I have an issue where in, I am trying to add copyrights message in all our files in the project. Since it will affect many directories and files, our team has split the task.
so each on of us will be updating the files manually. Can I automate it.
I tried with:
find -exec sed -i "1i # x CONFIDENTIAL\n# _____________________\n#\n# 1997 - 2012 x Incorporated\n# All Rights Reserved.\n#\n# NOTICE: All information contained herein is, and remains\n# the property of x Incorporated and its suppliers,\n# if any. The intellectual and technical concepts contained\n# herein are proprietary to x Incorporated\n# and its suppliers and may be covered by U.S. and Foreign Patents,\n# patents in process, and are protected by trade secret or copyright law.\n# Dissemination of this information or reproduction of this material\n# is strictly forbidden unless prior written permission is obtained\n# from x Incorporated.\n" -- {} \;
It just stops, as soon as it encounters the . folder and any folder under the current directory.
Can we control the command to affect some of the files in the directory by specifying the complete/partial name of the file?
You can do so by executing the following commands for each file:
cp file temp
cat copy_right_notice temp > file
Note that > overwrites file (while >> appends to file, which is not what you want (referring to your comment))
Related
I am trying to copy files over from an old file structure where data are stored in folders with improper names to a new (better) structure, but as there are 671 participants I need to copy, I want to use regex in order to streamline it (each participant has files saved in the same format). However, I keep getting a cp: cannot stat error message saying that no file/directory exists. I had assumed this meant that I had missed a / or put "" in the wrong location but I cannot see anything in the code that would suggest it.
My code is as follows (which I add a lot of comments so other collaborators can understand):
#!/bin/bash
# This code below copies the initial .nii file.
# These data are copied into my Trial Participant folders.
# Create a variable called parent_folder1 that describes initial mask directory e.g. folders for each participant which contains the files.
parent_folder1="/this/path/here/contains/Trial_Participants"
# The original folders are named according to ClinicalID_scandate_randomdigits e.g. folder 1234567890_20000101_987654.
# The destination folders are named according to TrialIDNumber e.g. LBC100001.
# The .nii files are saved under TrialIDNumber_1_ICV.nii.gz e.g. LBC1000001_1_ICV.nii.gz.
# These files need copied over from their directories into the Trial Participant folders, using the for loop function.
# The * symbol is used as a wildcard.
for i in $(ls -1d "${parent_folder1}"/*_20*); do
lbc=$(ls ${i}/finalMasks/*ICV* | sed 's/^.*\///'); lbc=${lbc:0:9}
cp "${parent_folder1}/${i}"/finalMasks/*_1_ICV.nii.gz /this/path/is/the/destination/path/${lbc}/
done
# This code uses regular expression to find the initial ICV file.
# ls asks for a list, -1 makes each new folder on a new line, d is for directory.
# *_20* refers to the name of the folders. The * covers the ClinicalID, _20* refers to the scan date and random digits.
# I have no idea what the | sed 's/^.*\///' does, but I think it strips the path.
# lbc=${lbc:0:9} is used to keep the ID numbers.
# cp copies the files that are named under TrialIDNumber(replaced by *)_1_ICV.nii.gz to the destination under the respective folder.
So after a bit of fooling around, I changed the code a lot (took out sed as it confuses me), and came up with this that worked. Thanks to those who commented!
# Create a variable called parent_folder1 that describes initial mask directory.
parent_folder1="/original/path/here"
# Iterate over directories in parent_folder1
for i in $(ls -1d "${parent_folder1}"/*_20*); do
# Extract the base name of the file in the finalMasks directory
lbc=$(basename $(ls "${i}"/finalMasks/*ICV*))
# Extract the LBC number from the file name
lbc=${lbc:0:9}
# Copy the file to the specific folder
cp "${i}"/finalMasks/${lbc}_1_ICV.nii.gz /destination/path/here/${lbc}/
done
I got a task to copy files with certain extensions from clear case while I need to :
find all files with certain extension and their map
copy the mapping but replace the file with a dir that has it's name
copy the file labels history to that dir
So I know what do to separately but can't figure how to connect things:
Code I used :
# for the latest label :
find . -name '*.extension' | cpio -pdm /path/to/save # this helped me to copy all files and their dir map
# to copy all labels for that file
\cp -r filename.extension##/main/ /path/to/save # the ##main/ gives me the view of the labels
and their map
The "map file" is more seen on Windows with a type manager
The map file, located in the ccase-home-dir\lib\mgrs directory, associates type manager methods with the programs that carry them out.
