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  • PHP/MySQL time zone migration

    - by El Yobo
    I have an application that currently stores timestamps in MySQL DATETIME and TIMESTAMP values. However, the application needs to be able to accept data from users in multiple time zones and show the timestamps in the time zone of other users. As such, this is how I plan to amend the application; I would appreciate any suggestions to improve the approach. Database modifications All TIMESTAMPs will be converted to DATETIME values; this is to ensure consistency in approach and to avoid having MySQL try to do clever things and convert time zones (I want to keep the conversion in PHP, as it involves less modification to the application, and will be more portable when I eventually manage to escape from MySQL). All DATETIME values will be adjusted to convert them to UTC time (currently all in Australian EST) Query modifications All usage of NOW() to be replaced with UTC_TIMESTAMP() in queries, triggers, functions, etc. Application modifications The application must store the time zone and preferred date format (e.g. US vs the rest of the world) All timestamps will be converted according to the user settings before being displayed All input timestamps will be converted to UTC according to the user settings before being input Additional notes Converting formats will be done at the application level for several main reasons The approach to converting time zones varies from DB to DB, so handing it there will be non-portable (and I really hope to be migrating away from MySQL some time in the not-to-distant future). MySQL TIMESTAMPs have limited ranges to the permitted dates (~1970 to ~2038) MySQL TIMESTAMPs have other undesirable attributes, including bizarre auto-update behaviour (if not carefully disabled) and sensitivity to the server zone settings (and I suspect I might screw these up when I migrate to Amazon later in the year). Is there anything that I'm missing here, or does anyone have better suggestions for the approach?

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  • getting an exception when refreshing the configuration in memory on change to external config file

    - by RKP
    Hi, I have a windows service which reads the config settings from an external file which is located at a different path than the path to the executable for the windows service. the windows service uses a FileSystemWatcher to monitor the changes to the external config file and when it the config file is changed, it should refresh the settings in memory by reading the updated settings from the config file. but this is where I am getting an exception "ConfigurationErrorsException" and the message is "An error occurred creating the configuration section handler for appSettings: The process cannot access the file 'M:\somefolder\WindowsService1.Config' because it is being used by another process." and the inner exception is actually "IOException" with same message. here is the code. I am not sure what is wrong with the code. Please help. protected void watcher_Changed(object sender, FileSystemEventArgs e) { ConfigurationManager.RefreshSection(ConfigSectionName); WriteToEventLog(ConfigKeyCheck); if (FileChanged != null) FileChanged(this, EventArgs.Empty); } private void WriteToEventLog(string key) { if (EventLog.SourceExists(ServiceEventSource)) { EventLog.WriteEntry(ServiceEventSource, string.Format("key:{0}, value:{1}", key, ConfigurationManager.AppSettings[key])); } }

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  • Fastest XML parser for small, simple documents in Java

    - by Varkhan
    I have to objectify very simple and small XML documents (less than 1k, and it's almost SGML: no namespaces, plain UTF-8, you name it...), read from a stream, in Java. I am using JAXP to process the data from my stream into a Document object. I have tried Xerces, it's way too big and slow... I am using Dom4j, but I am still spending way too much time in org.dom4j.io.SAXReader. Does anybody out there have any suggestion on a faster, more efficient implementation, keeping in mind I have very tough CPU and memory constraints? [Edit 1] Keep in mind that my documents are very small, so the overhead of staring the parser can be important. For instance I am spending as much time in org.xml.sax.helpers.XMLReaderFactory.createXMLReader as in org.dom4j.io.SAXReader.read [Edit 2] The result has to be in Dom format, as I pass the document to decision tools that do arbitrary processing on it, like switching code based on the value of arbitrary XPaths, but also extracting lists of values packed as children of a predefined node. [Edit 3] In any case I eventually need to load/parse the complete document, since all the information it contains is going to be used at some point. (This question is related to, but different from, http://stackoverflow.com/questions/373833/best-xml-parser-for-java )

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  • More efficient R / Sweave / TeXShop work-flow?

