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How to have the list of files represented by a regex given in input to a bash script
I'm creating a code for the automatic extraction of bib records from scientific papers.
In an old version of the script i gave in input the name of the folder where all the pdfs were stored, now I want to give a regex. E.g. before:
./AutoBib.sh Papers/
Now:
./Autobib.sh Papers/*.pdf
In the folder there are, for example 3 pdf files: Shrek.pdf, Fiona.pdf, Donkey.pdf, using my script I should be able to retrieve the doi from all files creating a file where all doi are listed but executing my script it returns the doi of the first file and nothing more.
Here there is my code:
for i in $1; do
doi $i
done
doi is a function that extract the doi from a pdf and puts it in a txt file. When i run the script it returns me only the doi of the first file.
How can I feed a regex in my script and being able to iterate though all files that matches that regex?
linux bash
edited Dec 30 '18 at 17:36
cody
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
add a comment |
I'm creating a code for the automatic extraction of bib records from scientific papers.
In an old version of the script i gave in input the name of the folder where all the pdfs were stored, now I want to give a regex. E.g. before:
./AutoBib.sh Papers/
Now:
./Autobib.sh Papers/*.pdf
In the folder there are, for example 3 pdf files: Shrek.pdf, Fiona.pdf, Donkey.pdf, using my script I should be able to retrieve the doi from all files creating a file where all doi are listed but executing my script it returns the doi of the first file and nothing more.
Here there is my code:
for i in $1; do
doi $i
done
doi is a function that extract the doi from a pdf and puts it in a txt file. When i run the script it returns me only the doi of the first file.
How can I feed a regex in my script and being able to iterate though all files that matches that regex?
linux bash
edited Dec 30 '18 at 17:36
cody
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
add a comment |
I'm creating a code for the automatic extraction of bib records from scientific papers.
In an old version of the script i gave in input the name of the folder where all the pdfs were stored, now I want to give a regex. E.g. before:
./AutoBib.sh Papers/
Now:
./Autobib.sh Papers/*.pdf
In the folder there are, for example 3 pdf files: Shrek.pdf, Fiona.pdf, Donkey.pdf, using my script I should be able to retrieve the doi from all files creating a file where all doi are listed but executing my script it returns the doi of the first file and nothing more.
Here there is my code:
for i in $1; do
doi $i
done
doi is a function that extract the doi from a pdf and puts it in a txt file. When i run the script it returns me only the doi of the first file.
How can I feed a regex in my script and being able to iterate though all files that matches that regex?
linux bash
edited Dec 30 '18 at 17:36
cody
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
I'm creating a code for the automatic extraction of bib records from scientific papers.
In an old version of the script i gave in input the name of the folder where all the pdfs were stored, now I want to give a regex. E.g. before:
./AutoBib.sh Papers/
Now:
./Autobib.sh Papers/*.pdf
In the folder there are, for example 3 pdf files: Shrek.pdf, Fiona.pdf, Donkey.pdf, using my script I should be able to retrieve the doi from all files creating a file where all doi are listed but executing my script it returns the doi of the first file and nothing more.
Here there is my code:
for i in $1; do
doi $i
done
doi is a function that extract the doi from a pdf and puts it in a txt file. When i run the script it returns me only the doi of the first file.
How can I feed a regex in my script and being able to iterate though all files that matches that regex?
linux bash
linux bash
edited Dec 30 '18 at 17:36
cody
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
edited Dec 30 '18 at 17:36
cody
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
edited Dec 30 '18 at 17:36
cody
8,20631226
edited Dec 30 '18 at 17:36
cody
8,20631226
edited Dec 30 '18 at 17:36
cody
8,20631226
8,20631226
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
asked Dec 30 '18 at 17:24
Giuseppe MinardiGiuseppe Minardi
869
869
add a comment |
add a comment |
3 Answers
3
active
oldest
votes
It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
answered Dec 30 '18 at 17:34
codycody
8,20631226
1
or evenfor i; do doi "$i"; done
– Paul Hodges
Dec 31 '18 at 14:58
add a comment |
If you want to filter files within directory by pattern, you can pass this pattern as second script parameter and search for matching files using find.
Here is the code. It's additionally resistant to filenames containing spaces:
find "$1" -maxdepth 1 -name "$2" -exec doi {} ;
Usage example: ./Autobib.sh Papers/ *.pdf
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
2
This has multiple problems. You don't want to uselsin scripts and*.pdfis not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.
– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to usefindinstead oflsand to make description more relevant.
– Robert Baldyga
Dec 31 '18 at 15:58
1
readis still not robust, you want something likewhile IFS="" read -r filenamebut a much better solution isfind ... -exec doi {} j;
– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
add a comment |
You can just run the ls command in loop and it will solve your problem.
for x in $(ls $@/*.pdf)
do
echo $x ## if you want only file name you can change this line to echo `basename $x`
done
I have created the same scenario as you mentioned above, refer the snapshot.
