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  • At which line in the following code should I commit my unit of work?

    - by Pure.Krome
    I have the following code which is in a transaction. I'm not sure where/when I should be commiting my unit of work. On purpose, I've not mentioned what type of Respoistory i'm using - eg. Linq-To-Sql, Entity Framework 4, NHibernate, etc. If someone knows where, can they please explain WHY they have said, where? (i'm trying to understand the pattern through example(s), as opposed to just getting my code to work). Here's what i've got :- using ( TransactionScope transactionScope = new TransactionScope ( TransactionScopeOption.RequiresNew, new TransactionOptions { IsolationLevel = IsolationLevel.ReadUncommitted } ) ) { _logEntryRepository.InsertOrUpdate(logEntry); //_unitOfWork.Commit(); // Here, commit #1 ? // Now, if this log entry was a NewConnection or an LostConnection, // then we need to make sure we update the ConnectedClients. if (logEntry.EventType == EventType.NewConnection) { _connectedClientRepository.Insert( new ConnectedClient { LogEntryId = logEntry.LogEntryId }); //_unitOfWork.Commit(); // Here, commit #2 ? } // A (PB) BanKick does _NOT_ register a lost connection, // so we need to make sure we handle those scenario's as a LostConnection. if (logEntry.EventType == EventType.LostConnection || logEntry.EventType == EventType.BanKick) { _connectedClientRepository.Delete( logEntry.ClientName, logEntry.ClientIpAndPort); //_unitOfWork.Commit(); // Here, commit #3 ? } _unitOfWork.Commit(); // Here, commit #4 ? transactionScope.Complete(); }

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  • Reading/Writing DataTables to and from an OleDb Database LINQ

    - by jsmith
    My current project is to take information from an OleDbDatabase and .CSV files and place it all into a larger OleDbDatabase. I have currently read in all the information I need from both .CSV files, and the OleDbDatabase into DataTables.... Where it is getting hairy is writing all of the information back to another OleDbDatabase. Right now my current method is to do something like this: OleDbTransaction myTransaction = null; try { OleDbConnection conn = new OleDbConnection("PROVIDER=Microsoft.Jet.OLEDB.4.0;" + "Data Source=" + Database); conn.Open(); OleDbCommand command = conn.CreateCommand(); string strSQL; command.Transaction = myTransaction; strSQL = "Insert into TABLE " + "(FirstName, LastName) values ('" + FirstName + "', '" + LastName + "')"; command.CommandType = CommandType.Text; command.CommandText = strSQL; command.ExecuteNonQuery(); conn.close(); catch (Exception) { // IF invalid data is entered, rolls back the database myTransaction.Rollback(); } Of course, this is very basic and I'm using an SQL command to commit my transactions to a connection. My problem is I could do this, but I have about 200 fields that need inserted over several tables. I'm willing to do the leg work if that's the only way to go. But I feel like there is an easier method. Is there anything in LINQ that could help me out with this?

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  • Pre-populate iPhone Safari SQLite DB

    - by Matt Rogish
    I'm working with a PhoneGap app that uses Safari local storage (SQlite DB) via Javascript: http://developer.apple.com/safari/library/documentation/iPhone/Conceptual/SafariJSDatabaseGuide/UsingtheJavascriptDatabase/UsingtheJavascriptDatabase.html On first load, the app creates the database, tables, and populates the data via a series of INSERT statements. If the user closes the app while this processing is happening, then my app database is left in an inconsistent state. What I prefer to do is deploy the SQLite DB as part of my iTunes App packaging so nothing must be populated at app cold start. However, I'm not sure if that is possible -- all of the google hits for this topic that I can find are referring to the core-data provided SQLite which is not what we're using... If it's not possible, could I wrap the entire thing in a transaction and keep re-trying it when the app is restarted? Failing that, I guess I can create a simple table with one boolean column "is_app_db_loaded?" and set it to true after I've processed all my inserts. But that's really gross... Ideas? Thanks!!

