First of all, I'm using Ubuntu 20.04 and Python 3.8.
I would like to run a program that takes command line inputs. I managed to start the program from python with the os.system() command, but after starting the program it is impossible to send the inputs. The program in question is a product interface application that uses the CubeSat Space Protocol (CSP) as a language. However, the inputs used are encoded in a .c file with their corresponding .h header.
In the shell, it looks like this:
starting the program
In python, it looks like this:
import os
os.chdir('/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1')
os.system('./waf')
os.system('./build/csp-client -k/dev/ttyUSB1')
os.system('cmp ident') #cmp ident is typically the kind of command that does not work on python
The output is the same as in the shell but without the "cmp ident output", that is to say it's impossible for me to use the csp-client#
As you can probably see, I'm a real beginner trying to be as clear and precise as possible. I can of course try to give more information if needed. Thanks for your help !
It sounds like the pexpect module might be what you're looking for rather than using os.system it's designed for controlling other applications and interacting with them like a human is using them. The documentation for it is available here. But what you want will probably look something like this:
import pexpect
p = pexpect.spawnu("/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client -k/dev/ttyUSB1")
p.expect("csp-client")
p.sendline("cmp indent")
print(p.read())
p.close()
I'll try and give you some hints to get you started - though bear in mind I do not know any of your tools, i.e. waf or csp-client, but hopefully that will not matter.
I'll number my points so you can refer to the steps easily.
Point 1
If waf is a build system, I wouldn't keep running that every time you want to run your csp-client. Just use waf to rebuild when you have changed your code - that should save time.
Point 2
When you change directory to /home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1 and then run ./build/csp-client you are effectively running:
/home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client -k/dev/ttyUSB1
But that is rather annoying, so I would make a symbolic link to that that from /usr/local/bin so that you can run it just with:
csp-client -k/dev/ttyUSB1
So, I would make that symlink with:
ln -s /home/augustin/workspaceGS/gs-sw-nanosoft-product-interface-application-2.5.1/build/csp-client /usr/local/bin/csp-client
You MAY need to put sudo at the start of that command. Once you have that, you should be able to just run:
csp-client -k/dev/ttyUSB1
Point 3
Your Python code doesn't work because every os.system() starts a completely new shell, unrelated to the previous line or shell. And the shell that it starts then exits before your next os.system() command.
As a result, the cmp ident command never goes to the csp-client. You really need to send the cmp ident command on the stdin or "standard input" of csp-client. You can do that in Python, it is described here, but it's not all that easy for a beginner.
Instead of that, if you just have aa few limited commands you need to send, such as "take a picture", I would make and test complete bash scripts in the Terminal, till I got them right and then just call those from Python. So, I would make a bash script in your HOME directory called, say csp-snap and put something like this in it:
#/bin/bash
# Extend PATH so we can find "/usr/local/bin/csp-client"
PATH=$PATH:/usr/local/bin
{
# Tell client to take picture
echo "nanoncam snap"
# Exit csp-client
echo exit
} | csp-client -k/dev/ttyUSB1
Now make that executable (only necessary once) with:
chmod +x $HOME/csp-snap
And then you can test it with:
$HOME/csp-snap
If that works, you can copy the script to /usr/local/bin with:
cp $HOME/csp-snap /usr/local/bin
You may need sudo at the start again.
Then you should be able to take photos from anywhere just with:
csp-snap
Then your Python code becomes easy:
os.system('/usr/local/bin/csp-snap')
Related
Sorry if the title is vague, I am fairly new to Linux and I don't really know how else to put it. I am creating a script and when I run it, I got it to run Sage but after it does so, the next command isn't executed. I presume this is because the first couple were in the standard Terminal (bash?) and everything after ./sage isn't -- here's the script:
#!/bin/bash
cd /home/alex/Desktop/sage-7.6
./sage
#I also tried wait ${!} here but it didn't work
notebook("/home/alex/Desktop/sage-7.6/projects/zero forcing.sagenb")
How might I enter the last command in Sage after it opens (assuming it's possible)? Thanks!
