o I am looking for the most performant way to turn rows into columns. I have a requirement to output the contents of the db (not actual schema above, but concept is similar) in both fixed width and delimited formats. The above FOR XML PATH query gives me the result I want, but when dealing with anything other than small amounts of data, can take awhile. I've looked at pivot but most of the examples I have found are aggregating information. I just to combine the child rows and tack them onto the parent. For example, for an order it would need to output: OrderId,Product1,Product2,Product3,etc Thoughts or suggestions? I am using SQL Server 2k5.

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• reading csv files in scipy/numpy in Python

  - by user248237

  I am having trouble reading a csv file, delimited by tabs, in python. I use the following function: def csv2array(filename, skiprows=0, delimiter='\t', raw_header=False, missing=None, with_header=True): """ Parse a file name into an array. Return the array and additional header lines. By default, parse the header lines into dictionaries, assuming the parameters are numeric, using 'parse_header'. """ f = open(filename, 'r') skipped_rows = [] for n in range(skiprows): header_line = f.readline().strip() if raw_header: skipped_rows.append(header_line) else: skipped_rows.append(parse_header(header_line)) f.close() if missing: data = genfromtxt(filename, dtype=None, names=with_header, deletechars='', skiprows=skiprows, missing=missing) else: if delimiter != '\t': data = genfromtxt(filename, dtype=None, names=with_header, delimiter=delimiter, deletechars='', skiprows=skiprows) else: data = genfromtxt(filename, dtype=None, names=with_header, deletechars='', skiprows=skiprows) if data.ndim == 0: data = array([data.item()]) return (data, skipped_rows) the problem is that genfromtxt complains about my files, e.g. with the error: Line #27100 (got 12 columns instead of 16) I am not sure where these errors come from. Any ideas? Here's an example file that causes the problem: #Gene 120-1 120-3 120-4 30-1 30-3 30-4 C-1 C-2 C-5 genesymbol genedesc ENSMUSG00000000001 7.32 9.5 7.76 7.24 11.35 8.83 6.67 11.35 7.12 Gnai3 guanine nucleotide binding protein alpha ENSMUSG00000000003 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 Pbsn probasin Is there a better way to write a generic csv2array function? thanks.

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• SQLiteDataAdapter Update method returning 0

  - by Lirik

  I loaded 83 rows from my CSV file, but when I try to update the SQLite database I get 0 rows... I can't figure out what I'm doing wrong. The program outputs: Num rows loaded is 83 Num rows updated is 0 The source code is: public void InsertData(String csvFileName, String tableName) { String dir = Path.GetDirectoryName(csvFileName); String name = Path.GetFileName(csvFileName); using (OleDbConnection conn = new OleDbConnection("Provider=Microsoft.Jet.OLEDB.4.0;Data Source=" + dir + @";Extended Properties=""Text;HDR=Yes;FMT=Delimited""")) { conn.Open(); using (OleDbDataAdapter adapter = new OleDbDataAdapter("SELECT * FROM " + name, conn)) { QuoteDataSet ds = new QuoteDataSet(); adapter.Fill(ds, tableName); Console.WriteLine("Num rows loaded is " + ds.Tags.Rows.Count); InsertData(ds, tableName); } } } public void InsertData(QuoteDataSet data, String tableName) { using (SQLiteConnection conn = new SQLiteConnection(_connectionString)) { using (SQLiteDataAdapter sqliteAdapter = new SQLiteDataAdapter("SELECT * FROM " + tableName, conn)) { using (new SQLiteCommandBuilder(sqliteAdapter)) { conn.Open(); Console.WriteLine("Num rows updated is " + sqliteAdapter.Update(data, tableName)); } } } } Any hints on why it's not updating the correct number of rows?

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• Python - Open default mail client using mailto, with multiple recipients

  - by victorhooi

  Hi, I'm attempting to write a Python function to send an email to a list of users, using the default installed mail client. I want to open the email client, and give the user the opportunity to edit the list of users or the email body. I did some searching, and according to here: http://www.sightspecific.com/~mosh/WWW_FAQ/multrec.html It's apparently against the RFC spec to put multiple comma-delimited recipients in a mailto link. However, that's the way everybody else seems to be doing it. What exactly is the modern stance on this? Anyhow, I found the following two sites: http://2ality.blogspot.com/2009/02/generate-emails-with-mailto-urls-and.html http://www.megasolutions.net/python/invoke-users-standard-mail-client-64348.aspx which seem to suggest solutions using urllib.parse (url.parse.quote for me), and webbrowser.open. I tried the sample code from the first link (2ality.blogspot.com), and that worked fine, and opened my default mail client. However, when I try to use the code in my own module, it seems to open up my default browser, for some weird reason. No funny text in the address bar, it just opens up the browser. The email_incorrect_phone_numbers() function is in the Employees class, which contains a dictionary (employee_dict) of Employee objects, which themselves have a number of employee attributes (sn, givenName, mail etc.). Full code is actually here (http://stackoverflow.com/questions/2963975/python-converting-csv-to-objects-code-design) from urllib.parse import quote import webbrowser .... def email_incorrect_phone_numbers(self): email_list = [] for employee in self.employee_dict.values(): if not PhoneNumberFormats.standard_format.search(employee.telephoneNumber): print(employee.telephoneNumber, employee.sn, employee.givenName, employee.mail) email_list.append(employee.mail) recipients = ', '.join(email_list) webbrowser.open("mailto:%s?subject=%s&body=%s" % (recipients, quote("testing"), quote('testing')) ) Any suggestions? Cheers, Victor

