I'm trying to do a simple tcsh script to look for a folder, then navigate to it if it exists. The statement evaluates properly, but if it evaluates false, I get an error "then: then/endif not found". If it evaluates true, no problem. Where am I going wrong?
#!/bin/tcsh
set icmanagedir = ""
set workspace = `find -maxdepth 1 -name "*$user*" | sort -r | head -n1`
if ($icmanagedir != "" && $workspace != "") then
setenv WORKSPACE_DIR `readlink -f $workspace`
echo "Navigating to workspace" $WORKSPACE_DIR
cd $WORKSPACE_DIR
endif
($icmanagedir is initialized elswehere, but I get the error regardless of which variable is empty)
The problem is that tcsh needs to have every line end in a newline, including the last line; it uses the newline as the "line termination character", and if it's missing it errors out.
You can use a hex editor/viewer to check if the file ends with a newline:
$ hexdump -C x.tcsh i:arch:21:49
00000000 69 66 20 28 22 78 22 20 3d 20 22 78 22 29 20 74 |if ("x" = "x") t|
00000010 68 65 6e 0a 09 65 63 68 6f 20 78 0a 65 6e 64 69 |hen..echo x.endi|
00000020 66 |f|
Here the last character if f (0x66), not a newline. A correct file has 0x0a as the last character (represented by a .):
$ hexdump -C x.tcsh
00000000 69 66 20 28 22 78 22 20 3d 20 22 78 22 29 20 74 |if ("x" = "x") t|
00000010 68 65 6e 0a 09 65 63 68 6f 20 78 0a 65 6e 64 69 |hen..echo x.endi|
00000020 66 0a |f.|
Ending the last line in a file with a newline is a common UNIX idiom, and some shell tools expect this. See What's the point in adding a new line to the end of a file? for some more info on this.
Most UNIX editors (such as Vim, Nano, Emacs, etc.) should do this by default, but some editors or IDEs don't do this by default, but almost all editors have a setting through which this can be enabled.
The best solution is to enable this setting in your editor. If you can't do this then adding a blank line at the end also solves your problem.
Related
I encounter a strange behaviour with bash string substitution.
I expected the same substitution on $r1 and $var to yield the exact same results.
both strings seem to have the same value.
But It is not the case and I can't understand what I am missing....
maybe is because of the glob? I just don't know... I am not pure IT guys and maybe it's something that will be evident for you.
(bottom a Repl.it link)
mkdir -p T21805
touch T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
r1=T21805/*R1*
echo $r1;
echo ${r1%%_S1*z}
var=T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
echo ${var%%_S1*z}
echo $r1| hexdump -C
echo $var | hexdump -C
output :
echo $r1
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
echo ${r1%%_S1*z}
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
echo ${var%%_S1*z}
T21805/T21805_SI-GA-D8-BH25N7DSXY
echo $r1| hexdump -C
00000000 54 32 31 38 30 35 2f 54 32 31 38 30 35 5f 53 49
|T21805/T21805_SI|
00000010 2d 47 41 2d 44 38 2d 42 48 32 35 4e 37 44 53 58
|-GA-D8-BH25N7DSX|
00000020 59 5f 53 31 5f 4c 30 30 31 5f 52 31 5f 30 30 31
|Y_S1_L001_R1_001|
00000030 2e 66 61 73 74 71 2e 67 7a 0a
|.fastq.gz.| 0000003a
echo $var | hexdump -C
00000000 54 32 31 38 30 35 2f 54 32 31 38 30 35 5f 53 49
|T21805/T21805_SI|
00000010 2d 47 41 2d 44 38 2d 42 48 32 35 4e 37 44 53 58
|-GA-D8-BH25N7DSX|
00000020 59 5f 53 31 5f 4c 30 30 31 5f 52 31 5f 30 30 31
|Y_S1_L001_R1_001|
00000030 2e 66 61 73 74 71 2e 67 7a 0a
|.fastq.gz.| 0000003a
Repl.it
I am interested on understanding why this is not working, I can achieve my desire output using sed for example.
Glob expansion doesn't happen at assignment time.
$ mkdir -p T21805
$ touch T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
$ touch T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_002.fastq.gz
$ r1=T21805/*R1*
$ printf '%s\n' "$r1"
T21805/*R1*
$ printf '%s\n' $r1
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_002.fastq.gz
It happens after the unquoted r1 has been expanded. When you write ${r1%%_S1*z}, the value of r1 doesn't contain the string S1; only after ${r1} expands is there an S1 you could match against.
