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• How can I apply a PSSM efficiently?

  - by flies

  I am fitting for position specific scoring matrices (PSSM aka Position Specific Weight Matrices). The fit I'm using is like simulated annealing, where I the perturb the PSSM, compare the prediction to experiment and accept the change if it improves agreement. This means I apply the PSSM millions of times per fit; performance is critical. In my particular problem, I'm applying a PSSM for an object of length L (~8 bp) at every position of a DNA sequence of length M (~30 bp) (so there are M-L+1 valid positions). I need an efficient algorithm to apply a PSSM. Can anyone help improve performance? My best idea is to convert the DNA into some kind of a matrix so that applying the PSSM is matrix multiplication. There are efficient linear algebra libraries out there (e.g. BLAS), but I'm not sure how best to turn an M-length DNA sequence into a matrix M x 4 matrix and then apply the PSSM at each position. The solution needs to work for higher order/dinucleotide terms in the PSSM - presumably this means representing the sequence-matrix for mono-nucleotides and separately for dinucleotides. My current solution iterates over each position m, then over each letter in word from m to m+L-1, adding the corresponding term in the matrix. I'm storing the matrix as a multi-dimensional STL vector, and profiling has revealed that a lot of the computation time is just accessing the elements of the PSSM (with similar performance bottlenecks accessing the DNA sequence). If someone has an idea besides matrix multiplication, I'm all ears.

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• How much of STL is too much?

  - by Darius Kucinskas

  I am using a lot of STL code with std::for_each, bind, and so on, but I noticed that sometimes STL usage is not good idea. For example if you have a std::vector and want to do one action on each item of the vector, your first idea is to use this: std::for_each(vec.begin(), vec.end(), Foo()) and it is elegant and ok, for a while. But then comes the first set of bug reports and you have to modify code. Now you should add parameter to call Foo(), so now it becomes: std::for_each(vec.begin(), vec.end(), std::bind2nd(Foo(), X)) but that is only temporary solution. Now the project is maturing and you understand business logic much better and you want to add new modifications to code. It is at this point that you realize that you should use old good: for(std::vector::iterator it = vec.begin(); it != vec.end(); ++it) Is this happening only to me? Do you recognise this kind of pattern in your code? Have you experience similar anti-patterns using STL?

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• Method that does conditional return of method calling it?

  - by Mattias Konradsson

  Ok this might be a bit of hack but bear with me :) The background is that i'm tired of methods that that some if-statement to that messes up indention for the whole method, like: public SomeClass DoStuff(string inputStr) { SomeClass result =null; if (IsOpenFilter(inputStr)) { .... } return result; } So I was thinking , wouldn't it be neat if I could do something like this instead: public SomeClass DoStuff(string inputStr) { Require(IsOpenFilter(inputStr),null); .... return result; } The idea is that if the statement does not evaluates to true it would return null. If there wasn't a return type for the method it would simply be: Require(IsOpenFilter(inputStr)); I realize that this is kinda overlapping with code contracts but these would be more like "conditional" or "soft" contracts evaluated at runtime rather than compile time. So I guess there's two questions, can this be done somehow? I'm stumped on how to do a conditional return from calling a method. The other question is, is this a good idea? It's a bit weird to monkeypatch the language like this but I'd rather like the way the code reads. I would be even cleaner if it could be put into an attribute above the method: [Require(IsOpenFilter(inputStr))]

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• Model login constraints based on time

