Is there a release of platform-etl-support that accompanies the 22.09 release?

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1

I am trying to create the platform-etl-support JAR files that would accompany and be compatible with the 22.09 release of the platform and data. On github I only see the 22.06.1 branch and the 22.06.2-ppp Partner preview but not one for 22.09.

The configuration in src/main/resources/reference.conf file in 22.06.1 does not correspond to the data in 22.09 (22.09 data uses ensembl version 107, while the 22.06.1 reference.conf file has verison 104, for instance).

I also see an issue with the target-input/uniprot/uniprot-ssl.tsv files in 22.09 and the code in 22.06, since that file in 22.09 uses “Name” for the ssl_match, while the code uses “Alias” in 22.06.1, so they don’t seem to match…

So, is there an official frozen release of platform-etl-support that matches the data in 22.09?

Thanks!

(p.s. here’s the piece of code that gives error when running 22.06.1 etl jar with 22.09 data

This is the offending section I think:

    val subcellOntologyDf = sslDf.select(
      col("Subcellular location ID") as "termSL",
      col("Alias") as "ssl_match",
      col("Category") as "labelSL"
    )
2

If you checkout commit 6178ef5 on the master branch and build a jar with sbt assembly the jar should work. Alternatively you can download the jar that we used to run the release from: gs://open-targets-data-releases/22.09/jars

3

Wow…I actually had found that commit and guessed it would correspond so I chose correctly…The JAR from 22.09 is not the FAT jar that i needed (does not have the spark jars) but since Cinzia works for us now, so showed me the “provided” trick in how to create it from source…I now have a working fork of OT UI (whihc we call iTAP Targets) with all our new data…Once I figured out how to run all the steps, modifying OT UI was easy and thanks for the great work!