I have an array which contains
commName[0]="ls"
commName[1]="date"
commName[2]="crontab"
commName[3]="uname"
commName[4]="hostname"
Now the array doesn't always contain these. Sometimes it can have more indices sometimes less. And the values are not always ls,date,... They can be different. Bottom line, I don't know the size nor the values of the array when I'm coding.
Every array value ls,date,... has its own unique address. So for example, ls would have /home/test/ and date would have /home/test/test2/ etc... These addresses need to be stored into a variable which will be used later on in the code. So I should have following variables according to the given array
$lsAddress
$dateAddress
$crontabAddress
$unameAddress
$hostnameAddress
Therefore, I need a way to make these variables (have in mind that I don't know ls,date,uname,....)
My approach was this
for ((j=0 ; j<${#commName[#]} ; j++))
do
set commName[$j]Nick="hi"
echo $(${commName[$j]}Nick)
done
What I expected this to do was to create new variables for every index of the array and set them equal to hi (just for test purposes) and then access those new variables.
Also, The new created variables Must be accessible anywhere. So, I can't have a temporary variable that keeps getting replaced.
However, this method isn't working... Is there any other way I can do this?
Use eval. Try this:
for ((j=0 ; j<${#commName[#]} ; j++))
do
param=`echo ${commName[$j]}Nick`
eval "$param=hi1"
eval "echo \$$param"
done
Use two parallel arrays, so that the entry in the command array matches with the corresponding entry in the address array.
commName[0]="ls"
commName[1]="date"
commName[2]="crontab"
commName[3]="uname"
commName[4]="hostname"
commAddress[0]="/home/test/" # ls
commAddress[1]="/home/test/test2" # date
# etc
Then, when you have a particular value of i, you know that ${commName[i]} and ${commAddress[i]} go together.
I recommend the two arrays, but you might also consider using bash's indirect parameter expansion instead.
$ commName[0]="ls"
$ lsAddress="/home/test"
$ name="${commName[0]}Address"
$ echo "${!name}"
/home/test
Related
I'm trying to create a for-loop to go through all the items from an array, and add the items to a string. The tags are given as a single string with format "tag1 tag2 tag3", and the tagging parameter can be given as many times as I want with the single command with syntax "-tag tag1 -tag -tag2 -tag tag3". I'm unable to create a for loop for the job, and I'm a little confused what is wrong with my code.
TAGS="asd fgh jkl zxc bnm" # Amount of tags varies, but there is always at least one
ARRAY=($TAGS)
TAGSTOBEADDED=""
for i in "$ARRAY[#]"
do
STRINGTOBEADDED="-tag ${ARRAY[$i]}"
$TAGSTOBEADDED=$TAGSTOBEADDED+$STRINGTOBEADDED
done
command $TAGSTOBEADDED
First, your array sintax is wrong as #oguz ismail said. To iter through array items you shold use this:
for i in "${ARRAY[#]}"; { echo $i;}
Second $TAGSTOBEADDED=$TAGSTOBEADDED+$STRINGTOBEADDED this is also fail.
Variables are set like so var="$var 123" you don't need $ in front of var name if you want to change it. Back to code. In this example you dont even need an array, just use TAGS var(without ""):
for i in $TAGS; { TAGSTOBEADDED+="-tag $i"; }
First: avoid storing lists of things in space-delimited strings (as you're currently doing with TAGS and TAGSTOBEADDED) -- there are a bunch of things that can go wrong if they have any "funny" characters (or if IFS gets changed). Use an array instead. Storing them as a string and then converting doesn't help; all of the same potential problems apply during the conversion.