Edit: Here's a picture of my problem. Sage runs but I can't get it to execute the notebook() command after it opens.
You need to run notebook() as sage code using the -c option mentioned [ here ]. Try the below code.
#!/bin/bash
/home/alex/Desktop/sage-7.6/sage # You can run the interactive shell directly
# At this point you have completely exited the sage interactive shell
# Presumably you want to run the below 'notebook()' after every interactive shell
# In that case do
/home/alex/Desktop/sage-7.6/sage -c 'notebook("/home/alex/Desktop/sage-7.6/projects/zero forcing.sagenb")'
I think what you really want is just to have one command that launches a notebook with a given name.
It turns out that in many Linux/Unix applications, there is automatic help at the command line. Try
/home/alex/.../sage -n -h
to get some help on the notebook. In particular,
sage -n -h --notebook=sagenb
gives a very, very long list of options, the first of which shows that
sage --notebook=sagenb directory=tp
will give you a new sage notebook server in the directory tp.sagenb.
All this said, I should also point out that the sagenb (sadly) is slowly becoming a legacy project in favor of the Jupyter notebook. In Sage 8.0 a conversion from sagenb to Jupyter will become the default, and even now you can just do
sage --notebook=jupyter --notebook-dir=/home/foo/bar
for that to start up.
So I am not experienced in dealing with a plethora of file types, and I haven't been able to find much info on exactly what .sh files are. Here's what I'm trying to do:
I'm trying to download map data sets which are arranged in tiles that can be downloaded individually: http://daymet.ornl.gov/gridded
In order to download a range of tiles at once, they say to download their script, which eventually leads to daymet-nc-retrieval.sh: https://github.com/daymet/scripts/blob/master/Bash/daymet-nc-retrieval.sh
So, what exactly am I supposed to do with this code? The website doesn't provide further instructions, assuming users know what to do with it. I'm guessing you're supposed to paste the code in to some other unmentioned application for a browser (using Chrome or Firefox in this case)? It almost looks like something that could be pasted in to Firefox/Greasemonkey, but not quite. Just by a quick Google on the file type I haven't been able to get heads or tails on it.
I'm sure there's a simple explanation on what to do with these files out there, but it seems to be buried in plenty of posts where people are already assuming you know what to do with these files. Anyone willing to just simply say what needs to be done from square one after getting to the page with the code to actually implementing it? Thanks.
What is a file with extension .sh?
It is a Bourne shell script. They are used in many variations of UNIX-like operating systems. They have no "language" and are interpreted by your shell (interpreter of terminal commands) or if the first line is in the form
#!/path/to/interpreter
they will use that particular interpreter. Your file has the first line:
#!/bin/bash
and that means that it uses Bourne Again Shell, so called bash. It is for all practical purposes a replacement for good old sh.
Depending upon the interpreter you will have different languages in which the file is written.
Keep in mind, that in UNIX world, it is not the extension of the file that determines what the file is (see "How to execute a shell script" below).
If you come from the world of DOS/Windows, you will be familiar with files that have .bat or .cmd extensions (batch files). They are not similar in content, but are akin in design.
How to execute a shell script
Unlike some unsafe operating systems, *nix does not rely exclusively on extensions to determine what to do with a file. Permissions are also used. This means that if you attempt to run the shell script after downloading it, it will be the same as trying to "run" any text file. The ".sh" extension is there only for your convenience to recognize that file.
You will need to make the file executable. Let's assume that you have downloaded your file as file.sh, you can then run in your terminal:
chmod +x file.sh
chmod is a command for changing file's permissions, +x sets execute permissions (in this case for everybody) and finally you have your file name.
You can also do it in your GUI. Most of the time you can right click on the file and select properties; in XUbuntu the permissions options look like this:
If you do not wish to change the permissions, you can also force the shell to run the command. In the terminal you can run:
bash file.sh
The shell should be the same as in the first line of your script.
How safe is it?
You may find it weird that you must perform another task manually in order to execute a file. But this is partially because of a strong need for security.