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• R: Why does read.table stop reading a file?

  - by Mike Dewar

  I have a file, called genes.txt, which I'd like to become a data.frame. It's got a lot of lines, each line has three, tab delimited fields: mike$ wc -l genes.txt 42476 genes.txt I'd like to read this file into a data.frame in R. I use the command read.table, like this: genes = read.table( genes_file, sep="\t", na.strings="-", fill=TRUE, col.names=c("GeneSymbol","synonyms","description") ) Which seems to work fine, where genes_file points at genes.txt. However, the number of lines in my data.frame is significantly less than the number of lines in my text file: > nrow(genes) [1] 27896 and things I can find in the text file: mike$ grep "SELL" genes.txt SELL CD62L|LAM1|LECAM1|LEU8|LNHR|LSEL|LYAM1|PLNHR|TQ1 selectin L don't seem to be in the data.frame > grep("SELL",genes$GeneSymbol) integer(0) it turns out that genes = read.delim( genes_file, header=FALSE, na.strings="-", fill=TRUE, col.names=c("GeneSymbol","synonyms","description"), ) works just fine. Why does read.delim work when read.table not? If it's of use, you can recreate genes.txt using the following commands which you should run from a command line curl -O ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz gzip -cd gene_info.gz | awk -Ft '$1==9606{print $3 "\t" $5 "\t" $9}' > genes.txt be warned, though, that gene_info.gz is 101MBish.

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• How to populate data from .txt file into Excel in VBA?

  - by swei

  I'm trying to create something to read data from a .txt file, then populate data into .xls, but after open the .txt file, how do I get the data out? Basically I'm trying to get the the third column of the lines dated '04/06/2010'. After I open the .txt file, when I use ActiveSheet.Cells(row, col), the ActiveSheet is not pointing to .txt file. My .txt file is like this (space delimited): 04/05/10 23 29226 04/05/10 24 26942 04/06/10 1 23166 04/06/10 2 22072 04/06/10 3 21583 04/06/10 4 21390 Here is the code I have: Dim BidDate As Date BidDate = '4/6/2010' Workbooks.OpenText Filename:=ForecastFile, StartRow:=1, DataType:=xlDelimited, Space:=True If Err.Number = 1004 Then MsgBox ("The forecast file " & ForecastFile & " was not found.") Exit Sub End If On Error GoTo 0 Dim row As Integer, col As Integer row = 1 col = 1 cell_value = activeSheet.Cells(row, col) MsgBox ("the cell_value=" & cell_value) Do While (cell_value <> BidDate) And (cell_value <> "") row = row + 1 cell_value = activeSheet.Cells(row, col) ' MsgBox ("the value is " & cell_value) Loop If cell_value = "" Then MsgBox ("A load forecast for " & BidDate & " was not found in your current load forecast file titled '" + ForecastFile + ". " + "Make sure you have a load forecast for the current bid date and then open this spreadsheet again.") ActiveWindow.Close Exit Sub End If Can anyone point out where it goes wrong here?

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• Recognize Dates In A String

  - by Tim Scott

  I want a class something like this: public interface IDateRecognizer { DateTime[] Recognize(string s); } The dates might exist anywhere in the string and might be any format. For now, I could limit to U.S. culture formats. The dates would not be delimited in any way. They might have arbitrary amounts of whitespace between parts of the date. The ideas I have are: ANTLR Regex Hand rolled I have never used ANTLR, so I would be learning from scratch. I wonder if there are libraries or code samples out there that do something similar that could jump start me. Is ANTLR too heavy for such a narrow use? I have used Regex a lot before, but I hate it for all the reasons that most people hate it. I could certainly hand roll it but I'd rather not re-solve a solved problem. Suggestions? UPDATE: Here is an example. Given this input: This is a date 11/3/63. Here is another one: November 03, 1963; and another one Nov 03, 63 and some more (11/03/1963). The dates could be in any U.S. format. They might have dashes like 11-2-1963 or weird extra whitespace inside like this: Nov   3,   1963, and even maybe the comma is missing like [Nov 3 63] but that's an edge case. The output should be an array of seven DateTimes. Each date would be the same: 11/03/1963 00:00:00.

