Using diff for two files and send by email [closed] - linux

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I have files like below. I use crontab every 5 min to check the files to see if the system's added one file, for example like this: AIR_2015xxxxT0yyyyyyyy.cfg. Then I need to use the diff command automatically between the last one and before the last one.
AIR_20151021T163514000.cfg
AIR_20151026T103845000.cfg
AIR_2015xxxxT0yyyyyyyy.cfg
I want to do this in a script like the one below:
#!/bin/bash
/var/opt/fds/
diff AIR_2015xxxxT0yyyyyyyy.cfg AIR_20151026T103845000.cfg > Test.txt
body(){
cat body.txt
}
(echo -e "$(body)") | -a Test.txt mailx -s 'Comparison' user#email.com

Given a list of files in the directory /var/opt/fds with names in the format:
AIR_YYYYmmddTHHMMSSfff.cfg
where the letter Y represents digits for the year, m for month, d for day, H for hour, M for minute, S for second, and f for fraction (milliseconds), then you need to establish the two most recent files in the directory to compare them.
One way to do this is:
cd /var/opt/fds || exit 1
old=
new=
for file in AIR_20[0-9][0-9]????T?????????.cfg
do
old=$new
new=$file
done
if [ -n "$old" ] && [ -n "$new" ]
then
diff "$old" "$new" > test.txt
mailx -a test.txt -s 'Comparison' user#example.com < body.txt
fi
Note that if the new file has a name containing letters x and y as shown in the question and comments, it will be listed after the names containing the time stamp as digits, so it will be picked up as the new file. It also assumes permission to write in the /var/opt/fds directory, and that the mail body file is present in that directory too. Those assumptions can be trivially fixed if necessary. The test.txt file should be deleted after it is sent, too, and you could check that it is non-empty before sending the email (just in case the two most recent files are in fact identical). You could embed a time-stamp in the generated file name containing the diffs instead of using test.txt:
output="diff.$(date +'%Y%m%dT%H%M%S000').txt"
and then use $output in place of test.txt.
The test ensures that there was both an old and a new name. The pattern match is sloppier than it could be, but using [0-9] or an appropriate subrange ([01], [0-3], [0-2], [0-5]) for the question marks makes the pattern unreadably long:
for file in AIR_20[0-9][0-9][01][0-9][0-3][0-9]T[0-2][0-9][0-5][0-9][0-5][0-9][0-9][0-9][0-9].cfg
It also probably provides very little extra in the way of protection. Of course, as shown, it imposes a Y2.1K crisis on the system, not that it is hard to fix that. You could also cut down the range of valid dates by basing it on today's date, but beware of the end of the year, etc. You might decide you only need entries from the last month or so.
Using globbing is generally better than trying to parse ls or find output. In this context, where the file names have a restricted set of characters in the name (no newlines, no blanks or tabs, no quotes, no dollar signs, etc), it is feasible to use either find or ls — but if you have to deal with arbitrary names created by random end users, those tools are not suitable. (The ls command does all sorts of weird stuff with weird names and basically is hard to use reliably in the face of user cussedness. The find command and its -print0 option can be used, especially if you have a sort that recognizes -z to work with null-terminated 'lines' and an xargs that supports -0 to handle such lines too — but you have to very careful.)
Note that this scheme does not keep a record of the last file analyzed (so if no new files appear for an hour, you might send a dozen copies of the same differences), nor does it directly report on the file names (but using diff -u or diff -c would include the file names being diffed in the output). Again, these issues can be worked around if that's appropriate (and it probably is). Keeping the record of which files have been compared is probably the hardest job; even that's not too bad:
echo "$old" "$new" >> reported.diffs
to record what's been processed; then
if grep -q "$old $new" reported.diffs
then : Already processed
else : Process $old and $new
fi

Related

How to pass multiple variables in grep

I have a json file that is download using curl. It has some information of a confluence page. I want to extract only 3 parts that downloaded information - that is page: id, status and title.
I have written a bash script for this and my constraint is that I am not sure how to pass multiple variables in grep command
id=id #hardcoded
status=status #hardcoded
echo Enter title you are looking for: #taking input from user here read title_name echo echo echo Here are details
curl -u username:password -sX GET "http://X.X.X.X:8090/rest/api/content?type=page&start=0&limit=200" | python -mjson.tool | grep -Eai "$title_name"|$id|$status"
Aside from a typo (you have an unbalanced quote - please always check the syntax for correctness before you are posting something), the basic idea of your approach would work in that
grep -Eai "$title_name|$id|$status"
would select those text lines which contain those lines which contain the content of one of the variables title_name, id or status.
However, it is a pretty fragile solution. I don't know what can be the actual content of those variables, but for instance, if title_name were set to X.Z, it would also match lines containing the string XYZ, since the dot matches any character. Similarily, if title_name would contain, say, a lone [ or (, grep would complained about an unmatched parentheses error.
If you want to match the string literally and not be taken as regular expressions, it is better to write those pattern into a file (one pattern per line) and use
grep -F -f patternfile
for searching. Of course, since you are using bash, you can also use process substitution if you prefer not using an explicit temporary file.