If you set an array, the assignment rules are different. The glob expands before the assignment, and so you can do your filtering on each element of the array.
$ r1=( T21805/*R1* )
$ printf '%2\n' "${r1[#]}"
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_002.fastq.gz
$ printf '%s\n' "${r1[#]%%_S1*z}"
T21805/T21805_SI-GA-D8-BH25N7DSXY
T21805/T21805_SI-GA-D8-BH25N7DSXY
I ran it after set -xv to see the contents of r1.
$ r1=T21805/*R1*
+ r1='T21805/*R1*'
$ var=T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
+ var=T21805/T21805_SI-GA-D8-BH25N7DSXY_S1_L001_R1_001.fastq.gz
The r1 of$ {r1 %% _ S1 * z}isT21805 / * R1 *.
r1 does not include_S1 * z.
I'm trying to run my shell script on Linux (Ubuntu).
It's running correctly on MacOS, but on Ubuntu it doesn't.
#!/usr/bin/env bash
while true
do
node Client/request -t 10.9.2.4 -p 4400 --flood
done
Ubuntu output this error for running: sh myScript.sh:
Syntax error: end of file unexpected (expecting "do")
Why is there any difference between them, since both of them are running by Bash? How can I avoid future errors caused by their differences?
I tried cat yourscript.sh | tr -d '\r' >> yournewscript.sh as related question was suggested to do, and also while [ true ].
The command hexdump -C util/runner.sh result is:
00000000 23 21 2f 75 73 72 2f 62 69 6e 2f 65 6e 76 20 62 |#!/usr/bin/env b|
00000010 61 73 68 0d 0a 0d 0a 77 68 69 6c 65 20 5b 20 74 |ash....while [ t|
00000020 72 75 65 20 5d 0d 0a 64 6f 0d 0a 20 20 20 6e 6f |rue ]..do.. no|
00000030 64 65 20 43 6c 69 65 6e 74 2f 72 65 71 75 65 73 |de Client/reques|
00000040 74 20 2d 74 20 31 39 32 2e 31 36 38 2e 30 2e 34 |t -t 192.168.0.4|
00000050 31 20 2d 70 20 34 34 30 30 20 2d 2d 66 6c 6f 6f |1 -p 4400 --floo|
00000060 64 0d 0a 64 6f 6e 65 0d 0a |d..done..|
00000069
The shebang #! line at the top of your file tells that this is a bash script. But then you run your script with sh myScript.sh, therefore using the sh shell.
The sh shell is not the same as the bash shell in Ubuntu, as explained here.
To avoid this problem in the future, you should call shell scripts using the shebang line. And also make sure to prefer bash over sh, because the bash shell is more convenient and standardized (IMHO). In order for the script to be directly callable, you have to set the executable flag, like this:
chmod +x yournewscript.sh
This has to be done only once (it's not necessary to do this on every call.)
Then you can just call the script directly:
./yournewscript.sh
and it will be interpreted by whatever command is present in the first line of the script.
in macOS, I use zsh terminal ,then input command 'man sort > sort-man.txt'.
When open sort-man.txt with Sublime text, I see many 'BS'.
What does 'BS' stands for in sublime text on macOS??
It can be some encoding issue??
question picture
The man command outputs a “bold” character by printing the character, then printing a backspace character, then printing the character again. Thus:
:; man sort | hexdump -C | head
00000000 0a 53 4f 52 54 28 31 29 20 20 20 20 20 20 20 20 |.SORT(1) |
00000010 20 20 20 20 20 20 20 20 20 20 20 42 53 44 20 47 | BSD G|
00000020 65 6e 65 72 61 6c 20 43 6f 6d 6d 61 6e 64 73 20 |eneral Commands |
00000030 4d 61 6e 75 61 6c 20 20 20 20 20 20 20 20 20 20 |Manual |
00000040 20 20 20 20 20 20 20 20 53 4f 52 54 28 31 29 0a | SORT(1).|
00000050 0a 4e 08 4e 41 08 41 4d 08 4d 45 08 45 0a 20 20 |.N.NA.AM.ME.E. |
^ ^ ^
| | +--- ASCII N
| +------ ASCII Backspace
+--------- ASCII N
Way back in the days of physical terminals that printed on paper, this would have the effect of overstriking the character, making it appear bolder.
