Bash to check directory and create missing folder from file


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# 1  
Bash to check directory and create missing folder from file

In the below bash I am trying to ensure that all folders (represented by $folders) in a given directory are created. In the file f1 the trimmed folder will be there somewhere (will be multiple trimmed folders).
When that trimmed folder is found (represented by $S5) the the contents of $2 printed to $STRING. If $STRING is the same as $folders then
that folder is already created in the directory and it can be skipped (this will be the case most of the time). If $STRING is not the same as $folders then the missing is created in the directory. The code seems to work as expected untill the If done, that is the variables are set correctly, but the actual match is portion below is not working and I am not sure how to mkdir. Thank you Smilie.


Code:
DIR=/home/cmccabe/folder

for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  TRIMSTR=${RDIR%%-v5.6*}  ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
     mv "$RDIR" "$TRIMSTR"  ## move trimmed folder to directory
     S5=${TRIMSTR##*/}  ## store run with no path as S5
# Iterate over each sample folder in run directory
cd "$TRIMSTR"
    folders=folders=`ls -d *[0-9]*/`  ## list only directories begining with digit 
done
for f in "$DIR"/f1; do STRING=$(awk -v ref="/$S5/" 'match($0, ref) {print $2}' "$f"); done
nl="  ## added newline boundry seperator 
"
    if [[ $nl$folders$nl == *$n$STRING/$nl* ]] || continue # only execute file on match
       else mkdir $STRING 
    fi

directory structure where variables come from
Code:
/path/to/run/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx

    --- /path/to/run/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123  --- this is $TRIMSTR and the blue is $S5

      --- 00-1111-xxx-xxx 00-2222-yyy-yy 00-3333-zz-zz id test   --- these are within $TRIMSTER id and test are not stored in $folders

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
zzzz_0005 00-1111-xxx-xxx
zzzz_0003 00-2222-yyy-yy
R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx

current
Code:
00-1111-xxx-xxx
00-2222-yyy-yy

desired
Code:
00-1111-xxx-xxx
00-2222-yyy-yy
00-3333-zz-zz


Last edited by cmccabe; 09-29-2019 at 08:31 AM.. Reason: updated script with comments
# 2  
You have a done statement on line 11 that doesn't match to anything.

S5=$(cut -d/ -f6 <<<"$TRIMSTR") ## store run with no path as S5
S5 will be empty because TRIMSTR doesn't contain 6 entries.

if [[ $folders = ${STRING[*]} ]]; then # only execute file on match
folders will contain space separated list of folders with a digit in their name, STRING is not an array, what are you trying to match here?
These 2 Users Gave Thanks to Chubler_XL For This Post:
# 3  
I made some edits to the code and am trying to match $TRIMSTER to the line in file f1. I think I should be looking for the pattern as f1 the file name is longer but includes [ICODE]$TRIMSTER[ICODE]. When a match is foung the values in$2 up to the empty line (which always seperates each block). I though those were being read into array $STRING which is then compared to $folders which is the sud-folders within $TRIMSTER. If $STRING[*] = $folders that means it is already there and can be skipped. However, if it is not equal then it is not there and a new folders is made in $TRIMSTR.. Thank you Smilie.

Last edited by RavinderSingh13; 09-28-2019 at 03:20 PM..
# 4  
A few suggestions:
Code:
for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  test -d "$RDIR" || continue  ## is a directory, or jump to the next cycle

As you see it is continue not next.
Code:
S5=${TRIMSTR##*/}  ## strip path and store in S5

Code:
folders=`ls -d *[0-9]*/`

The trailing / ensures only directories match. But the trailing / is now part of the names.

To match a string in a list you can use a case-esac or as you tried, a [[ == ]]
The RHS takes the * wildcards.
For an exact match use boundaries. Here $folders is newline-separated, so we enclose the STRING in newlines, and we must enclose the LHS (folder list) in newlines so the first and last element can be matched.

