I have two properties files that are not the same and I need to find the differences. The second file is sorted by key.
Is there a tool that can help me with it? From what I've seen every merge tool cares very much about the order.
I've done it in bash on Linux by sorting both files and then merge them. If you are on Windows you could install Cygwin for running Linux programs.
However, I think you are best served by creating a small program to do it, probably takes you less time than learning to use Cygwin.
Edit: You could look at it as a small project to learn a new technology. I often use projects like these to learn things like Ruby or Python. Although it may not be accepted if it is at work.
Sort one or both files.
Then run "diff".
Related
I have a radio chip (connected to an embedded processor) which I have written a library for. I want to develop the protocol to use with the rf chip on a PC (Ubuntu). In order to do so I have copied the header file of my library into a new folder, but created an entirely new implementation in a new c file and compile for the PC with gcc. This approach has worked better than expected and I'm able to prototype code that calls the rf lib on the PC and simply copy it right over to the real project with little or no changes.
I do have one small problem. Any changes I make in the the library's header file need to be manually copied between the two project folders. Not a big deal, but since this has worked so well, I can see doing things like this again in the future, and would like to link the API headers between the real and "emulated" environments when doing so. I have thought about using git submodules to do so, but I'm not fond of lots of folders in my projects especially if most of them only contain one or two files each. I could use the c preprocessor to swap in the right code at compile time, but that doesn't cover the changes in my Makefile to call the right compiler with the right fags.
I'm wondering if anyone else has ever done something similar, and what their approach was?
Thanks guys!
maybe you should create a "rflib" and treat it as an external library that you use within your embedded project.
develop on one side and update to the newest version on the other.
An obvious (but fairly hacky) solution is to use a symlink.
I think the best solution, since they will share so much code, would be to just merge the two projects and have two different makefile targets for the binaries.
Apologies if I explain this badly or am asking something bleeding obvious but I'm new to the Linux kernel and kinda in at the deep end...
We have an embedded-linux system which arrives with a (very badly documented) SDK containing hundreds of folders of stuff, most folders containing a rules.make, make, make.config or some variation of... and the root folder containing a "master" makefile & rules.make which mean that you can, from the root folder, type "make sysall" and it builds the entire package.
So far so good, but trying to debug it is a bit of an issue as the documentation will say something like:
"To get the kernel to output debug messages, just define #outputdebugmessagesplz"
OK, but some of these things are defined in the "master" make/rules file, some of these are defined in the child make/rules/config files, some are in .h files... and of course it's far nicer to turn these things on/off from the "top" make.config rather than modifying individual .h files and then having to remember to turn them off again.
So I thought it would be a useful thing to recursively build a tree, starting from the master "make" file and following everything it does, everything that gets defined or re-defined, etc... but there doesn't seem to be a simple way of doing that?
I assume I am missing a "make" option here that spits this info out, or a usage of the makefile/config that will just work?
Your situation is not uncommon. When developing for embedded systems, you might encounter many custom systems that solve a problem in a specific way. As people already commented on your question, there's no easy way to generate a dependency graph for your makefile structure/framework. But there are some things you can try, and I'll try to base my suggestions based on your situation. Since you've said:
Im new to the Linux kernel and kinda in at the deep end...
and
We have an embedded-linux system which arrives with a (very badly
documented) SDK containing hundreds of folders of stuff
You could try the following things:
If your SDK is provided by a third-party vendor, try contacting them and get some support.
SDK's usually provide an abstraction to work with several components without a deep understanding of how each one of them really works. Try to pinpoint your problem, like if you want to customize only the kernel configuration, you could find the linux kernel folder on your SDK (assuming your SDK is composed of a set of folders with things like libraries, source code of applications and stuff, one of them might be the kernel one) and run make menuconfig. This will open a ncurses-based configuration GUI that you can navigate and choose kernel options.
