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• MySQL died during the night on a 12.04.1 Ubuntu

  - by Olivier

  I can't explain why, but somehow during the night, one of my MySQL running on an Ubuntu 12.04.1 box broke. The service is running but I can't login anymore (to SQL), the previous password is not working anymore. It does not looks like the server has been compromised (nothing in /var/auth.log) It looks like some automatic security upgrade (server is configured to perform those) has occured and broke something. The MySQL server has restarted a couple of times in the logs at the time errors started to happen (I get email when CRON task fail). In the logs it complains about an unset root password (I do have cron job running all day using SQL so the password was set & working for months). Anyway I can't login without password either! Do you have any idea of what could have happened? How do I get my databases back? This line looks strange : Nov 6 06:36:12 ns398758 mysqld_safe[6676]: ERROR: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'ALTER TABLE user ADD column Show_view_priv enum('N','Y') CHARACTER SET utf8 NOT ' at line 1 Here is the full log below : Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: PLEASE REMEMBER TO SET A PASSWORD FOR THE MySQL root USER ! Nov 6 06:36:06 ns398758 mysqld_safe[6586]: To do so, start the server, then issue the following commands: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: /usr/bin/mysqladmin -u root password 'new-password' Nov 6 06:36:06 ns398758 mysqld_safe[6586]: /usr/bin/mysqladmin -u root -h ns398758.ovh.net password 'new-password' Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Alternatively you can run: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: /usr/bin/mysql_secure_installation Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: which will also give you the option of removing the test Nov 6 06:36:06 ns398758 mysqld_safe[6586]: databases and anonymous user created by default. This is Nov 6 06:36:06 ns398758 mysqld_safe[6586]: strongly recommended for production servers. Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: See the manual for more instructions. Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Please report any problems with the /usr/scripts/mysqlbug script! Nov 6 06:36:06 ns398758 mysqld_safe[6586]: Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 [Note] Plugin 'FEDERATED' is disabled. Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: The InnoDB memory heap is disabled Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: Mutexes and rw_locks use GCC atomic builtins Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: Compressed tables use zlib 1.2.3.4 Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: Initializing buffer pool, size = 128.0M Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: Completed initialization of buffer pool Nov 6 06:36:06 ns398758 mysqld_safe[6632]: 121106 6:36:06 InnoDB: highest supported file format is Barracuda. Nov 6 06:36:07 ns398758 mysqld_safe[6632]: 121106 6:36:07 InnoDB: Waiting for the background threads to start Nov 6 06:36:08 ns398758 mysqld_safe[6632]: 121106 6:36:08 InnoDB: 1.1.8 started; log sequence number 29276459701 Nov 6 06:36:08 ns398758 mysqld_safe[6632]: 121106 6:36:08 InnoDB: Starting shutdown... Nov 6 06:36:09 ns398758 mysqld_safe[6632]: 121106 6:36:09 InnoDB: Shutdown completed; log sequence number 29276459701 Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 [Note] Plugin 'FEDERATED' is disabled. Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: The InnoDB memory heap is disabled Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: Mutexes and rw_locks use GCC atomic builtins Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: Compressed tables use zlib 1.2.3.4 Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: Initializing buffer pool, size = 128.0M Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: Completed initialization of buffer pool Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: highest supported file format is Barracuda. Nov 6 06:36:11 ns398758 mysqld_safe[6676]: 121106 6:36:11 InnoDB: Waiting for the background threads to start Nov 6 06:36:12 ns398758 mysqld_safe[6676]: 121106 6:36:12 InnoDB: 1.1.8 started; log sequence number 29276459701 Nov 6 06:36:12 ns398758 mysqld_safe[6676]: ERROR: 1064 You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'ALTER TABLE user ADD column Show_view_priv enum('N','Y') CHARACTER SET utf8 NOT ' at line 1 Nov 6 06:36:12 ns398758 mysqld_safe[6676]: 121106 6:36:12 [ERROR] Aborting Nov 6 06:36:12 ns398758 mysqld_safe[6676]: Nov 6 06:36:12 ns398758 mysqld_safe[6676]: 121106 6:36:12 InnoDB: Starting shutdown... Nov 6 06:36:13 ns398758 mysqld_safe[6676]: 121106 6:36:13 InnoDB: Shutdown completed; log sequence number 29276459701 Nov 6 06:36:13 ns398758 mysqld_safe[6676]: 121106 6:36:13 [Note] /usr/sbin/mysqld: Shutdown complete Nov 6 06:36:13 ns398758 mysqld_safe[6676]: Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 [Note] Plugin 'FEDERATED' is disabled. Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: The InnoDB memory heap is disabled Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: Mutexes and rw_locks use GCC atomic builtins Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: Compressed tables use zlib 1.2.3.4 Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: Initializing buffer pool, size = 128.0M Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: Completed initialization of buffer pool Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: highest supported file format is Barracuda. Nov 6 06:36:13 ns398758 mysqld_safe[6697]: 121106 6:36:13 InnoDB: Waiting for the background threads to start Nov 6 06:36:14 ns398758 mysqld_safe[6697]: 121106 6:36:14 InnoDB: 1.1.8 started; log sequence number 29276459701 Nov 6 06:36:14 ns398758 mysqld_safe[6697]: 121106 6:36:14 InnoDB: Starting shutdown... Nov 6 06:36:15 ns398758 mysqld_safe[6697]: 121106 6:36:15 InnoDB: Shutdown completed; log sequence number 29276459701 Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 [Note] Plugin 'FEDERATED' is disabled. Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: The InnoDB memory heap is disabled Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: Mutexes and rw_locks use GCC atomic builtins Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: Compressed tables use zlib 1.2.3.4 Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: Initializing buffer pool, size = 128.0M Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: Completed initialization of buffer pool Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: highest supported file format is Barracuda. Nov 6 06:36:15 ns398758 mysqld_safe[6718]: 121106 6:36:15 InnoDB: Waiting for the background threads to start Nov 6 06:36:16 ns398758 mysqld_safe[6718]: 121106 6:36:16 InnoDB: 1.1.8 started; log sequence number 29276459701 Nov 6 06:36:16 ns398758 mysqld_safe[6718]: ERROR: 1050 Table 'plugin' already exists Nov 6 06:36:16 ns398758 mysqld_safe[6718]: 121106 6:36:16 [ERROR] Aborting Nov 6 06:36:16 ns398758 mysqld_safe[6718]: Nov 6 06:36:16 ns398758 mysqld_safe[6718]: 121106 6:36:16 InnoDB: Starting shutdown... Nov 6 06:36:17 ns398758 mysqld_safe[6718]: 121106 6:36:17 InnoDB: Shutdown completed; log sequence number 29276459701 Nov 6 06:36:17 ns398758 mysqld_safe[6718]: 121106 6:36:17 [Note] /usr/sbin/mysqld: Shutdown complete Nov 6 06:36:17 ns398758 mysqld_safe[6718]: Nov 6 06:36:19 ns398758 /etc/mysql/debian-start[6816]: Upgrading MySQL tables if necessary. Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: /usr/bin/mysql_upgrade: the '--basedir' option is always ignored Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: Looking for 'mysql' as: /usr/bin/mysql Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: col_digitas.acos OK Nov 6 06:36:20 ns398758 /etc/mysql/debian-start[6819]: col_digitas.aros OK ...