  - by DaDaDom

  Good morning, for an existing web application I need to implement "time based login constraints". It means that for each user, later maybe each group, I can define timeslots when they are (not) allowed to log in into the system. As all data for the application is stored in database tables, I need to somehow create a way to model this idea in that way. My first approach, I will try to explain it here: Create a tree of login constraints (called "timeslots") with the main "categories", like "workday", "weekend", "public holiday", etc. on the top level, which are in a "sorted" order (meaning "public holiday" has a higher priority than "weekday") for each top level node create subnodes, which have a finer timespan, like "monday", "tuesday", ... below that, create an "hour" level: 0, 1, 2, ..., 23. No further details are necessary. set every member to "allowed" by default For every member of the system create a 1:n relationship member:timeslots which defines constraints, e.g. a member A may have A:monday-forbidden and A:tuesday-forbidden Do a depth-first search at every login and check if the member has a constraint. Why a depth first search? Well, I thought that it may be that a member has the rules: A:monday->forbidden, A:monday-10->allowed, A:mondey-11->allowed So a login on monday at 12:30 would fail, but one at 10:30 succeed. For performance reasons I could break the relational database paradigm and set a flag for every entry in the member-to-timeslots-table which is set to true if the member has information set for "finer" timeslots, but that's a second step. Is this model in principle a good idea? Are there existing models? Thanks.

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• When I try to run vim in command line I get Python errors

  - by Eduan

  When I try running vim in the Terminal (so as to follow @romainl's suggestion in my other question) I get lots of Python errors, which all boil down to: IOError: invalid Python installation: unable to open /usr/include/python2.7/pyconfig.h (No such file or directory) Why is this? I can use Python or Sublime Text even, without any problems. The full list of errors is the following: Traceback (most recent call last): File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py", line 565, in <module> File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py", line 547, in main File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py", line 278, in addusersitepackages File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py", line 253, in getusersitepackages File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py", line 243, in getuserbase File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.py", line 523, in get_config_var File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.py", line 419, in get_config_vars File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.py", line 298, in _init_posix IOError: invalid Python installation: unable to open /usr/include/python2.7/pyconfig.h (No such file or directory) Extra info: I am on Mac OS X Mountain Lion (OS 10.8) EDIT: I tried @BobDunakey idea with no success, the idea was to use sudo. I still get the same errors. EDIT 2: I was able to solve the problem thanks to Zirak's solution, which is the following: http://clearfix.be/2012/08/05/fix-mountain-lion-10-8-python-ioerror-pyconfig-h-error/

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• Strange Problem with Webservice and IIS

  - by Rene

  Hello there, I have a Problem which confuses me a little bit, resp. where I don't have any Idea about what it could be. The System I'm using is Windows Vista, IIS 7.0, VS2008, Windows Software Factory, Entity Framework, WCF. The Binding for all Webservices is wshttpbinding. I'm using a Webservice hosted in IIS. This Webservice uses/calls another Webservice (also installed in the IIS). If I use a client calling the first Webservice (which calls the second Webservice) it works fine for about 4-10 Times. And then (it is repeatable to get this Problem, but sometimes it happens after 4, sometimes after 10 Time, but it always will happen), the Service and the IIS gets stuck. Stuck means, that this Webservice isn't callable anymore and generates an timeout after 1 minute. Even increasing Timeout doesn't change anything. If i try to restart the IIS I get an timeout error. So the IIS is also "stuck" (it is not really stuck, but I can't restart it). Only if I kill the w3wp.exe IIS is restartable and the Webservice will work again (until i again call this service several times). The logfiles (i'm no expert in things like logging or where to find/enable such logs, so to say : i'm a newbie) like http-logging, Event Viewer or WCF-Message Logging don't show any hints upon the source of the problem. I don't have this problem when I'm using a Webservice which doesn't call another Service. Calling a Webservice is done by Service Reference (I'm using no Proxy-Classes), but I think this should be no Problem. I have no idea of what is happening, nor how to solve this Problem. Regards Rene

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• javascript plugin - singleton pattern?