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  • Entity Framework autoincrement key

    - by Tommy Ong
    I'm facing an issue of duplicated incremental field on a concurrency scenario. I'm using EF as the ORM tool, attempting to insert an entity with a field that acts as a incremental INT field. Basically this field is called "SequenceNumber", where each new record before insert, will read the database using MAX to get the last SequenceNumber, append +1 to it, and saves the changes. Between the getting of last SequenceNumber and Saving, that's where the concurrency is happening. I'm not using ID for SequenceNumber as it is not a unique constraint, and may reset on certain conditions such as monthly, yearly, etc. InvoiceNumber | SequenceNumber | DateCreated INV00001_08_14 | 1 | 25/08/2014 INV00001_08_14 | 1 | 25/08/2014 <= (concurrency is creating two SeqNo 1) INV00002_08_14 | 2 | 25/08/2014 INV00003_08_14 | 3 | 26/08/2014 INV00004_08_14 | 4 | 27/08/2014 INV00005_08_14 | 5 | 29/08/2014 INV00001_09_14 | 1 | 01/09/2014 <= (sequence number reset) Invoice number is formatted based on the SequenceNumber. After some research I've ended up with these possible solutions, but wanna know the best practice 1) Optimistic Concurrency, locking the table from any reads until the current transaction is completed (not fancy of this idea as I guess performance will be of a great impact?) 2) Create a Stored Procedure solely for this purpose, does select and insert on a single statement as such concurrency is at minimum (would prefer a EF based approach if possible)

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  • PHP Commercial Project Function define

    - by Shiro
    Currently I am working with a commercial project with PHP. I think this question not really apply to PHP for all programming language, just want to discuss how your guys solve it. I work in MVC framework (CodeIgniter). all the database transaction code in model class. Previously, I seperate different search criteria with different function name. Just an example function get_student_detail_by_ID($id){} function get_student_detail_by_name($name){} as you can see the function actually can merge to one, just add a parameter for it. But something you are rushing with project, you won't look back previously got what similar function just make some changes can meet the goal. In this case, we found that there is a lot function there and hard to maintenance. Recently, we try to group the entity to one ultimate search something like this function get_ResList($is_row_count=FALSE, $record_start=0, $arr_search_criteria='', $paging_limit=20, $orderby='name', $sortdir='ASC') we try to make this function to fit all the searching criteria. However, our system getting bigger and bigger, the search criteria not more 1-2 tables. It require join with other table with different purpose. What we had done is using IF ELSE, if(bla bla bla) { $sql_join = JOIN_SOME_TABLE; $sql_where = CONDITION; } at the end, we found that very hard to maintance the function. it is very hard to debug as well. I would like to ask your opinion, what is the commercial solution they solve this kind of issue, how to define a function and how to revise it. I think this is link project management skill. Hope you willing to share with us. Thanks.

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  • Storing Credit Card Numbers in SESSION - ways around it?

    - by JM4
    I am well aware of PCI Compliance so don't need an earful about storing CC numbers (and especially CVV nums) within our company database during checkout process. However, I want to be safe as possible when handling sensitive consumer information and am curious how to get around passing CC numbers from page to page WITHOUT using SESSION variables if at all possible. My site is built in this way: Step 1) collect Credit Card information from customer - when customer hits submit, the information is first run through JS validation, then run through PHP validation, if all passes he moves to step 2. Step 2) Information is displayed on a review page for customer to make sure the details of their upcoming transaction are shown. Only the first 6 and last 4 of the CC are shown on this page but card type, and exp date are shwon fully. If he clicks proceed, Step 3) The information is sent to another php page which runs one last validation, sends information through secure payment gateway, and string is returned with details. Step 4) If all is good and well, the consumer information (personal, not CC) is stored in DB and redirected to a completion page. If anything is bad, he is informed and told to revisit the CC processing page to try again (max of 3 times). Any suggestions?