A map file entry has three fields: type manager, method, and program.
On Linux:
On UNIX, and Linux a type manager is a collection of programs in a subdirectory of ccase-home-dir /lib/mgrs; the subdirectory name is the name by which the type manager is specified with the –manager option in a mkeltype command.
Each program in a type manager subdirectory implements one method (data-manipulation operation).
A method can be a compiled program, a shell script, or a link to an executable.
This differs from your "dir map".
You can list labels on the current version with: cleartool descr -fmt "%l" myFile.
Using extended paths can work in a dynamic view, but it is best (to get all labels on all branches) to do a:
cleartool find . -version "!lbtype(x)" -name "yourelement" -exec "cleartool descr -fmt \"%n labels:%l\n\" \"%CLEARCASE_XPN%\""
To combine both code, do a loop on the result of the first find command.
# Make sure globstar is enabled
shopt -s globstar
for i in **/*.extension; do # Whitespace-safe and recursive
cpio -pdm "${i}" /path/to/save
cp -r "${i}"##/main/ /path/to/save
done
Upon looping a directory to delete txt files ONLY - a message is returned indicating The System cannot find the file specified: 'File.txt'.
I've made sure the txt files that I'm attempting to delete exist in the directory I'm looping. I've also checked my code and to make sure it can see my files by printing them in a list with the print command.
import os
fileLoc = 'c:\\temp\\files'
for files in os.listdir(fileLoc):
if files.endswith('.txt'):
os.unlink(files)
Upon initial execution, I expected to see all txt files deleted except for other non-txt files. The actual result was an error message "FileNotFoundError: [WinError 2] The system cannot find the file specified: 'File.txt'.
Not sure what I'm doing wrong, any help would be appreciated.
It isn't found because the the path you intended to unlink is relative to fileLoc. In fact with your code, the effect is to unlink the file relative to the current working directory. If there were *.txt files
in the cwd then the code would have unfortunate side-effects.
Another way to look at it:
Essentially, by analogy, in the shell what you're trying to do is equivalent to this:
# first the setup
$ mkdir foo
$ touch foo/a.txt
# now your code is equvalent to:
$ rm *.txt
# won't work as intended because it removes the *.txt files in the
# current directory. In fact the bug is also that your code would unlink
# any *.txt files in the current working directory unintentionally.
# what you intended was:
$ rm foo/*.txt
The missing piece was the path to the file in question.
I'll add some editorial: The Old Bard taught us to "when in doubt, print variables". In other words, debug it. I don't see from the OP an attempt to do that. Just a thing to keep in mind.
Anyway the new code:
Revised:
import os
fileLoc = 'c:\\temp\\files'
for file in os.listdir(fileLoc):
if file.endswith('.txt'):
os.unlink(os.path.join(fileLoc,file))
The fix: os.path.join() builds a path for you from parts. One part is the directory (path) where the file exists, aka: fileLoc. The other part is the filename, aka file.
os.path.join() makes a whole valid path from them using whatever OS directory separator is appropriate for your platform.
Also, might want to glance through:
https://docs.python.org/2/library/os.path.html
I am trying to zip a file using shell script command. I am using following command:
zip ./test/step1.zip $FILES
where $FILES contain all the input files. But I am getting a warning as follows
zip warning: name not matched: myfile.dat
and one more thing I observed that the file which is at last in the list of files in a folder has the above warning and that file is not getting zipped.
Can anyone explain me why this is happening? I am new to shell script world.
zip warning: name not matched: myfile.dat
This means the file myfile.dat does not exist.
You will get the same error if the file is a symlink pointing to a non-existent file.