  - by Adam Kiss

  intro Hello, I'm trying to develop some plugin or/*and* object in javascript, which will control some properties over some object. It will also use jQuery, to ease development. idea This is in pseudocode to give you an idea, since I can't really describe it in english with the right words, it's impossible to go and use google to find out what I want to use (and learn). I will have plugin (maybe object?) with some variables and methods: plugin hideshow(startupconfig){ var c, //collection add: function(what){ c += what; }, do: function(){ c.show().hide().stop(); //example code } } and I will use it this way (or sort-of): var p = new Plugin(); p .add($('p#simple')) .add($('p#simple2')) .do(); note I'm not really looking for jQuery plugin tutorials - it's more like usage of singleton pattern in document in javascript, jQuery is mentione only because it will be used to modify dom and simplify selectors, jQuery plugin maybe just for that one little function add. I'm looking for something, that will sit on top of my document and call functions from itselft based on timer, or user actions, or whatever. problems I don't really know where to start with construction of this object/plugin I'm not really sure how to maintain one variable, which is collection of jQuery objects (something like $('#simple, #simple2');) I would maybe like to extedn jQuery with $.fn.addToPlugin to use chaining of objects, but that should be simple (really just each( p.add($(this)); )) I hope I make any sense, ideas, links or advices appreciated.

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• svnserve not strictly required?

  - by Kev

  I was reading the Red Bean book and noticed this paragraph: Do not be seduced by the simple idea of having all of your users access a repository directly via file:// URLs. Even if the repository is readily available to everyone via a network share, this is a bad idea. It removes any layers of protection between the users and the repository: users can accidentally (or intentionally) corrupt the repository database, it becomes hard to take the repository offline for inspection or upgrade, and it can lead to a mess of file permission problems (see the section called “Supporting Multiple Repository Access Methods”). Note that this is also one of the reasons we warn against accessing repositories via svn+ssh:// URLs—from a security standpoint, it's effectively the same as local users accessing via file://, and it can entail all the same problems if the administrator isn't careful. I realized that, since I'm the only one accessing the repository, ever, none of these caveats seem to apply. Can I safely down svnserve then and only ever have to worry about upgrading my TortoiseSVN client, not both the client and the server whenever there's a new version out? (I've tried it already--just needed to use the Relocate feature to switch from svn:// to file://--but I wanted to make sure something wouldn't be sneaking up on me if I left it this way.)

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• proper use of volatile keyword

  - by luke

  I think i have a pretty good idea about the volatile keyword in java, but i'm thinking about re-factoring some code and i thought it would be a good idea to use it. i have a class that is basically working as a DB Cache. it holds a bunch of objects that it has read from a database, serves requests for those objects, and then occasionally refreshes the database (based on a timeout). Heres the skeleton public class Cache { private HashMap mappings =....; private long last_update_time; private void loadMappingsFromDB() { //.... } private void checkLoad() { if(System.currentTimeMillis() - last_update_time > TIMEOUT) loadMappingsFromDB(); } public Data get(ID id) { checkLoad(); //.. look it up } } So the concern is that loadMappingsFromDB could be a high latency operation and thats not acceptable, So initially i thought that i could spin up a thread on cache startup and then just have it sleep and then update the cache in the background. But then i would need to synchronize my class (or the map). and then i would just be trading an occasional big pause for making every cache access slower. Then i thought why not use volatile i could define the map reference as volatile private volatile HashMap mappings =....; and then in get (or anywhere else that uses the mappings variable) i would just make a local copy of the reference: public Data get(ID id) { HashMap local = mappings; //.. look it up using local } and then the background thread would just load into a temp table and then swap the references in the class HashMap tmp; //load tmp from DB mappings = tmp;//swap variables forcing write barrier Does this approach make sense? and is it actually thread-safe?