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  • SQL Server race condition issue with range lock

    - by Freek
    I'm implementing a queue in SQL Server (please no discussions about this) and am running into a race condition issue. The T-SQL of interest is the following: set transaction isolation level serializable begin tran declare @RecordId int declare @CurrentTS datetime2 set @CurrentTS=CURRENT_TIMESTAMP select top 1 @RecordId=Id from QueuedImportJobs with (updlock) where Status=@Status and (LeaseTimeout is null or @CurrentTS>LeaseTimeout) order by Id asc if @@ROWCOUNT> 0 begin update QueuedImportJobs set LeaseTimeout = DATEADD(mi,5,@CurrentTS), LeaseTicket=newid() where Id=@RecordId select * from QueuedImportJobs where Id = @RecordId end commit tran RecordId is the PK and there is also an index on Status,LeaseTimeout. What I'm basically doing is select a record of which the lease happens to be expired, while simultaneously updating the lease time with 5 minutes and setting a new lease ticket. So the problem is that I'm getting deadlocks when I run this code in parallel using a couple of threads. I've debugged it up to the point where I found out that the update statement sometimes gets executing twice for the same record. Now, I was under the impression that the with (updlock) should prevent this (it also happens with xlock btw, not with tablockx). So it actually look like there is a RangeS-U and a RangeX-X lock on the same range of records, which ought to be impossible. So what am I missing? I'm thinking it might have something to do with the top 1 clause or that SQL Server does not know that where Id=@RecordId is actually in the locked range? Deadlock graph: Table schema (simplified):

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  • Downloading Images to a specific directory using Automator / Applescript

    - by fighella
    Im trying to use a variable in Automator to save images into a specific folder. Strangely when you create a new folder and you use a variable, it allows you to set the base path... but if you try to "Download URL" it does not allow you to select the base path to add the variable onto and it breaks the transaction. Im sure applescript could do a better job, but I can't seem to figure it out. Example. There is a photo gallery called Cats and Dogs. I am able to grab the Cats and Dogs title and make it my variable... it makes a new folder on my desktop called Cats and Dogs (from the Variable)... I am then able to grab all the images in the gallery as a result from "Get Image URL's from webpage"... This works great... then I try to "Download the URLs" and I want to download them to the new "Cats and Dogs" folder I have created. But I can't seem to make that work, because I can't set the path in the Download the URLs box in automator... This ends up being really useful when I have 100 galleries I need to rip to my desktop... Of course I could move the files in the newly created folder by hand once saved... but then I would have to do this for each gallery... Any suggestions?

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  • How to write this snippet in Python?

    - by morpheous
    I am learning Python (I have a C/C++ background). I need to write something practical in Python though, whilst learning. I have the following pseudocode (my first attempt at writing a Python script, since reading about Python yesterday). Hopefully, the snippet details the logic of what I want to do. BTW I am using python 2.6 on Ubuntu Karmic. Assume the script is invoked as: script_name.py directory_path import csv, sys, os, glob # Can I declare that the function accepts a dictionary as first arg? def getItemValue(item, key, defval) return !item.haskey(key) ? defval : item[key] dirname = sys.argv[1] # declare some default values here weight, is_male, default_city_id = 100, true, 1 # fetch some data from a database table into a nested dictionary, indexed by a string curr_dict = load_dict_from_db('foo') #iterate through all the files matching *.csv in the specified folder for infile in glob.glob( os.path.join(dirname, '*.csv') ): #get the file name (without the '.csv' extension) code = infile[0:-4] # open file, and iterate through the rows of the current file (a CSV file) f = open(infile, 'rt') try: reader = csv.reader(f) for row in reader: #lookup the id for the code in the dictionary id = curr_dict[code]['id'] name = row['name'] address1 = row['address1'] address2 = row['address2'] city_id = getItemValue(row, 'city_id', default_city_id) # insert row to database table finally: f.close() I have the following questions: Is the code written in a Pythonic enough way (is there a better way of implementing it)? Given a table with a schema like shown below, how may I write a Python function that fetches data from the table and returns is in a dictionary indexed by string (name). How can I insert the row data into the table (actually I would like to use a transaction if possible, and commit just before the file is closed) Table schema: create table demo (id int, name varchar(32), weight float, city_id int); BTW, my backend database is postgreSQL