I also recommend using lower- or mixed-case variable names in scripts, since there are a bunch of all-caps names with special meanings, and accidentally using one of those for something else can have weird effects. So, to define the array of tags, I'd just use this:
tags=(asd fgh jkl zxc bnm)
You also have a number of syntax errors in the script. In this line:
for i in "$ARRAY[#]"
... the shell will try to expand $ARRAY as a plain variable (not an array), and then treat "[#]" as just some unrelated characters that go after it. You need braces around the variable refence (like "${ARRAY[#]}") any time you're doing anything nontrivial with a variable reference. BTW, this idiom -- including double-quotes, braces, square-brackets and at-sign -- is what you almost always want when getting the contents of an array.
In this line:
STRINGTOBEADDED="-tag ${ARRAY[$i]}"
$i will expand to one of the array elements, not its index. That is, it'll expand to something like:
STRINGTOBEADDED="-tag ${ARRAY[asd]}"
...which doesn't make any sense. You just want
STRINGTOBEADDED="-tag $i"
...except you don't want that either, because (as I said before) storing lists of things space-delimited in a string is a bad idea. But I'll get to that because fixing it will involve the next line:
$TAGSTOBEADDED=$TAGSTOBEADDED+$STRINGTOBEADDED
There are two problems here: you don't want a dollar sign on the variable being assigned to ($varname gets the value of a variable; anytime you're setting it, don't use the $). Also the + isn't needed to add strings, you just stick them end to end. Well, you'd need to add a space in between, something like one of these:
TAGSTOBEADDED=$TAGSTOBEADDED" "$STRINGTOBEADDED
TAGSTOBEADDED="$TAGSTOBEADDED $STRINGTOBEADDED"
(Generally, you should have double-quotes around all variable references; on the right side of a plain assignment is one of the few places it's safe to leave them unquoted, but I tend to prefer to just double-quote always rather than try to remember all of the exceptions about where it's safe and where it isn't. Plus, quoting just the space looks weird.)
But you don't want to do that either, because (again) space-delimited strings are a bad way to do things. Use an array. So before the loop, create an empty array instead of an empty string:
tagstobeadded=()
...and then inside the loop, append to it with +=( ):
tagstobeadded+=(-tag "$i")
...and then at the end, use it with all the appropriate quotes, braces, etc:
command "${tagstobeadded[#]}"
So, with all of these changes, here's what I'd recommend:
tags=(asd fgh jkl zxc bnm)
tagstobeadded=()
for i in "${tags[#]}"
do
tagstobeadded+=(-tag "$i")
done
command "${tagstobeadded[#]}"
I am new to R and I have a Perl Script in which I want to call a R Script, which calculates something for me (not important what in this context). I want to give as arguments an input file, an array which contains some numbers and a number for a total number of clusters. medoid.r is the name of my R Script.
my $R_out;
$R_out = qx{./script/medoid.r $output #cluster $NUMBER_OF_CLUSTERS}
My current R code looks like this. Right now I just print cluster to see what is inside.
args <- commandArgs(TRUE)
filename = args[1]
cluster = as.vector(args[2])
number_of_cluster = args[3]
matrix = read.table(filename, sep='\t', header=TRUE, row.names=1, quote="")
print(cluster)
Is it possible to give an array as an argument? How can I save it in R? Right now only the first number of the array is stored and printed, but I would like to have every number in a vector or something similar.
If you do this in Perl
$R_out = qx{./script/medoid.r $output #cluster $NUMBER_OF_CLUSTERS};
your command line will look similar to this
./scriptmedoid.r output 111 222 333 3
assuming that $output is 'output' and #clusters = (111, 222, 333).
If you want to read that in R, you need to assign all elements after the first one in args to cluster but the last one, and the last one to number_of_cluster. In Perl you can use shift and pop for that.
my #args = #_;
my $output = shift #args;
my $number = pop #args;
# now #args only contains the clusters
I don't know if those operators exist in R.
You cannot pass a full data structure unless you serialize it in some way.
In perl, qx will expect a string as an argument. You may certainly use an array to generate that string, but ultimately it will still be a string. You cannot "pass an array" to a system call, you can only pass command-line text/arguments.