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• How to distribute an offline cube for excel

  - by Mike M

  I have the following scenario. A cube created in SSAS 2008. I can connected to this cube via Excel. I can create an offline cube file. I can connect to this offline cube file. Now, say I want to email this excel file along with the cube file so that another user can view it. I run into the problem that the connection path the offline cube is hard coded into the excel file. Its the same problem this person had. http://stackoverflow.com/questions/1253950/opening-offline-cube-from-another-machine Their solution was to just make sure the other user saved the cube in the same directory structure. I don't love that solution. I also came across this idea: http://www.pcreview.co.uk/forums/thread-948974.php I tried that, it errored out, but I am not an Excel VBA programmer and really have no idea if I even put the code in the right place. So anyway, anyone out there have any ideas about who to do this? If the VBA solution is the best, could someone give me some tips on where to actually put that code?

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• keep HTMLformat after replace some text (using PHP and JS)

  - by Sadi

  I would like modify HTML like I am <b>Sadi, novice</b> programmer. to I am <b>Sadi, learner</b> programmer. To do it I will search using a string "novice programmer". How can I do it please? Any idea? Thank you Sadi More clarification: I get some nice reply with possible solution. But please keep posting if you have any idea in mind. I would like to more clarify the problem just in case anyone missed it. Main post shows the problem as an example scenario. 1) Now the problem is find and replace some string without considering the tags. The tags may shows up within a single word. String may contain multiple word. Tag only appear in the content string or the document. The search phrase never contain any tags. We can easily remove all tags and do some text operation. But here the another problem shows up. 2) The tags must be preserve, even after replacing the text. That is what the example shows. Thank you Again for helping

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• Free Memory Occupied by Std List, Vector, Map etc

  - by Graviton

  Coming from a C# background, I have only vaguest idea on memory management on C++-- all I know is that I would have to free the memory manually. As a result my C++ code is written in such a way that objects of the type std::vector, std::list, std::map are freely instantiated, used, but not freed. I didn't realize this point until I am almost done with my programs, now my code is consisted of the following kinds of patterns: struct Point_2 { double x; double y; }; struct Point_3 { double x; double y; double z; }; list<list<Point_2>> Computation::ComputationJob(list<Point_3> pts3D, vector<Point_2> vectors) { map<Point_2, double> pt2DMap=ConstructPointMap(pts3D); vector<Point_2> vectorList = ConstructVectors(vectors); list<list<Point_2>> faceList2D=ConstructPoints(vectorList , pt2DMap); return faceList2D; } My question is, must I free every.single.one of the list usage ( in the above example, this means that I would have to free pt2DMap, vectorList and faceList2D)? That would be very tedious! I might just as well rewrite my Computation class so that it is less prone to memory leak. Any idea how to fix this?

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• Can't install do_mysql gem?

  - by maccy1

  I'm trying to install the do_mysql on my Snow Leopord system Macbook Pro 13", but I keep getting this error: n216-160:~ myself$ sudo gem1.9 install do_mysql Password: Building native extensions. This could take a while... ERROR: Error installing do_mysql: ERROR: Failed to build gem native extension. /opt/local/bin/ruby1.9 extconf.rb checking for mysql_query() in -lmysqlclient... no *** extconf.rb failed *** Could not create Makefile due to some reason, probably lack of necessary libraries and/or headers. Check the mkmf.log file for more details. You may need configuration options. Provided configuration options: --with-opt-dir --without-opt-dir --with-opt-include --without-opt-include=${opt-dir}/include --with-opt-lib --without-opt-lib=${opt-dir}/lib --with-make-prog --without-make-prog --srcdir=. --curdir --ruby=/opt/local/bin/ruby1.9 --with-mysql-config --without-mysql-config --with-mysql-dir --without-mysql-dir --with-mysql-include --without-mysql-include=${mysql-dir}/include --with-mysql-lib --without-mysql-lib=${mysql-dir}/lib --with-mysqlclientlib --without-mysqlclientlib Gem files will remain installed in /opt/local/lib/ruby1.9/gems/1.9.1/gems/do_mysql-0.10.0 for inspection. Results logged to /opt/local/lib/ruby1.9/gems/1.9.1/gems/do_mysql-0.10.0/ext/do_mysql_ext/gem_make.out n216-160:~ myself$ I have no idea why. I also reinstalled my verison of MySQL with the MySQL 5.4.3 beta, 64-bit as others suggested but no dice. Does anyone have any idea what is wrong?