    - by user594795
    I've now got everything to work properly on my Mac OS X 10.6 machine so that I can create decent looking LaTeX documents with Sweave that include snippets of R code, output, and LaTeX formatting together. Unfortunately, I feel like my work-flow is a bit clunky and inefficient: Using TextWrangler, I write LaTeX code and R code (surrounded by <<= above and @ below R code chunk) together in one .Rnw file. After saving changes, I call the .Rnw file from R using the Sweave command Sweave(file="/Users/mymachine/Documents/Assign4.Rnw", syntax="SweaveSyntaxNoweb") In response, R outputs the following message: You can now run LaTeX on 'Assign4.tex' So then I find the .tex file (Assign4.tex) in the R directory and copy it over to the folder in my documents ~/Documents/ where the .Rnw file is sitting (to keep everything in one place). Then I open the .tex file (e.g. Assign4.tex) in TeXShop and compile it there into pdf format. It is only at this point that I get to see any changes I have made to the document and see if it 'looks nice'. Is there a way that I can compile everything with one button click? Specifically it would be nice to either call Sweave / R directly from TextWrangler or TeXShop. I suspect it might be possible to code a script in Terminal to do it, but I have no experience with Terminal. Please let me know if there's any other things I can do to streamline or improve my work flow.

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  • C# + Querying XML with LINQ

    - by user336786
    Hello, I'm learning to use LINQ. I have seen some videos online that have really impressed me. In an effort to learn LINQ myself, I decided to try to write a query to the NOAA web service. If you put "http://www.weather.gov/forecasts/xml/sample_products/browser_interface/ndfdBrowserClientByDay.php?zipCodeList=20001&format=24+hourly&startDate=2010-06-10&numDays=5" in your browser's address bar, you will see some XML. I have successfully retrieved that XML in a C# program. I am loading the XML into a LINQable entity by doing the following: string xml = QueryWeatherService(); XDocument weather = XDocument.Parse(xml); I have a class called DailyForecast defined as follows: public class DailyForecast { public float HighTemperature { get; set; } public float LowTemperature { get; set; } public float PrecipitationPossibility { get; set; } public string WeatherSummary { get; set; } } I'm trying write a LINQ query that adheres to the structure of my DailyForecast class. At this time, I've only gotten to this far: var results = from day in response.Descendants("parameters") select day; Not very far I know. Because of the structure of the XML returned, I'm not sure it is possible to solely use a LINQ query. I think the only way to do this is via a loop and traverse the XML. I'm seeking someone to correct me if I'm wrong. Can someone please tell me if I can get results using purely LINQ that adhere to the structure of the DailyForecast class? If so, how? Thank you!

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  • PHP Session variable isset(..)=1 after session_start()

    - by Nicsoft
    Hello! I guess I am not understanding the scope of session variables, or the session itself, in PHP, hence this question: This is my code if(!session_id()==""){ echo "Getting rid of session"."</br>"; session_destroy(); } echo "Before session_start(): ".isset($_SESSION["first_date_of_week"])."</br>"; session_start(); echo "After session_start(): ".isset($_SESSION["first_date_of_week"])." ".$_SESSION["first_date_of_week"]->format("Y-m-d")."</br>"; The output is: Before session_start(): After session_start(): 1 2011-01-09 How come that when doing the isset(..) on the session variable it is set directly after starting the session, even though I haven't even used it or set it yet? It does, however, still have the same value as before. Also, session_id()="" since the if-clause is never triggered. I never kill the session, how come it is set to ""? I.e. I refresh the page and expects the session to still be alive. Using the isset(..) function is then pretty useless testing if it has been set already... Thanks in advance! /Niklas

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  • Weird problem with PHP mail() under Linux.

    - by Vilx-
    This is the case when it "works on my machine". Except that my machine is Windows, and the target is some sort of Linux. The idea is that the mail() function puts a newline between the MIME-Version and Content-Type headers, thus breaking the whole thing. Here's the code, simpliefied as much as possible: <?php $HTMLPart = chunk_split(base64_encode('<html><body style="color: red">Test.</body></html>')); $PlaintextPart = chunk_split(base64_encode('>>> TEST <<<')); $Headers =<<<AKAM From: "My Test" <[email protected]> Reply-To: [email protected] MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="9-1410065408-1410065408=:27514" AKAM; $Body =<<<AKAM This is a multi-part message in MIME format. --9-1410065408-1410065408=:27514 Content-Type: text/plain; charset="windows-1252" Content-Transfer-Encoding: base64 $PlaintextPart --9-1410065408-1410065408=:27514 Content-Type: text/html; charset="windows-1252" Content-Transfer-Encoding: base64 $HTMLPart --9-1410065408-1410065408=:27514-- AKAM; echo 'Try 3: '; echo mail('[email protected]', 'Testmail', $Body, $Headers) ? 'WIN' : 'FAIL'; ?>

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  • Is it possible to De-Serialize a new Derived class using Old Binary?

