I've got a bash script that wraps mvn (Apache Maven) to add colour to its output. A cut-down version of what it does is:
mvn "$#" | sed -e "s/^\[INFO\] \-.*/$bldblu&$rst/g"
where $bldblu is the ANSI color escape characters for bold blue, and $rst resets the colours.
The issue I'm having is that sometimes mvn writes a line that doesn't end in a newline, thus (as far as I can tell) sed keeps waiting for input and never prints the prompt (which makes it seem like Maven is hanging). I've tried adding -u to sed but that just forces sed to do line-by-line buffering instead of buffering more than one line - not helpful for me.
So far this is what I've come up with:
mvn "$#" | perl -pe "$| = 1; s/^(\[INFO\] \-.*)/$bldblu\$1$rst/g"
but I think the use of -p is not correct here. Any help?
A substitution may be overkill, especially when the replacement pattern has special characters in it. How about this?
export bldblu
export rst
mvn "$#" | perl -pe 'if(/^.INFO. -/){ $_=$ENV{bldblu}.$_.$ENV{rst} }'
or rather than reinventing the wheel
mvn "$#" | perl -MTerm::ANSIColor -pe
'$_=color("bold blue").$_.color("reset") if /^.INFO. -/'
(workaround) Use sed --unbuffered
I couldn't figure out the solution but thankfully this is good enough for my particular usage:
cat - | sed --unbuffered 's/.*?from//g'
But I too would like to know the answer. Perl one line substitution is a key idiom in my toolbelt.
BSD
Looks like there is no common flag for GNU and BSD. For the latter, you'd need:
-l Make output line buffered.
Related
I'm looking for an equivalent of perl -pe. Ideally, it would be replace with sed if it's possible. Any help is highly appreciated.
The code is:
perl -pe 's/^\[([^\]]+)\].*$/$1/g'
$ echo '[foo] 123' | perl -pe 's/^\[([^\]]+)\].*$/$1/g'
foo
$ echo '[foo] 123' | sed -E 's/^\[([^]]+)\].*$/\1/'
foo
sed by default accepts code from command line, so -e isn't needed (though it can be used)
printing the pattern space is default, so -p isn't needed and sed -n is similar to perl -n
-E is used here to be as close as possible to Perl regex. sed supports BRE and ERE (not as feature rich as Perl) and even that differs from implementation to implementation.
with BRE, the command for this example would be: sed 's/^\[\([^]]*\)\].*$/\1/'
\ isn't special inside character class unless it is an escape sequence like \t, \x27 etc
backreferences use \N format (and limited to maximum 9)
Also note that g flag isn't needed in either case, as you are using line anchors
I have a string like below
abc="where session = '001122' and indicator = 'X'"
I want to convert it to
eng="where session in ('001122') and indicator in ('X')"
I have tried like below using sed in bash
eng=$(echo $abc | sed -r "s/=\s+('[^']+')/in (\1)/g")
I am still get the input itself. What am I doing wrong.
You can use unadorned sed with escaped to escape the capture group parentheses (\( and \)), as well as one-or-more quantifiers (\+):
$ eng=$(echo "$abc" | sed "s/=\s\+'\([^']\+\)'/in ('\1')/g"
$ echo "$eng"
where session in ('001122') and indicator in ('X')
It is also probably a good idea to quote your expansion of abc, since it has spaces in it, but not strictly necessary in this context.
Your original code may not have worked because -r is a GNU extension. The synonym -E used to be as well, but is now part of the POSIX standard, and should therefore be relatively portable. The following version should therefore have no problems either:
$ eng=$(echo "$abc" | sed -E "s/=\s+'([^']+)'/in ('\1')/g"
Using sed I want to parse Heroku's log-runtime-metrics like this one:
2016-01-29T00:38:43.662697+00:00 heroku[worker.2]: source=worker.2 dyno=heroku.17664470.d3f28df1-e15f-3452-1234-5fd0e244d46f sample#memory_total=54.01MB sample#memory_rss=54.01MB sample#memory_cache=0.00MB sample#memory_swap=0.00MB sample#memory_pgpgin=17492pages sample#memory_pgpgout=3666pages
the desired output is:
worker.2: 54.01MB (54.01MB is being memory_total)
I could not manage although I tried several alternatives including:
sed -E 's/.+source=(.+) .+memory_total=(.+) .+/\1: \2/g'
What is wrong with my command? How can it be corrected?