Basically when you download and run a bash script, it is the same thing as somebody telling you "run all these commands in sequence on your computer, I promise that the results will be good and safe". Ask yourself if you trust the party that has supplied this file, ask yourself if you are sure that you have downloaded the file from the same place as you thought, maybe even have a glance inside to see if something looks out of place (although that requires that you know something about *nix commands and bash programming).
Unfortunately apart from the warning above I cannot give a step-by-step description of what you should do to prevent evil things from happening with your computer; so just keep in mind that any time you get and run an executable file from someone you're actually saying, "Sure, you can use my computer to do something".
If you open your second link in a browser you'll see the source code:
#!/bin/bash
# Script to download individual .nc files from the ORNL
# Daymet server at: http://daymet.ornl.gov
[...]
# For ranges use {start..end}
# for individul vaules, use: 1 2 3 4
for year in {2002..2003}
do
for tile in {1159..1160}
do wget --limit-rate=3m http://daymet.ornl.gov/thredds/fileServer/allcf/${year}/${tile}_${year}/vp.nc -O ${tile}_${year}_vp.nc
# An example using curl instead of wget
#do curl --limit-rate 3M -o ${tile}_${year}_vp.nc http://daymet.ornl.gov/thredds/fileServer/allcf/${year}/${tile}_${year}/vp.nc
done
done
So it's a bash script. Got Linux?
In any case, the script is nothing but a series of HTTP retrievals. Both wget and curl are available for most operating systems and almost all language have HTTP libraries so it's fairly trivial to rewrite in any other technology. There're also some Windows ports of bash itself (git includes one). Last but not least, Windows 10 now has native support for Linux binaries.
sh files are unix (linux) shell executables files, they are the equivalent (but much more powerful) of bat files on windows.
So you need to run it from a linux console, just typing its name the same you do with bat files on windows.
Typically a .sh file is a shell script which you can execute in a terminal. Specifically, the script you mentioned is a bash script, which you can see if you open the file and look in the first line of the file, which is called the shebang or magic line.
I know this is an old question and I probably won't help, but many Linux distributions(e.g., ubuntu) have a "Live cd/usb" function, so if you really need to run this script, you could try booting your computer into Linux. Just burn a .iso to a flash drive (here's how http://goo.gl/U1wLYA), start your computer with the drive plugged in, and press the F key for boot menu. If you choose "...USB...", you will boot into the OS you just put on the drive.
How do I run .sh scripts?
Give execute permission to your script:
chmod +x /path/to/yourscript.sh
And to run your script:
/path/to/yourscript.sh
Since . refers to the current directory: if yourscript.sh is in the current directory, you can simplify this to:
./yourscript.sh
or with GUI
https://askubuntu.com/questions/38661/how-do-i-run-sh-scripts/38666#38666
https://www.cyberciti.biz/faq/run-execute-sh-shell-script/
open the location in terminal then type these commands
1. chmod +x filename.sh
2. ./filename.sh
that's it
I am trying to create a script that will run a program on each file in a list. I have been trying to do this using a .csh file (I have no clue if this is the best way), and I started with something as simple as hello world
echo "hello world"
The problem is that I cannot execute this script, or verify that it works correctly. (I was trying to do ./testscript.csh which is obviously wrong). I haven't been able to find anything that really explains how to run C Scripts, and I'm guessing there's a better way to do this too. What do I need to change to get this to work?
You need to mark it as executable; Unix doesn't execute things arbitrarily based on extension.
chmod +x testscript.csh
Also, I strongly recommend using sh or bash instead of csh, or you will soon learn about the idiosyncrasies of csh's looping and control flow constructs (some things only work inside them if done a particular way, in particular with the single-line versions things are very limited).
You can use ./testscript.csh. You will however need to make it executable first:
chmod u+x testscript.csh
Which means set testscript to have execute permissions for the user (who ever the file is owned by - which in this case should be yourself!)
Also to tell the OS that this is a csh script you will need put
#! /path/to/csh
on the first line (where /path/to/csh is the full path to csh on your system. You can find that out by issuing the command which csh).