    - by Anand
    In my project I have a class which I Serialize in Binary format to the disk. Due to some new requirement I need to create a new class which is derived from the original class. eg [Serializable] public class Sample { String someString; int someInt; public Sample() { } public Sample(String _someString, int _someInt) { this.someInt = _someInt; this.someString = _someString; } public String SomeString { get { return someString; } } public int SomeInt { get { return someInt; } } } [Serializable] public class DerivedSample : Sample { String someMoreString; int someMoreInt; public DerivedSample () : base() { } public DerivedSample (String _someString, int _someInt, String _someMoreString, int _someMoreInt) : base(_someString, _someInt) { this.someMoreString = _someMoreString; this.someMoreInt = _someMoreInt; } public String SomeMoreString { get { return someMoreString; } } public int SomeMoreInt { get { return someMoreInt; } } } When I try to De serialize an old file which contains only object of Sample it works fine, in the current assembly. That means backward compatibility is there. But when I try to deserialize the file which contains object of DerivedSample using the previous version of the assembly application crashes. Which means forward compatibilty needs to be taken care off... It it possible to say read only the base class part of the object from new version of the file?

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  • django: results in in_bulk style without IDs

    - by valya
    in django 1.1.1, Place.objects.in_bulk() does not work and Place.objects.in_bulk(range(1, 100)) works and returns a dictionary of Ints to Places with indexes - primary keys. How to avoid using range in this situation (and avoid using a special query for ids, I just want to get all objects in this dictionary format) >>> Place.objects.in_bulk() Traceback (most recent call last): File "<console>", line 1, in <module> File "/usr/lib/python2.5/site-packages/Django-1.1.1-py2.5.egg/django/db/models/manager.py", line 144, in in_bulk return self.get_query_set().in_bulk(*args, **kwargs) TypeError: in_bulk() takes exactly 2 arguments (1 given) >>> Place.objects.in_bulk(range(1, 100)) {1L: <Place: "??? ????">, 3L: <Place: "???????????? ?????">, 4L: <Place: "????????? "??????"">, 5L: <Place: "????????? "??????"">, 8L: <Place: "????????? "??????????????"">, 9L: <Place: "??????? ????????">, 10L: <Place: "????????? ???????">, 11L: <Place: "??????????????? ???">, 14L: <Place: "????? ????? ??????">}

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  • How can I write an XML on my hard drive to GetRequestStream

    - by swolff1978
    I need to post raw xml to a site and read the response. With the following code I keep getting an "Unknown File Format" error and I'm not sure why. XmlDocument sampleRequest = new XmlDocument(); sampleRequest.Load(@"C:\SampleRequest.xml"); byte[] bytes = Encoding.UTF8.GetBytes(sampleRequest.ToString()); string uri = "https://www.sample-gateway.com/gw.aspx"; req = WebRequest.Create(uri); req.Method = "POST"; req.ContentLength = bytes.Length; req.ContentType = "text/xml"; using (var requestStream = req.GetRequestStream()) { requestStream.Write(bytes, 0, bytes.Length); } // Send the data to the webserver rsp = req.GetResponse(); XmlDocument responseXML = new XmlDocument(); using (var responseStream = rsp.GetResponseStream()) { responseXML.Load(responseStream); } I am fairly certain my issue is what/how I am writing to the requestStream so.. How can I modify that code so that I may write an xml located on the hard drive to the request stream?

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  • Simplest way to mix sequences of types with iostreams?

    - by Kylotan
    I have a function void write<typename T>(const T&) which is implemented in terms of writing the T object to an ostream, and a matching function T read<typename T>() that reads a T from an istream. I am basically using iostreams as a plain text serialisation format, which obviously works fine for most built-in types, although I'm not sure how to effectively handle std::strings just yet. I'd like to be able to write out a sequence of objects too, eg void write<typename T>(const std::vector<T>&) or an iterator based equivalent (although in practice, it would always be used with a vector). However, while writing an overload that iterates over the elements and writes them out is easy enough to do, this doesn't add enough information to allow the matching read operation to know how each element is delimited, which is essentially the same problem that I have with a single std::string. Is there a single approach that can work for all basic types and std::string? Or perhaps I can get away with 2 overloads, one for numerical types, and one for strings? (Either using different delimiters or the string using a delimiter escaping mechanism, perhaps.)

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  • Is there a table of OpenGL extensions, versions, and hardware support somewhere?