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• InstallShield-2009: Basic MSI: How to run a custom action after user cancels uninstall (rollback)

  - by Samir

  InstallShield-2009 Premier: Basic msi project: What to do when I want a custom action to run when user clicks cancel button during uninstall? I put a custom action (a C# exe which would just show a message box) with Action Type: Type: Launch an executable Location: Stored in the Binary table Action Parameters: Source: exe path Target: a b c (doesn't matter, I don't need it) Additional Options: Return Processing: Synchronous (Check exit code) Run Only During Path Uninstall: unchecked Respond Options: In-Script Execution: Rollback Execution in System Context Executing Scheduling: disabled Insert into Sequence: Install UI-Sequence: <Absent from sequence> Install Execute Sequence: After InstallServices (what should I set here?) Install Execute Condition: (do I need to set? I left it blank) but it didn't fire the message box when I canceled the uninstall. How?

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• How to blacklist a problem Wi-Fi access point by MAC address in Mac OS X

  - by Sam Alexander

  So I am a small Mac-user cog in a larger Windows-based network machine. The network here works fine for most everyone else (on PCs), but I have random timeouts and issues with the Wi-Fi. Luckily, I have identified a few problem access points by MAC address (via their log messages in Console.app). Is it possible to tell my AirPort on my Macbook to avoid those access points, and only speak with the access points who are far less touchy about me drinking the Apple kool-aid? All of the points are on the same network SSID.

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• Creating a GraphicsPath from a semi-transparent bitmap

  - by Moozhe

  I want to create a GraphicsPath and a list of Points to form the outline of the non-transparent area of a bitmap. If needed, I can guarantee that each image has only one solid collection of nontransparent pixels. So for example, I should be able to record the points either clockwise or counter-clockwise along the edge of the pixels and perform a full closed loop. The speed of this algorithm is not important. However, the efficiency of the resulting points is semi-important if I can skip some points to reduce in a smaller and less complex GraphicsPath. I will list my current code below which works perfectly with most images. However, some images which are more complex end up with paths which seem to connect in the wrong order. I think I know why this occurs, but I can't come up with a solution. public static Point[] GetOutlinePoints(Bitmap image) { List<Point> outlinePoints = new List<Point>(); BitmapData bitmapData = image.LockBits(new Rectangle(0, 0, image.Width, image.Height), ImageLockMode.ReadOnly, PixelFormat.Format32bppArgb); byte[] originalBytes = new byte[image.Width * image.Height * 4]; Marshal.Copy(bitmapData.Scan0, originalBytes, 0, originalBytes.Length); for (int x = 0; x < bitmapData.Width; x++) { for (int y = 0; y < bitmapData.Height; y++) { byte alpha = originalBytes[y * bitmapData.Stride + 4 * x + 3]; if (alpha != 0) { Point p = new Point(x, y); if (!ContainsPoint(outlinePoints, p)) outlinePoints.Add(p); break; } } } for (int y = 0; y < bitmapData.Height; y++) { for (int x = bitmapData.Width - 1; x >= 0; x--) { byte alpha = originalBytes[y * bitmapData.Stride + 4 * x + 3]; if (alpha != 0) { Point p = new Point(x, y); if (!ContainsPoint(outlinePoints, p)) outlinePoints.Add(p); break; } } } for (int x = bitmapData.Width - 1; x >= 0; x--) { for (int y = bitmapData.Height - 1; y >= 0; y--) { byte alpha = originalBytes[y * bitmapData.Stride + 4 * x + 3]; if (alpha != 0) { Point p = new Point(x, y); if (!ContainsPoint(outlinePoints, p)) outlinePoints.Add(p); break; } } } for (int y = bitmapData.Height - 1; y >= 0; y--) { for (int x = 0; x < bitmapData.Width; x++) { byte alpha = originalBytes[y * bitmapData.Stride + 4 * x + 3]; if (alpha != 0) { Point p = new Point(x, y); if (!ContainsPoint(outlinePoints, p)) outlinePoints.Add(p); break; } } } // Added to close the loop outlinePoints.Add(outlinePoints[0]); image.UnlockBits(bitmapData); return outlinePoints.ToArray(); } public static bool ContainsPoint(IEnumerable<Point> points, Point value) { foreach (Point p in points) { if (p == value) return true; } return false; } And when I turn the points into a path: GraphicsPath outlinePath = new GraphicsPath(); outlinePath.AddLines(_outlinePoints); Here's an example showing what I want. The red outline should be an array of points which can be made into a GraphicsPath in order to perform hit detection, draw an outline pen, and fill it with a brush.

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• How to blacklist a problem wifi access point by MAC address in OSX

  - by Sam Alexander

  So I am a small mac-user cog in a larger windows-based network machine. The network here works fine for most everyone else (on PCs), but I have random timeouts and issues with the Wifi. Luckily, I have identified a few problem access points by MAC address (via their log messages in Console.app). Is it possible to tell my Airport on my Macbook to avoid those access points, and only speak with the access points who are far less touchy about me drinking the Apple kool-aid? All of the points are on the same network SSID.

