I am checking to see if a file I am hoping to create conflicts with a file that has the same name.
FILEPATH=/root/logs/pData*.csv
COMPPATH=/root/logs/pData*.csv.gz
shopt -s nullglob
thisYear="$(date +"%Y")"
thisMonth="$(date +"%m")"
thisDay="$(date +"%d")"
thisTime="$(date | cut -d ' ' -f 4 | tr : _)"
for file in $FILEPATH
do
fileYear="$(stat -c %y $file | cut -d'-' -f 1)"
fileMonth="$(stat -c %y $file | cut -d'-' -f 2)"
fileDay="$(stat -c %y $file | cut -d'-' -f 3 | cut -d' ' -f 1)"
fileTime="$(stat -c %y $file | cut -d ' ' -f 2 | cut -d '.' -f 1 | tr : _)"
if (("$fileYear" < '1990'))
then
fName="pData_"$thisYear"_"$thisMonth"_"$thisDay"_"$thisTime".csv.gz"
else
fName="pData_"$fileYear"_"$fileMonth"_"$fileDay"_"$fileTime".csv.gz"
fi
echo $fName
for file in $COMPPATH
do
if ('/root/logs/'$fName == $file)
then
echo "OOPS"
fi
done
done
The script works as intended for the most part, printing OOPS when I run into a file of the same name, but for files that don't exist it prints
./compress.sh: line 31: /root/logs/pData_2015_09_18_22_25_44.csv.gz: No such file or directory
Why is this printed?
How do I prevent this from happening?
The string comparison is wrong. Using single parentheses is creating a sub-shell and trying to execute '/root/logs/'$fName
Set your string compare to be:
if [[ '/root/logs/'$fName = $file ]]
See: http://www.tldp.org/LDP/abs/html/comparison-ops.html
Related
I'm extracting two md5sums by using this code:
md5sum test{1,2} | cut -d' ' -f1-2
I'm receiving two md5sums as in example below:
02eace9cb4b99519b49d50b3e44ecebc
d8e8fca2dc0f896fd7cb4cb0031ba249
Afterwards I'm not sure how to compare them. I have tried using the xargs:
md5sum test{1,2} | cut -d' ' -f1-2 | xargs bash -c '$0 == $1'
However, it tries to execute md5sum as a command
Any advice?
Try using a command subsitution instead
#!/bin/bash
echo 1 > file_a
echo 2 > file_b
echo 1 > file_c
file1=file_a
# try doing "file2=file_b" as well
file2=file_c
if [[ $(sha1sum $file1 | cut -d ' ' -f1-2) = $(sha1sum $file2 | cut -d ' ' -f1-2) ]]; then
echo same
else
echo different
fi
I use youtube-dl to archive specific blogs. I use a custom bash script (called tvify) to help me organize my content into Plex-ready filenames for later replay via my home Plex server.
Archiving the content works fine, unless a blogger posts more than one video on the same date - if that happens my script creates more than one file for a given month/date and plex sees a duplicate episode. In the plex app, it stuffs them together as distinct 'versions' of the same episode. The result is that the description of the video no longer matches its contents, and only one 'version' appears unless I access an additional sub menu.
The videos get downloaded by you tube-dl kicked off from a cron-job, and that downloader script runs the following to help format their filenames and stuff them into appropriate folders for 'seasons'.
The season is the year when the video was released, and the episode is the combination of the month and date in MMDD format.
Below is my 'tvify' script, which helps perform the filename manipulation and stuffs the file into the proper folder for the season.
#!/bin/bash
mySuff="$1"
echo mySuff="$mySuff"
if [ -z "$1" ]; then
mySuff="*.mp4"
fi
for i in $mySuff
do
prb=`ffprobe -- "$i" 2>&1`
myDate=`echo "$prb" | grep -E 'date\s+:' | cut -d ':' -f 2`
myartist=`echo "$prb" | grep -E 'artist\s+:' | cut -d ':' -f 2`
myTitle=`echo "$prb" | grep -E 'title\s+:' | cut -d ':' -f 2 | sed 's/\//_/g'`
cwd_stub=`pwd | awk -F'/' '{print $NF}'`
if [ -d "s${myDate:1:4}" ]; then echo "Directory found" > /dev/null; else mkdir "s${myDate:1:4}"; fi
[ -d "s${myDate:1:4}" ] && mv -- "$i" "s${myDate:1:4}/${myartist[#]:1} - s${myDate:1:4}e${myDate:5:8} - ${myTitle[#]:1:40} _$i" || mv -- "$i" "${myartist[#]:1} - s${myDate:1:4}e${myDate:5:8} - ${myTitle[#]:1:40} _$i"
done
How can I modify that script to identify if a conflicting year/MMDD file exists, and if so, append an appropriate suffix to the episode number so that plex will interpret them as distinct episodes?