    - by Thomas
    I'm looking for some resource that can help me decide what OpenGL version my game needs at minimum, and what features to support through extensions. Ideally, a table of the following format: 1.0 1.1 1.2 1.2.1 1.3 ... multitexture - ARB ARB core core texture_float - EXT EXT ARB ARB ... (Not sure about the values I put in, but you get the idea.) The extension specs themselves, at opengl.org, list the minimum OpenGL version they need, so that part is easy. However, many extensions have been accepted and became core standard in subsequent OpenGL versions, but it is very hard to find when that happened. The only way I could find is to compare the full OpenGL standards document for each version. On a related note, I would also very much like to know which extensions/features are supported by which hardware, to help me decide what features I can safely use in my game, and which ones I need to make optional. For example, a big honkin' table like this: MAX_TEXTURE_IMAGE_UNITS MAX_VERTEX_TEXTURE_IMAGE_UNITS ... GeForce 6xxx 8 4 GeForce 7xxx 16 8 ATi x300 8 4 ... (Again, I'm making the values up.) The table could list hardware limitations from glGet but also support for particular extensions, and limitations of such extension support (e.g. what floating-point texture formats are supported in hardware). Any pointers to these or similar resources would be hugely appreciated!

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  • submittingthe form even if the form is in invalid state

    - by Abu Hamzah
    i am using asp.net web forms and i am using bassistance.de jquery validation.. i have bunch of fields in the form and its validatating how it suppose to but its still executing my code behind code, why is it doing that? here is my code: form: <script type="text/javascript"> $(document).ready(function() { $("#aspnetForm").validate({ rules: { <%=txtVisitName.UniqueID %>: { maxlength:1, //minlength: 12, required: true } ................. }, messages: { <%=txtVisitName.UniqueID %>: { required: "Enter visit name", minlength: jQuery.format("Enter at least {0} characters.") } ............ }, success: function(label) { label.html("&nbsp;").addClass("checked"); } }); $("#aspnetForm").validate(); }); </script> <div > <h1> Page</h1> <asp:Label runat="server" ID='Label1'>Visit Name:</asp:Label> <asp:TextBox ID="txtVisitName" runat='server'></asp:TextBox> ............ ............... <button id="btnSubmit" name="btnSubmit" type="submit"> Submit</button> </div> and i have a external .js file referencing to my web form page. $(document).ready(function() { $("#btnSubmit").click(function() { SavePage(); }); }); i have a WebMethod .cs and i have bookmark and it does hitting that line of code even thoug my page is in invalid state. how would i fix this? thanks.

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  • Element not found blocks execution in Selenium

    - by Mariano
    In my test, I try to verify if certain text exists (after an action) using find_element_by_xpath. If I use the right expression and my test pass, the routine ends correctly in no time. However if I try a wrong text (meaning that the test will fail) it hangs forever and I have to kill the script otherwise it does not end. Here is my test (the expression Thx user, client or password you entered is incorrect does not exist in the system, no matter what the user does): # -*- coding: utf-8 -*- import gettext import unittest from selenium import webdriver class TestWrongLogin(unittest.TestCase): def setUp(self): self.driver = webdriver.Firefox() self.driver.get("http://10.23.1.104:8888/") # let's check the language try: self.lang = self.driver.execute_script("return navigator.language;") self.lang = self.lang("-")[0] except: self.lang = "en" language = gettext.translation('app', '/app/locale', [self.lang], fallback=True) language.install() self._ = gettext.gettext def tearDown(self): self.driver.quit() def test_wrong_client(self): # test wrong client inputElement = self.driver.find_element_by_name("login") inputElement.send_keys("root") inputElement = self.driver.find_element_by_name("client") inputElement.send_keys("Unleash") inputElement = self.driver.find_element_by_name("password") inputElement.send_keys("qwerty") self.driver.find_element_by_name("form.submitted").click() # wait for the db answer self.driver.implicitly_wait(10) ret = self.driver.find_element_by_xpath( "//*[contains(.,'{0}')]".\ format(self._(u"Thx user, client or password you entered is incorrect"))) self.assertTrue(isinstance(ret, webdriver.remote.webelement.WebElement)) if __name__ == '__main__': unittest.main() Why does it do that and how can I prevent it?

