I have code that runs something like
python extract_info.py -f file.txt | sort -k1 | gzip -c >> gzipped_file.txt.gz
python extract_info.py -f file2.txt | sort -k1 | gzip -c >> gzipped_file.txt.gz
Yet when I try to extract information from that file using zcat like this:
zcat gzipped_file.txt.gz | python do_stuff.py | gzip -c > output.txt.gz
I get this error:
gzip: gzipped_file.txt.gz: invalid compressed data--format violated
invalid input
Is there a way that I can append gzipped information to the end of a file that works in a pipeline like this?
Related
I want to check some file on the remote website.
Here is bash command to generate commands that calculate the file md5
[root]# head -n 3 zrcpathAll | awk '{print $3}' | xargs -I {} echo wget -q -O - -i {}e \| md5sum\;
wget -q -O - -i https://example.com/zrc/3d2f0e76e04444f4ec456ef9f11289ec.zrce | md5sum;
wget -q -O - -i https://example.com/zrc/e1bd7171263adb95fb6f732864ceb556.zrce | md5sum;
wget -q -O - -i https://example.com/zrc/5300b80d194f677226c4dc6e17ba3b85.zrce | md5sum;
Then I pipe the outputed commands to bash, but only the first command was executed.
[root]# head -n 3 zrcpathAll | awk '{print $3}' | xargs -I {} echo wget -q -O - -i {}e \| md5sum\; | bash -v
wget -q -O - -i https://example.com/zrc/3d2f0e76e04444f4ec456ef9f11289ec.zrce | md5sum;
3d2f0e76e04444f4ec456ef9f11289ec -
[root]#
Would you please try the following instead:
while read -r _ _ url _; do
wget -q -O - "$url"e | md5sum
done < <(head -n 3 zrcpathAll)
we should not put -i in front of "$url" here.
[Explanation about -i option]
Manpage of wget says:
-i file
--input-file=file
Read URLs from a local or external file. [snip]
If this function is used, no URLs need be present on the command line. [snip]
If the file is an external one, the document will be automatically treated as html if the Content-Type matches text/html.
Furthermore, the file's location will be implicitly used as base
href if none was specified.
where the file will contain line(s) of url such as:
https://example.com/zrc/3d2f0e76e04444f4ec456ef9f11289ec.zrce
https://example.com/zrc/e1bd7171263adb95fb6f732864ceb556.zrce
https://example.com/zrc/5300b80d194f677226c4dc6e17ba3b85.zrce
Whereas if we use the option as -i url, wget first
downloads the url as a file which contains the lines of urls
as above. In our case, the url is the target to download itself,
not the list of urls, wget causes an error: No URLs found in url.
Even if the wget fails, why the command outputs just one line, not
three lines as the result of md5sum?
This seems to be because the head command immediately flushes the remaining
lines when the piped subprocess fails.
I am using grep to extract data from a log file. The log file is dynamically updating new rows. and I need to send the grepped data to a REST endpoint using curl. This can be done easily for a static file but cannot find a solution fo a running log file. How can I realize this situation?
eg: tail -f | grep "<string>" > ~/<fileName>.log
The above can put the data in a file. Need to send it using a POST curl.
Maybe using a function like
send_data(){
curl -s -k -X POST –header Content-Type: application/json’ \
–header ‘Accept: application/json’ \
“http://${HOST}${PORT}/v1/notify” \
-d $1
}
If tail -f | grep "<string>" > ~/<fileName>.log is working for you then you could do:
tail -f file | stdbuf -i0 -o0 -e0 grep "<string>" | xargs -n 1 -d $'\n' curl ...
or:
while IFS= read -r line; do
curl ... "$line"
done < <(tail -f file | stdbuf -i0 -o0 -e0 grep "<string>")
I have a md5sum file containing lots of lines. I want to use GNU parallel to accelerate the md5sum checking process. In the md5sum, when no file input, it will take the md5 string from stdin. I tried this:
cat checksums.md5 | parallel md5sum -c {}
But getting this error:
md5sum 445350b414a8031d9dd6b1e68a6f2367 testing.gz: No such file or directory
How can I parallel the md5sum checking?