As people already pointed out, you can try to run make -n and check the output. You could also try to run make -p | less and inspect the output, but I don't recommend this since it will only print the data base (rules and variable values) that results from reading the makefiles. You would have to parse this output to find out what you want in it.
Basically, you should try to pinpoint what you want to customize and see how this interacts with your SDK. If it's the kernel, then working only with it will give you a starting point. The linux kernel has its own makefile-build system, named kbuild. You can find more information about it at the kernel's Documentation folder.
Besides that, trying to understand how makefiles work will help you if you have a complex makefile structure controlling several components. The following are good resources to learn about makefiles:
GNU Make official documentation
O'Reilly's Open Book "Managing Projects with GNU Make"
Also, before trying to build your own tool, you can check if there's an open source project that does what you want. A quick search on google gave me this:
makegrapher
Also, check this question and this one. You might find useful information from people that had the same problems as you did.
Hope it helps!
I'm working on a small application and thinking about integrating BLAST or other local alignment searches into my application. My searching has only brought up programs, which need to be installed and called as an external program.
Is there a way short of me implementing it from scratch? Any pre-made library perhaps?
Does it have to be in C, or would C++ also be OK? If so, you might want to look at the SeqAn library here.
This is a topic which has also to do with reproducibility of results: it is always better to use the raw blast binary provided by NCBI or UCSC, because it will make your results easeir to reproduce by other scientists and will save you a lot of time spent on writing tests (more time than you can imagine).
For the day-to-day work I have often used exonerate, a tool written in C which can do both global and local alignment, has a simple unix-like interface, and doesn't require to format your input as with blast.
Moreover, take in mind that people usually use a combination of makefiles and scripts to define a pipeline, instead of calling everything from a script: most programming languages are not good to define pipelines, while automated build tools like Make are not useful for scripting tasks. Have a look at these examples: http://skam.sourceforge.net/skam-intro.html http://swc.scipy.org/lec/build.html
I just stumbled across the thing I would have wanted: The NCBI C++ Toolkit. Thanks for all the suggestions though.
The BLAST algorithm was implemented ~20 years ago, it is now a very big algorithm and I cannot imagine it can be easily implemented from scratch. You can try to learn about it when looking at the sources of the 'blastall' program in the NCBI toolkit.
A simpler pairwise algorithm (Swith Waterman, Needleman-Wunsch )should be easier to implement:
Computational Molecular Biology: An Introduction has code for Smith-Waterman and other dynamic programming alignment algorithms.
I use NetBLAST through the blastcl3 client binary. I believe that the blastcl3 binary is a pretty thin client for the NetBLAST web service.
If so, it shouldn't be too hard to sniff the packets and implement your own client. Depending on your use case, this might be faster/easier than implementing your own alignment algorithm. It does, however, introduce a dependency to NCBI's web services.
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/netblast.html
I posted a similar question (running BLAST (bl2seq) without creating sequence files)
Basically, the answer I came up with was running this command:
bl2seq -i<(echo sequence1) -j(echo sequence2) -p blastn
That pipes the result of the echo command to the bl2seq (blast 2 sequences) program.
But I couldn't get it to work via calling system from Python
I'm looking for a make platform. I've read a little about gnu make, and that its got some issues on windows platforms (from slash/backslash, to shell determination ... ) so I would like to hear what are my alternatives to it ?
If it matters, i'm doing fortran development combined with (very)little c on small sized projects (50k lines max), but I don't think that matters since most of those are of the language agnostic type.
What are gnu make drawbacks, and what alternatives do I have, with what advantages?
There are a couple of good tools for continuous integration and building on windows. The two I have in mind are NAnt which describes itself as .Net build tool, but could be used to build anything - its open source and very extensible, although the UI is lacking. I've recently started to use Hudson which is brilliant, the output is way better than NAnt, making it much easier to use. I have zero experience with these tools and Fortran, so good luck there.
