Using substituteInPlace on ${..} expression gives bad substitution

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1

hi,

I have this line (java pom.xml):

${gatk.shell.directory}/check_utils_engine_tools.sh

maven executes this as a bash script during build phase.

It gives the following error:

Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:exec 
(check-utils-engine-tools) on project gatk-aggregator: 
Command execution failed.: Cannot run program
"/build/source/public/src/main/scripts/shell/check_utils_engine_tools.sh" 
(in directory "/build/source"): error=2, No such file or directory -> [Help 1]

the path /build/source is sandboxed right?

I think I could put the relative path into that value. I tried escaping $ with ‘’, but it gives me bad substitution error :

substituteInPlace pom.xml \                                                                                                                                                       
  --replace "''${gatk.shell.directory}/check_utils_engine_tools.sh" "./public/src/main/scripts/shell/check_utils_engine_tools.sh"

any way to do this?

2

You’re using ''$ to escape the shell variable, except that’s only the escape inside of a ''multiline string''. In a "double-quoted string" you just escape with \ instead.

3

Thank you very much @lilyball :slight_smile:

however I still get gatk as an undefined variable when I do this:

       substituteInPlace pom.xml \                                                                                                                                                        
         --replace "\${gatk.shell.directory}/check_utils_engine_tools.sh"  "..."

I think I’ll just go with creating a patch using git instead. At least I get to test that out as well :slight_smile:

I’ve put a gist up, if anyone wants to test it out:

4

Oh I know what happened. substituteInPlace is a shell function so I assume you actually had something like

postPatch = ''
substituteInPlace pom.xml \                                                                                                                                                        
         --replace "\${gatk.shell.directory}/check_utils_engine_tools.sh"  "..."
''

This means you need to worry about both Nix and Bash variable escaping. This can be handled by using your original ''$ escape but adding the \ for bash, as in

postPatch = ''
substituteInPlace pom.xml \                                                                                                                                                        
         --replace "\''${gatk.shell.directory}/check_utils_engine_tools.sh"  "..."
''

Alternatively you could change the " to ' but I’m not sure offhand how to do that given the ''$ immediately following.

5

Thanks again @lilyball :slight_smile:

I tried this too, seems that it also escapes the replace script (it’s not able to see the pattern). I did fix it with a git diff patch. Needed to do some other changes as well, so think it’s the best way in anyway.

Thanks a lot for the help though!! I think the substituteInPlace function is very convenient.