I ended up implementing an array, counting the number of elements in the array, and using that to append the integer:
#!/bin/bash
mySuff="$1"
echo mySuff="$mySuff"
if [ -z "$1" ]; then
mySuff="*.mp4"
fi
for i in $mySuff
do
prb=`ffprobe -- "$i" 2>&1`
myDate=`echo "$prb" | grep -E 'date\s+:' | cut -d ':' -f 2`
myartist=`echo "$prb" | grep -E 'artist\s+:' | cut -d ':' -f 2`
myTitle=`echo "$prb" | grep -E 'title\s+:' | cut -d ':' -f 2 | sed 's/\//_/g'`
cwd_stub=`pwd | awk -F'/' '{print $NF}'`
readarray -t conflicts < <(find . -maxdepth 2 -iname "*s${myDate:1:4}e${myDate:5:8}*" -type f -printf '%P\n')
[ ${#conflicts[#]} -gt 0 ] && _inc=${#conflicts[#]} || _inc=
if [ -d "s${myDate:1:4}" ]; then echo "Directory found" > /dev/null; else mkdir "s${myDate:1:4}"; fi
[ -d "s${myDate:1:4}" ]
&& mv -- "$i" "s${myDate:1:4}/${myartist[#]:1} - s${myDate:1:4}e${myDate:5:8}$_inc - ${myTitle[#]:1:40} _$i"
|| mv -- "$i" "${myartist[#]:1} - s${myDate:1:4}e${myDate:5:8}$_inc - ${myTitle[#]:1:40} _$i"
done
I need to read a json file and take value like 99XXXXXXXXXXXX0 and cccs and write in csv which having column BASE_No and Schedule.
Input file: classedFFDCD_5666_4888_45_2018_02112018012106.021.json
"bfgft":"99XXXXXXXXXXXX0","fp":"XXXXXX","cur_gt":225XXXXXXXX0,"cccs"
"bfgft":"21XXXXXXXXXXXX0","fp":"XXXXXX","cur_gt":225XXXXXXXX0,"nncs"
"bfgft":"56XXXXXXXXXXXX0","fp":"XXXXXX","cur_gt":225XXXXXXXX0,"fgbs"
"bfgft":"44XXXXXXXXXXXX0","fp":"XXXXXX","cur_gt":225XXXXXXXX0,"ddss"
"bfgft":"94XXXXXXXXXXXX0","fp":"XXXXXX","cur_gt":225XXXXXXXX0,"jjjs"
Expected output:
BASE_No,Schedule
99XXXXXXXXXXXX0,cccs
21XXXXXXXXXXXX0,nncs
56XXXXXXXXXXXX0,fgbs
44XXXXXXXXXXXX0,ddss
94XXXXXXXXXXXX0,jjjs
I am using below code for reading file name and date, but unable to read file for BASE_No,Schedule.
SAVEIFS=$IFS
IFS=$(echo -en "\n\b")
for line in `ls -lrt *.json`; do
date=$(echo $line |awk -F ' ' '{print $6" "$7}');
file=$(echo $line |awk -F ' ' '{print $9}');
echo ''$file','$(date "+%Y/%m/%d %H.%M.%S")'' >> $File_Tracker`
Assuming the structure of the json doesnt change for every line, the sample code checks through line by line to retrieve the particular value and concatenates using printf. The output is then stored as new output.txt file.
#!/bin/bash
input="/home/kj4458/winhome/Downloads/sample.json"
printf "Base,Schedule \n" > output.txt
while IFS= read -r var
do
printf "`echo "$var" | cut -d':' -f 2 | cut -d',' -f 1`,`echo "$var" | cut -d':' -f 4 | cut -d',' -f 2` \n" | sed 's/"//g' >> output.txt
done < "$input"
awk -F " \" " ' {print $4","$12 }' file
99XXXXXXXXXXXX0,cccs
21XXXXXXXXXXXX0,nncs
56XXXXXXXXXXXX0,fgbs
44XXXXXXXXXXXX0,ddss
94XXXXXXXXXXXX0,jjjs
I got that result!
