I tried it two ways both resulting in file or directory not found, but I can manually ssh to them. This is not the full code but I hope it's enough as I don't want to post code that is not needed. Thank you .
attempt 1
Code:
# match unique run in list and extract samples
run=$(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list)
# create array of samples from $run
readarray -t array <<< "$(printf '%s\n' $run)"
for ((i=0; i<${#array[@]}; i++ )) ; do
echo "${array[$i]}"
done
# loop through array and append with ID
for ID in "${array[@]}" ; do
"( cd /path/to/${ID}*/*/folder && exec sshpass -f file.txt scp xxx@xxx.xx.xx.xxx:path/to/destination/${ID}-cn_results.png )"
done | sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxxx@xxx.xx.xxx.xx
attempt 2
Code:
# match unique run in list and extract samples
run=$(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)
# create array of samples from $run
readarray -t array <<< "$(printf '%s\n' $run)"
for ((i=0; i<${#array[@]}; i++ )) ; do
echo "${array[$i]}"
done
# loop through array and append with ID
for ID in "${array[@]}" ; do
"( cd /path/to/${ID}*/*/folder && exec sshpass -f file.txt scp "$ID" xxx@xxx.xx.xx.xxx:path/to/destination/"${ID%}"-cn_results.png )"
done | sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxxx@xxx.xx.xxx.xx
attempt 1 error:
Code:
script.sh: line 39: ( cd /path/to/ID1*/*/folder && exec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:path/to/destination/ID1-cn_results.png ): No such file or directory
script.sh: line 39: ( cd /path/to/ID2*/*/folder && exec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:path/to/destination/ID2-cn_results.png ): No such file or directory
attempt 2 error: --- in the server these exsist as ID1-xxxx-xxxxxxx-xxxxxx so I added * but thats not expanding it seems ----
Code:
ID1: No such file or directory
ID2: No such file or directory
Last edited by cmccabe; 10-16-2019 at 01:40 PM..
Reason: fixed format
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Discussion started by: wisecracker
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LEARN ABOUT CENTOS
git-symbolic-ref
GIT-SYMBOLIC-REF(1) Git Manual GIT-SYMBOLIC-REF(1)NAME
git-symbolic-ref - Read, modify and delete symbolic refs
SYNOPSIS
git symbolic-ref [-m <reason>] <name> <ref>
git symbolic-ref [-q] [--short] <name>
git symbolic-ref --delete [-q] <name>
DESCRIPTION
Given one argument, reads which branch head the given symbolic ref refers to and outputs its path, relative to the .git/ directory.
Typically you would give HEAD as the <name> argument to see which branch your working tree is on.
Given two arguments, creates or updates a symbolic ref <name> to point at the given branch <ref>.
Given --delete and an additional argument, deletes the given symbolic ref.
A symbolic ref is a regular file that stores a string that begins with ref: refs/. For example, your .git/HEAD is a regular file whose
contents is ref: refs/heads/master.
OPTIONS -d, --delete
Delete the symbolic ref <name>.
-q, --quiet
Do not issue an error message if the <name> is not a symbolic ref but a detached HEAD; instead exit with non-zero status silently.
--short
When showing the value of <name> as a symbolic ref, try to shorten the value, e.g. from refs/heads/master to master.
-m
Update the reflog for <name> with <reason>. This is valid only when creating or updating a symbolic ref.
NOTES
In the past, .git/HEAD was a symbolic link pointing at refs/heads/master. When we wanted to switch to another branch, we did ln -sf
refs/heads/newbranch .git/HEAD, and when we wanted to find out which branch we are on, we did readlink .git/HEAD. But symbolic links are
not entirely portable, so they are now deprecated and symbolic refs (as described above) are used by default.
git symbolic-ref will exit with status 0 if the contents of the symbolic ref were printed correctly, with status 1 if the requested name is
not a symbolic ref, or 128 if another error occurs.
GIT
Part of the git(1) suite
Git 1.8.3.1 06/10/2014 GIT-SYMBOLIC-REF(1)
10-16-2019
.