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• Do you like Twisted?

  - by Luca

  I use Python Twisted for web development, and I don't like it? I know async programming is a great idea, I know there are may async web servers now, I know it's the only way to solve some problems you'd have with threads but I don't like. The problem is that, you're forced to program in a twisted way. So, the architecture you have in mind, very often have to be modified to fit the way twisted works. The architecture have to follow the technology, I don't think this is good. When we use callback in javascript, we don't have too many difficulties: things are usually simpler, we use a callback in response to an Ajax call. But in a server web app things are, very often, a bit more complex. Writing chain of callbacks don't seem to me a wonderful way of programming. The code is not simple, and so it is difficult to understand and to maintain. Writing twisted code we very often lost the linear intuitive idea of the algorithm we wanted to implement, especially when things grow in complexity. What's your point of view?

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• Adding exclusive filter for <static initializer> in findbugs

  - by MilanAleksic

  Hi all, I want my findbugs report not show the following error: DM_NUMBER_CTOR: Method invokes inefficient Number constructor; use static valueOf instead The problem is that this happens in groovy-generated code files, so I can't control the source code - that is why I want to exclude it and add it to my exclude filter. I do not want to add explicitly class (since I make API that many tools will use, I want my filter to be generic). I would not like to completely remove this bug from the report by type, I would really like to only exclude this bug from appearing if it happenned in "static initializer" methods. Any idea? I tried the filter below but no luck, maybe somebody has better idea? <Match> <Method name="~.*static initializer.*" /> <Bug pattern="DM_NUMBER_CTOR" /> </Match> Here is the "stacktrace" of FindBugs in that case: In class net.milanaleksic.cuc.tools.sound.SoundPlayerTool In method net.milanaleksic.cuc.tools.sound.SoundPlayerTool.() Called method new Long(long) Should call Long.valueOf(long) instead In SoundPlayerTool.groovy

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• Memory problems while code is running (Python, Networkx)

  - by MIN SU PARK

  I made a code for generate a graph with 379613734 edges. But the code couldn't be finished because of memory. It takes about 97% of server memory when it go through 62 million lines. So I killed it. Do you have any idea to solve this problem? My code is like this: import os, sys import time import networkx as nx G = nx.Graph() ptime = time.time() j = 1 for line in open("./US_Health_Links.txt", 'r'): #for line in open("./test_network.txt", 'r'): follower = line.strip().split()[0] followee = line.strip().split()[1] G.add_edge(follower, followee) if j%1000000 == 0: print j*1.0/1000000, "million lines done", time.time() - ptime ptime = time.time() j += 1 DG = G.to_directed() # P = nx.path_graph(DG) Nn_G = G.number_of_nodes() N_CC = nx.number_connected_components(G) LCC = nx.connected_component_subgraphs(G)[0] n_LCC = LCC.nodes() Nn_LCC = LCC.number_of_nodes() inDegree = DG.in_degree() outDegree = DG.out_degree() Density = nx.density(G) # Diameter = nx.diameter(G) # Centrality = nx.betweenness_centrality(PDG, normalized=True, weighted_edges=False) # Clustering = nx.average_clustering(G) print "number of nodes in G\t" + str(Nn_G) + '\n' + "number of CC in G\t" + str(N_CC) + '\n' + "number of nodes in LCC\t" + str(Nn_LCC) + '\n' + "Density of G\t" + str(Density) + '\n' # sys.exit() # j += 1 The edge data is like this: 1000 1001 1000245 1020191 1000 10267352 1000653 10957902 1000 11039092 1000 1118691 10346 11882 1000 1228281 1000 1247041 1000 12965332 121340 13027572 1000 13075072 1000 13183162 1000 13250162 1214 13326292 1000 13452672 1000 13844892 1000 14061830 12340 1406481 1000 14134703 1000 14216951 1000 14254402 12134 14258044 1000 14270791 1000 14278978 12134 14313332 1000 14392970 1000 14441172 1000 14497568 1000 14502775 1000 14595635 1000 14620544 1000 14632615 10234 14680596 1000 14956164 10230 14998341 112000 15132211 1000 15145450 100 15285998 1000 15288974 1000 15300187 1000 1532061 1000 15326300 Lastly, is there anybody who has an experience to analyze Twitter link data? It's quite hard to me to take a directed graph and calculate average/median indegree and outdegree of nodes. Any help or idea?