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
add a comment |
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3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
answered Dec 30 '18 at 17:34
codycody
8,20631226
1
or evenfor i; do doi "$i"; done
– Paul Hodges
Dec 31 '18 at 14:58
add a comment |
It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
answered Dec 30 '18 at 17:34
codycody
8,20631226
1
or evenfor i; do doi "$i"; done
– Paul Hodges
Dec 31 '18 at 14:58
add a comment |
It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
answered Dec 30 '18 at 17:34
codycody
8,20631226
It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
answered Dec 30 '18 at 17:34
codycody
8,20631226
edited Dec 30 '18 at 17:50
answered Dec 30 '18 at 17:34
codycody
8,20631226
answered Dec 30 '18 at 17:34
codycody
8,20631226
answered Dec 30 '18 at 17:34
codycody
8,20631226
8,20631226
1
or evenfor i; do doi "$i"; done
– Paul Hodges
Dec 31 '18 at 14:58
add a comment |
1
or evenfor i; do doi "$i"; done
– Paul Hodges
Dec 31 '18 at 14:58
1
1
or even
for i; do doi "$i"; done– Paul Hodges
Dec 31 '18 at 14:58
or even
for i; do doi "$i"; done– Paul Hodges
Dec 31 '18 at 14:58
add a comment |
If you want to filter files within directory by pattern, you can pass this pattern as second script parameter and search for matching files using find.
Here is the code. It's additionally resistant to filenames containing spaces:
find "$1" -maxdepth 1 -name "$2" -exec doi {} ;
Usage example: ./Autobib.sh Papers/ *.pdf
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
2
This has multiple problems. You don't want to uselsin scripts and*.pdfis not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.
– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to usefindinstead oflsand to make description more relevant.
– Robert Baldyga
Dec 31 '18 at 15:58
1
readis still not robust, you want something likewhile IFS="" read -r filenamebut a much better solution isfind ... -exec doi {} j;
– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
add a comment |
If you want to filter files within directory by pattern, you can pass this pattern as second script parameter and search for matching files using find.
Here is the code. It's additionally resistant to filenames containing spaces:
find "$1" -maxdepth 1 -name "$2" -exec doi {} ;
Usage example: ./Autobib.sh Papers/ *.pdf
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
2
This has multiple problems. You don't want to uselsin scripts and*.pdfis not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.
– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to usefindinstead oflsand to make description more relevant.
– Robert Baldyga
Dec 31 '18 at 15:58
1
readis still not robust, you want something likewhile IFS="" read -r filenamebut a much better solution isfind ... -exec doi {} j;
– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
add a comment |
If you want to filter files within directory by pattern, you can pass this pattern as second script parameter and search for matching files using find.
Here is the code. It's additionally resistant to filenames containing spaces:
find "$1" -maxdepth 1 -name "$2" -exec doi {} ;
Usage example: ./Autobib.sh Papers/ *.pdf
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
If you want to filter files within directory by pattern, you can pass this pattern as second script parameter and search for matching files using find.
Here is the code. It's additionally resistant to filenames containing spaces:
find "$1" -maxdepth 1 -name "$2" -exec doi {} ;
Usage example: ./Autobib.sh Papers/ *.pdf
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
edited Jan 1 at 12:52
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
answered Dec 30 '18 at 19:13
Robert BaldygaRobert Baldyga
7715
7715
2
This has multiple problems. You don't want to uselsin scripts and*.pdfis not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.
– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to usefindinstead oflsand to make description more relevant.
– Robert Baldyga
Dec 31 '18 at 15:58
1
readis still not robust, you want something likewhile IFS="" read -r filenamebut a much better solution isfind ... -exec doi {} j;
– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
add a comment |
2
This has multiple problems. You don't want to uselsin scripts and*.pdfis not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.
– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to usefindinstead oflsand to make description more relevant.
– Robert Baldyga
Dec 31 '18 at 15:58
1
readis still not robust, you want something likewhile IFS="" read -r filenamebut a much better solution isfind ... -exec doi {} j;
– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
2
2
This has multiple problems. You don't want to use
ls in scripts and *.pdf is not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.– tripleee
Dec 31 '18 at 7:48
This has multiple problems. You don't want to use
ls in scripts and *.pdf is not a valid regex. Even if it were, you'd need to quote it in order to prevent the shell from expanding it into a list of arguments.– tripleee
Dec 31 '18 at 7:48
Thanks. I edited answer to use
find instead of ls and to make description more relevant.– Robert Baldyga
Dec 31 '18 at 15:58
Thanks. I edited answer to use
find instead of ls and to make description more relevant.– Robert Baldyga
Dec 31 '18 at 15:58
1
1
read is still not robust, you want something like while IFS="" read -r filename but a much better solution is find ... -exec doi {} j;– tripleee
Jan 1 at 12:20
read is still not robust, you want something like while IFS="" read -r filename but a much better solution is find ... -exec doi {} j;– tripleee
Jan 1 at 12:20
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
Yeah, looks great to me! Thanks!
– Robert Baldyga
Jan 1 at 12:54
add a comment |
You can just run the ls command in loop and it will solve your problem.
for x in $(ls $@/*.pdf)
do
echo $x ## if you want only file name you can change this line to echo `basename $x`
done
I have created the same scenario as you mentioned above, refer the snapshot.
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
add a comment |
You can just run the ls command in loop and it will solve your problem.
for x in $(ls $@/*.pdf)
do
echo $x ## if you want only file name you can change this line to echo `basename $x`
done
I have created the same scenario as you mentioned above, refer the snapshot.
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
add a comment |
You can just run the ls command in loop and it will solve your problem.
for x in $(ls $@/*.pdf)
do
echo $x ## if you want only file name you can change this line to echo `basename $x`
done
I have created the same scenario as you mentioned above, refer the snapshot.
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
You can just run the ls command in loop and it will solve your problem.
for x in $(ls $@/*.pdf)
do
echo $x ## if you want only file name you can change this line to echo `basename $x`
done
I have created the same scenario as you mentioned above, refer the snapshot.
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
answered Jan 2 at 2:56
Mohit RathoreMohit Rathore
1004
1004
add a comment |
add a comment |
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