The .+ after source= and memory_total= are both greedy, so they accept as much of the line as possible. Use [^ ] to mean "anything except a space" so that it knows where to stop.
sed -E 's/.+source=([^ ]+) .+memory_total=([^ ]+) .+/\1: \2/g'
Putting your content into https://regex101.com/ makes it really obvious what's going on.
I'd go for the old-fashioned, reliable, non-extended sed expressions and make sure that the patterns are not too greedy:
sed -e 's/.*source=\([^ ]*\) .*memory_total=\([^ ]*\) .*/\1: \2/'
The -e is not the opposite of -E, which is primarily a Mac OS X (BSD) sed option; the normal option for GNU sed is -r instead. The -e simply means that the next argument is an expression in the script.
This produces your desired output from the given line of data:
worker.2: 54.01MB
Bonus question: There are some odd lines within the stream, I can usually filter them out using a grep pipe like | grep memory_total. However if I try to use it along with the sed command, it does not work. No output is produced with this:
heroku logs -t -s heroku | grep memory_total | sed.......
Sometimes grep | sed is necessary, but it is often redundant (unless you are using a grep feature that isn't readily supported by sed, such as Perl regular expressions).
You should be able to use:
sed -n -e '/memory_total=/ s/.*source=\([^ ]*\) .*memory_total=\([^ ]*\) .*/\1: \2/p'
The -n means "don't print by default". The /memory_total=/ matches the lines you're after; the s/// content is the same as before. I removed the g suffix that was there previously; the regex would never match multiple times anyway. I added the p to print the line when the substitution occurs.
I have a bash script in which I have a few qsubs. Each of them are waiting for a preivous qsub to be done before starting.
My first qsub consist of sending files in a certain directory to a perl program and having the outfiles printed in a new directory. At the end, I echo the array with all my jobs names. This script works as intented.
mkdir -p /perl_files_dir
for ID_FILES in `ls Infiles_dir/*.txt`;
do
JOB_ID=`echo "perl perl_scirpt.pl $ID_FILES" | qsub -j oe `
JOB_ID_ARRAY="${JOB_ID_ARRAY}:$JOB_ID"
done
echo $JOB_ID_ARRAY
My second qsub is meant to sort all my previous files made with my perl script in a new outfile and to start after all these jobs are done (about 100 jobs) with depend=afterany. Again, this part is working fine.
SORT_JOB=`echo "sort -m -n perl_files_dir/*.txt >>sorted_file.txt" | qsub -j oe -W depend=afterany$JOB_ID_ARRAY`
SORT_ARRAY="${SORT_ARRAY}:$SORT_JOB"
My issue is that in my sorted file, I have a few columns I wish to remove (2 to 6), so I came up with this last line using awk piped to sed with another depend=afterany
SED=`echo "awk '{\$2="";\$3="";\$4="";\$5="";\$6=""; print \$0}' sorted_file.txt \
| sed 's/ //g' >final_file.txt" | qsub -j oe -W depend=afterany$SORT_ARRAY`
This last step creates final_file.txt, but leaves it empty. I added SED= before my echo because it would otherwise give me Command not found.
I tried without the pipe so it would just print everything. Unfortunately it prints nothing.
I assume it is not opening my sorted file and this is why my final file is empty after my sed. If it's the case, then why won't awk read it?
In my script, I am using variables to define my directories and files (with the correct path). I know my issue is not about find my files or directories since they are perfectly defined at the beginning and used throughout the script. I tried to write the whole path instead of a variable and I get the same results.
for ID_FILES in `ls Infiles_dir/*.txt`
Simplify this to
for ID_FILES in Infiles_dir/*.txt
ls lists the files you pass it (except when you pass it directories, then it lists their content). Rather than telling it to display a list of files and parse the output, use the list of files you already have! This is more reliable (parsing the output of ls will fail if the file names contain whitespace or wildcard characters), clearer and faster. Don't parse the output of ls.
SORT_JOB=`echo "sort -m -n perl_files_dir/*.txt >>sorted_file.txt" | qsub -j oe -W depend=afterany$JOB_ID_ARRAY`
You'd make your life simpler if you used the right form of quoting in the right place. Don't use backquotes, because it's difficult to know how to quote things inside. Use $(…) instead, it's exactly equivalent except that it is parsed in a sane way.