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• FILE* issue PPU side code

  - by Cristina

  We are working on a homework on CELL programming for college and their feedback response to our questions is kinda slow, thought i can get some faster answers here. I have a PPU side code which tries to open a file passed down through char* argv[], however this doesn't work it cannot make the assignment of the pointer, i get a NULL. Now my first idea was that the file isn't in the correct directory and i copied in every possible and logical place, my second idea is that maybe the PPU wants this pointer in its LS area, but i can't deduce if that's the bug or not. So... My question is what am i doing wrong? I am working with a Fedora 7 SDK Cell, with Eclipse as an IDE. Maybe my argument setup is wrong tho he gets the name of the file correctly. Code on request: images_t *read_bin_data(char *name) { FILE *file; images_t *img; uint32_t *buffer; uint8_t buf; unsigned long fileLen; unsigned long i; //Open file file = (FILE*)malloc(sizeof(FILE)); file = fopen(name, "rb"); printf("[Debug]Opening file %s\n",name); if (!file) { fprintf(stderr, "Unable to open file %s", name); return NULL; } //....... } Main launch: int main(int argc,char* argv[]) { int i,img_width; int modif_this[4] __attribute__ ((aligned(16))) = {1,2,3,4}; images_t *faces, *nonfaces; spe_context_ptr_t ctxs[SPU_THREADS]; pthread_t threads[SPU_THREADS]; thread_arg_t arg[SPU_THREADS]; //intializare img_width img_width = atoi(argv[1]); printf("[Debug]Img size is %i\n",img_width); faces = read_bin_data(argv[3]); //....... } Thanks for the help.

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• Is there a tool I can use to generate interfaces and wrappers for object mocking in c#

  - by fostandy

  Given a class like System.Timers.Timer, or ANY managed class (whether user defined, from the .net framework, or some 3rd party library) is there some program I can use to (a) generate an interface based on this class and (b) generate a wrapper for the given class? for example if I have a public class Foo { public object MyProperty { get { ... } set { ... } } public int SomeMethod(object a) { ... } } it will create an interface interface IFoo { object MyProperty { get; set; } int SomeMethod(object a) { ... } } and maybe even a wrapper class FooWrap { // something for relay constructor here ... Foo _me; public object MyProperty { get { return _me.MyProperty; } set { _me.MyProperty = value; } } public int SomeMethod(object a) { return _me.SomeMethod(); } } Obviously there's stuff I haven't thought about like events, generics etc. I want a DWIMNWIS-PSICHTO(-Plus-Stuff-I-Clearly-Haven't-Thought-Of). I'm aware resharper can be used to extract an interface but I've only been able to use this on my own classes. Aside: Wow, it is amazing how simply becoming accustomed to a previously 'unacceptable' idea eventually gives it legitimacy. A year ago the idea of having to create interfaces for all objects I want to mock and adopting an injection framework would have seemed like the height of madness. It turns out that while it's not quite death and taxes, it is sparta. I am aware of and have used typemock. It certainly is the work of elvish wizards. One day when $800 does not seem like quite so much money I intend to buy it.