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• PHP SOAP error: Method element needs to belong to the namespace

  - by kdm

  I'm unable to retrieve data from an XML document, any help is greatly appreciated. I'm using PHP 5.2.10 and the WSDL url is an internal link within my company. The following code produces an error. $url = "http://dta-info/IVR/IVRINFO?WSDL"; $params = array("zANI" => "12345"); try{ $client = new SoapClient($url, array( 'trace' => 1, 'connection_timeout' => 2, 'location' => $url ) ); }catch(SoapFault $fault){ echo "faultstring: {$fault->faultstring})\n"; } try{ $result = $client->GetIVRinfo($params); }catch(SoapFault $fault){ echo "(faultcode: {$fault->faultcode}, faultstring: {$fault->faultstring} )\n"; } (faultcode: SOAP-ENV:Client, faultstring: There should be no path or parameters after a SOAP vname. ) So i tried to use a non-wsdl mode but i receive a different error no matter how i try to format the params. $url = "http://dta-info/IVR/IVRINFO"; $params = array("zANI" => "12345"); try{ $client = new SoapClient(null, array( 'trace' => 1, 'connection_timeout' => 2, 'location' => $url, 'uri' => $uri, 'style' => SOAP_DOCUMENT, 'use' => SOAP_LITERAL, 'soap_version' => SOAP_2 ) ); }catch(SoapFault $fault){ echo "faultstring: {$fault->faultstring})\n"; } try{ $result = $client->GetIVRinfo($params); }catch(SoapFault $fault){ echo "(faultcode: {$fault->faultcode}, faultstring: {$fault->faultstring} )\n"; } (faultcode: SOAP-ENV:Client, faultstring: The method element needs to belong to the namespace 'http://GETIVRINFO/IVR/IVRINFO'. ) I have tested this WSDL with a tool called SoapUI and it returns the results with no errors. So it leads me to believe I'm not formatting the vars or headers correctly with PHP. I also tried passing in a xml fragment as the param but that returns the same error. What am i doing wrong?????? $params = '<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:ivr="http://GETIVRINFO/IVR/IVRINFO"> <soapenv:Header/> <soapenv:Body> <ivr:GetIVRinfo> <!--Optional:--> <ivr:zANI>12345</ivr:zANI> </ivr:GetIVRinfo> </soapenv:Body> </soapenv:Envelope>'; Here is the WSDL document: <?xml version="1.0"?><wsdl:definitions name="IVR" targetNamespace="http://GETIVRINFO/IVR/IVRINFO" xmlns:tns="http://GETIVRINFO/IVR/IVRINFO" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:sql="http://schemas.microsoft.com/SQLServer/2001/12/SOAP" xmlns:sqltypes="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types" xmlns:sqlmessage="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlMessage" xmlns:sqlresultstream="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlResultStream"> <wsdl:types><xsd:schema targetNamespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types' elementFormDefault='qualified' attributeFormDefault='qualified'> <xsd:import namespace='http://www.w3.org/2001/XMLSchema'/> <xsd:simpleType name='nonNegativeInteger'> <xsd:restriction base='xsd:int'> <xsd:minInclusive value='0'/> </xsd:restriction> </xsd:simpleType> <xsd:attribute name='IsNested' type='xsd:boolean'/> <xsd:complexType name='SqlRowSet'> <xsd:sequence> <xsd:element ref='xsd:schema'/> <xsd:any/> </xsd:sequence> <xsd:attribute ref='sqltypes:IsNested'/> </xsd:complexType> <xsd:complexType name='SqlXml' mixed='true'> <xsd:sequence> <xsd:any/> </xsd:sequence> </xsd:complexType> <xsd:simpleType name='SqlResultCode'> <xsd:restriction base='xsd:int'> <xsd:minInclusive value='0'/> </xsd:restriction> </xsd:simpleType> </xsd:schema> <xsd:schema targetNamespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlMessage' elementFormDefault='qualified' attributeFormDefault='qualified'> <xsd:import namespace='http://www.w3.org/2001/XMLSchema'/> <xsd:import namespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types'/> <xsd:complexType name='SqlMessage'> <xsd:sequence minOccurs='1' maxOccurs='1'> <xsd:element name='Class' type='sqltypes:nonNegativeInteger'/> <xsd:element name='LineNumber' type='sqltypes:nonNegativeInteger'/> <xsd:element name='Message' type='xsd:string'/> <xsd:element name='Number' type='sqltypes:nonNegativeInteger'/> <xsd:element name='Procedure' type='xsd:string'/> <xsd:element name='Server' type='xsd:string'/> <xsd:element name='Source' type='xsd:string'/> <xsd:element name='State' type='sqltypes:nonNegativeInteger'/> </xsd:sequence> <xsd:attribute ref='sqltypes:IsNested'/> </xsd:complexType> </xsd:schema> <xsd:schema targetNamespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlResultStream' elementFormDefault='qualified' attributeFormDefault='qualified'> <xsd:import namespace='http://www.w3.org/2001/XMLSchema'/> <xsd:import namespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types'/> <xsd:import namespace='http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlMessage'/> <xsd:complexType name='SqlResultStream'> <xsd:choice minOccurs='1' maxOccurs='unbounded'> <xsd:element name='SqlRowSet' type='sqltypes:SqlRowSet'/> <xsd:element name='SqlXml' type='sqltypes:SqlXml'/> <xsd:element name='SqlMessage' type='sqlmessage:SqlMessage'/> <xsd:element name='SqlResultCode' type='sqltypes:SqlResultCode'/> </xsd:choice> </xsd:complexType> </xsd:schema> <xsd:schema targetNamespace="http://GETIVRINFO/IVR/IVRINFO" elementFormDefault="qualified" attributeFormDefault="qualified"> <xsd:import namespace="http://www.w3.org/2001/XMLSchema"/> <xsd:import namespace="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types"/> <xsd:import namespace="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlMessage"/> <xsd:import namespace="http://schemas.microsoft.com/SQLServer/2001/12/SOAP/types/SqlResultStream"/> <xsd:element name="GetIVRinfo"> <xsd:complexType> <xsd:sequence> <xsd:element minOccurs="0" maxOccurs="1" name="zANI" type="xsd:string" nillable="true"/> </xsd:sequence> </xsd:complexType> </xsd:element> <xsd:element name="GetIVRinfoResponse"> <xsd:complexType> <xsd:sequence> <xsd:element minOccurs="1" maxOccurs="1" name="GetIVRinfoResult" type="sqlresultstream:SqlResultStream"/> </xsd:sequence> </xsd:complexType> </xsd:element> </xsd:schema> </wsdl:types> <wsdl:message name="GetIVRinfoIn"> <wsdl:part name="parameters" element="tns:GetIVRinfo"/> </wsdl:message> <wsdl:message name="GetIVRinfoOut"> <wsdl:part name="parameters" element="tns:GetIVRinfoResponse"/> </wsdl:message> <wsdl:portType name="SXSPort"> <wsdl:operation name="GetIVRinfo"> <wsdl:input message="tns:GetIVRinfoIn"/> <wsdl:output message="tns:GetIVRinfoOut"/> </wsdl:operation> </wsdl:portType> <wsdl:binding name="SXSBinding" type="tns:SXSPort"> <soap:binding style="document" transport="http://schemas.xmlsoap.org/soap/http"/> <wsdl:operation name="GetIVRinfo"> <soap:operation soapAction="http://GETIVRINFO/IVR/IVRINFO/GetIVRinfo" style="document"/> <wsdl:input> <soap:body use="literal"/> </wsdl:input> <wsdl:output> <soap:body use="literal"/> </wsdl:output> </wsdl:operation> </wsdl:binding> <wsdl:service name="IVR"> <wsdl:port name="SXSPort" binding="tns:SXSBinding"> <soap:address location="http://GETIVRINFO/IVR/IVRINFO"/> </wsdl:port> </wsdl:service> </wsdl:definitions>

