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I am trying to use a shell script file in the Bash shell. In this script, 2 sed commands are there. The second sed command is following.

sed -e s:MACRO_NAME:"${runmacro}":g \ -e s:INFILE_PATH_NAME:"${filedir}"/"${filename}":g \ -e s:INFILE_NAME:"${filename%.*}":g \ -e s:INDEX:"${index}":g \ -e s:TREE_NAME:"${treename}":g \ -e s:SUFFIX:"${suffix}":g \ -e s:SMEAR_TEMPLATE_NAME:"${smeartemplatename}":g \ -e s:IS_MC:"${ismc}":g \ -e s:PWD:.:g \ -e s:SCRAM_DIR:"${scramdir}":g \ -e s:OUTFILE_NAME:"${outfilename}":g \ -e s:OUTFILE_DIR:"${outputpath}":g \ -e s:PREFIX:"${prefix}":g \ -e s:OUTPUT_DIR:"${outputdir}":g \ template_files/submit_script_template.sh > tempfile \
&& mv tempfile ../"${outputdir}"/submit_"${outputdir}"_"${index}".sh

By executing the .sh file, I am getting this error:

sed: -e expression #2, char 25: unknown option to `s'

I added echo to sed also. The result is:

sed -e s:MACRO_NAME:QCDSmearedSkimmer.C:g \ -e s:INFILE_PATH_NAME:root:// \ -e s:INFILE_NAME:qcd_ht1000to1500-ext_10_ntuple_postproc:g \ -e s:INDEX:2:g \ -e s:TREE_NAME:Events:g \ -e s:SUFFIX:SmearedQCD:g \ -e s:SMEAR_TEMPLATE_NAME:resTailOut_combined_filtered_CHEF_puWeight_weight_WoH.root:g \ -e s:IS_MC:1:g \ -e s:PWD:.:g \ -e s:SCRAM_DIR:${CMSSW_BASE}:g \ -e s:OUTFILE_NAME:qcd_ht1000to1500-ext_10_ntuple_postproc_1_SmearedQCD.root:g \ -e s:OUTFILE_DIR:/ddash/nobackup/mywork/qcd/CMSSW_9_4_6_patch1/src/AnalysisMethods/macros/Skims/generate_smear_scripts/smeared_file/:g \ -e s:PREFIX:root:// \ -e s:OUTPUT_DIR:qcd_smeared_file3:g \ template_files/submit_script_template.sh > tempfile \
&& mv tempfile ../qcd_smeared_file3/submit_qcd_smeared_file3_2.sh

Please help me to fix this problem.

7

2 Answers

In the sed expression s:INFILE_PATH_NAME:"${filedir}"/"${filename}":g, there are five parts:

  • the sed command s,
  • the search pattern for that command (INFILE_PATH_NAME),
  • the replacement text (whatever "${filedir}"/"${filename}" - in this example, that's root://),
  • options to the s command (here g),
  • and the delimiter that separates all these, which is : (colon) here.

Now, if the replacement text contains :, then sed will think that the replacement text ends there, and whatever follows are options to s. So instead of

  • replacement: root://
  • option: g,

we get:

  • replacement: root
  • option: //

which is invalid as far as sed is concerned.

Suggested solutions:

  1. use a different delimiter, some character which won't appear in the replacement text, such as , (comma), ; (semicolon), etc. For example:

    sed -e "s,INFILE_PATH_NAME,${filedir}/${filename},g" ...
  2. Wherever you get your input from, escape : with a backslash so that it becomes \:.
2

The error appears because your variables (at least some of them) contain colons (:) and you use a colon as the delimiter for the s/…/…/ command. Actually for the s:…:…: command in your case.

When you have

var="ex:ample"

and then try to issue

sed -e "s:${var}:sample:g" some_file

then the shell interpolates the variable before handing it over to sed, and sed is called like so:

sed -e "s:ex:ample:sample:g" some_file

and the s:…:…: is now broken. It looks like you are telling sed to replace ex with ample and apply the options s, a, m, p, l, and e.

To avoid this, use a different delimiter which you are sure of it doesn't appear in your text. Popular delimiters are + and # but you can choose any character. The delimiter is in fact the first character after the s, so 

sed -e "s#…#…#" some_file
sed -e "s+…+…+" some_file
sed -e "s'…'…'" some_file

will all do.

1

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