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Make qlever get-data for UniProt fail on errors and convert ChEBI and Rhea - #359
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…nd Rhea So far, `qlever get-data` for UniProt could download all 1.5 TB of RDF/XML and then fail every conversion to Turtle without reporting an error. The conversion runs `rdfxml` from Apache Jena for each file in parallel, and its errors only went to the `.stderr` file next to each output. When `rdfxml` was not on the `PATH`, all 552 conversions failed and left empty `.ttl.gz` files, while `get-data` finished as if it had succeeded. With this change, `get-data` first checks that all required commands exist and that `rdfxml` runs. A failed conversion or download now makes `get-data` fail, and running `get-data` again continues an interrupted download. The conversion also never handled the ChEBI and Rhea files, which are compressed with `gzip` instead of `xz`. So `chebi.ttl.gz` and `rhea.ttl.gz` were missing, although `MULTI_INPUT_JSON` uses them. With recent Java versions, Rhea also fails because its RDF/XML exceeds the default XML entity size limit of the JDK, so the conversion now lifts these limits for `rdfxml`. In addition, `DATE` is updated to the current release, and the unused `raptor2-utils` is dropped from the install instructions.
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So far,
qlever get-datafor UniProt could download all 1.5 TB of RDF/XML and then fail every conversion to Turtle without reporting an error. The conversion runsrdfxmlfrom Apache Jena for each file in parallel, and its errors only went to the.stderrfile next to each output. Whenrdfxmlwas not on thePATH, all 552 conversions failed and left empty.ttl.gzfiles, whileget-datafinished as if it had succeeded. With this change,get-datafirst checks that all required commands exist and thatrdfxmlruns. A failed conversion or download now makesget-datafail, and runningget-dataagain continues an interrupted download.The conversion also never handled the ChEBI and Rhea files, which are compressed with
gzipinstead ofxz. Sochebi.ttl.gzandrhea.ttl.gzwere missing, althoughMULTI_INPUT_JSONuses them. With recent Java versions, Rhea also fails because its RDF/XML exceeds the default XML entity size limit of the JDK, so the conversion now lifts these limits forrdfxml. In addition,DATEis updated to the current release, and the unusedraptor2-utilsis dropped from the install instructions.