My thought on make and its derivatives is to avoid based on it's age, a good tool in its time but it must 20 years old now, and tech (even in the build area) has moved on a fair bit since then.
You can have a look at cmake. It's a kind of "meta-make" system: You write a make-file for it, which says how your project is structured, what libs and sources it needs, and so on. And it can build make-files for you for GNU make, nmake (i believe), project files for Kdevelop and Visual Studio.
KDE has adopted it for KDE4 onwards and it was since greatly enhanced: CMake
Another such system is Bakefile which was built to generate make-files and project-files for the wxWidgets GUI toolkit. It can be used for non-wx applications too, and is relatively young and modern (uses XML as its makefile description).
There is also nmake, which is Microsoft's version of nmake. I would recommend to stick with gnu make though. My advise is to always use Unix like slashes; they also work for Windows. Gnu make is widely used, you can easily find tutorials and get advices about it's use. It is also a better investment, since you can also use it in other areas in the future. Finally, it is much richer in functionality.
I use GNU make under Windows and have no problems with it. However, I also use bash as my shell. Both make and bash are available as part of the Cygwin package from www.cygwin.com and I strongly recommend you install bash & all the common command line tools (grep, sed etc.) if you are going to use make from the command line.
Make has stood the test of time even on windows, and I use it everyday, but there's also msbuild
Details, details...
Given your small project, I wuld just start with MS nmake. Then if that doesn't suffice, move on to GNUmake. Other advice above is also good. Ant and CMake are fine, but you don't need them and there are so many make users who can help you if you have problems.
For that matter, since you are on windows, doesn't the MS IDE have buil tools built in. Just click and go.
keep it simple. Plan to throw the first on away, you will anyway.
Wikipedia also has this to say:
http://en.wikipedia.org/wiki/List_of_build_automation_software
I'm looking for a tool that, given a bit of C, will tell you what symbols (types, precompiler definitions, functions, etc) are used from a given header file. I'm doing a port of a large driver from Solaris to Windows and figuring out where things are coming from is getting to be difficult, so this would be a huge help. Any ideas?
Edit: Not an absolute requirement, but tools that work on Windows would be a plus.
Edit #2: To clarify what I'm trying to do, I have a codebase I'm trying to port, which brings in a large number of headers. What I'd like is a tool that, given foo.c, will tell me which symbols it uses from bar.h.
I like KScope, which copes with very large projects.
KScope http://img110.imageshack.us/img110/4605/99101zd3.png
I use on both Linux and Windows :
gvim + ctags + cscope.
Same environment will work on solaris as well, but this is of course force you to use vim as editor, i pretty sure that emacs can work with both ctags and cscope as well.
You might want give a try to vim, it's a bit hard at first, but soon you can't work another way. The most efficient editor (IMHO).
Comment replay:
Look into the cscope man:
...
Find functions called by this function:
Find functions calling this function:
...
I think it's exactly what are you looking for ... Please clarify if not.
Comment replay 2:
ok, now i understand you. The tools i suggested can help you understand code flow, and find there certain symbol is defined, but not what are you looking for.
Not what you asking for but since we are talking i have some experience with porting and drivers (feel free to ignore)
It seems like compiler is good enough for your task. You just starting with original file and let compiler find what missing part, it will be a lot of empty stubs and you will get you code compiled.
At least for beginning i suggest you to create a lot of stubs and modifying original code as less as possible, later on once you get it working you can optimize.
It's might be more complex depending on the type of driver your are porting (I'm assuming kernel driver), the Windows and Solaris subsystems are not so alike. We do have a driver working on both solaris and windows, but it was designed to be multi platform from the beginning.
emacs and etags.
And I leverage make to run the tag indexing for me---that way I can index a large project with one command. I've been thinking about building a master index and separate module indecies, but haven't gotten around to implementing this yet...
#Ilya: Would pistols at dawn be acceptable?
Try doxygen, it can produce graphs and/or HTML and highly customizable