I have a problem
I Have a program general like this gene.sh
that for all file (es file: geneX.csv) make a directory with the name of gene (example: Genex/geneX.csv) next this program compile an other program inside gene.sh but this progrm need a varieble and I dont know how do it.
this is the program gene.sh
#!/bin/bash
# Create a dictory for each file *.xls and *.csv
for fname in *.xlsx *csv
do
dname=${fname%.*}
[[ -d $dname ]] || mkdir "$dname"
mv "$fname" "$dname"
done
# For each gene go inside the directory and compile the programs getChromosomicPositions.sh to have the positions, and getHapolotipeStings.sh to have the variants
for geni in */; do
cd $geni
z=$(tail -n 1 *.csv | tr ';' "\n" | wc -l)
cd ..
cp getChromosomicPositions.sh $geni --->
cp getHaplotypeStrings.sh $geni
cd $geni
export z
./getChromosomicPositions.sh *.csv
export z
./getHaplotypeStrings.sh *.csv
cd ..
done
This is the program getChromosomichPositions.sh:
rm chrPosRs.txt
grep '^Haplotype\ ID' $1 | cut -d ";" -f 4-61 | tr ";" "\n" | awk '{print "select chrom,chromStart,chromEnd,name from snp147 where name=\""$1"\";"}' > listOfQuery.txt
while read l; do
echo $l > query.txt
mysql -h genome-mysql.cse.ucsc.edu -u genome -A -D hg38 --skip-column-names < query.txt > queryResult.txt
if [[ "$(cat queryResult.txt)" == "" ]];
then
cat query.txt |
while read line; do
echo $line | awk '$6 ~/rs/ {print $6}' > temp.txt;
if [[ "$(cat temp.txt)" != "" ]];
then cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g' > temp.txt;
./getHGSVposHG19.sh temp.txt ---> Hear the problem--->
else
echo $line | awk '{num=sub(/.*:g\./,"");num+=sub(/\".*/,"");if(num==2){print};num=""}' > temp2.txt
fi
done
cat query.txt >> varianti.txt
echo "Missing Data" >> chrPosRs.txt
else
cat queryResult.txt >> chrPosRs.txt
fi
done < listOfQuery.txt
rm query*
hear the problem:
I need to enter in the file temp.txt and put automatically at the beginning of the file the variable $geni of the program gene.sh
How can I do that?
Why not pass "$geni" as say the first argument when invoking your script, and treating the rest of the arguments as your expected .csv files.
./getChromosomicPositions.sh "$geni" *.csv
Alternatively, you can set it as environment variable for the script, so that it can be used there (or just export it).
geni="$geni" ./getChromosomicPositions.sh *.csv
In any case, once you have it available in the second script, you can do
if passed as the first argument:
echo "${1}:$(cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g')
or if passed as environment variable:
echo "${geni}:$(cat temp.txt | awk -F'name="' '{print $2}' | sed -e 's/";//g')
I am trying a simple shell script like the following:
#!/bin/bash
up_cap=$( cat result.txt | cut -d ":" -f 6,7 | sort -n | cut -d " " -f 2 | sort -n)
down_cap=$( cat result.txt | cut -d : -f 6,7 | sort -n | cut -d " " -f 6| sort -n)
for value in "${down_cap[#]}";do
if [ $value > 80000 ]; then
cat result.txt | grep -B 1 "$value"
fi
done
echo " All done, exiting"
when I execute the above script as ./script.sh, I get the error:
./script.sh: line 5: [: too many arguments
All done, exiting
I have googled enough, and still not able to rectify this.
You want
if [ "$value" -gt 80000 ]; then
You use -gt for checking if A is bigger than B, not >. The quotation marks I merely added to prevent the script from failing in case $value is empty.
Try to declare variable $value explicitly:
declare -i value
So, with the dominikh's and mine additions the code should look like this:
#!/bin/bash
up_cap=$( cat result.txt | cut -d ":" -f 6,7 | sort -n | cut -d " " -f 2 | sort -n)
down_cap=$( cat result.txt | cut -d : -f 6,7 | sort -n | cut -d " " -f 6| sort -n)
for value in "${down_cap[#]}";do
declare -i value
if [ $value -gt 80000 ]; then
cat result.txt | grep -B 1 "$value"
fi
done
echo " All done, exiting"