Keep in mind, you are executing a system call running Rscript as a child process. The way you're describing the issue, there is no inter-process communication beyond the command line. Think of it this way: how would you type an array on the command line? You may have some textual way of representing an array, but you can't type an array on the command line. Arrays are stored and accessed in memory differently by various different languages, and thus are not really portable between two languages like you're suggesting.
One solution: all that said, there may be a simple solution for you. You haven't provided any information on the type of data you want to pass in your array. If it is simple enough, you may try passing it on the command line as delimited text, and then break it up to use in your Rscript.
Here is an Rscript that shows you what I mean:
args = commandArgs(trailingOnly=TRUE)
filename = args[1]
cluster <- c(strsplit(args[2],"~"))
sprintf("Filename: %s",filename)
sprintf("Cluster list: %s",cluster)
print("Cluster:")
cluster
sprintf("First Item: %s",cluster[[1]][1])
Save it as "test.r" and try executing it with "Rscript test.r test.txt one~two" and you'll get the following output (tested on Rscript 46084, OpenBSD):
[1] "Filename: test.txt"
[1] "Cluster list: c(\"one\", \"two\")"
[1] "Cluster:"
[[1]]
[1] "one" "two"
[1] "First Item: one"
So, all you'd have to do on the perl side of things is join() your array using "~" or any other delimiter- it is highly dependent on your data, and you haven't provided it.
Summary: re-think how you want to communicate between perl and Rscript. Consider sending the data as a delimited string (if it's the right size) and breaking it up on the other side. Look into IPC if that won't work, consider environment variables or other options. There is no way to send an array reference on the command-line.
Note: you may want to read up on security risks of different system calls in perl.
I want to make an array with string values that have square brackets. but every time I keep getting output unexpected.
selections=()
for i in $choices
do
selections+=("role[${filenames[$i]}]")
done
echo ${selections[#]}
If choices were 1 and 2, and the array filenames[1] and filenames[2] held the values 'A', 'B' I want the selections array to hold the strings role[A], and role[B]
instead the output I get is just roles.
I can make the code you presented produce the output you wanted, or not, depending on the values I assign to variables filenames and choices.
First, I observe that bash indexed arrays are indexed starting at 0, not 1. If you are using the values 1 and 2 as indices into array filenames, and if that is an indexed array with only two elements, then it may be that ${filenames[2]} expands to nothing. This would be the result if you initialize filenames like so:
# NOT WHAT YOU WANT:
filenames=(A B)
Instead, either assign array elements individually, or add a dummy value at index 0:
# Could work:
filenames=('' A B)
Next, I'm suspicious of choices. Since you're playing with arrays, I speculate that you may have initialized choices as an array, like so:
# NOT CONSISTENT WITH YOUR LATER USAGE:
choices=(1 2)
If you expand an array-valued variable without specifying an index, it is as if you specified index 0. With the above initialization, then, $choices would expand to just 1, not 1 2 as you intend. There are two possibilities: either initialize choices as a flat string:
# Could work:
choices='1 2'
or expand it differently:
# or expand it this way:
for i in "${choices[#]}"
. Do not overlook the quotes, by the way: that particular form will expand to one word per array element, but without the quotes the array elements would be subject to word splitting and other expansions (though that's moot for the particular values you're using in this case).
The quoting applies also, in general, to your echo command: if you do not quote the expansion then you have to analyze the code much more carefully to be confident that it will do what you intend in all cases. It will be subject not only to word splitting, but pathname expansion and a few others. In your case, there is a potential for pathname expansion to be performed, depending on the names of the files in the working directory (thanks #CharlesDuffy). It is far safer to just quote.
Anyway, here is a complete demonstration incorporating your code verbatim and producing the output you want:
#!/bin/bash
filenames=('' 'A' 'B')
choices="1 2"
selections=()
for i in $choices
do
selections+=("role[${filenames[$i]}]")
done
echo ${selections[#]}
# better:
# echo "${selections[#]}"
Output:
role[A] role[B]
Finally, as I observed in comments, there is no way that your code could output "roles", as you claim it does, given the inputs (variable values) you claim it has. If that's in fact what you see, then either it is not related to the code you presented at all, or your inputs are different than you claim.
