I am trying to upload all changed files to my FTP server. However, I cannot use -S .tmp and -v when I use the -bb flag - and I can't use those options with ncftpbatch at all. Here is my code:
#!/bin/bash -eo pipefail
IN=$(git diff-tree --no-commit-id --name-only -r HEAD)
OUT=$(echo $IN | tr ";" "\n")
for file in "${OUT[#]}"; do
ncftpput -bb -S .tmp -v -u "zeussite#kolechia.heliohost.org" -p "*****" ftp.kolechia.heliohost.org "/" $file
done
ncftpbatch
As you can see, I need the -S .tmp to avoid breaking the site during uploads. -v provides output to prevent my CI service from timing out.
How can I upload only the changed files - without temporarily breaking the site? I'm thinking of just logging in separately for each file, but that is bad practice.
Why not launch a function in background which just prints dummy values like uploading, please wait and then sleeps for few seconds and do it again. Outside the loop you can kill that background job
If you don't want any output
printf "\0"
or
printf "a\b"
Related
My problem is that I have a cluster-server with Torque PBS and want to use it to run a sequence-comparison with the program rapsearch.
The normal RapSearch command is:
./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32
Now I want to run it with 2 nodes on the cluster-server.
I've tried with: echo "./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32" | qsub -l nodes=2 but nothing happened.
Do you have any suggestions? Where I'm wrong? Help please.
Standard output (and error output) files are placed in your home directory by default; take a look. You are looking for a file named STDIN.e[numbers], it will contain the error message.
However, I see that you're using ./rapsearch but are not really being explicit about what directory you're in. Your problem is therefore probably a matter of changing directory into the directory that you submitted from. When your terminal is in the directory of the rapsearch executable, try echo "cd \$PBS_O_WORKDIR && ./rapsearch [arguments]" | qsub [arguments] to submit your job to the cluster.
Other tips:
You could add rapsearch to your path if you use it often. Then you can use it like a regular command anywhere. It's a matter of adding the line export PATH=/full/path/to/rapsearch/bin:$PATH to your .bashrc file.
Create a submission script for use with qsub. Here is a good example.
Looking for the origin of this error message:
Processing: +([^_]).flv
date: +([^_]).flv: No such file or directory
I started getting this at some point in the last few months (can't say when as I wasn't logging my cron output. I know, I know!).
When I originally wrote this, it worked ok for at least two months. I'm wondering if there was an sh update that broke it?
The script runs via crontab and gets all .flv files in the current directory without an underscore and processes each one. It then checks the modified date for files that have been created in the last 24 hours and runs the yamdi meta tag injector for .flv files.
It seems like it's not recognizing the pattern as a pattern and looking for it as an actual file to me. If I run this script from an ssh shell it works ok, it's only when running via cron that it gives this error.
shopt -s extglob
now=$(date +"%s")
for f in +([^_]).flv; do
echo "Processing: $f"
age=$(date -r "$f" +"%s")
calc=$(((now-age) / 60 / 60))
if(( calc < 24 )); then
echo "$f age=$calc"
yamdi -i "$f" -o "$f".seek
rm "$f"
cp "$f".seek "$f"
touch -d #$age "$f"
fi
done
This is most likely a problem of the wrong shell being used; make sure your script's first line represents the right shell:
#!/bin/bash
for bash, or whatever shell you wrote this for. You might want to check your environment variables that cron may set (that's a very common problem -- one assumes everything is set up correctly, but the environment that cron offers to scripts it executes is different).
I'd like to compare a few files from the bazaar branch lp:ubuntu/nvidia-graphics-drivers. I'm mainly interested in the debian subdirectory inside that branch, but due to the binary blob in http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files, it takes ages to get just the text files. I've already downloaded 555MB and it's still counting.
Is it possible to retrieve a bazaar branch, including or excluding certain files by one of the following properties:
file size
file extension
file name (include only debian/ for example)
I do not need to push back any changes, nor do I need to view the history of a file. I just want to compare two files in the debian/ directory, files with the .in extension and files without.
As far as I'm aware, no. You're downloading the branch history, not just the individual files. And each file is an integral part of the branch's history.
On the bright side, you only have to check it out once. Unless those binary files change, they'll be skipped the next time you pull from Launchpad.
Depending on the branch's history, you may be able to cut down on the download size if you use a lightweight checkout (bzr checkout --lightweight). But of course, that may come back and bite you later, as it means you won't get a local copy of the branch, only the checked-out files. So it'll work much like SVN, where every operation has to go through the server. And as long as you don't need to look at the branch history, or commit your changes, that should serve you just fine, I believe.
I ended up doing some dirty grep-ing on the HTTP response since bzr info "$branch" and bzr ls -d "$branch" "$directory" did not provide enough information to me.