That should give you the behvaiour you want.
EDIT As discussed in some of the comments, you may want to choose an alternative shell to C Shell (csh). It is not the friendliest one for scripting.
You have several options.
You can run the script from within your current shell. If you're running csh or tcsh, the syntax is source testscript.csh. If you're running sh, bash, ksh, etc., the syntax is . ./testscript.sh. Note that I've changed the file name suffix; source or . runs the commands in the named file in your current shell. If you have any shell-specific syntax, this won't work unless your interactive shell matches the one used by the script. If the script is very simple (just a sequence of simple commands), that might not matter.
You can make the script an executable program. (I'm going to repeat some of what others have already written.) Add a "shebang" as the first line. For a csh script, use #!/bin/csh -f. The -f avoids running commands in your own personal startup scripts (.cshrc et al), which saves time and makes it more likely that others will be able to use it. Or, for a sh script (recommended), used #!/bin/sh (no -f, it has a completely different meaning). In either case, run chmod +x the_script, then ./the_script.
There's a trick I often use when I want to perform some moderately complex action. Say I want to delete some, but not all, files in the current directory, but the criterion can't be expressed conveniently in a single command. I might run ls > tmp.sh, then edit tmp.h with my favorite editor (mine happens to be vim). Then I go through the list of files and delete all the ones that I want to leave alone. Once I've done that, I can replace each file name with a command to remove it; in vim, :%s/.*/rm -f &/. I add a #!/bin/sh at the top save it, chmod +x foo.sh, then ./foo.sh. (If some of the file names might have special characters, I can use :%s/.*/rm -f '&'/.)
I feel silly asking this...
I am not an expert on shell scripting, but I am finally in enough of a sysadmin role that I want to do this correctly.
I have a production server that hosts a webapp. Here is my routine.
1 - ssh to server
2 - cd django_src/django_apps/team_proj
3 - svn update
4 - sudo /etc/init.d/apache2 restart
5 - logout
I want to create a shell script for steps 2,3,4.
I can do this, but it will be a very plain and simple bash script simply containing the actual commands I type at the command line.
My question: What is the best way to script this kind of repetitive procedure in bash (Linux, Ubuntu) for a remote server?
Thanks!
The best way is simply as you suggest. Some things you should do for your script would be:
put set -e at the top of the script (after the shebang). This will cause your script to stop if any of the commands fail. So if it cannot cd to the directory, it will not run svn update or restart apache. You can do this programmatically by putting || exit 0 after each command, but if that's all you're doing, you may as well use set -e
Use full paths in your script. Do not assume the directory that the script is run from. In this specific case, the cd command has a relative path. Use a full (absolute) path, or use an environment variable like $HOME.
You may want to set up sudo so that it can run the command without asking for a password. This makes your script non-interactive which means it can be run in the background and from cron jobs and such.
As time goes by, you may add features and take command line arguments to parameterise the script. But don't bother doing this up front. Just evolve your scripts as you need.
There is nothing wrong with a simple bash script simply containing the actual commands you type at the command line. Don't make it more complicated than necessary.
I'd setup a cron job doing that automatically.
Since you're using python, check out fabric - you can use it to automate these kind of tasks. First install fabric:
$ sudo easy_install fabric
then write your fabric script:
from __future__ import with_statement
from fabric.api import *
def svnupdate():
with cd('django_src/django_apps/team_proj'):
run('svn update')
sudo('/etc/init.d/apache2 restart')
Save as fabfile.py, then run using the fab command:
$ fab -H hostname svnupdate
Tell me that's not cool! :-)
you can do this with the shell (bash,ksh,zsh + ssh + tools), or programming languages such as Python,Perl(Ruby or PHP or Java) etc, basically a language that supports SSH protocol and operating system functions. The "best" one is the one that you are more comfortable and have knowledge in. If you are doing sysadmin, the shell is the closest thing you can use. Then after you have done your script, you can use the crontab (cron) , or the at command to schedule your task. check their man page for more information
You can easily do the above using bash/Bourne etc.