These days, your terminal emulator app interprets a sequence like this by changing the color or font of the character.
I guess Sublime Text shows the backspace character as BS.
Consulting the man man page, I find this under “TIPS”:
To get a plain text version of a man page, without backspaces and underscores, try
# man foo | col -b > foo.mantxt
This is the script I've constructed
It takes a list of files according to the extension supplied as an argument.
It then removes everything before the pattern 00000000: in those files.
The pattern 00000000: is preceded by the string <pre>, it then removes those five first characters.
The script then removes the last three lines of the file
The script the outputs only the hexdump data of the file.
The script runs xxd to convert the hexdump to a file.jpg
if [[ $# -eq 0 ]] ; then
echo 'Run script as ./hexconv ext'
exit 0
fi
for file in *.$1
do
filename=$(basename $file)
extension="${filename##*.}"
filename="${filename%.*}"
sed -n '/00000000:/,$p' $file | sed '1s/^.....//' | head -n -3 | awk '{print $2" "$3" "$4" "$5" "$6" "$7" "$8" "$9" "$10" "$11" "$12" "$13" "$14" "$15" "$16" "$17}' | xxd -p -r > $filename.jpg
done
It works as I want it too, but I suspect there are things to improve it by, but alas, I am a novice in the use of awk and sed.
Excerpt from file
<th>response-head:</th>
<td>HTTP/1.1 200 OK
Date: Sun, 15 Dec 2013 04:27:04 GMT
Server: PWS/8.0.18
X-Px: ms h0-s34.p6-lhr ( h0-s35.p6-lhr), ht-d h0-s35.p6-lhr.cdngp.net
Etag: "4556354-9fbf8-4e40387aadfc0"
Cache-Control: no-store, no-cache, must-revalidate, post-check=0, pre-check=0, max-age=0
Accept-Ranges: bytes
Content-Length: 654328
Content-Type: image/jpeg
Last-Modified: Thu, 15 Aug 2013 21:55:19 GMT
Pragma: no-cache
</td>
</tr>
</table>
<hr/>
<pre>00000000: ff d8 ff e0 00 10 4a 46 49 46 00 01 01 01 00 48 ......JFIF.....H
00000010: 00 48 00 00 ff e1 00 18 45 78 69 66 00 00 49 49 .H......Exif..II
00000020: 2a 00 08 00 00 00 00 00 00 00 00 00 00 00 ff ed *...............
00000030: 00 48 50 68 74 73 68 70 20 33 2e 30 00 .HPhotoshop 3.0.
00000040: 38 42 49 4d 04 04 00 00 00 00 00 1c 01 5a 00 8BIM..........Z.
00000050: 03 1b 25 47 1c 02 00 00 02 00 02 00 38 42 49 4d ..%G........8BIM
00000060: 04 25 00 00 00 00 00 10 fc e1 89 c8 b7 c9 78 .%.............x
00000070: 34 62 34 07 58 77 eb ff e1 03 a5 68 74 74 70 /4b4.Xw.....http
00000080: 3a 6e 73 2e 61 64 62 65 2e 63 6d ://ns.adobe.com/
00000090: 78 61 70 31 2e 30 00 3c 78 70 61 63 6b xap/1.0/.<?xpack
000000a0: 65 74 20 62 65 67 69 6e 3d 22 ef bb bf 22 20 69 et begin="..." i
000000b0: 64 3d 22 57 35 4d 30 4d 70 43 65 68 69 48 7a 72 d="W5M0MpCehiHzr
000000c0: 65 53 7a 4e 54 63 7a 6b 63 39 64 22 3e 20 3c eSzNTczkc9d"?> <
000000d0: 78 3a 78 6d 70 6d 65 74 61 20 78 6d 6c 6e 73 3a x:xmpmeta xmlns:
000000e0: 78 3d 22 61 64 62 65 3a 6e 73 3a 6d 65 74 61 x="adobe:ns:meta
000000f0: 22 20 78 3a 78 6d 70 74 6b 3d 22 41 64 62 /" x:xmptk="Adob
00000100: 65 20 58 4d 50 20 43 72 65 20 35 2e 30 2d 63 e XMP Core 5.0-c
00000110: 30 36 31 20 36 34 2e 31 34 30 39 34 39 2c 20 32 061 64.140949, 2
00000120: 30 31 30 31 32 30 37 2d 31 30 3a 35 37 3a 010/12/07-10:57:
Although #CodeGnome is right and this might belong to Code Review SE, here you go anyway:
Slightly more efficient to combine the multiple sed commands into one, for example:
sed -n -e 's/^<pre>//' -e '/00000000:/,$p'
I decided to retract this part, as I'm not all that sure it's any better or clearer. Your version is fine, except that s/^<pre>// is better than s/^.....//.