The below Bash script relies on the working of Launchpads front-end Loggerhead. It recursively downloads from a given URL. Currently, it ignores *.run files. Save it as bzrdl in a directory available from $PATH and run it with bzrdl http://launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files/head:/debian/. All files will be saved in the current directory, be sure that it's empty to avoid conflicts.
#!/bin/bash
max_retries=5
rooturl="$1"
if ! [[ $rooturl =~ /$ ]]; then
echo "Usage: ${0##*/} URL"
echo "URL must end with a slash. Example URL:"
echo "http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-graphics-drivers/oneiric/files/head:/"
exit 1
fi
tmpdir="$(mktemp -d)"
target="$(pwd)"
# used for holding HTTP response before extracting data
tmp="$(mktemp)"
# url_filter reads download URLs from stdin (piped)
url_filter() {
grep -v '\.run$'
}
get_files_from_dir() {
local slash=/
local dir="$1"
# to avoid name collision: a/b/c/ -> a.d/b.d/c.d/
local storedir="${dir//$slash/.d${slash}}"
mkdir -p "$tmpdir/$storedir" "$target/$dir"
local i subdir
for ((i=0; i<$max_retries; i++ )); do
if wget -O "$tmp" "$rooturl$dir"; then
# store file list
grep -F -B 1 '<img src="/static/images/ico_file_download.gif" alt="Download File" />' "$tmp" |\
grep '^<a' | cut -d '"' -f 2 | url_filter \
> "$tmpdir/$storedir/files"
IFS=$'\n'
for subdir in $(grep -F -B 1 '<img src="/static/images/ico_folder.gif" ' "$tmp" | \
grep -F '<a ' | rev | cut -d / -f 2 | rev); do
IFS=$' \t\n'
get_files_from_dir "$dir$subdir/"
done
return
fi
done
echo "Failed to download directory listing of: $dir" >> "$tmpdir/errors"
}
download_files() {
local slash=/
local dir="$1"
# to avoid name collision: a/b/c/ -> a.d/b.d/c.d/
local storedir="${dir//$slash/.d${slash}}"
local done=false
local subdir
cd "$tmpdir/$storedir"
for ((i=0; i<$max_retries; i++)); do
if wget -B "$rooturl$dir" -nc -i files -P "$target/$dir"; then
done=true
break
fi
done
$done || echo "Failed to download all files from $dir" >> "$tmpdir/errors"
for subdir in *.d; do
download_files "$dir${subdir%%.d}/"
done
}
get_files_from_dir ''
# make *.d expand to nothing if no directories are found
shopt -s nullglob
download_files ''
echo "TMP dir: $tmpdir"
echo "Errors : $(wc -l "$tmpdir/errors" 2>/dev/null | cut -d ' ' -f 2 || echo 0)"
The temporary directory and file is not removed afterwards, that must be done manually. Any errors (failures to download) will be written to $tmpdir/errors
It's confirmed to work with:
bzrdl http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-settings/oneiric/files/head:/debian/
Feel free to correct any mistakes or add improvements.
There is no way to selectively check out a specific directory from a Bazaar branch at the moment, although we do have plans to add such support in the future.
There is definitely too much traffic for the clone you are doing, considering the size of the branch. It's probably a bug in the client implementation.
Here on bzr 2.4 it is still quite slow but not too bad (60s):
localhost:/tmp% bzr branch http://bazaar.launchpad.net/~ubuntu-branches/ubuntu/oneiric/nvidia-settings/oneiric
Most recent Ubuntu Oneiric version: 275.09.07-0ubuntu1
Packaging branch status: CURRENT
Branched 37 revision(s).
From the log:
[11866] 2011-07-31 00:56:57.007 INFO: Branched 37 revision(s).
56.786 Transferred: 5335kB (95.8kB/s r:5314kB w:21kB)
I've got:
$ rsync -azv zope#myserver:/smb/Data/*/*/* ~/rsynced_samples/
And I want it to run forever, syncing any new file as soon as it appears on myserver:
(specifying a poll interval, such as 4 seconds would be an ok comprise)
Instead of rsync you can use inotifywait which use kernel specific file changes triggers.
This script (inotify.sh) can you give an idea:
#!/bin/bash
directory=$1
inotifywait -q -m --format '%f' -e modify -e move -e create -e delete ${directory} | while read line
do
echo "doing something with: $line";
# for example:
# cp $line to <somewhere>
You can invoke this script specifying the "monitor" directory, in this way
./inotify.sh ~/Desktop/
The $line variable contains the full file path.