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  • Data historian queries

    - by Scott Dennis
    Hi, I have a table that contains data for electric motors the format is: DATE(DateTime) | TagName(VarChar(50) | Val(Float) | 2009-11-03 17:44:13.000 | Motor_1 | 123.45 2009-11-04 17:44:13.000 | Motor_1 | 124.45 2009-11-05 17:44:13.000 | Motor_1 | 125.45 2009-11-03 17:44:13.000 | Motor_2 | 223.45 2009-11-04 17:44:13.000 | Motor_2 | 224.45 Data for each motor is inserted daily, so there would be 31 Motor_1s and 31 Motor_2s etc. We do this so we can trend it on our control system displays. I am using views to extract last months max val and last months min val. Same for this months data. Then I join the two and calculate the difference to get the actual run hours for that month. The "Val" is a nonresetable Accumulation from a PLC(Controller). This is my query for Last months Max Value: SELECT TagName, Val AS Hours FROM dbo.All_Data_From_Last_Mon AS cur WHERE (NOT EXISTS (SELECT TagName, Val FROM dbo.All_Data_From_Last_Mon AS high WHERE (TagName = cur.TagName) AND (Val > cur.Val))) This is my query for Last months Max Value: SELECT TagName, Val AS Hours FROM dbo.All_Data_From_Last_Mon AS cur WHERE (NOT EXISTS (SELECT TagName, Val FROM dbo.All_Data_From_Last_Mon AS high WHERE (TagName = cur.TagName) AND (Val < cur.Val))) This is the query that calculates the difference and runs a bit slow: SELECT dbo.Motors_Last_Mon_Max.TagName, STR(dbo.Motors_Last_Mon_Max.Hours - dbo.Motors_Last_Mon_Min.Hours, 12, 2) AS Hours FROM dbo.Motors_Last_Mon_Min RIGHT OUTER JOIN dbo.Motors_Last_Mon_Max ON dbo.Motors_Last_Mon_Min.TagName = dbo.Motors_Last_Mon_Max.TagName I know there is a better way. Ultimately I just need last months total and this months total. Any help would be appreciated. Thanks in advance

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  • Suggestions for a django db structure

    - by rh0dium
    Hi Say I have the unknown number of questions. For example: Is the sky blue [y/n] What date were your born on [date] What is pi [3.14] What is a large integ [100] Now each of these questions poses a different but very type specific answer (boolean, date, float, int). Natively django can happily deal with these in a model. class SkyModel(models.Model): question = models.CharField("Is the sky blue") answer = models.BooleanField(default=False) class BirthModel(models.Model): question = models.CharField("What date were your born on") answer = models.DateTimeField(default=today) class PiModel(models.Model) question = models.CharField("What is pi") answer = models.FloatField() But this has the obvious problem in that each question has a specific model - so if we need to add a question later I have to change the database. Yuck. So now I want to get fancy - How do a set up a model where by the answer type conversion happens automagically? ANSWER_TYPES = ( ('boolean', 'boolean'), ('date', 'date'), ('float', 'float'), ('int', 'int'), ('char', 'char'), ) class Questions(models.model): question = models.CharField(() answer = models.CharField() answer_type = models.CharField(choices = ANSWER_TYPES) default = models.CharField() So in theory this would do the following: When I build up my views I look at the type of answer and ensure that I only put in that value. But when I want to pull that answer back out it will return the data in the format specified by the answer_type. Example 3.14 comes back out as a float not as a str. How can I perform this sort of automagic transformation? Or can someone suggest a better way to do this? Thanks much!!

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  • Resize my image on upload not working - what must my buffer be?

    - by Etienne
    This is the code i got from This Link I want the user to upload a picture and then resize it............. Public Sub ResizeFromStream(ByVal ImageSavePath As String, ByVal MaxSideSize As Integer, ByVal Buffer As System.IO.Stream) Dim intNewWidth As Integer Dim intNewHeight As Integer Dim imgInput As System.Drawing.Image = System.Drawing.Image.FromStream(Buffer) 'Determine image format Dim fmtImageFormat As ImageFormat = imgInput.RawFormat 'get image original width and height Dim intOldWidth As Integer = imgInput.Width Dim intOldHeight As Integer = imgInput.Height 'determine if landscape or portrait Dim intMaxSide As Integer If (intOldWidth >= intOldHeight) Then intMaxSide = intOldWidth Else intMaxSide = intOldHeight End If If (intMaxSide > MaxSideSize) Then 'set new width and height Dim dblCoef As Double = MaxSideSize / CDbl(intMaxSide) intNewWidth = Convert.ToInt32(dblCoef * intOldWidth) intNewHeight = Convert.ToInt32(dblCoef * intOldHeight) Else intNewWidth = intOldWidth intNewHeight = intOldHeight End If 'create new bitmap Dim bmpResized As Drawing.Bitmap = New Drawing.Bitmap(imgInput, intNewWidth, intNewHeight) 'save bitmap to disk bmpResized.Save(ImageSavePath, fmtImageFormat) 'release used resources imgInput.Dispose() bmpResized.Dispose() Buffer.Close() End Sub Now when i click on my submit button it must execute my code but i am not sure what the input must be for the Buffer field? Protected Sub btnUpload_Click() Handles btnUpload.Click ResizeFromStream("~Pics", 200, ??????????) End Sub Thanks in advanced! Edit I need to get my Image from the File Upload control!