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  • SQL Server stored procedure + set error message from the records of a table

    - by lucky
    Hello, My question is I have a table with the set of records. I am calling a stored procedure for some other purpose. But when ever it finds some duplicate records. It need to return as error message back to php. C1 C2 c3 abc 32 21.03.2010 def 35 04.04.2010 pqr 45 30.03.2010 abc 12 04.05.2010 xyz 56 01.03.2010 ghi 21 06.05.2010 def 47 17.02.2010 klm 93 04.03.2010 xyz 11 01.03.2010 For the above set it need to check for the records that has the same c1. The stored procedure should return as abc,def,xyz are duplicate. I tried something like this. This will not work it has more than 1 set of duplicate records. Please help me to enhance this to solve the purpose. SET @duplicate = (SELECT c1 FROM temp GROUP BY c1 HAVING count(c1) > 1) --Check for duplicate concession Nr. IF(len(@duplicate) > '1') BEGIN SET @error = @error + ' Duplicate C1 Number:- ' + @duplicate SET @errorcount = @errorcount + 1 END As this one type error I am checking for errorcount. IF @errorcount <> '0' BEGIN GOTO E_General_Error END -- If an error occurs, rollback and exit E_General_Error: PRINT 'Error' SET @error = @error IF @@error <> 0 SET @error = 'Database update failed' ROLLBACK TRANSACTION update_database RETURN END Now it is able to return Duplicate c1 number abc. If there are more than 1 problem comes. Thanks in advance!

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  • Dealing with SQLException with spring,hibernate & Postgres

    - by mad
    Hi im working on a project using HibernateDaoSUpport from my Daos from Spring & spring-ws & hibernate & postgres who will be used in a national application (means a lot of users) Actually, every exception from hibernate is automatically transformed into some specific Spring dataAccesException. I have a table with a keyword on the dabatase & a unique constraint on the keywords : no duplicate keywords is allowed. I have found twows ways to deal with with that in the Insert Dao: 1- Check for the duplicate manually (with a select) prior to doing your insert. I means that the spring transaction will have a SERIALIZABLE isolation level. The obvious drawback is that we have now 2 queries for a simple insert.Advantage: independent of the database 2-let the insert gone & catch the SqlException & convert it to a userfriendly message & errorcode to the final consumer of our webservices. Solution 2: Spring has developped a way to translate specific exeptions into customized exceptions. see http://www.oracle.com/technology/pub/articles/marx_spring.html In my case i would have a ConstraintViolationException. Ideally i would like to write a custom SQLExceptionTranslator to map the duplicate word constraint in the database with a DuplicateWordException. But i can have many unique constraints on the same table. So i have to get the message of the SQLEXceptions in order to find the name of the constraint declared in the create table "uq_duplicate-constraint" for example. Now i have a strong dependency with the database. Thanks in advance for your answers & excuse me for my poor english (it is not my mother tongue)

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  • IBM WESB/WAS JCA security configuration

    - by user594883
    I'm working with IBM tools. I have a Websphere ESB (WESB) and a CICS transaction gateway (CTG). The basic set-up is as follows: A SOAP service needs data from CICS. The SOAP-service is connecting to service bus (WESB) to handle data and protocol transformation and then WESB calls the CTG which in turn calls CICS and the reply is handled vice verse (synchronously). WESB calls the CTG using Resource Adapter and JCA connector (or CICS adapter as it is called in WESB). Now, I have all the pieces in place and working. My question is about the security, and even though I'm working with WESB, the answer is probably the same as in Websphere Application Server (WAS). The Resource Adaper is secured using JAAS - J2C authentication data. I have configured the security using J2C authentication data entry, so basically I have a reference in the application I'm running and at runtime the application does a lookup for the security attributes from the server. So basically I'm always accessing the CICS adapter with the same security reference. My problem is that I need to access the resource in more dynamic way in the future. The security cannot be welded into the application anymore but instead given as a parameter. Could some WESB or WAS guru help me out, how this could be done in WESB/WAS exactly?