I'm working on a script that has a number of functions in place which pull data from a few different arrays. We hope to keep the arrays individualized for reporting purposes. The information in the arrays does not change and the only thing different between each function is which array name is being used. Since all of the functions have 98% the same content I'm trying to pull them into 1 single array for simplified management.
The issue I'm facing though is that I'm not able to figure out the correct syntax to obtain the length of an array based on the array title that is passed in the function argument. I can't post the actual script, but here is a mock up that details a simplified version of what I'm testing with. I believe if we can get it working using the mock script below I can transfer the needed changes to the actual script.
array1=(
"item1 123"
"item2 456"
)
array2=(
"stockA qwe"
"stockB asd"
"stockC zxc"
)
test() {
local ref=${1}[#]
IFS=$'\n'; for i in ${!ref}; do echo $i ; done
}
test array1
test array2
The script above so far will echo the content of each array line based on argument 1 when the function and it's argument is called; which is working as needed. I've tried many different combinations such as len=${#${1}[#]} but I always receive a "bad substitution" error. The functions I mention before have while loops and for statements that use the array length to know when to stop, so being able to pull that information really ties it all together. What I'm hoping for is something like the flow below
I plan to continue my research on this, but thank you for any help and knowledge that can be provided!
-Cyanide
I think the only solution is to create a copy of the array, then take the length of that array:
local ref=${1}[#]
copy=( "${!ref}" )
len=${#copy[#]}
Since bash does not allow chaining of the parameter expansion operators, I know of no shorter way to use both ${#...} and ${!...} on the same line.
Two things, first this is my first question in this forum and I do apologise if the formating is all over the place. Second I have not written that many bash scripts, and it tend to be quite a long time between the scripts I produce.
That said, here is my question.
Is it possible to do something like this in bash (Clear array $array contains):
$array=()
Basically this is what I would like to do. I have a variable with array variable names in it:
array1=()
array2=()
arrayList="array1 array2"
# In a function far far away
for array in $arrayList
do
eval arr=("\"\${$array[#]\"")
for index in ${!arr[#]}
do
echo "${arr[$index]}"
done
# Here is the big "?", I like to clear the array that $array refers to.
$array=()
done
My arrays contain strings that include "" (space) and this is why I use the eval statement. Not sure it's needed but at least it's working. The script is more or less working as I want it too, but I need to clear the arrays in the $arrayList, and I rather not hardcode it somewhere, even though that would be easy.
Probably the simplest thing to do is just unset them. An unset variable will act identically to an empty array in most contexts, and unset $array ought to work fine.
You can't do $foo=bar ever -- that isn't how indirect assignments in bash work. Unfortunately, while being able to do indirect array assignments is an available feature in ksh93, it isn't a formally documented available feature in bash.
Quoting BashFAQ #6 (which should be read in full if you're interested in knowing more about using indirect variables in general):
We are not aware of any trick that can duplicate that functionality in POSIX or Bourne shells (short of using eval, which is extremely difficult to do securely). Bash can almost do it -- some indirect array tricks work, and others do not, and we do not know whether the syntax involved will remain stable in future releases. So, consider this a use at your own risk hack.
# Bash -- trick #1. Seems to work in bash 2 and up.
realarray=(...) ref=realarray; index=2
tmp="$ref[$index]"
echo "${!tmp}" # gives array element [2]
# Bash -- trick #2. Seems to work in bash 3 and up.
# Does NOT work in bash 2.05b.
tmp="$ref[#]"
printf "<%s> " "${!tmp}"; echo # Iterate whole array.
However, clearing is simpler, as unset $array will work fine.
array=()
It clears the array. I guess that is what you wanted..