As you say, whatever is the last file at the of $FILES, it will not be added to the zip along with the warning. So I think something's wrong with the way you create $FILES. Chances are there is a newline, carriage return, space, tab, or other invisible character at the end of the last filename, resulting in something that doesn't exist. Try this for example:
for f in $FILES; do echo :$f:; done
I bet the last line will be incorrect, for example:
:myfile.dat :
...or something like that instead of :myfile.dat: with no characters before the last :
UPDATE
If you say the script started working after running dos2unix on it, that confirms what everybody suspected already, that somehow there was a carriage-return at the end of your $FILES list.
od -c shows the \r carriage-return. Try echo $FILES | od -c
Another possible cause that can generate a zip warning: name not matched: error is having any of zip's environment variables set incorrectly.
From the man page:
ENVIRONMENT
The following environment variables are read and used by zip as described.
ZIPOPT
contains default options that will be used when running zip. The contents of this environment variable will get added to the command line just after the zip command.
ZIP
[Not on RISC OS and VMS] see ZIPOPT
Zip$Options
[RISC OS] see ZIPOPT
Zip$Exts
[RISC OS] contains extensions separated by a : that will cause native filenames with one of the specified extensions to be added to the zip file with basename and extension swapped.
ZIP_OPTS
[VMS] see ZIPOPT
In my case, I was using zip in a script and had the binary location in an environment variable ZIP so that we could change to a different zip binary easily without making tonnes of changes in the script.
Example:
ZIP=/usr/bin/zip
...
${ZIP} -r folder.zip folder
This is then processed as:
/usr/bin/zip /usr/bin/zip -r folder.zip folder
And generates the errors:
zip warning: name not matched: folder.zip
zip I/O error: Operation not permitted
zip error: Could not create output file (/usr/bin/zip.zip)
The first because it's now trying to add folder.zip to the archive instead of using it as the archive. The second and third because it's trying to use the file /usr/bin/zip.zip as the archive which is (fortunately) not writable by a normal user.
Note: This is a really old question, but I didn't find this answer anywhere, so I'm posting it to help future searchers (my future self included).
eebbesen hit the nail in his comment for my case (but i cannot vote for comment).
Another possible reason missed in the other comments is file exceeding the file size limit (4GB).
I converted my script for unix environment using dos2unix command and executed my script as ./myscript.sh instead bash myscript.sh.
I just discovered another potential cause for this. If the permissions of the directory/subdirectory don't allow the zip to find the file, it will report this error. Actually, if you run a chmod -R 444 on the directory, and then try to zip it, you will reproduce this error, and also have a "stored 0%" report, like this:
zip warning: name not matched: borrar/enviar
adding: borrar/ (stored 0%)
Hence, try changing the permissions of the file. If you are trying to send them through email, and those email filters (like Gmail's) invent silly filters of not sending executables, don't forget that making permissions very strict when making zip compression can be the cause of the error you are reporting, of "name not matched".
spaces are not allowed:
it would fail if there are more than one files(s) in $FILES unless you put them in loop
I also encountered this issue. In my case, the line separate is CRLF in my zip shell script which causes the problem. Using LF fixed it.
I working with linux, bash.
I have one directory with 100 folders in it, each one named different.
In each of these 100 folders, there is a file called first.bars (so I have 100 files named first.bars). Although all named first.bars, the files are actually slightly different.
I want to get all these files moved to one new folder and rename/number these files so that I know which file comes from which folder. So the first first.bars file must be renamed to 001.bars, the second to 002.bars.. etc.
I have tried the following:
ls -d * >> /home/directorywiththe100folders/list.txt
cat list.txt | while read line;
do cd $line;
mv first.bars /home/newfolder
This does not work because I can't have 100 files, named the same, in one folder. So I only need to know how to rename them. The renaming must be connected to the cat list.txt, because the first line is the folder containing the first file wich is moved and renamed. That file will be called 001.bars.
Try doing this :
$ rename 's/^.*?\./sprintf("%03d.", $c++)/e' *.bar
If you want more information about this command, see this recent response I gave earlier : How do I rename multiple files beginning with a Unix timestamp - imapsync issue
If the rename command is not available,
for d in /home/directorywiththe100folders/*/; do
newfile=$(printf "/home/newfolder/%d.bars" $(( c++ )) )
mv "$d/first.bars" "$newfile"
done