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  • Logic for rate approximation

    - by Rohan
    I am looking for some logic to solve the below problem. There are n transaction amounts : T1,T2,T3.. Tn. Commission for these transactions are calculated using a rate table provided as below. if amount between 0 and A1 - rate is r1 if amount between A1 and A2 - rate is r2 if amount between A2 and A1 - rate is r3 ... ... if amount greater than An - rate is r4 So if T1 < A1 then rate table returns r1 else if r1 < T1 < r2;it returns r2. So,lets says the rate table results for T1,T2 and T3 are r1,r2 and r3 respectively. Commission C = T1 * r1 + T2 * r2 + T3 * r3 e.g; if rate table is defined(rates are in %) 0 - 2500 - 1 2501 - 5000 - 2 5001 - 10000 - 4 10000 or more- 6 If T1 = 6000,T2 = 3000, T3 = 2000, then C= 6000 * 0.04 + 3000* 0.02 + 2000 * 0.01 = 320 Now my problem is whether we can approximate the commission amount if instead of individual values of T1,T2 and T3 we are provided with T1+T2+T3 (T) In the above example if T (11000) is applied to the rate tablewe would get 6% and which would result in a commision of 600. Is there a way to approximate the commission value given T instead of individual values of T1,T2,T3?

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  • how to use a list containing the query result with hibernate and display it in jsp

    - by kawtousse
    hi everyone, In my servlet I construct the query like the following: net.sf.hibernate.Session s = null; net.sf.hibernate.Transaction tx; try { s= HibernateUtil.currentSession(); tx=s.beginTransaction(); Query query = s.createQuery("select opcemployees.Nom,opcemployees.Prenom,dailytimesheet.TrackingDate,dailytimesheet.Activity," + "dailytimesheet.ProjectCode,dailytimesheet.WAName,dailytimesheet.TaskCode," + "dailytimesheet.TimeSpent,dailytimesheet.PercentTaskComplete from Opcemployees opcemployees,Dailytimesheet dailytimesheet " + "where opcemployees.Matricule=dailytimesheet.Matricule and dailytimesheet.Etat=3 " + "group by opcemployees.Nom,opcemployees.Prenom" ); List opdts= query.list(); request.setAttribute("items", opdts); request.getRequestDispatcher("EspaceValidation.jsp").forward(request, response); } catch (HibernateException e){ e.printStackTrace();} But in the jsp I can't display the result correctly. I do the following in JSP: <table> <c:forEach items="${items}" var="item"> <tr> <td>${item}</td> </tr> </c:forEach> </table> thanks for help.

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  • how to remove subsets form given text file

    - by user324887
    i have a problem like this 10 20 30 40 70 20 30 70 30 40 10 20 29 70 80 90 20 30 40 40 45 65 10 20 80 45 65 20 I want to remove all subset transaction from this file. output file should be like follows 10 20 30 40 70 29 70 80 90 20 30 40 40 45 65 10 20 80 Where records like 20 30 70 30 40 10 20 45 65 20 are removed because of they are subset of other records. i AM using set for this but i am not able to create one set for one line can anybody know how to do this please help me here i am sending you my code include include include using namespace std; using namespace std; set s1; int main() { FILE fp = fopen ( "abc.txt", "r" ); if ( fp != NULL ) { char line [ 128 ]; / or other suitable maximum line size */ while ( fgets ( line, sizeof line, fp ) != NULL ) /* read a line */ { istringstream iss(line); do { string sub; iss >> sub; s1.insert(sub); } while (iss); for (set<string>::const_iterator p = s1.begin( );p != s1.end( ); ++p) cout << *p << endl; } } }

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  • Anyone NOT using a Web Framework? Why?