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  • Using list() to extract a data.table inside of a function

    - by Nathan VanHoudnos
    I must admit that the data.table J syntax confuses me. I am attempting to use list() to extract a subset of a data.table as a data.table object as described in Section 1.4 of the data.table FAQ, but I can't get this behavior to work inside of a function. An example: require(data.table) ## Setup some test data set.seed(1) test.data <- data.table( X = rnorm(10), Y = rnorm(10), Z = rnorm(10) ) setkey(test.data, X) ## Notice that I can subset the data table easily with literal names test.data[, list(X,Y)] ## X Y ## 1: -0.8356286 -0.62124058 ## 2: -0.8204684 -0.04493361 ## 3: -0.6264538 1.51178117 ## 4: -0.3053884 0.59390132 ## 5: 0.1836433 0.38984324 ## 6: 0.3295078 1.12493092 ## 7: 0.4874291 -0.01619026 ## 8: 0.5757814 0.82122120 ## 9: 0.7383247 0.94383621 ## 10: 1.5952808 -2.21469989 I can even write a function that will return a column of the data.table as a vector when passed the name of a column as a character vector: get.a.vector <- function( my.dt, my.column ) { ## Step 1: Convert my.column to an expression column.exp <- parse(text=my.column) ## Step 2: Return the vector return( my.dt[, eval(column.exp)] ) } get.a.vector( test.data, 'X') ## [1] -0.8356286 -0.8204684 -0.6264538 -0.3053884 0.1836433 0.3295078 ## [7] 0.4874291 0.5757814 0.7383247 1.5952808 But I cannot pull a similar trick for list(). The inline comments are the output from the interactive browser() session. get.a.dt <- function( my.dt, my.column ) { ## Step 1: Convert my.column to an expression column.exp <- parse(text=my.column) ## Step 2: Enter the browser to play around browser() ## Step 3: Verity that a literal X works: my.dt[, list(X)] ## << not shown >> ## Step 4: Attempt to evaluate the parsed experssion my.dt[, list( eval(column.exp)] ## Error in `rownames<-`(`*tmp*`, value = paste(format(rn, right = TRUE), (from data.table.example.R@1032mCJ#7) : ## length of 'dimnames' [1] not equal to array extent return( my.dt[, list(eval(column.exp))] ) } get.a.dt( test.data, "X" ) What am I missing? Update: Due to some confusion as to why I would want to do this I wanted to clarify. My use case is when I need to access a data.table column when when I generate the name. Something like this: set.seed(2) test.data[, X.1 := rnorm(10)] which.column <- 'X' new.column <- paste(which.column, '.1', sep="") get.a.dt( test.data, new.column ) Hopefully that helps.

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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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  • Will this class cause memory leaks, and does anything need disposing of? (asp.net vb)

    - by Phil
    Here is the class to export a gridview to an excel sheet: Imports System Imports System.Data Imports System.Configuration Imports System.IO Imports System.Web Imports System.Web.Security Imports System.Web.UI Imports System.Web.UI.WebControls Imports System.Web.UI.WebControls.WebParts Imports System.Web.UI.HtmlControls Namespace ExcelExport Public NotInheritable Class GVExportUtil Private Sub New() End Sub Public Shared Sub Export(ByVal fileName As String, ByVal gv As GridView) HttpContext.Current.Response.Clear() HttpContext.Current.Response.AddHeader("content-disposition", String.Format("attachment; filename={0}", fileName)) HttpContext.Current.Response.ContentType = "application/ms-excel" Dim sw As StringWriter = New StringWriter Dim htw As HtmlTextWriter = New HtmlTextWriter(sw) Dim table As Table = New Table table.GridLines = GridLines.Vertical If (Not (gv.HeaderRow) Is Nothing) Then GVExportUtil.PrepareControlForExport(gv.HeaderRow) table.Rows.Add(gv.HeaderRow) End If For Each row As GridViewRow In gv.Rows GVExportUtil.PrepareControlForExport(row) table.Rows.Add(row) Next If (Not (gv.FooterRow) Is Nothing) Then GVExportUtil.PrepareControlForExport(gv.FooterRow) table.Rows.Add(gv.FooterRow) End If table.RenderControl(htw) HttpContext.Current.Response.Write(sw.ToString) HttpContext.Current.Response.End() End Sub Private Shared Sub PrepareControlForExport(ByVal control As Control) Dim i As Integer = 0 Do While (i < control.Controls.Count) Dim current As Control = control.Controls(i) If (TypeOf current Is LinkButton) Then control.Controls.Remove(current) control.Controls.AddAt(i, New LiteralControl(CType(current, LinkButton).Text)) ElseIf (TypeOf current Is ImageButton) Then control.Controls.Remove(current) control.Controls.AddAt(i, New LiteralControl(CType(current, ImageButton).AlternateText)) ElseIf (TypeOf current Is HyperLink) Then control.Controls.Remove(current) control.Controls.AddAt(i, New LiteralControl(CType(current, HyperLink).Text)) ElseIf (TypeOf current Is DropDownList) Then control.Controls.Remove(current) control.Controls.AddAt(i, New LiteralControl(CType(current, DropDownList).SelectedItem.Text)) ElseIf (TypeOf current Is CheckBox) Then control.Controls.Remove(current) control.Controls.AddAt(i, New LiteralControl(CType(current, CheckBox).Checked)) End If If current.HasControls Then GVExportUtil.PrepareControlForExport(current) End If i = (i + 1) Loop End Sub End Class End Namespace Will this class cause memory leaks? And does anything here need to be disposed of? The code is working but I am getting the app pool falling over frequently when it is in use. Thanks.

