Bash to check directory and create missing folder from file


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# 8  
STRING is empty. I believe this is because of / character before and after ref variable:

Code:
$ echo "test" | awk 'match($0, /est/) { print $1 }'
test
$ echo "test" | awk -v ref=/est/ 'match($0, ref) { print $1 }'
$ echo "test" | awk -v ref=est 'match($0, ref) { print $1 }'
test

Notice how the / characters are not needed when the 2nd match argument is a variable.
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# 9  
I made some edits to the code and am closer but am not performing the $STRING to $folder comparison correctly and the wrong folder gets created. I don't know if there is a better way but hopefullt I am closer Thank you Smilie.

Code:
DIR=/home/cmccbe/folder
for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  S5=${RDIR##*/}  ## store run with no path as S5
  TRIMSTR=${RDIR%%-v5.6*}  ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
    mv "$RDIR" "$TRIMSTR"  ## move trimmed folder to directory
  cd "$TRIMSTR"
   folders=`ls -d *[0-9]*/`  ## list folders
    STRING=$(awk -F '\n' -v RS="" -v ref="$S5" '$0 ~ ref {print $2}' "$DIR"/f1)
if [[ $folders == $STRING* ]] ## only execute folder on match
    then
      continue
  if [[ $folders != $STRING* ]] ## only execute folder on mis-match
   then
     mkdir -p "$TRIMSTR"/variants
 fi
  fi
done

set -x
Code:
+ for rdir in '"$dir"/R_2019*'
+ s5=R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx
+ trimstr=/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ mv /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx 
/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ cd /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
++ ls --color=auto -d 00-1111-xxx-xxx/ 00-2222-yyy-yy/
+ folders='00-1111-xxx-xxx/
00-2222-yyy-yy/'
++ awk -F '\n' -v RS= -v ref=R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx '$0 ~ ref {print $2}' 
/home/cmccabe/folder/f1
+ string='zzzz_0005 00-1111-xxx-xxx'
+ [[ 00-1111-xxx-xxx/
00-2222-yyy-yy/ != zzzz_0005 00-1111-xxx-xxx* ]]
+ mkdir -p '/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000- 
123/zzzz_0005 00-1111-xxx-xxx/folder'

desired
Code:
  --- $TRIMSTR/$STRIG/folder ---
R_2019_00_00_00_00_00_xxxx_x0-00000-123
       00-1111-xxx-xxx
           folder
       00-2222-yyy-yy
           folder
       00-3333-zz-zz
           folder

--- Post updated at 06:53 AM ---

I made some edits to the code and am closer but am not performing the $STRING to $folder comparison correctly and the wrong folder gets created. Thank you Smilie.

Code:
DIR=/home/cmccbe/folder
for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  S5=${RDIR##*/}  ## store run with no path as S5
  TRIMSTR=${RDIR%%-v5.6*}  ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
    mv "$RDIR" "$TRIMSTR"  ## move trimmed folder to directory
  cd "$TRIMSTR"
   folders=`ls -d *[0-9]*/`  ## list folders
    STRING=$(awk -F '\n' -v RS="" -v ref="$S5" '$0 ~ ref {print $2}' "$DIR"/f1)
  if [[ $folders != $STRING* ]] ## only execute folder on mis-match
   then
     mkdir -p "$TRIMSTR"/$STRING/folder
  fi
done

set -x
Code:
+ for rdir in '"$dir"/R_2019*'
+ s5=R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx
+ trimstr=/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ mv /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx 
/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ cd /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
++ ls --color=auto -d 00-1111-xxx-xxx/ 00-2222-yyy-yy/
+ folders='00-1111-xxx-xxx/
00-2222-yyy-yy/'
++ awk -F '\n' -v RS= -v ref=R_2019_00_00_00_00_00_xxxx_x0-00000-123- 
v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx '$0 ~ ref {print $2}' 
/home/cmccabe/folder/f1
+ string='zzzz_0005 00-1111-xxx-xxx'
+ [[ 00-1111-xxx-xxx/
00-2222-yyy-yy/ != zzzz_0005 00-1111-xxx-xxx* ]]
+ mkdir -p '/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000- 
123/zzzz_0005 00-1111-xxx-xxx/folder'

desired
Code:
  --- $TRIMSTR/$STRING/folder ---
R_2019_00_00_00_00_00_xxxx_x0-00000-123
       00-1111-xxx-xxx
           folder
       00-2222-yyy-yy
           folder
       00-3333-zz-zz
           folder

