Bash to append array value to file before copying


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# 15  
Directory structure:
Code:
/path/to/${ID}*/path/to/folder (always this format)

The ${ID} will always be unique and have some random text after it that the * is used for. At the last folder in the path there is a .png always named cn_results that I am trying to append the unique ${ID} on front of ${ID}-cn_results.png, then scp that .png to xxxx@xxx.xx.xxx.xx:/path/to/destination/${ID}-cn_results.png)

There are two values in array, but only the first is printed:

Code:
# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run with samples
echo "This is array" "$array" > /tmp/out

Contents of out
Code:
This is array ID1

I added a loop to iterate though each ID in array, but only the second value is printed:
Code:
# Set an array in one step in bash
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' "$run_dir"/rna.barcodes | tr -d '\r') )  ## match run with samples
   for file in "${array[@]}" ; do
    echo "This is array" "$file" > /tmp/loop.out
done

Contents of loop.out
Code:
This is array ID2

In this example array has two values in it ID1 and ID2, but there may be more or less it just depends on the run which the values for array come from. Thank you very much Smilie

Last edited by cmccabe; 4 Weeks Ago at 12:54 PM.. Reason: fixed format
# 16  
Show your actual directory structure EXPLICITLY, like
Code:
tree -d
.
├── D1
│   ├── D2
│   │   └── L1
│   ├── D3
│   │   └── L2
│   └── D4
│       ├── L1
│       ├── L2
│       └── L3
└── test
    └── D1
        └── D3
            ├── L1
            └── L2

14 directories

If your system doesn't have tree, use e.g. an editor to compose it.
This User Gave Thanks to RudiC For This Post:
# 17  
Hopefully this is better. Thank you Smilie.

Code:
├──/path/to/
│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder
│   ├── ${ID}*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID/folder

# 18  
No, it's not. How do you expect people to bug hunt if they don't see what is actually going wrong? Show the directory listing from your target system. If that is confidential, build a dummy one but adapt your code to reproduce the error.
This User Gave Thanks to RudiC For This Post:
# 19  
Hopefully, this is better and helps:
Code:
# Set run array
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run in rna.barcode and extract patient

# iterate through array
for ID in "${array[*]}" ; do
echo "$ID" > /tmp/out.txt
       echo "( cd /path/to/${ID}*/path/to/folder && xec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/${ID}-cn_results)"
       sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxx@xxx.xx.xx.xx
done

Contents of out --- This is array with all samples one one line ---
Code:
ID1 ID2

echo to terminal
Code:
( cd /path/to/ID1 ID2*/*/path/to/folder && exec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/ID1 ID2-cn_results.png)

Code:
├──/path/to/   ---- common path after ssh ---
│   ├── ID1*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID1/folder
│   ├── ID2*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID2/folder
Description:

After ssh to the common path on the server, each unique ID is used to further navigate to folder. In each folder there is a png (cn_results), that the unique ID is append to (ID-cn_results) and this 
append file is scp to xxx@xxx.xx.xx.xxx:/path/to/destination. It seems that since array is one line both are being used and that is causing the error?

# 20  
Well that's not going to work. You're just printing the statements to the screen and not giving anything to sshpass at all.

Does your script change the variable IFS? Strings are supposed to split when you do ARRAY=( 1 2 3 ) and not doing so is very weird unless IFS was changed.

That's why you need to be careful to do

Code:
OLDIFS="$IFS"
IFS="."

...

IFS="$OLDIFS"

...whenever you alter IFS for anything. If you don't put it back when you're done, that changes how all splitting works later.
This User Gave Thanks to Corona688 For This Post:
# 21  
I only printed the array to see what values were there and didn't change IFS (I don't think anyway). Thank you Smilie.
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Awk's built-in variables include the field variables: $1, $2, $3, and so on ($0 represents the entire record).
True or False?

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