    - by tom
    I'm well aware of the many reasons to use a web framework. I'm just wondering whether anyone out there is using absolutely no web framework whatsoever to develop their web projects. I would really love to know the reason(s) why you're not using a web framework. For the sake of this discussion, your programming language of choice does not matter. Some possibilities for discussion: You don't hide behind an ORM. You don't rely on any sort of templating system. You think MVC is a really nice TLA but lacks an essential vowel or two. No need for any additional javascript framework tomfoolery. You just write as much code as possible in your native programming language(s). Summary of reasons thus far: Language learning opportunities. Specific performance reasons (write-intensive transaction processing). Seeking more nuanced control over your data and applications (less abstraction). You're building your own framework! Prove to yourself that you can succeed (or fail) just like the big framework-building gurus. Integration issues with unpopular/legacy technologies (exotic databases or protocols come to mind). Big company, lots of code, no talent nor buy-in present to move to a web framework. Some frameworks really lock you in and cannot perpetually grow along with your needs. These few black sheep don't make it easy to jump outside of the framework, write some custom code, and easily jump back in. When you finally escape the asylum, you'll never look back.

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  • C#: HTTPWebResponse using application/x-www-form-urlencoded

    - by CSharpened
    So I sent an HTTPWebRequest using application/x-www-form-urlencoded as my content type. I assume that this means the reponse will be returned in a similar type? (EDIT: Have now been told this isn't the case) My question is this. How do I access the different key/value pairs returned in the response. My code so far looks like this. I can of course read the string but surely there is a better way to access the data other than ripping the string apart. HttpWebResponse response = SendPOSTRequest("https://site/page?Service=foo", content.ToString(), "", "", true); string responseCode = response.StatusCode.ToString(); string responseStatusDescription = response.StatusDescription; StreamReader sr = new StreamReader(response.GetResponseStream()); string result = sr.ReadToEnd(); I tried using XML/linq to read the elements into an XDocument but of course it is not being returned in XML form. Assume I have 3 or 4 different pieces of information in there how could I read them out? EDIT: I have just checked and the data is being returned as text/plain. How can this be processed easily? EDIT: The response string once retrieved via a streamreader is: VPSProtocol=2.23 Status=OK StatusDetail=Server transaction registered successfully. VPSTxId={FDC93F3D-FC64-400D-875F-0B7E855AD81F} SecurityKey=***** NextURL=https://foo.com/PaymentPage.asp?TransactionID={875F-0B7E855AD81F}

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  • How would you code an efficient Circular Buffer in Java or C#

    - by Cheeso
    I want a simple class that implements a fixed-size circular buffer. It should be efficient, easy on the eyes, generically typed. EDIT: It need not be MT-capable, for now. I can always add a lock later, it won't be high-concurrency in any case. Methods should be: .Add and I guess .List, where I retrieve all the entries. On second thought, Retrieval I think should be done via an indexer. At any moment I will want to be able to retrieve any element in the buffer by index. But keep in mind that from one moment to the next Element[n] may be different, as the Circular buffer fills up and rolls over. This isn't a stack, it's a circular buffer. Regarding "overflow": I would expect internally there would be an array holding the items, and over time the head and tail of the buffer will rotate around that fixed array. But that should be invisible from the user. There should be no externally-detectable "overflow" event or behavior. This is not a school assignment - it is most commonly going to be used for a MRU cache or a fixed-size transaction or event log.

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  • PayPal sandbox anomalies

    - by Christian
    When testing some donations on my local machine, I set various key=value pairs to do various things (return to specific thank you page, get POST data from PayPal and not GET data and others) I also built my code around the response from the PayPal sandbox. BUT, when my code goes to the production server and we switch on live payments and test with real accounts and money, a few strange things happen; We get a GET response from PayPal - the URL is filled with crap. We get no transaction details. This is the biggie, no name, no txn_id, no dates, nothing. We get a handful of keys etc, its not totally empty and the payment has gone through, but nowhere near the verbosity of the sandbox. Curious about why this might be? It doesn't really make sense to have a sandbox (or dev environment) that is substantially different from the production environment. Or, am I missing something? EDIT: Still no response to my question in the PayPal Developer Forums. I don't even get a donation amount back from PayPal. Is this a setting maybe? EDIT #2: Two of you have suggested to check PDT and Auto-Return. The data analytics guy for the project only 2 hrs ago suggested the same. I have asked the client to confirm this. I can't see a setting for it in the Sandbox so can assume that it is enabled by default?