How to rename files in bash to increase number in name?

I have a few thousand files named as follows:
Cyprinus_carpio_600_nanopore_trim_reads.fasta
Cyprinus_carpio_700_nanopore_trim_reads.fasta
Cyprinus_carpio_800_nanopore_trim_reads.fasta
Cyprinus_carpio_900_nanopore_trim_reads.fasta
Vibrio_cholerae_3900_nanopore_trim_reads.fasta
for 80 variations of the first two words (80 different species), i would like to rename all of these files such that the number is increased by 100 - for example:
Vibrio_cholerae_3900_nanopore_trim_reads.fasta
would become
Vibrio_cholerae_4000_nanopore_trim_reads.fasta
or
Cyprinus_carpio_300_nanopore_trim_reads.fasta
would become
Cyprinus_carpio_400_nanopore_trim_reads.fasta
Unfortunately I can't work out how to get to rename them, i've had some luck with following the solutions on https://unix.stackexchange.com/questions/40523/rename-files-by-incrementing-a-number-within-the-filename
But i can't get it to work for the inside of the name, i'm running on Ubuntu 18.04 if that helps
If you can get hold of the Perl-flavoured version of rename, that is simple like this:
rename -n 's/(\d+)/$1 + 100/e' *fasta
Sample Output
'Ciprianus_maximus_11_fred.fasta' would be renamed to 'Ciprianus_maximus_111_fred.fasta'
'Ciprianus_maximus_300_fred.fasta' would be renamed to 'Ciprianus_maximus_400_fred.fasta'
'Ciprianus_maximus_3900_fred.fasta' would be renamed to 'Ciprianus_maximus_4000_fred.fasta'
If you can't read Perl, that says... "Do a single substitution as follows. Wherever you see a bunch of digits next to each other in a row (\d+), remember them (because I put that in parentheses), and then replace them with the evaluated expression of that bunch of digits ($1) plus 100.".
Remove the -n if the dry-run looks correct. The only "tricky part" is the use of e at the end of the substitution which means evaluate the expression in the substitution - or I call it a "calculated replacement".
If there is only one number in your string then below two line of code should provide help you resolve your issue
filename="Vibrio_cholerae_3900_nanopore_trim_reads.fasta"
var=$(echo $filename | grep -oP '\d+')
echo ${filename/${var}/$((var+100))}
Instead of echoing the changed file name, you can take it into a variable and use mv command to rename it
Considering the filename conflicts in the increasing order, I first thought of reversing the order but there still remains the possibility of conflicts in the alphabetical (standard) sort due to the difference to the numerical sort.
Then how about a two-step solution: in the 1st step, an escape character (or whatever character which does not appear in the filename) is inserted in the filename and it is removed in the 2nd step.
#!/bin/bash
esc=$'\033' # ESC character
# 1st pass: increase the number by 100 and insert a ESC before it
for f in *.fasta; do
num=${f//[^0-9]/}
num2=$((num + 100))
f2=${f/$num/$esc$num2}
mv "$f" "$f2"
done
# 2nd pass: remove the ESC from the filename
for f in *.fasta; do
f2=${f/$esc/}
mv "$f" "$f2"
done
Mark's perl-rename solution looks great but you should apply it twice with a bump of 50 to avoid name conflict. If you can't find this flavor of rename you could try my rene.py (https://rene-file-renamer.sourceforge.io) for which the command would be (also applied twice) rene *_*_*_* *_*_?_* B/50. rene would be a little easier because it automatically shows you the changes and asks whether you want to make them and it has an undo if you change your mind.