I recommend using a here document for the shell snippet that you're feeding to qsub. You have fewer quoting issues to worry about, and it's more readable.
While we're at it, always put double quotes around variable substitutions and command substitutions: "$some_variable", "$(some_command)". Annoyingly, $var in shell syntax doesn't mean “take the value of the variable var”, it means “take the value of the variable var, parse it as a list of wildcard patterns, and replace each pattern by the list of matching files if there are matching files”. This extra stuff is turned off if the substitution happens inside double quotes (or in a here document, by the way): "$var" means “take the value of the variable var”.
SORT_JOB=$(qsub -j oe -W depend="afterany$JOB_ID_ARRAY" <<'EOF'
sort -m -n perl_files_dir/*.txt >>sorted_file.txt
EOF
)
We now get to the snippet where the quoting was actually causing a problem.
SED=`echo "awk '{\$2="";\$3="";\$4="";\$5="";\$6=""; print \$0}' sorted_file.txt \
| sed 's/ //g' >final_file.txt" | qsub -j oe -W depend=afterany$SORT_ARRAY`
The string that becomes the argument to the echo command is:
awk '{$2=;$3=;$4=;$5=;$6=; print $0}' sorted_file.txt | sed 's/ //g' >final_file.txt
This is syntactically incorrect, and that's why you're not getting any output.
You didn't escape the double quotes inside what was meant to be the awk snippet. It's a lot clearer if you use a here document. Also, you don't need the SED= part. You added it because you had a command substitution (a command between …), which substitutes the output of a command. But since you aren't interested in the output of the qsub command, don't take its output, just execute it.
qsub -j oe -W depend="afterany$SORT_ARRAY" <<'EOF'
awk '{$2="";$3="";$4="";$5="";$6=""; print $0}' sorted_file.txt |
sed 's/ //g' >final_file.txt
EOF
I'm not familiar with qsub, but presumably there's a way to get the error output and the return status of the commands it runs. Inspect that error output, you should have seen the errors from awk.
The version of awk that I am using, does not like the character escapes
awk --version
GNU Awk 3.1.7
spuder#cent64$ awk '{\$2="";\$3="";\$4=""; print \$0}' foo.txt
awk: {\$2="";\$3="";\$4=""; print \$0}
awk: ^ backslash not last character on line
Try the following syntax
awk '{for(i=2;i<=7;i++) $i="";print}' foo.txt
As a side note, if you are using Torque 4.x you may not be able to use a comma separated list of jobs with -W depend=, instead you may need to create a new PBS declarative (-W) for each job.
eg...
#Invalid syntax in newer versions of torque
qsub -W depend=foo,bar
Resources
backslash in gawk fields
Print all but the first three columns
http://docs.adaptivecomputing.com/torque/help.htm#topics/commands/qsub.htm#-W
I am trying to write a sed expression that can remove urls from a file
example
http://samgovephotography.blogspot.com/ updated my blog just a little bit ago. Take a chance to check out my latest work. Hope all is well:)
Meet Former Child Star & Author Melissa Gilbert 6/15/09 at LA's B&N https://hollywoodmomblog.com/?p=2442 Thx to HMB Contributor #kdpartak :)
But I dont get it:
sed 's/[\w \W \s]*http[s]*:\/\/\([\w \W]\)\+[\w \W \s]*/ /g' posFile
FIXED!!!!!
handles almost all cases, even malformed URLs
sed 's/[\w \W \s]*http[s]*[a-zA-Z0-9 : \. \/ ; % " \W]*/ /g' positiveTweets | grep "http" | more
The following removes http:// or https:// and everything up until the next space:
sed -e 's!http\(s\)\{0,1\}://[^[:space:]]*!!g' posFile
updated my blog just a little bit ago. Take a chance to check out my latest work. Hope all is well:)
Meet Former Child Star & Author Melissa Gilbert 6/15/09 at LA's B&N Thx to HMB Contributor #kdpartak :)
Edit:
I should have used:
sed -e 's!http[s]\?://\S*!!g' posFile
"[s]\?" is a far more readable way of writing "an optional s" compared to "\(s\)\{0,1\}"
"\S*" a more readable version of "any non-space characters" than "[^[:space:]]*"
I must have been using the sed that came installed with my Mac at the time I wrote this answer (brew install gnu-sed FTW).