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  • UIDocumentInteractionController & ARC: [UIPopoverController dealloc] reached while popover is still visible

    - by muffel
    This issue or similar issues have been discussed here before, but I didn't find any working solution for me. I am using the following code to display a UIDocumentInteractionController on an ARC-enabled iOS 7 project: - (void) exportDoc{ // [...] docController = [UIDocumentInteractionController interactionControllerWithURL:[NSURL fileURLWithPath:path]]; docController.delegate = self; [docController presentOpenInMenuFromBarButtonItem:mainMenuButton animated:YES]; } First I didn't want to create a property that holds the controller reference, but as many people said that there are not alternatives to it. It is defined as @property (strong) UIDocumentInteractionController* docController; exportDoc is run in the main thread using NSOperationQueue. Whenever it is executed, I get the following error message: Terminating app due to uncaught exception 'NSGenericException', reason: '-[UIPopoverController dealloc] reached while popover is still visible.' This is what the backtrace says: (lldb) bt * thread #1: tid = 0x1c97d9, 0x000000019a23c1c0 libobjc.A.dylibobjc_exception_throw, queue = 'com.apple.main-thread', stop reason = breakpoint 2.1 frame #0: 0x000000019a23c1c0 libobjc.A.dylibobjc_exception_throw frame #1: 0x000000018d982e90 CoreFoundation+[NSException raise:format:] + 128 frame #2: 0x0000000190bc348c UIKit-[UIPopoverController dealloc] + 96 frame #3: 0x0000000190e18fc8 UIKit-[UIDocumentInteractionController dealloc] + 168 frame #4: 0x000000019a255474 libobjc.A.dylib(anonymous namespace)::AutoreleasePoolPage::pop(void*) + 524 frame #5: 0x000000018d881988 CoreFoundation_CFAutoreleasePoolPop + 28 frame #6: 0x000000018e42cb18 Foundation-[NSOperationInternal _start:] + 892 frame #7: 0x000000018e4eea38 Foundation__NSOQSchedule_f + 76 frame #8: 0x000000019a813fd4 libdispatch.dylib_dispatch_client_callout + 16 frame #9: 0x000000019a8171dc libdispatch.dylib_dispatch_main_queue_callback_4CF + 336 frame #10: 0x000000018d942c2c CoreFoundation__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE + 12 frame #11: 0x000000018d940f6c CoreFoundation__CFRunLoopRun + 1452 frame #12: 0x000000018d881c20 CoreFoundationCFRunLoopRunSpecific + 452 frame #13: 0x0000000193511c0c GraphicsServicesGSEventRunModal + 168 frame #14: 0x00000001909b2fdc UIKitUIApplicationMain + 1156 * frame #15: 0x000000010000947c MyApplicationmain(argc=1, argv=0x000000016fdfbc80) + 108 at main.m:16 frame #16: 0x000000019a82faa0 libdyld.dylibstart + 4 As far as I understand the autoreleasepool just releases the controller. Shouldn't this be prevented by using a strong property just as I did? Do you have any idea what the problem can be and how I can solve it?