Find and Replace Incrementally Across Multiple Files - Bash

I apologize in advance if this belongs in SuperUser, I always have a hard time discerning whether these scripting in bash questions are better placed here or there. Currently I know how to find and replace strings in multiple files, and how to find and replace strings within a single file incrementally from searching for a solution to this issue, but how to combine them eludes me.
Here's the explanation:
I have a few hundred files, each in sets of two: a data file (.data), and a message file (data.ms).
These files are linked via a key value unique to each set of two that looks like: ab.cdefghi
Here's what I want to do:
Step through each .data file and do the following:
Find:
MessageKey ab.cdefghi
Replace:
MessageKey xx.aaa0001
MessageKey xx.aaa0002
...
MessageKey xx.aaa0010
etc.
Incrementing by 1 every time I get to a new file.
Clarifications:
For reference, there is only one instance of "MessageKey" in every file.
The paired files have the same name, only their extensions differ, so I could simply step through all .data files and then all .data.ms files and use whatever incremental solution on both and they'd match fine, don't need anything too fancy to edit two files in tandem or anything.
For all intents and purposes whatever currently appears on the line after each MessageKey is garbage and I am completely throwing it out and replacing it with xx.aaa####
String length does matter, so I need xx.aa0009, xx.aaa0010 not xx.aa0009, xx.aa00010
I'm using cygwin.
I would approach this by creating a mapping from old key to new and dumping that into a temp file.
grep MessageKey *.data \
| sort -u \
| awk '{ printf("%s:xx.aaa%04d\n", $1, ++i); }' \
> /tmp/key_mapping
From there I would confirm that the file looks right before I applied the mapping using sed to the files.
cat /tmp/key_mapping \
| while read old new; do
sed -i -e "s:MessageKey $old:MessageKey $new:" * \
done
This will probably work for you, but it's neither elegant or efficient. This is how I would do it if I were only going to run it once. If I were going to run this regularly and efficiency mattered, I would probably write a quick python script.
#Carl.Anderson got me started on the right track and after a little tweaking, I ended up implementing his solution but with some syntax tweaks.
First of all, this solution only works if all of your files are located in the same directory. I'm sure anyone with even slightly more experience with UNIX than me could modify this to work recursively, but here goes:
First I ran:
-hr "MessageKey" . | sort -u | awk '{ printf("%s:xx.aaa%04d\n", $2, ++i); }' > MessageKey
This command was used to create a find and replace map file called "MessageKey."
The contents of which looked like:
In.Rtilyd1:aa.xxx0087
In.Rzueei1:aa.xxx0088
In.Sfricf1:aa.xxx0089
In.Slooac1:aa.xxx0090
etc...
Then I ran:
MessageKey | while IFS=: read old new; do sed -i -e "s/MessageKey $old/MessageKey $new/" *Data ; done
I had to use IFS=: (or I could have alternatively find and replaced all : in the map file with a space, but the former seemed easier.
Anyway, in the end this worked! Thanks Carl for pointing me in the right direction.

Using sed to delete lines present in similar file

I have a file listing from an original and a duplicate drive consisting of 985257 lines and 984997 lines respectfully.
As the number of lines do not match I am certain that some of the files have not duplicated.
In order to establish which files are not present I wish to use sed to filter the original file listing by deleting any lines present in the duplicate listing from the source listing.
I had thought about using a match formula in excel but due to the number of lines the program crashes. I thought using this approach in sed would be a viable option.
I have had no success with my approach so far however.
echo "Start"
# Cat the passed argument which is the duplicate file listing
for line in $(cat $1)
do
#sed the $line variable over the larger file and remove
#sed "${line}/d" LiveList.csv
#sed -i "${line}/d" LiveList.csv
#sed -i '${line}' 'd' LiveList.csv
sed -i "s/'${line}'//" /home/listings/LiveList.csv
done
There is a temporary file which is created and fills to the 103.4mb of the listing file however the listing file itself is not altered at all.
My other concern is that as the listing has been created in windows the '\' character may be escaping the string leading to no matches and therefore no alteration.
Example path:
Path,Length,Extension
Jimmy\tail\images\Jimmy\0001\0014\Text\A0\20\A056TH01-01.html,71982,.html
Please help.
This might work for you:
sort orginal_list.txt duplicate_list.txt | uniq -u
First thing that comes to my mind is just using rsync to take care of copying the missing files as fast as possible. It really works wonders.
If not, you can first sort both files to identify where they differ. You can use some paste trickery to put side by side differences, or even use the diff side-by-side output. When files are ordered, I think diff finds it easily to identify what lines have been added.

Comparison script help

I'm trying to write a Bash script that will go through a set of directories for a cache and make some comparisons on the contents. (I want to find the two that have the smallest differences for purposes of a project I'm working on).
The structure is that there is a root directory; two subdirectories after that; under that up to 52 directories (a AA b BB etc); and under each of those a variable number of directories where the contents actually are. Basically:
root >> a/b >> a/AA/b/BB/.../z/ZZ >> <some hex-named directory>
So I need to get to that last level, then run diff on the file in that directory (the contents are always named identically) and all the other cached files and figure out what the most similar files are.
The two directories at the top never change name, so that's easy. The directories under those follow a set format (they fill sequentially starting with 'a' and 'AA' up through 'z' and 'ZZ'), so I could just hard code an array for that. The best way I can think to do the last level is to run 'ls > dirList', then read dirList into an array, and use that to go into the directories, and run diff through a loop on every other cache thing using the same algorithm (yes, run time is going to be awful, but it will save a tremendous amount of time in the long run).
Is this a reasonable approach? Is there a better, or more efficient way?
Also, is there a way to get diff to count the number of lines that are different?
I know this is a bit long, but any help would be greatly appreciated.
Thanks!
Assuming the 2 directories in your root directory are the ones to compare (a & b), I would try something like that:
min_diff=9999 # big value
file2remember=''
cd a || return $?
find * -type f |while read f
do
n=`diff "$f" "../b/$f"|wc -l`
if [ $n -lt $min_diff ]
then min_diff=$n ; file2remember="$f"
fi
done
echo $file2remember
NB: I do not have a linux or unix box to test that.

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