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monarch-initiative / HpoCaseAnnotator

Next-generation Biocuration App for annotating cases and PhenoPackets
https://hpocaseannotator.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
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Liftover - MalformedURLException #81

Closed pnrobinson closed 3 years ago

pnrobinson commented 3 years ago

downloadLiftoverChainFiles leads to this error

java.net.MalformedURLException
    at java.net.URL.<init>(URL.java:644)
    at java.net.URL.<init>(URL.java:507)
    at java.net.URL.<init>(URL.java:456)
    at org.monarchinitiative.hpo_case_annotator.gui.controllers.SetResourcesController.downloadLiftoverChainFiles(SetResourcesController.java:451)
    (...)
Caused by: java.lang.NullPointerException
    at java.net.URL.<init>(URL.java:549)
    ... 118 more

However, the URL in hpo-case-annotator.properties appears to be OK

hg19.hg38.chain.url=https://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
ielis commented 3 years ago

Yeah, you need to remove the properties file that is stored in $HOME/.hpo.case.annotator/hpo-case-annotator.properties. From some reason we need to remove the file and only after that start the app

pnrobinson commented 3 years ago

sorry, forgot. Works now!