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• Problem deserializing xml file

  - by Andy

  I auto generated an xsd file from the below xml and used xsd2code to get a c# class. The problem is the entire xml doesn't deserialize. Here is how I'm attempting to deserialize: static void Main(string[] args) { using (TextReader textReader = new StreamReader("config.xml")) { // string temp = textReader.ReadToEnd(); XmlSerializer deserializer = new XmlSerializer(typeof(project)); project p = (project)deserializer.Deserialize(textReader); } } here is the actual XML: <?xml version='1.0' encoding='UTF-8'?> <project> <scm class="hudson.scm.SubversionSCM"> <locations> <hudson.scm.SubversionSCM_-ModuleLocation> <remote>https://svn.xxx.com/test/Validation/CPS DRTest DLL/trunk</remote> </hudson.scm.SubversionSCM_-ModuleLocation> </locations> <useUpdate>false</useUpdate> <browser class="hudson.scm.browsers.FishEyeSVN"> <url>http://fisheye.xxxx.net/browse/Test/</url> <rootModule>Test</rootModule> </browser> <excludedCommitMessages></excludedCommitMessages> </scm> <openf>Hello there</openf> <buildWrappers/> </project> When I run the above, the locations node remains null. Here is the xsd that I'm using: <?xml version="1.0" encoding="utf-8"?> <xs:schema id="NewDataSet" xmlns="" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:msdata="urn:schemas-microsoft-com:xml-msdata"> <xs:element name="project"> <xs:complexType> <xs:all> <xs:element name="openf" type="xs:string" minOccurs="0" /> <xs:element name="buildWrappers" type="xs:string" minOccurs="0" /> <xs:element name="scm" minOccurs="0"> <xs:complexType> <xs:sequence> <xs:element name="useUpdate" type="xs:string" minOccurs="0" msdata:Ordinal="1" /> <xs:element name="excludedCommitMessages" type="xs:string" minOccurs="0" msdata:Ordinal="2" /> <xs:element name="locations" minOccurs="0"> <xs:complexType> <xs:sequence> <xs:element name="hudson.scm.SubversionSCM_-ModuleLocation" minOccurs="0"> <xs:complexType> <xs:sequence> <xs:element name="remote" type="xs:string" minOccurs="0" /> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="browser" minOccurs="0"> <xs:complexType> <xs:sequence> <xs:element name="url" type="xs:string" minOccurs="0" msdata:Ordinal="0" /> <xs:element name="rootModule" type="xs:string" minOccurs="0" msdata:Ordinal="1" /> </xs:sequence> <xs:attribute name="class" type="xs:string" /> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="class" type="xs:string" /> </xs:complexType> </xs:element> </xs:all> </xs:complexType> </xs:element> <xs:element name="NewDataSet" msdata:IsDataSet="true" msdata:UseCurrentLocale="true"> <xs:complexType> <xs:choice minOccurs="0" maxOccurs="unbounded"> <xs:element ref="project" /> </xs:choice> </xs:complexType> </xs:element> </xs:schema>

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• SNMP: ASN.1 MIB Definitions. Referencing a table within a table

  - by Doug

  Its's been a while since I've written ASN.1 so.. Our data model is comprised of several table definitions within a table. This is not workable in SNMP, so we need to flatten the definitions. The easiest way to do this would be to have the embedded table indexed by the same OID as the parent table. Thus someTableEntry ::= SEQUENCE { someTableIndex Integer32, someTableDomain Integer32, someTableFooTable SEQUENCE OF SomeTableFooTable } becomes someTableEntry ::= SEQUENCE { someTableIndex Integer32, someTableDomain Integer32, } someTableFooTable ::= SEQUENCE { someTableIndex Integer32, .... } The good thing is that in our application there will NEVER be any kind of SET, GET or GET NEXT so no need for SNMP walk (there are some very good reasons for this that supersede the need for network management elegance. All attributes will be reported via traps only. I think this is a valid SNMP MIB definitions but wanted to get some feedback. Thanks in advance.

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• Why is XML Deserilzation not throwing exceptions when it should.