Code:
nl="
"
    if [[ $nl$folders$nl == *$n$STRING$nl* ]]

If folder names have a trailing / you can add it to the STRING
Code:
    if [[ $nl$folders$nl == *$n$STRING/$nl* ]]

I hope this is helpful rather than confusing.
These 2 Users Gave Thanks to MadeInGermany For This Post:
# 5  
I updated the script in the original post with the helpful suggestions and added set -x. There are some syntax error and the $STRING variable doesn't get populated, though it looks like the expected values are being used. Thank you Smilie.


Code:
set -x
cmccabe@Satellite-M645:~$ DIR=/home/cmccabe/folder
+ DIR=/home/cmccabe/folder
cmccabe@Satellite-M645:~$ 
cmccabe@Satellite-M645:~$ for RDIR in "$DIR"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
>   TRIMSTR=${RDIR%%-v5.6*}  ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
>      mv "$RDIR" "$TRIMSTR"  ## move trimmed folder to directory
>      S5=${TRIMSTR##*/}  ## store run with no path as S5
> # Iterate over each sample folder in run directory
> cd "$TRIMSTR"
>     folders=folders=`ls -d *[0-9]*/`  ## list only directories begining with digit 
> done
+ for RDIR in '"$DIR"/R_2019*'
+ TRIMSTR=/home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ mv /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ S5=R_2019_00_00_00_00_00_xxxx_x0-00000-123
+ cd /home/cmccabe/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123
++ ls --color=auto -d 00-1111-xxx-xxx/ 00-2222-yyy-yy/
+ folders='folders=00-1111-xxx-xxx/
00-2222-yyy-yy/'
cmccabe@Satellite-M645:~/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123$ for f in "$DIR"/f1; do STRING=$(awk -v ref="/$S5/" 'match($0, ref) {print $2}' "$f"); done
+ for f in '"$DIR"/f1'
++ awk -v ref=/R_2019_00_00_00_00_00_xxxx_x0-00000-123/ 'match($0, ref) {print $2}' /home/cmccabe/folder/f1
+ STRING=
cmccabe@Satellite-M645:~/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123$ nl="
> "
+ nl='
'
cmccabe@Satellite-M645:~/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123$     if [[ $nl$folders$nl == *$n$STRING/$nl* ]] || continue # only execute file on match
>        else mkdir $STRING 
bash: syntax error near unexpected token `else'
cmccabe@Satellite-M645:~/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123$     fi

# 6  
The syntax requires then between if and else.
And what does the for loop with STRING?
You probably want
Code:
## added newline boundry seperator
nl="
"
for f in "$DIR"/f1
do
    STRING=$(awk -v ref="/$S5/" 'match($0, ref) {print $2}' "$f")
    if [[ $nl$folders$nl != *$n$STRING/$nl* ]] ## only execute file on match
    then
       mkdir $STRING 
    fi
done

Note that in [[ ]] the == operator is a glob match, and != is the opposite (no match). Some shells allow = instead of == but == is the standard in [[ ]].
(While in [ ] the = operator is true if the strings are equal, and the != is the opposite (not equal).) Some shells allow == instead of = but = is the standard in [ ].

Last edited by MadeInGermany; 09-30-2019 at 07:37 AM..
These 2 Users Gave Thanks to MadeInGermany For This Post:
# 7  
set x showed the same as the previous post, I initially thought there may be multiple files so used a for, but quickly realized that wasn't going to work. Is there a better approach? Thank you Smilie.

Code:
for f in "$DIR"/all ; do
>     STRING=$(awk -v ref="/$S5/" 'match($0, ref) {print $2}' "$f")
>     if [[ $nl$folders$nl != *$n$STRING/$nl* ]] ## only execute file on match
>     then
>        mkdir -p $STRING 
>     fi
> done
+ for f in '"$DIR"/f1'
++ awk -v ref=/R_2019_00_00_00_00_00_xxxx_x0-00000-123/ 'match($0, ref) {print $2}' /home/cmccabe/Desktop/new/f1
+ STRING=
+ [[ 

 != */
* ]]
+ mkdir -p

This User Gave Thanks to cmccabe For This Post:
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