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• Interesting questions related to lighttpd on Amazon EC2

  - by terence410

  This problem appeared today and I have no idea what is going on. Please share you ideas. I have 1 EC2 DB server (MYSQL + NFS File Sharing + Memcached). And I have 3 EC2 Web servers (lighttpd) where it will mounted the NFS folders on the DB server. Everything going smoothly for months but suddenly there is an interesting phenomenon. In every 8 minutes to 10 minutes, PHP file will be unreachable. This will last about 1 minute and then back to normal. Normal files like .html file are unaffected. All servers have the same problem exactly at the same time. I have spent one whole day to analysis the reason. Finally, I find out when the problem appear, the file descriptor of lighttpd suddenly increased a lot. I used ls /proc/1234/fd | wc -l to check the number of fd. The # of fd is around 250 in normal time. However, when the problem appeared, it will be raised to 1500 and then back to normal. It sounds funny, right? Do you have any idea what's going on? ======================== The CPU graph of one of the web server.

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• Is it legal to extend the Class class?

  - by spiralganglion

  I've been writing a system that generates some templates, and then generates some objects based on those templates. I had the idea that the templates could be extensions of the Class class, but that resulted in some magnificent errors: VerifyError: Error #1107: The ABC data is corrupt, attempt to read out of bounds. What I'm wondering is if subclassing Class is even possible, if there is perhaps some case where doing this would be appropriate, and not just a gross misuse of OOP. I believe it should be possible, as ActionScript allows you to create variables of the Class type. This use is described in the LiveDocs entry for Class, yet I've seen no mentions of subclassing Class. Here's a pseudocode example: class Foo extends Class var a:Foo = new Foo(); trace(a is Class) // true, right? var b = new a(); I have no idea what the type of b would be. In summary: can you subclass the Class class? If so, how can you do it without errors, and what type are the instances of the instances of the Class subclass?

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• ACL architechture for a Software As a service in Sprgin 3.0

  - by geoaxis

  I am making a software as a service using Spring 3.0 (Spring MVC, Spring Security, Spring Roo, Hibernate) I have to come up with a flexible access control list mechanism.I have three different kinds of users System (who can do any thing to the system, includes admin and internal daemons) Operations (who can add and delete users, organizations, and do maintenance work on behalf of users and organizations) End Users (they belong to one or more organization, for each organization, the user can have one or more roles, like being organization admin, or organization read-only member) (role like orgadmin can also add users for that organization) Now my question is, how should i model the entity of User? If I just take the End User, it can belong to one or more organizations, so each user can contain a set of references to its organizations. But how do we model the users role for each organization, So for example User UX belongs to organizations og1, og2 and og3, and for og1 he is both orgadmin, and org-read-only-user, where as for og2 he is only orgadmin and for og3 he is only org-read-only-user I have the possibility of making each user belong to one organization alone, but that's making the system bounded and I don't like that idea (although i would still satisfy the requirement) If you have a better extensible ACL architecture, please suggest it. Since its a software as a service, one would expect that alot of different organizations would be part if the same system. I had one concern that it is not a good idea to keep og1 and og2 data on the same DB (if og1 decides to spawn a 100 reports on the system, og2 should not suffer) But that is some thing advanced for now and is not directly related to ACL but to the physical distribution of data and setup of services based on those ACLs This is a community Wiki question, please correct any thing which you wish to do so. Thanks

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• Really annoying bug with Topmost property in Windows Forms

  - by Nazgulled

  Hi, I have this Windows Forms application where it sits in the notification area. Clicking on the icon brings it up front, clicking it again (or clicking on the app X icon) sends it back. This is the type of app that having the window always on top is important when it's displayed by clicking the icon, but it's optional. Right-clicking the icon brings up a context menu where one can select to enable the "always on top" option or not. When the application first starts up, the app settings are read from an XML file and I'm 99% that this is working as it should, the Topmost properly is properly read (and written). After some time (minutes, hours, days, whatever, I normally hibernate and rarely shutdown) the Topmost stops working. I don't change the option, I don't think anything is changing the option but I click the notification area icon and app is not brought up front. It shows up (it displays on Alt+Tab) but it's on the background, it's not topmost as it should. I bring up the context menu, disable the option (cause it's enabled) and enable it back and it starts to work after that. The app is now topmost. However, it can lose this ability anytime after while. I can't understand why this happens and how this happens. Does anyone have any idea why? If not, any idea how could I try to debug such behavior?