There are better URL regular expressions out there (those that take into account schemes other than HTTP(S), for instance), but this will work for you, given the examples you give. Why complicate things?
The accepted answer provides the approach that I used to remove URLs, etc. from my files. However it left "blank" lines. Here is a solution.
sed -i -e 's/http[s]\?:\/\/\S*//g ; s/www\.\S*//g ; s/ftp:\S*//g' input_file
perl -i -pe 's/^'`echo "\012"`'${2,}//g' input_file
The GNU sed flags, expressions used are:
-i Edit in-place
-e [-e script] --expression=script : basically, add the commands in script
(expression) to the set of commands to be run while processing the input
^ Match start of line
$ Match end of line
? Match one or more of preceding regular expression
{2,} Match 2 or more of preceding regular expression
\S* Any non-space character; alternative to: [^[:space:]]*
However,
sed -i -e 's/http[s]\?:\/\/\S*//g ; s/www\.\S*//g ; s/ftp:\S*//g'
leaves nonprinting character(s), presumably \n (newlines). Standard sed-based approaches to remove "blank" lines, tabs and spaces, e.g.
sed -i 's/^[ \t]*//; s/[ \t]*$//'
do not work, here: if you do not use a "branch label" to process newlines, you cannot replace them using sed (which reads input one line at a time).
The solution is to use the following perl expression:
perl -i -pe 's/^'`echo "\012"`'${2,}//g'
which uses a shell substitution,
'`echo "\012"`'
to replace an octal value
\012
(i.e., a newline, \n), that occurs 2 or more times,
{2,}
(otherwise we would unwrap all lines), with something else; here:
//
i.e., nothing.
[The second reference below provides a wonderful table of these values!]
The perl flags used are:
-p Places a printing loop around your command,
so that it acts on each line of standard input
-i Edit in-place
-e Allows you to provide the program as an argument,
rather than in a file
References:
perl flags: Perl flags -pe, -pi, -p, -w, -d, -i, -t?
ASCII control codes: https://www.cyberciti.biz/faq/unix-linux-sed-ascii-control-codes-nonprintable/
remove URLs: sed to remove URLs from a file
branch labels: How can I replace a newline (\n) using sed?
GNU sed manual: https://www.gnu.org/software/sed/manual/sed.html
quick regex guide: https://www.gnu.org/software/sed/manual/html_node/Regular-Expressions.html
Example:
$ cat url_test_input.txt
Some text ...
https://stackoverflow.com/questions/4283344/sed-to-remove-urls-from-a-file
https://www.google.ca/search?dcr=0&ei=QCsyWtbYF43YjwPpzKyQAQ&q=python+remove++citations&oq=python+remove++citations&gs_l=psy-ab.3...1806.1806.0.2004.1.1.0.0.0.0.61.61.1.1.0....0...1c.1.64.psy-ab..0.0.0....0.-cxpNc6youY
http://scikit-learn.org/stable/modules/generated/sklearn.feature_extraction.text.TfidfVectorizer.html
https://bbengfort.github.io/tutorials/2016/05/19/text-classification-nltk-sckit-learn.html
http://datasynce.org/2017/05/sentiment-analysis-on-python-through-textblob/
https://www.google.ca/?q=halifax&gws_rd=cr&dcr=0&ei=j7UyWuGKM47SjwOq-ojgCw
http://www.google.ca/?q=halifax&gws_rd=cr&dcr=0&ei=j7UyWuGKM47SjwOq-ojgCw
www.google.ca/?q=halifax&gws_rd=cr&dcr=0&ei=j7UyWuGKM47SjwOq-ojgCw
ftp://ftp.ncbi.nlm.nih.gov/
ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/alignment_indices/20100804.alignment.index
Some more text.
$ sed -e 's/http[s]\?:\/\/\S*//g ; s/www\.\S*//g ; s/ftp:\S*//g' url_test_input.txt > a
$ cat a
Some text ...
Some more text.
$ perl -i -pe 's/^'`echo "\012"`'${2,}//g' a
Some text ...
Some more text.
$