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  • ecommerce platform or from scratch? customer specific catalogs and purchase orders

    - by rafi
    I have a possible freelance job in front of me for a distributor who wants product ordering set up but the orders are all P.O.s basically - no actual credit card or paypal transaction. The customer is simply billed and the order archived. Customers will need to login to this site and each customer will have their own custom catalog of a few dozen products which have been setup via a control panel this distributor uses. So there will be a master catalog of over 1,000 products (perhaps browsable but not to be ordered from on the site) but each customer will only be able to order from the products specified for their accounts. I know I can build this from scratch but I figured it's worth looking into what ecommerce platforms would get me a nice head start. Obviously shopping cart, order history, catalog management are concepts that I can reuse but are any of the ecommerce systems out there also capable of handling custom catalogs (maybe as multi-stores?) or transactions billed to accounts without credit card? The more I could reuse the better. I've messed with OSCommerce (way back) and a little Zen Cart more recently. I've also worked on a number of totally custom e-commerce sites. But my knowledge of the open source e-commerce tools is pretty limited and I'm trying to keep the effort as simple as I possibly can on this. I'm pretty flexible on the language of the platform by the way. Thanks in advance.

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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • Building "isolated" and "automatically updated" caches (java.util.List) in Java.

    - by Aidos
    Hi Guys, I am trying to write a framework which contains a lot of short-lived caches created from a long-living cache. These short-lived caches need to be able to return their entier contents, which is a clone from the original long-living cache. Effectively what I am trying to build is a level of transaction isolation for the short-lived caches. The user should be able to modify the contents of the short-lived cache, but changes to the long-living cache should not be propogated through (there is also a case where the changes should be pushed through, depending on the Cache type). I will do my best to try and explain: master-cache contains: [A,B,C,D,E,F] temporary-cache created with state [A,B,C,D,E,F] 1) temporary-cache adds item G: [A,B,C,D,E,F] 2) temporary-cache removes item B: [A,C,D,E,F] master-cache contains: [A,B,C,D,E,F] 3) master-cache adds items [X,Y,Z]: [A,B,C,D,E,F,X,Y,Z] temporary-cache contains: [A,C,D,E,F] Things get even harder when the values in the items can change and shouldn't always be updated (so I can't even share the underlying object instances, I need to use clones). I have implemented the simple approach of just creating a new instance of the List using the standard Collection constructor on ArrayList, however when you get out to about 200,000 items the system just runs out of memory. I know the value of 200,000 is excessive to iterate, but I am trying to stress my code a bit. I had thought that it might be able to somehow "proxy" the list, so the temporary-cache uses the master-cache, and stores all of it's changes (effectively a Memento for the change), however that quickly becomes a nightmare when you want to iterate the temporary-cache, or retrieve an item at a specific index. Also given that I want some modifications to the contents of the list to come through (depending on the type of the temporary-cache, whether it is "auto-update" or not) and I get completly out of my depth. Any pointers to techniques or data-structures or just general concepts to try and research will be greatly appreciated. Cheers, Aidos

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  • Maintenance tool for Application Database

    - by Thierry
    Hello ! Does anybody know about a good tool which help maintaining the database of an application ? I'm working on an application which uses a database (Microsoft Sql Server). When a development requires to change something in the database (e.g., structure, data migration...), we create a script (Transact-SQL script) and add it into our revision control tool (subversion - that tool also contains our code). Each script must add a line in a log table to keep a trace of all the scripts that have been ran into a database. In order to build a database for our application, one needs to run all scripts ordered by their creation date. I'm not really happy with this technique notably because it make application migration a bit hard. If we want to install a new version of the application somewhere, e.g., migrate from version 1.3 to 2.1, we must get all the scripts between these two versions. Then run them and ensure that everything is done in a transaction... For sure we could built home-made tools to help but I wonder if some tools already exists to do that kind of job.