thought process
Code:
DIR=/home/cmccabe/Desktop/new    --- define directory ---
for RDIR in "$DIR"/R_2019* ; do  ---  /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx ---
  S5=${RDIR##*/}  --- R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx ---
  TRIMSTR=${RDIR%%-v5.6*}  --- --- R_2019_00_00_00_00_00_xxxx_x0-00000-123 ---
    mv "$RDIR" "$TRIMSTR"  --- /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx >>> /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6
  cd "$TRIMSTR"   --- look in /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6 ---
   folders=`ls -d *[0-9]*/`  --- 00-1111-xxx-xxx/ 00-2222-yyy-yy/ --- 
     STRING=$(awk -F '\n' -v RS="" -v ref="$S5" '$0 ~ ref {print $2}' "$DIR"/f1)   --- match R_2019 from $S5 line in f1 and print 00-1111-xxx-xxx/ 00-2222-yyy-yy 00-3333-zz-zz to $STRING --
if [[ $folders == $STRING/* ]] ## only folder on match --- 00-1111-xxx-xxx/ 00-2222-yyy-yy are skipped as they match $STRING ---
    then
      continue
   if [[ $folders != $STRING/* ]] ## only execute folder on mis-match   --- 00-3333-zz-zz is not equal to $STRING  ---
    then
      mkdir -p "$TRIMSTR"/variants  --- 00-3333-zz-zz/variants is made in /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6 ---
   fi
  fi
done


Last edited by cmccabe; 10-02-2019 at 06:10 PM.. Reason: fixed format, updated awk, added thought process
# 10  
I'm still a little confused on what you want to happen.

You end up with variables as follows:
folders
Code:
00-1111-xxx-xxx/
00-2222-yyy-yy/

string
Code:
zzzz_0005 00-1111-xxx-xxx

You seem to imply there is some sort of looping thru the folders variable and a comparison with stringwhich then results in creating folders. However you are just performing a single comparison between the two variables.
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# 11  
Quote:
You seem to imply there is some sort of looping thru the folders variable and a comparison with string which then results in creating folders. However you are just performing a single comparison between the two variables.
Yes that is correct. If the $folder variable does not match $STRING then it does not exist, so it is created (this will happen ocassionally). If the $folder variable does match $STRING then it already exists and can be skipped (this will be the majority of the time). Thank you Smilie.
# 12  
Is this closer to what you need?

Code:
DIR=/home/cmccbe/folder
for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  S5=${RDIR##*/}  ## store run with no path as S5
  TRIMSTR=${RDIR%%-v5.6*}  ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
    mv "$RDIR" "$TRIMSTR"  ## move trimmed folder to directory
  cd "$TRIMSTR"
  STRING=$(awk -F '\n' -v RS="" -v ref="$S5" '$0 ~ ref {print $2}' "$DIR"/f1)
  for folder in *[0-9]*/ ; do
      folder=${folder%/}   ## remove trailing slash
      if ! [[ " $STRING " == *\ $folder\ * ]]
      then
           ## folder is not within $STRING so make variants folder and leave
           mkdir -p "$TRIMSTR"/variants
           break
       end
  done
done

This User Gave Thanks to Chubler_XL For This Post:
# 13  
I added set -x and the $STRING variable looks to contain only one of the $2 values from f1, instead of the three so the directory created is not the right one. Thank you very much Smilie.

f1
Code:
yyy_009 00-0000-xxx-xxx-xxx
yyy_004 00-0011-xxx-xxx-xxx
R_2019_00_00_00_00_00_xxxx_x0-00000-200_yyyyyyy

zzzz_0000 00-3333-zz-zz  --- not printed to $STRING currently, but should be for the comparison ---
zzzz_0005 00-1111-xxx-xxx  --- printed to $STRING currently ---
zzzz_0003 00-2222-yyy-yy   --- not printed to $STRING currently, but should be for the comparison  ---
R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx   ---- this is matched ---

$folder
Code:
zzzz_0005 00-1111-xxx-xxx  --- this is correct ---
zzzz_0003 00-2222-yyy-yy

so since
Code:
00-3333-zz-zz

is not in folder 00-3333-zz-zz/variants is created

Code:
+ for RDIR in '"$DIR"/R_2019*'
+ S5=R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx
+ TRIMSTR=/home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ mv /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ cd /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123
++ awk -F '\n' -v RS= -v ref=R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx '$0 ~ ref {print $2}' /home/cmccabe/Desktop/new/f1
+ STRING='zzzz_0005 00-1111-xxx-xxx'
+ for folder in '*[0-9]*/'
+ folder=00-1111-xxx-xxx
+ [[  zzzz_0005 00-1111-xxx-xxx  == *\ 00-1111-xxx-xxx\ * ]]
+ for folder in '*[0-9]*/'
+ folder=00-2222-yyy-yy
+ [[  zzzz_0005 00-1111-xxx-xxx  == *\ 00-2222-yyy-yy\ * ]]
+ mkdir -p /home/cmccabe/Desktop/new/R_2019_00_00_00_00_00_xxxx_x0-00000-123/00-2222-yyy-yy/variants
+ break

# 14  
I believe you will need an awk script like this:

Code:
STRING=$(awk -F '\n' -v RS="" -v ref="$S5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' "$DIR"/f1)

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