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  • How to append new elements to Xml from stream

    - by Wololo
    I have a method which returns some xml in a memory stream private MemoryStream GetXml() { XmlWriterSettings settings = new XmlWriterSettings(); settings.Indent = true; using (MemoryStream memoryStream = new MemoryStream()) { using (XmlWriter writer = XmlWriter.Create(memoryStream, settings)) { writer.WriteStartDocument(); writer.WriteStartElement("root"); writer.WriteStartElement("element"); writer.WriteString("content"); writer.WriteEndElement(); writer.WriteEndElement(); writer.WriteEndDocument(); writer.Flush(); } return memoryStream; } } In this example the format of the xml will be: <?xml version="1.0" encoding="utf-8"?> <root> <element>content</element> </root> How can i insert a new element under the root e.g <?xml version="1.0" encoding="utf-8"?> <root> <element>content</element> ----->New element here <------ </root>

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  • Having trouble uploading a file

    - by neo skosana
    Hi I am having trouble uploading a file. First of all I have a class: class upload { private $name; private $document; public function __construct($nme,$doc) { $this->setName($nme); $this->setDocument($doc); } public function setName($nme) { $this->name = $nme; } public function setDocument($doc) { $this->document = $doc; } public function fileNotPdf() { /* Was the file a PDF? */ if ($this->document['type'] != "application/pdf") { return true; } else { return false; } } public function fileNotUploaded() { /* Make sure that the file was POSTed. */ if (!(is_uploaded_file($this->document['tmp_name']))) { return true; } else { return false; } } public function fileNotMoved($repositry) { /* move uploaded file to final destination. */ $result = move_uploaded_file($this->document['tmp_name'], "$repositry/$this->name.pdf"); if($result) { return false; } else { return true; } } } Now for my main page: $docName = $_POST['name']; $page = $_FILES['doc']; if($_POST['submit']) { /* Set a few constants */ $filerepository = "np"; $uploadObj = new upload($docName, $page); if($uploadObj->fileNotUploaded()) { promptUser("There was a problem uploading the file.",""); } elseif($uploadObj->fileNotPdf()) { promptUser("File must be in pdf format.",""); } elseif($uploadObj->fileNotMoved($filerepository)) { promptUser("File could not be uploaded to final destination.",""); } else { promptUser("File has been successfully uploaded.",""); } } The errors that I get: Warning: move_uploaded_file(about.pdf)[function.move-uploaded-file]: failed to open stream: No such file or directory in... Warning: move_uploaded_file()[function.move-uploaded-file]: Unable to move 'c:\xampp\tmp\php13.tmp' to 'about.pdf' in... File could not be uploaded to final destination.

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  • Programming texts and reference material for my Kindle DX, creating the ultimate reference device?

    - by mwilliams
    (Revisiting this topic with the release of the Kindle DX) Having owned both generation Kindle readers and now getting a Kindle DX; I'm very excited for true PDF handling on an e-ink device! An image of _Why's book on my Kindle (from my iPhone). This gives me a device capable of storing hundreds of thousands of pages that are full text search capable in the form factor of a magazine. What references (preferably PDF to preserve things such as code samples) would you recommend? Ultimately I would like reference material for every modern and applicable programming language (C, C++, Objective-C, Python, Ruby, Java, .NET (C#, Visual Basic, ASP.NET), Erlang, SQL references) as well as general programming texts and frameworks (algorithms, design patterns, theory, Rails, Django, Cocoa, ORMs, etc) and anything else that could be thought of. With so many developers here using such a wide array of languages, as a professional in your particular field, what books or references would you recommend to me for my Kindle? Creative Commons material a plus (translate that to free) as well as the material being in the PDF file format. File size is not an issue. If this turns out to be a success, I will update with a follow-up with a compiled list generated from all of the answers. Thanks for the assistance and contributing! UPDATE I have been using the Kindle DX a lot now for technical books. Check out this blog post I did for high resolution photos of different material: http://www.matthewdavidwilliams.com/2009/06/12/technical-document-pdfs-on-the-kindle-dx/

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  • Nested Routes Show Action: What objects does it expect?

    - by NoahClark
    Here is the relevant line from my rake routes: client_note GET /clients/:client_id/notes/:id(.:format) notes#show When I try passing in the objects like <%= client_note_path([client, @notes.first]) %>> I get: No route matches {:action=>"show", :controller=>"notes", :client_id=>[#<Client id: 5, ... , #<Note id: 9, ...]} Which made me think to try a client ID. So, I tried: <%= client_note_path([client.id, @notes.first]) %> which gives me: No route matches {:action=>"show", :controller=>"notes", :client_id=>[5, #<Note id: 9,content: "He just bought a brand new bobcat, be sure to charg...", client_id: 5, created_at: "2012-06-11 16:18:16", updated_at: "2012-06-11 16:18:16">]} Which, made me want to try just passing in a client ID. <%= client_note_path(client.id) %> No route matches {:action=>"show", :controller=>"notes", :client_id=>5} Still not what I'm looking for. I want to be able to show an individual note which can normally be found at a url like looks like: http://localhost:3000/clients/2/notes/3/

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