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  • Spring Security ACL: NotFoundException from JDBCMutableAclService.createAcl

    - by user340202
    Hello, I've been working on this task for too long to abandon the idea of using Spring Security to achieve it, but I wish that the community will provide with some support that will help reduce the regret that I have for choosing Spring Security. Enough ranting and now let's get to the point. I'm trying to create an ACL by using JDBCMutableAclService.createAcl as follows: [code] public void addPermission(IWFArtifact securedObject, Sid recipient, Permission permission, Class clazz) { ObjectIdentity oid = new ObjectIdentityImpl(clazz.getCanonicalName(), securedObject.getId()); this.addPermission(oid, recipient, permission); } @Override @Transactional(propagation = Propagation.REQUIRED, isolation = Isolation.READ_UNCOMMITTED, readOnly = false) public void addPermission(ObjectIdentity oid, Sid recipient, Permission permission) { SpringSecurityUtils.assureThreadLocalAuthSet(); MutableAcl acl; try { acl = this.mutableAclService.createAcl(oid); } catch (AlreadyExistsException e) { acl = (MutableAcl) this.mutableAclService.readAclById(oid); } // try { // acl = (MutableAcl) this.mutableAclService.readAclById(oid); // } catch (NotFoundException nfe) { // acl = this.mutableAclService.createAcl(oid); // } acl.insertAce(acl.getEntries().length, permission, recipient, true); this.mutableAclService.updateAcl(acl); } [/code] The call throws a NotFoundException from the line: [code] // Retrieve the ACL via superclass (ensures cache registration, proper retrieval etc) Acl acl = readAclById(objectIdentity); [/code] I believe this is caused by something related to Transactional, and that's why I have tested with many TransactionDefinition attributes. I have also doubted the annotation and tried with declarative transaction definition, but still with no luck. One important point is that I have used the statement used to insert the oid in the database earlier in the method directly on the database and it worked, and also threw a unique constraint exception at me when it tried to insert it in the method. I'm using Spring Security 2.0.8 and IceFaces 1.8 (which doesn't support spring 3.0 but definetely supprorts 2.0.x, specially when I keep caling SpringSecurityUtils.assureThreadLocalAuthSet()). My AppServer is Tomcat 6.0, and my DB Server is MySQL 6.0 I wish to get back a reply soon because I need to get this task off my way

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  • MSMQ - Message Queue Abstraction and Pattern

    - by Maxim Gershkovich
    Hi All, Let me define the problem first and why a messagequeue has been chosen. I have a datalayer that will be transactional and EXTREMELY insert heavy and rather then attempt to deal with these issues when they occur I am hoping to implement my application from the ground up with this in mind. I have decided to tackle this problem by using the Microsoft Message Queue and perform inserts as time permits asynchronously. However I quickly ran into a problem. Certain inserts that I perform may need to be recalled (ie: retrieved) immediately (imagine this is for POS system and what happens if you need to recall the last transaction - one that still hasn’t been inserted). The way I decided to tackle this problem is by abstracting the MessageQueue and combining it in my data access layer thereby creating the illusion of a single set of data being returned to the user of the datalayer (I have considered the other issues that occur in such a scenario (ie: essentially dirty reads and such) and have concluded for my purposes I can control these issues). However this is where things get a little nasty... I’ve worked out how to get the messages back and such (trivial enough problem) but where I am stuck is; how do I create a generic (or at least somewhat generic) way of querying my message queue? One where I can minimize the duplication between the SQL queries and MessageQueue queries. I have considered using LINQ (but have very limited understanding of the technology) and have also attempted an implementation with Predicates which so far is pretty smelly. Are there any patterns for such a problem that I can utilize? Am I going about this the wrong way? Does anyone have an of their own ideas about how I can tackle this problem? Does anyone even understand what I am talking about? :-) Any and ALL input would be highly appreciated and seriously considered… Thanks again.

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