  - by chobo2

  Hi Here is some dummy xml and dummy xml schema I made. schema <?xml version="1.0" encoding="utf-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://www.domain.com" xmlns="http://www.domain.com" elementFormDefault="qualified"> <xs:element name="vehicles"> <xs:complexType> <xs:sequence> <xs:element name="owner" minOccurs="1" maxOccurs="1"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:minLength value="2" /> <xs:maxLength value="8" /> </xs:restriction> </xs:simpleType> </xs:element> <xs:element name="Car" minOccurs="1" maxOccurs="1"> <xs:complexType> <xs:sequence> <xs:element name="Information" type="CarInfo" minOccurs="0" maxOccurs="unbounded" /> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="Truck"> <xs:complexType> <xs:sequence> <xs:element name="Information" type="CarInfo" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="SUV"> <xs:complexType> <xs:sequence> <xs:element name="Information" type="CarInfo" minOccurs="0" maxOccurs="unbounded" /> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> <xs:complexType name="CarInfo"> <xs:sequence> <xs:element name="CarName"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:minLength value="1"/> <xs:maxLength value="50"/> </xs:restriction> </xs:simpleType> </xs:element> <xs:element name="CarPassword"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:minLength value="6"/> <xs:maxLength value="50"/> </xs:restriction> </xs:simpleType> </xs:element> <xs:element name="CarEmail"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:pattern value="\w+([-+.']\w+)*@\w+([-.]\w+)*\.\w+([-.]\w+)*"/> </xs:restriction> </xs:simpleType> </xs:element> </xs:sequence> </xs:complexType> </xs:schema> xml sample <?xml version="1.0" encoding="utf-8" ?> <vehicles> <owner>Car</owner> <Car> <Information> <CarName>Bob</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> <Information> <CarName>Bob2</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> </Car> <Truck> <Information> <CarName>Jim</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> <Information> <CarName>Jim2</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> </Truck> <SUV> <Information> <CarName>Jane</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> <Information> <CarName>Jane</CarName> <CarPassword>123456</CarPassword> <CarEmail>[email protected]</CarEmail> </Information> </SUV> </vehicles> Serialization Class using System; using System.Collections.Generic; using System.Xml; using System.Xml.Serialization; [XmlRoot("vehicles")] public class MyClass { public MyClass() { Cars = new List<Information>(); Trucks = new List<Information>(); SUVs = new List<Information>(); } [XmlElement(ElementName = "owner")] public string Owner { get; set; } [XmlElement("Car")] public List<Information> Cars { get; set; } [XmlElement("Truck")] public List<Information> Trucks { get; set; } [XmlElement("SUV")] public List<Information> SUVs { get; set; } } public class CarInfo { public CarInfo() { Info = new List<Information>(); } [XmlElement("Information")] public List<Information> Info { get; set; } } public class Information { [XmlElement(ElementName = "CarName")] public string CarName { get; set; } [XmlElement("CarPassword")] public string CarPassword { get; set; } [XmlElement("CarEmail")] public string CarEmail { get; set; } } Now I think this should all validate. If not assume it is write as my real file does work and this is what this dummy one is based off. Now my problem is this. I want to enforce as much as I can from my schema. Such as the "owner" tag must be the first element and should show up one time and only one time ( minOccurs="1" maxOccurs="1"). Right now I can remove the owner element from my dummy xml file and deseriliaze it and it will go on it's happy way and convert it to object and will just put that property as null. I don't want that I want it to throw an exception or something saying this does match what was expected. I don't want to have to validate things like that once deserialized. Same goes for the <car></car> tag I want that to appear always even if there is no information yet I can remove that too and it will be happy with that. So what tags do I have to add to make my serialization class know that these things are required and if they are not found throw an exception.

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• Deserializing classes from XML generated using XSD.exe

  - by heap

  I have classes generated (using xsd.exe) from an .xsd that I can serialize just fine, but when I try and deserialize it, I get the error: {"<XMLLanguages xmlns='http://tempuri.org/XMLLanguages.xsd'> was not expected."} I've searched for a couple of hours and found most peoples problems lie in not declaring namespaces in their xsd/xml, not defining namespaces in their classes, etc, but I can't find a solution for my problem. Here are code snippets for the relevant classes. <?xml version="1.0" encoding="utf-8"?> <xs:schema id="SetupData" targetNamespace="http://tempuri.org/XMLLanguages.xsd" elementFormDefault="qualified" xmlns="http://tempuri.org/XMLLanguages.xsd" xmlns:xs="http://www.w3.org/2001/XMLSchema" > <xs:element name="XMLLanguages"> <xs:complexType> <xs:sequence> <xs:element name="Tier" minOccurs="1" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="L" minOccurs="1" maxOccurs="unbounded" type="Language"/> </xs:sequence> <xs:attribute name="TierID" type="xs:int"/> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> <xs:complexType name="Language"> <xs:sequence> <xs:element name="LangID" type="xs:int"/> <xs:element name="Tier" type="xs:int"/> <xs:element name ="Name" type="xs:string"/> </xs:sequence> <xs:attribute name ="PassRate" type="xs:int"/> </xs:complexType> </xs:schema> And the class: /// <remarks/> [System.CodeDom.Compiler.GeneratedCodeAttribute("xsd", "4.0.30319.1")] [System.SerializableAttribute()] [System.Diagnostics.DebuggerStepThroughAttribute()] [System.ComponentModel.DesignerCategoryAttribute("code")] [System.Xml.Serialization.XmlTypeAttribute(Namespace = "http://tempuri.org/XMLLanguages.xsd")] [System.Xml.Serialization.XmlRootAttribute(Namespace = "http://tempuri.org/XMLLanguages.xsd", IsNullable = false)] public partial class XMLLanguages { private List<XMLLanguagesTier> tierField; /// <remarks/> [System.Xml.Serialization.XmlElementAttribute("Tier")] public List<XMLLanguagesTier> Tiers { get { return this.tierField; } set { this.tierField = value; } } } And a the line in XML causing the error: <XMLLanguages xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://tempuri.org/XMLLanguages.xsd">

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• Validate xsl fo in xslt styleesheet