Assuming checksums.md5 has the format:
d41d8cd98f00b204e9800998ecf8427e My file name
Run:
cat checksums.md5 | parallel --pipe -N1 md5sum -c
If your files are small: -N100
If that does not speed up your processing make sure your disks are fast enough: md5sum can process 500 MB/s. iostat -dkx 1 can tell you if your disks are a bottleneck.
You need option --pipe. In this mode parallel splits stdin into blocks and supplies each block to the command via stdin, see man parallel for details:
cat checksums.md5 | parallel --pipe md5sum -c -
By default size of the block is 1 MB, can be changed with --block option.
I'm trying to get 2 files using curl based on some pattern but that doesn't seem to work:
Files:
SystemOut_15.04.01_21.12.36.log
SystemOut_15.04.01_15.54.05.log
curl -f -k -u "login:password" https://myserver/cgi-bin/logviewer/index.cgi?getlogfile=SystemOut_15.04.01_21.12.36.log'&'server=qwerty123.com'&'numlines=100000000'&'appenv=MBL%20-%20PROD'&'directory=/app/WAS/was85/profiles/node/logs/mbl-server1
I know there is -A key but it doesn't work since my file is inside the link.
How can I extract those 2 files using a pattern?
Did that myself. One curl gets the list of logs on the webpage. Another downloads those files.
The code looks like:
for file in $(curl -f -k -u "user:pwd" https://selfservice.pwj.com/cgi-bin/logviewer/index.cgi?listdirectory=/app/smx_client_mob/data/log'&'appenv=MBL%20-%20PROD'&'server=xshembl04pap.she.pwj.com | grep href | sed 's/.*href="//' | sed 's/".*//' | sed 's/javascript:getLog//g' | sed "s/['();]//g" | grep -i 'service' | grep '^[a-zA-Z].*'); do
curl -o $file -f -k -u "user:pwd" https://selfservice.pwj.com/cgi-bin/logviewer/index.cgi?getlogfile="$file"'&'server=xshembl04pap.she.pwj.com'&'numlines=100000000'&'appenv=MBL%20-%20PROD'&'directory=/app/smx_client_mob/data/log; done
So I have the equivalent of a list of files being output by another command, and it looks something like this:
http://somewhere.com/foo1.xml.gz
http://somewhere.com/foo2.xml.gz
...
I need to run the XML in each file through xmlstarlet, so I'm doing ... | xargs gzip -d | xmlstarlet ..., except I want xmlstarlet to be called once for each line going into gzip, not on all of the xml documents appended to each other. Is it possible to compose 'gzip -d' 'xmlstarlet ...', so that xargs will supply one argument to each of their composite functions?
Why not read your file and process each line separately in the shell? i.e.
fileList=/path/to/my/xmlFileList.txt
cat ${fileList} \
| while read fName ; do
gzip -d ${fName} | xmlstartlet > ${fName}.new
done
I hope this helps.
Although the right answer is the one suggested by shelter (+1), here is a one-liner "divertimento" providing that the input is the proposed by Andrey (a command that generates the list of urls) :-)
~$ eval $(command | awk '{a=a "wget -O - "$0" | gzip -d | xmlstartlet > $(basename "$0" .gz ).new; " } END {print a}')
It just generates a multi command line that does wget http://foo.xml.gz | gzip -d | xmlstartlet > $(basenname foo.xml.gz .gz).new for each of the urls in the input; after the resulting command is evaluated
Use GNU Parallel:
cat filelist | parallel 'zcat {} | xmlstarlet >{.}.out'
or if you want to include the fetching of urls:
cat urls | parallel 'wget -O - {} | zcat | xmlstarlet >{.}.out'
It is easy to read and you get the added benefit of having on job per CPU run in parallel. Watch the intro video to learn more: http://www.youtube.com/watch?v=OpaiGYxkSuQ
If xmlstarlet can operate on stdin instead of having to pass it a filename, then:
some command | xargs -i -n1 sh -c 'zcat "{}" | xmlstarlet options ...'
The xargs option -i means you can use the "{}" placeholder to indicate where the filename should go. Use -n 1 to indicate xargs should only one line at a time from its input.