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• Retrieve OpenId FullName from Google

  - by user294711

  I'm using DotNetOpenAuth lib to work with Google(only) OpenId. And I'm retrieving Email without any problem. But I can't get FullName, it is always null. request.AddExtension(new ClaimsRequest { Email = DemandLevel.Require, FullName = DemandLevel.Require }); ClaimsResponse claimsResponse = relyingPartyResponse.GetExtension<ClaimsResponse>(); if (claimsResponse != null) { var email = claimsResponse.Email; var fullName = claimsResponse.FullName; } I googled this problem and found that: Glad you got it working. Google will not give a full name or nickname for their users. They ONLY give email address, and (I think, but perhaps only on a white list) the timezone. It's not a matter of figuring out how to rig your RP so that it works. Google just won't do it yet. – Andrew Arnott Sep 8 at 14:22 stackoverflow.com/questions/1387438/retrieve-openid-user-information-claims-across-providers But it was in Sep 2009, maybe something was changed from that moment... I've found that in http://code.google.com/apis/accounts/docs/OpenID.html: openid.ax.required -- (required) Specifies the attribute being requested. Valid values include: "country", "email", "firstname", "language", "lastname". To request multiple attributes, set this parameter to a comma-delimited list of attributes. So, my question is how can I get FullName (FirstName, LastName) from Google OpenId?

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• Java: Efficiency of the readLine method of the BufferedReader and possible alternatives

  - by Luhar

  We are working to reduce the latency and increase the performance of a process written in Java that consumes data (xml strings) from a socket via the readLine() method of the BufferedReader class. The data is delimited by the end of line separater (\n), and each line can be of a variable length (6KBits - 32KBits). Our code looks like: Socket sock = connection; InputStream in = sock.getInputStream(); BufferedReader inputReader = new BufferedReader(new InputStreamReader(in)); ... do { String input = inputReader.readLine(); // Executor call to parse the input thread in a seperate thread }while(true) So I have a couple of questions: Will the inputReader.readLine() method return as soon as it hits the \n character or will it wait till the buffer is full? Is there a faster of picking up data from the socket than using a BufferedReader? What happens when the size of the input string is smaller than the size of the Socket's receive buffer? What happens when the size of the input string is bigger than the size of the Socket's receive buffer? I am getting to grips (slowly) with Java's IO libraries, so any pointers are much appreciated. Thank you!

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• Facebook like button issue.

  - by Ross Hale

  Hello community, We're having some trouble getting our like button to work. It seemed to work last week but suddenly it's stopped working. Basically when clicking "Like", we get an error saying: You failed to provide a valid list of administators. You need to supply the administors using either a "fb:app_id" meta tag, or using a "fb:admins" meta tag to specify a comma-delimited list of Facebook users. Our section looks like this: <html xmlns="http://www.w3.org/1999/xhtml" xmlns:og="http://opengraphprotocol.org/schema/" xmlns:fb="http://www.facebook.com/2008/fbml" xml:lang="en" lang="en"> <head> <meta property="fb:app_id" content="number"/> <meta property="fb:admins" content="number"/> <meta property="og:title" content="title"/> <meta property="og:type" content="website"/> <meta property="og:url" content="url with trailing slash"/> <meta property="og:image" content="url to image"/> <meta property="og:site_name" content="Site Name"/> </head> Help?

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• Is this a variation of the traveling salesman problem?

  - by Ville Koskinen

  I'm interested in a function of two word lists, which would return an order agnostic edit distance between them. That is, the arguments would be two lists of (let's say space delimited) words and return value would be the minimum sum of the edit (or Levenshtein) distances of the words in the lists. Distance between "cat rat bat" and "rat bat cat" would be 0. Distance between "cat rat bat" and "fat had bad" would be the same as distance between "rat bat cat" and "had fat bad", 4. In the case the number of words in the lists are not the same, the shorter list would be padded with 0-length words. My intuition (which hasn't been nurtured with computer science classes) does not find any other solution than to use brute force: |had|fat|bad| a solution ---+---+---+---+ +---+---+---+ cat| 2 | 1 | 2 | | | 1 | | ---+---+---+---+ +---+---+---+ rat| 2 | 1 | 2 | | 3 | | | ---+---+---+---+ +---+---+---+ bat| 2 | 1 | 1 | | | | 4 | ---+---+---+---+ +---+---+---+ Starting from the first row, pick a column and go to the next rows without ever revisiting a column you have already visited. Do this over and over again until you've tried all combinations. To me this sounds a bit like the traveling salesman problem. Is it, and how would you solve my particular problem?

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