  - by Biegal

  Hi, i have a little problem with validating xml, xslt in details. I have a xslt stylesheet that, transforms xml data source to xsl:fo document. Something like this: <?xml version="1.0" encoding="utf-8"?> <xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <xsl:template match="/"> <fo:root xmlns:fo="http://www.w3.org/1999/XSL/Format" xmlns="http://www.w3.org/1999/xhtml"> <fo:layout-master-set> <fo:simple-page-master margin-top="25mm" margin-bottom="25mm" margin-left="25mm" margin-right="25mm" page-width="210mm" page-height="297mm" master-name="simplePageLayout"> <fo:region-body region-name="xsl-region-body" column-gap="0.25in" /> <fo:region-before region-name="xsl-region-before" display-align="after" extent="0.1mm" padding-top="0pt" padding-left="0.4in" padding-right="0.4in" padding-bottom="0pt" /> <fo:region-after region-name="xsl-region-after" display-align="before" extent="0.4in" padding-top="4pt" padding-left="0.4in" padding-right="0.4in" padding-bottom="0pt" /> </fo:simple-page-master> <fo:page-sequence-master master-name="default-sequence"> <fo:repeatable-page-master-reference master-reference="simplePageLayout" /> </fo:page-sequence-master> </fo:layout-master-set> <fo:page-sequence master-reference="default-sequence"> <fo:flow flow-name="xsl-region-body"> <fo:block font-family="Segoe UI" color="#000000" font-size="9pt" /> </fo:flow> </fo:page-sequence> </fo:root> </xsl:template> What I want to do, is to validate written xsl:fo elements, ignoring xsl tags. Is it posible? For now I use dtd validation (I have xsd schema too) for validating Fo, but it give me an error on each xsl tag. Summary. Is it posiible to validate only fo elements against the schema, ignoring xsl tags, and how should I do it? Maybe a code snnippet in C#, or a hint how to modify documents? Thanks in advance!

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• Iterator blocks in Clojure?

  - by Checkers

  I am using clojure.contrib.sql to fetch some records from an SQLite database. (defn read-all-foo [] (with-connection *db* (with-query-results res ["select * from foo"] (into [] res)))) Now, I don't really want to realize the whole sequence before returning from the function (i.e. I want to keep it lazy), but if I return res directly or wrap it some kind of lazy wrapper (for example I want to make a certain map transformation on result sequence), SQL-related bindings will be reset and connection will be closed after I return, so realizing the sequence will throw an exception. How can I enclose the whole function in a closure and return a kind of iterator block (like yield in C# or Python)? Or is there another way to return a lazy sequence from this function?

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• db:migrate creates sequences but doesn't alter table?

  - by RewbieNewbie

  Hello, I have a migration that creates a postres sequence for auto incrementing a primary identifier, and then executes a statement for altering the column and specifying the default value: execute 'CREATE SEQUENCE "ServiceAvailability_ID_seq";' execute <<-SQL ALTER TABLE "ServiceAvailability" ALTER COLUMN "ID" set DEFAULT NEXTVAL('ServiceAvailability_ID_seq'); SQL If I run db:migrate everything seems to work, in that no errors are returned, however, if I run the rails application I get: Mnull value in column "ID" violates not-null constraint I have discovered by executing the sql statement in the migration manually, that this error is because the alter statement isn't working, or isn't being executed. If I manually execute the following statement: CREATE SEQUENCE "ServiceAvailability_ID_seq; I get: error : ERROR: relation "serviceavailability_id_seq" already exists Which means the migration successfully created the sequence! However, if I manually run: ALTER TABLE "ServiceProvider" ALTER COLUMN "ID" set DEFAULT NEXTVAL('ServiceProvider_ID_seq'); SQL It runs successfully and creates the default NEXTVAL. So the question is, why is the migration file creating the sequence with the first execute statement, but not altering the table in the second execute? (Remembering, no errors are output on running db:migrate) Thank you and apologies for tl:dr

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• Initialization of std::vector<unsigned int> with a list of consecutive unsigned integers

  - by Thomas

  I want to use a special method to initialize a std::vector<unsigned int> which is described in a C++ book I use as a reference (the German book 'Der C++ Programmer' by Ulrich Breymann, in case that matters). In that book is a section on sequence types of the STL, referring in particular to list, vector and deque. In this section he writes that there are two special constructors of such sequence types, namely, if Xrefers to such a type, X(n, t) // creates a sequence with n copies of t X(i, j) // creates a sequence from the elements of the interval [i, j) I want to use the second one for an interval of unsigned int, that is std::vector<unsigned int> l(1U, 10U); to get a list initialized with {1,2,...,9}. What I get, however, is a vector with one unsigned int with value 10 :-| Does the second variant exist, and if yes, how do I force that it is called?

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• Using optimization to assign by preference

  - by Aarthi

  I have 100 objects ("candies") that I need to distribute between five people so that each has an equal number of candies (in this case, 20 candies per person). However, each person has also expressed their preferences of candy to me in a chart, similar to below. Top-favored candies receive 10 points, least-favored candies receive -10 points, and neutral-favored candies receive 0.5 points. I need to sort the items out so that: Each person receives the same number of candies Each person's total "satisfaction" (points) is maximized My output is a list of each person's assigned items I'm familiar with Excel's in-house Monte Carlo simulation tools (Solver, F9 diceroll, etc) and would like to stick to those tools. While I know how to set up the chart, and how to use the column summation to input into Solver, I don't know how to get it to give me the desired output. Furthermore, how do I adjust the solver so it takes into account individual preferences rather than empirical ones? To wit: how do I begin setting up this model?

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• database schema eligible for delta synchronization

  - by WilliamLou

  it's a question for discussion only. Right now, I need to re-design a mysql database table. Basically, this table contains all the contract records I synchronized from another database. The contract record can be modified, deleted or users can add new contract records via GUI interface. At this stage, the table structure is exactly the same as the Contract info (column: serial number, expiry date etc.). In that case, I can only synchronize the whole table (delete all old records, replace with new ones). If I want to delta(only synchronize with modified, new, deleted records) synchronize the table, how should I change the database schema? here is the method I come up with, but I need your suggestions because I think it's a common scenario in database applications. 1)introduce a sequence number concept/column: for each sequence, mark the new added records, modified records, deleted records with this sequence number. By recording the last synchronized sequence number, only pass those records with higher sequence number; 2) because deleted contracts can be added back, and the original table has primary key constraints, should I create another table for those deleted records? or add a flag column to indicate if this contract has been deleted? I hope I explain my question clearly. Anyway, if you know any articles or your own suggestions about this, please let me know. Thanks!

