[InterMine Dev] Any way to pass an input file to a post-process task?

justincc at intermine.org justincc at intermine.org
Wed Jul 20 22:55:02 BST 2016


Hi Sam,

Are you trying to add a post processing operation to a <source> or a new 
<post-process> step in <post-processing>?

PostProcessOperationsTask handles <post-process> steps (and hardcodes 
all possible steps such as create-references which is really quite 
shocking).

However, do you really want post-processing on an individual source 
<source> (confusing, I know).  This is done by providing a class in that 
source's directory that extends org.intermine.postprocess.PostProcessor. 
  This should accept the properties in <source> as usual (as described at 
[1]).  One existing example is BioPAXPostProcess.java

[1] 
https://intermine.readthedocs.io/en/latest/database/data-sources/custom/

On 2016-07-20 21:45, Sam Hokin wrote:
> Hi, devs. I'm writing a post-processor that takes an input file
> (interpro.xml) and adds a bunch of data from that to proteins and
> protein domains (which I already have from a different data source). I
> see that PostProcessOperationsTask.java has a method to set an output
> file (setOutputFile), presumably from project.xml, but there is none
> to set an input file. I naively added a setter to do so, but it does
> not work when I use:
> 
>       <property name="input.file"
> location="/home/intermine/data/interpro/interpro.xml"/>
> 
> in project.xml. The setter that I added is simply:
> 
>     /**
>      * Set the value of inputFile
>      *
>      * @param inputFile an input file for operations that require one
>      */
>     public void setInputFile(File inputFile) {
>         this.inputFile = inputFile;
>     }
> 
> Any suggestions? I thought I'd ask before I start digging deeper.
> _______________________________________________
> dev mailing list
> dev at lists.intermine.org
> https://lists.intermine.org/mailman/listinfo/dev



More information about the dev mailing list