If you want to limit to only newly created files you can use on the flag "-e create"
Use cron to set up a check based on your time interval (say, every minute, perhaps?) . This link should help: http://www.cyberciti.biz/faq/how-do-i-add-jobs-to-cron-under-linux-or-unix-oses/
Note that a cron tab is set up on your machine side, not in your bash script
also useful: http://benr75.com/pages/using_crontab_mac_os_x_unix_linux
and here is a code example:
1) crontab -e // this opens up your current crontab or creates one if it does not exist
2) enter: * * * * * file.sh >> log.txt // this would pipe the output of your file to a log file and run it every minute.
hope that helps
I want to download a lot of urls in a script but I do not want to save the ones that lead to HTTP errors.
As far as I can tell from the man pages, neither curl or wget provide such functionality.
Does anyone know about another downloader who does?
I think the -f option to curl does what you want:
-f, --fail
(HTTP) Fail silently (no output at all) on server errors. This is mostly done to better
enable scripts etc to better deal with failed attempts. In normal cases when an HTTP
server fails to deliver a document, it returns an HTML document stating so (which often
also describes why and more). This flag will prevent curl from outputting that and
return error 22. [...]
However, if the response was actually a 301 or 302 redirect, that still gets saved, even if its destination would result in an error:
$ curl -fO http://google.com/aoeu
$ cat aoeu
<HTML><HEAD><meta http-equiv="content-type" content="text/html;charset=utf-8">
<TITLE>301 Moved</TITLE></HEAD><BODY>
<H1>301 Moved</H1>
The document has moved
here.
</BODY></HTML>
To follow the redirect to its dead end, also give the -L option:
-L, --location
(HTTP/HTTPS) If the server reports that the requested page has moved to a different
location (indicated with a Location: header and a 3XX response code), this option will
make curl redo the request on the new place. [...]
One liner I just setup for this very purpose:
(works only with a single file, might be useful for others)
A=$$; ( wget -q "http://foo.com/pipo.txt" -O $A.d && mv $A.d pipo.txt ) || (rm $A.d; echo "Removing temp file")
This will attempt to download the file from the remote Host. If there is an Error, the file is not kept. In all other cases, it's kept and renamed.
Ancient thread.. landed here looking for a solution... ended up writing some shell code to do it.
if [ `curl -s -w "%{http_code}" --compress -o /tmp/something \
http://example.com/my/url/` = "200" ]; then
echo "yay"; cp /tmp/something /path/to/destination/filename
fi
This will download output to a tmp file, and create/overwrite output file only if status was a 200. My usecase is slightly different.. in my case the output takes > 10 seconds to generate... and I did not want the destination file to remain blank for that duration.
NOTE: I am aware that this is an older question, but I believe I have found a better solution for those using wget than any of the above answers provide.
wget -q $URL 2>/dev/null
Will save the target file to the local directory if and only if the HTTP status code is within the 200 range (Ok).
Additionally, if you wanted to do something like print out an error whenever the request was met with an error, you could check the wget exit code for non-zero values like so:
wget -q $URL 2>/dev/null
if [ $? != 0]; then
echo "There was an error!"
fi
I hope this is helpful to someone out there facing the same issues I was.
Update:
I just put this into a more script-able form for my own project, and thought I'd share:
function dl {
pushd . > /dev/null
cd $(dirname $1)
wget -q $BASE_URL/$1 2> /dev/null
if [ $? != 0 ]; then
echo ">> ERROR could not download file \"$1\"" 1>&2
exit 1
fi
popd > /dev/null
}
I have a workaround to propose, it does download the file but it also removes it if its size is 0 (which happens if a 404 occurs).
wget -O <filename> <url/to/file>
if [[ (du <filename> | cut -f 1) == 0 ]]; then
rm <filename>;
fi;
It works for zsh but you can adapt it for other shells.
But it only saves it in first place if you provide the -O option
As alternative you can create a temporal rotational file:
wget http://example.net/myfile.json -O myfile.json.tmp -t 3 -q && mv list.json.tmp list.json
The previous command will always download the file "myfile.json.tmp" however only when the wget exit status is equal to 0 the file is rotated as "myfile.json".
This solution will prevent to overwrite the final file when a network failure occurs.
The advantage of this method is that in case that something is wrong you can inspect the temporal file and see what error message is returned.
The "-t" parameter attempt to download the file several times in case of error.
The "-q" is the quiet mode and it's important to use with cron because cron will report any output of wget.
The "-O" is the output file path and name.
Remember that for Cron schedules it's very important to provide always the full path for all the files and in this case for the "wget" program it self as well.
You can download the file without saving using "-O -" option as
wget -O - http://jagor.srce.hr/
You can get mor information at http://www.gnu.org/software/wget/manual/wget.html#Advanced-Usage