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• Another serialization ? - c#

  - by ltech

  I had asked this Yesterday If my xsd schema changes to <xs:element name="Document" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="MetaDoc" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="ATTRIBUTES" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="author" type="xs:string" minOccurs="0" /> <xs:element name="max_versions" type="xs:string" minOccurs="0" /> <xs:element name="summary" type="xs:string" minOccurs="0" /> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> My xsd - class generation becomes /// <remarks/> [System.Xml.Serialization.XmlArrayAttribute(Form=System.Xml.Schema.XmlSchemaForm.Unqualified)] [System.Xml.Serialization.XmlArrayItemAttribute("MetaDoc", typeof(DocumentMetaDocATTRIBUTES[]), Form=System.Xml.Schema.XmlSchemaForm.Unqualified, IsNullable=false)] [System.Xml.Serialization.XmlArrayItemAttribute("ATTRIBUTES", typeof(DocumentMetaDocATTRIBUTES), Form=System.Xml.Schema.XmlSchemaForm.Unqualified, IsNullable=false, NestingLevel=1)] public DocumentMetaDocATTRIBUTES[][][] Document { get { return this.documentField; } set { this.documentField = value; } } If I am deriving to CollectionBase, as shown in my previous post, how would I manage the XmlArrayItemAttribute ? so that I can read this part of my input xml into my strongly types object <Document> <MetaDoc> <ATTRIBUTES> <author>asas</author> <max_versions>1</max_versions> <summary>aasasqqqq</summary> </ATTRIBUTES> </MetaDoc> </Document>

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• splitting A and MX records

  - by market

  I have a domain name which currently points to a shared hosting service. I've set up a dedicated Apache server for the web hosting, but would like to keep using the mail server of the old host. Is the correct way to do this to add an A record that points to the IP of the new server, and an MX record that points to the hostname of the mail server? does anything need to be done with the NS records?

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• I am confused -- Will this code always work?

  - by Shekhar

  Hello, I have written this piece of code public class Test{ public static void main(String[] args) { List<Integer> list = new ArrayList<Integer>(); for(int i = 1;i<= 4;i++){ new Thread(new TestTask(i, list)).start(); } while(list.size() != 4){ // this while loop required so that all threads complete their work } System.out.println("List "+list); } } class TestTask implements Runnable{ private int sequence; private List<Integer> list; public TestTask(int sequence, List<Integer> list) { this.sequence = sequence; this.list = list; } @Override public void run() { list.add(sequence); } } This code works and prints all the four elements of list on my machine. My question is that will this code always work. I think there might be a issue in this code when two/or more threads add element to this list at the same point. In that case it while loop will never end and code will fail. Can anybody suggest a better way to do this? I am not very good at multithreading and don't know which concurrent collection i can use? Thanks Shekhar

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• Is this code well-defined?

  - by Nawaz

  This code is taken from a discussion going on here. someInstance.Fun(++k).Gun(10).Sun(k).Tun(); Is this code well-defined? Is ++k Fun() evaluated before k in Sun()? What if k is user-defined type, not built-in type? And in what ways the above function calls order is different from this: eat(++k);drink(10);sleep(k); As far as I can say, in both situations, there exists a sequence point after each function call. If so, then why can't the first case is also well-defined like the second one? Section 1.9.17 of the C++ ISO standard says this about sequence points and function evaluation: When calling a function (whether or not the function is inline), there is a sequence point after the evaluation of all function arguments (if any) which takes place before execution of any expressions or statements in the function body. There is also a sequence point after the copying of a returned value and before the execution of any expressions outside the function.

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• XML Schema for a .NET type that inherits and implements

  - by John Ruiz

  Hi, Please consider the following three .NET types: I have an interface, an abstract class, and a concrete class. My question is how to write the XML Schema to include the properties from the interface and from the abstract class. public interface IStartable { bool RequiresKey { get; set; } void Start(object key); } public abstract class Vehicle { uint WheelCount { get; set; } } public class Car : Vehicle, IStartable { public bool RequiresKey { get; set; } public string Make { get; set; } publilc string Model { get; set; } public Car() {} public void Start(object key) { // start car with key } } I don't know how to complete this schema: <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="cars" xmlns="cars" xmlns:c="cars"> <!-- How do I get car to have vehicle's wheelcount AND IStartable's RequiresKey? --> <xs:element name="Car" type="c:Car" /> <xs:complexType name="Car"> <xs:complexContent> <xs:extension base="c:Vehicle"> <xs:group ref=c:CarGroup" /> </xs:extension> </xs:complexContent> </xs:complexType> <xs:group name="CarGroup"> <xs:sequence> <xs:element name="Make" type="xs:token" /> <xs:element name="Model" type="xs:token" /> </xs:sequence> </xs:group> <xs:complexType name="Vehicle"> <xs:sequence> <xs:element name="WheelCount" type="xs:unsignedInt" /> </xs:sequence> </xs:complexType> <xs:complexType name="IStartable"> <xs:sequence> <xs:element name="RequiresKey" type="xs:boolean" /> </xs:sequence> </xs:complexType> </xs:schema>

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• Parse a text file into multiple text file