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• Designing a general database interface in PHP

  - by lamas

  I'm creating a small framework for my web projects in PHP so I don't have to do the basic work over and over again for every new website. It is not my goal to create a second CakePHP or Codeigniter and I'm also not planning to build my websites with any of the available frameworks as I prefer to use things I've created myself in general. I have no problems in designing that framework when it comes to parts like the core structure, request handling, and so on but I'm getting stuck with designing the database interface for my modules. I've already thought about using the MVC pattern but thought that it would be a bit of a overkill. So the exact problem I'm facing is how my frameworks modules (viewCustomers could be a module, for example) should interact with the database. Is it a good idea to write SQL directly in PHP (mysql_query( 'SELECT firstname, lastname(.....))? How could I abstract a query like SELECT firstname, lastname FROM customers WHERE id=X Would MySQL helper functions like $this->db->get( array('firstname', 'lastname'), array('id'=>X) ) be a good idea? I suppose not because they actually make everything more complicated by requiring arrays to be created and passed. Is the Model pattern from MVC my only real option?

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• Creating Mobile Cross-Platform Scripting Solution

  - by Aplomb

  I am having the dream to design a Mobile cross-platform scripting solution to achieve Developer only need to code once by scripting language(it's possible be Javascript or others need further investigation), then the solution will be able to generate the installation files for multiple mobile platforms like J2me, Android, Symbian, BlackBerry, Palm, Windows Mobile/Phone, iPhone, etc. Using the scripting language, developer can code with unified platform API. And other extension frameworks under scripting language, like, 1. 2D UI framework Most probably using for Mobile Applications, the UI style will compete with native UI framework and no longer every application in particular platform looks similar. 2. 3D UI framework Provide the platforms who has 3D capability can represent their Mobile Application with more fashion 3D style which will be much more abstractive. 3. Variable game engine Developers can can use it for easily and high-quality build games. 4. etc This Mobile solution is providing three points, 1. Cross-Platform 2. Scripting 3. Middleware So guys, what do you think about this idea, is it good for Developers? is it profitable? where is the better direction for this idea?

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• Voting on Hacker News stories programmatically?

  - by igorgue

  I decided to write an app like: http://michaelgrinich.com/hackernews/ but for Android devices, my idea will use a web application backend (because I rather code in Python and for the web than completely in Java for Android devices). What I have right now implemented is something like this: $ curl -i http://localhost:8080/stories.json?page=1\&stories=1 HTTP/1.0 200 OK Date: Sun, 25 Apr 2010 07:59:37 GMT Server: WSGIServer/0.1 Python/2.6.5 Content-Length: 296 Content-Type: application/json [{"title": "Don\u2019t talk to aliens, warns Stephen Hawking", "url": "http://www.timesonline.co.uk/tol/news/science/space/article7107207.ece?", "unix_time": 1272175177, "comments": 15, "score": 38, "user": "chaostheory", "position": 1, "human_time": "Sun Apr 25 01:59:37 2010", "id": "1292241"}] The next step (and final I think) is voting, my design is doing something like this: $ curl -i http://localhost:8080/stories/1?vote=up -u username:password Will vote up and: $ curl -i http://localhost:8080/stories/1?vote=down -u username:password Down. I have no idea how to do it though... I was planning to use Twill but the login link is always different, e.g.: http://news.ycombinator.com/x?fnid=7u89ccHKln Later the Android app will consume this API. Any experience with programmatically browsing Hacker News?

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