Use exit 1 when checking the number of arguments to signal an error
What is for file in *. there? Iterate for all files ending with a dot? Typo?
Unless you're 100% sure the filenames will never contain spaces, you should quote them, but don't quote where you don't need, for example:
filename=$(basename "$file") # need to quote
extension=${filename##*.} # no need,
filename=${filename%.*} # no need
sed ... "$file" # need to quote
... | xxd > "$filename".jpg # need to quote
The last awk could be shorter and less error prone as a loop:
... | awk '{printf $2; for (i=3; i<=17; ++i) printf " " $i; print ""}'
It seems you want to learn. You might be interested in this other answer too: What are the rules to write robust shell scripts?
The error message should be sent to stderr, should not hard-code the name of the script in case you rename it later, and should exit with a nonzero value.
if (( ! $# )); then
echo >&2 "Run script as '$0' \$extension"
exit 1
fi
If you're going to put the then on the same line as the if, then you should put the do on the same line as the for, too, for consistency:
for file in *.$1; do
Using file for the full name and filename for the basename is confusing variable name choice. I would use basename for the variable, to match the operation. And you need to quote the parameter expansion:
basename=$(basename "$file")
But you don't need to quote the right hand side of an assignment:
extension=${basename##*.}
The part of a filename without the extension is sometimes called the root (in vi and csh :-modifiers, you get it with :r)... using that name would be less confusing than changing an existing variable and reusing it:
root=${basename%.*}
As far as the actual pipeline, I would reorder it to put the head before the awk, since the sed and the head are all about what lines to print out and should be grouped together before the awk which modifies those selected lines. I would also use a loop and printf to make the awk a little more wieldy:
sed -n '/0\{8\}:/,$p' "$file" |
head -n -3 |
awk '{ printf "%s", $2; for (f=3;f<=17;++f) { printf " %s", $f }; print "" }' |
xxd -p -r > "$root.jpg"
done
I am using sed on Windows (the GNU port).
I execute:
$> sed "s/$/./" < /data.txt
And get:
.ne
.wo
.hree
But expect.
one.
two.
three.
The following works though I don't think it should. The way I read it is "replace the last character of the line with a period." I'm afraid it won't work consistently when used elsewhere. The intent isn't to replace the last character with a period but to append a period.
$> sed "s/.$/./" < /data.txt
I am not sure if the file encoding or something specific to windows is causing the issues I'm having or if it's just lack of experience with sed. Ideas?
hexdump -C sheds some light:
$ sed 's/$/./' < t.dos | hexdump -C
00000000 6f 6e 65 0d 2e 0a 74 77 6f 0d 2e 0a 74 68 72 65 |one...two...thre|
00000010 65 0d 2e 0a |e...|
00000014
There, 2e is the dot, the 0d before it is carriage return aka \r, and after that is the newline aka \n. In other words, sed treats \r as the end of the line instead of \r\n together, and thus \r is still part of the line, so it puts the dot after it, then adds back the newline as usual.
I think this does what you want, but it's not exactly pretty:
$ sed 's/.$/.\r/' < t.dos | hexdump -C
00000000 6f 6e 65 2e 0d 0a 74 77 6f 2e 0d 0a 74 68 72 65 |one...two...thre|
00000010 65 2e 0d 0a |e...|
00000014
The above is not so good, because it will only work if the input is in dos format, otherwise it will break the file. A better solution might be to first strip any \r and add them back manually later, like this:
$ tr -d '\r' < t.dos | sed -e 's/$/.\r/' | hexdump -C
00000000 6f 6e 65 2e 0d 0a 74 77 6f 2e 0d 0a 74 68 72 65 |one...two...thre|
00000010 65 2e 0d 0a |e...|
00000014