  - by Vijay Kumar Singh

  I want to get multiple file by parsing a input file Through Java. The Input file contains many fasta format of thousands of protein sequence and I want to generate raw format(i.e., without any comma semicolon and without any extra symbol like "", "[", "]" etc) of each protein sequence. A fasta sequence starts form "" symbol followed by description of protein and then sequence of protein. For example ? lcl|NC_000001.10_cdsid_XP_003403591.1 [gene=LOC100652771] [protein=hypothetical protein LOC100652771] [protein_id=XP_003403591.1] [location=join(12190..12227,12595..12721,13403..13639)] MSESINFSHNLGQLLSPPRCVVMPGMPFPSIRSPELQKTTADLDHTLVSVPSVAESLHHPEITFLTAFCL PSFTRSRPLPDRQLHHCLALCPSFALPAGDGVCHGPGLQGSCYKGETQESVESRVLPGPRHRH Like above formate the input file contains 1000s of protein sequence. I have to generate thousands of raw file containing only individual protein sequence without any special symbol or gaps. I have developed the code for it in Java but out put is : Cannot open a file followed by cannot find file. Please help me to solve my problem. Regards Vijay Kumar Garg Varanasi Bharat (India) The code is /*Java code to convert FASTA format to a raw format*/ import java.io.*; import java.util.*; import java.util.regex.*; import java.io.FileInputStream; // java package for using regular expression public class Arrayren { public static void main(String args[]) throws IOException { String a[]=new String[1000]; String b[][] =new String[1000][1000]; /*open the id file*/ try { File f = new File ("input.txt"); //opening the text document containing genbank ids FileInputStream fis = new FileInputStream("input.txt"); //Reading the file contents through inputstream BufferedInputStream bis = new BufferedInputStream(fis); // Writing the contents to a buffered stream DataInputStream dis = new DataInputStream(bis); //Method for reading Java Standard data types String inputline; String line; String separator = System.getProperty("line.separator"); // reads a line till next line operator is found int i=0; while ((inputline=dis.readLine()) != null) { i++; a[i]=inputline; a[i]=a[i].replaceAll(separator,""); //replaces unwanted patterns like /n with space a[i]=a[i].trim(); // trims out if any space is available a[i]=a[i]+".txt"; //takes the file name into an array try // to handle run time error /*take the sequence in to an array*/ { BufferedReader in = new BufferedReader (new FileReader(a[i])); String inline = null; int j=0; while((inline=in.readLine()) != null) { j++; b[i][j]=inline; Pattern q=Pattern.compile(">"); //Compiling the regular expression Matcher n=q.matcher(inline); //creates the matcher for the above pattern if(n.find()) { /*appending the comment line*/ b[i][j]=b[i][j].replaceAll(">gi",""); //identify the pattern and replace it with a space b[i][j]=b[i][j].replaceAll("[a-zA-Z]",""); b[i][j]=b[i][j].replaceAll("|",""); b[i][j]=b[i][j].replaceAll("\\d{1,15}",""); b[i][j]=b[i][j].replaceAll(".",""); b[i][j]=b[i][j].replaceAll("_",""); b[i][j]=b[i][j].replaceAll("\\(",""); b[i][j]=b[i][j].replaceAll("\\)",""); } /*printing the sequence in to a text file*/ b[i][j]=b[i][j].replaceAll(separator,""); b[i][j]=b[i][j].trim(); // trims out if any space is available File create = new File(inputline+"R.txt"); try { if(!create.exists()) { create.createNewFile(); // creates a new file } else { System.out.println("file already exists"); } } catch(IOException e) // to catch the exception and print the error if cannot open a file { System.err.println("cannot create a file"); } BufferedWriter outt = new BufferedWriter(new FileWriter(inputline+"R.txt", true)); outt.write(b[i][j]); // printing the contents to a text file outt.close(); // closing the text file System.out.println(b[i][j]); } } catch(Exception e) { System.out.println("cannot open a file"); } } } catch(Exception ex) // catch the exception and prints the error if cannot find file { System.out.println("cannot find file "); } } } If you provide me correct it will be much easier to understand.

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• Unable to serialize correctly- c#

  - by ltech

  I had asked this Yesterday If my xsd schema changes to <xs:element name="Document" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="MetaDoc" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="ATTRIBUTES" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="author" type="xs:string" minOccurs="0" /> <xs:element name="max_versions" type="xs:string" minOccurs="0" /> <xs:element name="summary" type="xs:string" minOccurs="0" /> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> </xs:complexType> </xs:element> My xsd - class generation becomes /// <remarks/> [System.Xml.Serialization.XmlArrayAttribute(Form=System.Xml.Schema.XmlSchemaForm.Unqualified)] [System.Xml.Serialization.XmlArrayItemAttribute("MetaDoc", typeof(DocumentMetaDocATTRIBUTES[]), Form=System.Xml.Schema.XmlSchemaForm.Unqualified, IsNullable=false)] [System.Xml.Serialization.XmlArrayItemAttribute("ATTRIBUTES", typeof(DocumentMetaDocATTRIBUTES), Form=System.Xml.Schema.XmlSchemaForm.Unqualified, IsNullable=false, NestingLevel=1)] public DocumentMetaDocATTRIBUTES[][][] Document { get { return this.documentField; } set { this.documentField = value; } } If I am deriving to CollectionBase, as shown in my previous post, how would I manage the XmlArrayItemAttribute ? so that I can read this part of my input xml into my strongly types object <Document> <MetaDoc> <ATTRIBUTES> <author>asas</author> <max_versions>1</max_versions> <summary>aasasqqqq</summary> </ATTRIBUTES> </MetaDoc> </Document>

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• Swift CMutablePointers in factories e.g. NewMusicSequence

  - by Gene De Lisa

  How do you use C level factory methods in Swift? Let's try using a factory such as NewMusicSequence(). OSStatus status var sequence:MusicSequence status=NewMusicSequence(&sequence) This errors out with "error: variable 'sequence' passed by reference before being initialized". Set sequence to nil, and you get EXC_BAD_INSTRUCTION. You can try being explicit like this: var sp:CMutablePointer<MusicSequence>=nil status=NewMusicSequence(sp) But then you get a bad access exception when you set sp to nil. If you don't set sp, you get an "error: variable 'sp' used before being initialized" Here's the reference.

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• "Anagram solver" based on statistics rather than a dictionary/table?

  - by James M.

  My problem is conceptually similar to solving anagrams, except I can't just use a dictionary lookup. I am trying to find plausible words rather than real words. I have created an N-gram model (for now, N=2) based on the letters in a bunch of text. Now, given a random sequence of letters, I would like to permute them into the most likely sequence according to the transition probabilities. I thought I would need the Viterbi algorithm when I started this, but as I look deeper, the Viterbi algorithm optimizes a sequence of hidden random variables based on the observed output. I am trying to optimize the output sequence. Is there a well-known algorithm for this that I can read about? Or am I on the right track with Viterbi and I'm just not seeing how to apply it?

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