However I would take the time and effort to learn Perl (or some similarly powerful scripting language). Why ?
the language constructs are much more powerful
there are no end of libraries to interface to the systems/features you want to script
because of the library support, you won't have to spawn off different commands to achieve what you want (possibly valuable on a loaded system)
you can decompose frequently-used scripts into your own libraries for later use
I choose Perl particularly because it's been designed (perhaps designed is too strong a word for Perl) for these sort of tasks. However you may want to check out Ruby/Python or other suggestions from SO contributers.
For the basic steps look at camh's answer. If you plan to run the script via cron, then implement some simple logging, e.g. by appending start time of each command with exit code to a textfile which you can later analyze for failures of the script.
Expect -- scripting interactive applications
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.... Expect can make easy all sorts of tasks that are prohibitively difficult with anything else. You will find that Expect is an absolutely invaluable tool - using it, you will be able to automate tasks that you've never even thought of before - and you'll be able to do this automation quickly and easily.
http://expect.nist.gov
bonus: Your tax dollars at work!
I would probably do something like this...
project_update.sh
#!/bin/bash
#
# $1 - user#host
# $2 - project directory
[[ -z $1 || -z $2 ]] && { echo "usage: $(basename $0) user#host project_dir"; exit 1; }
declare host=$1 proj_dir=$2
ssh $host "cd $proj_dir;svn update;sudo /etc/init.d/apache2 restart" && echo "Success"
Just to add another tip - you should not give users access to some application in an unknown state. svn up might break during the update, users might see a page that's half-new half-old, etc. If you're deploying the whole application at once, I'd suggest doing svn export instead to a new directory and then either mv current old ; mv new current, or even keeping current as a link to the directory you're using now. Still not perfect and not blocking every possible race condition, but it definitely takes less time than svn up on the live copy.
Problem: Customer X is a Windows user who wants to be able to trigger pre-packaged bash commands by using mnemonic keywords or "tag hints" when she is logged in to her RedHat box via shell.
Example: Customer X logs into host using ssh and wants to do some routine file operations. She wants to be able to type
copy file
and get back a listing of pre-fab fill-in-the-blank bash commands to choose from
cp <#source#> <#dest#> ### simple copy
cp -R <#startdir#> <#destdir#> ### recursive copy
she then wants to be able to select one of these items, fill in the blank(s) and just hit enter to run the command.
Customer X is willing to specify ahead of time what commands she is likely to want to use (in windows-speak) and then hire the developer to translate those into bash commands, and then put them together in a script that allows her to talk windows-speak to bash and get back the list of commands.
NOTE: Customer X doesn't like apropos because it assumes familiarity with terms used in bash, as opposed to windows-speak. For example:
apropos shortcut
doesn't give her anything about creating symlinks (even though that is exactly what she wants) because she doesn't know what windows shortcuts are called in linux. Obviously, windows concepts don't carry over 100% so she will have to learn eventually, but she's a busy person and is asking for this as a way to "ease" her into linux understanding.
Question: What is the best way to get started on something like this? Is there a perl, python, ruby script out there that does something like this already? Is there something in bash that can simulate this kind of feature request?
What you probably want is to override bash's command-not-found handler. Here's the section in /etc/bash.bashrc in a standard Ubuntu install that installs the handler:
...
# if the command-not-found package is installed, use it
if [ -x /usr/lib/command-not-found ]; then
function command_not_found_handle {
# check because c-n-f could've been removed in the meantime
if [ -x /usr/lib/command-not-found ]; then
/usr/bin/python /usr/lib/command-not-found -- $1
return $?
else
return 127
fi
}
fi
...
In effect, if a command is not found, a user specified program is executed with that command as a parameter. In the case of Ubuntu, it's a Python program that checks to see if the command the user typed is a valid application that can be installed, and if it is, informs the user that he/she can install it.
What you probably want to do is compare it to you hashref of commands and usage strings and display the appropriate one if there's a match.