Make SemanticHash Resilient to FileNotFoundExceptions - #13919
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Fixes hail-is#13915 `MatrixVCFReader` accepts glob patterns (wildcards in glob names). This bamboozled `SemanticHash` which had assumed all files had been resolved. This change fixes this by adding explicit `FileNotFoundException` handling to `SemanticHash` and replacing the `params.files` object of `MatrixVCFReader` with the resolved paths.
| log.warn( | ||
| """An internal compiler error occurred. | ||
| |Please report this to the Hail Team using the link below, | ||
| |including the stack trace at the end of this message. | ||
| |https://github.com/hail-is/hail/issues/new/choose | ||
| |""".stripMargin, | ||
| error |
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Seems right that a failure in semhash shouldn't bring the whole query down. It's not that important. Simmer down.
We want to know about these failures though, so a shouty log might be appropriate. Though this needs to be more shouty.
| """AN INTERNAL COMPILER ERROR OCCURRED. | ||
| |PLEASE REPORT THIS TO THE HAIL TEAM USING THE LINK BELOW, | ||
| |INCLUDING THE STACK TRACE AT THE END OF THIS MESSAGE. | ||
| |https://github.com/hail-is/hail/issues/new/choose | ||
| |""".stripMargin, |
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Indeed appropriately shouty
danking
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danking
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I confirmed that, with this change, #13915 is resolved. In the interest of fixing that for 0.2.125, I'm gonna approve and get it into this release.
However, I left a comment inline. It seems that the meaning of pathsUsed was always a bit buggy and I think we should kill that tech debt now before it trips us again.
I'm also still concerned that test_glob didn't catch this bug; we should nail down why.
| """AN INTERNAL COMPILER ERROR OCCURRED. | ||
| |PLEASE REPORT THIS TO THE HAIL TEAM USING THE LINK BELOW, | ||
| |INCLUDING THE STACK TRACE AT THE END OF THIS MESSAGE. | ||
| |https://github.com/hail-is/hail/issues/new/choose | ||
| |""".stripMargin, |
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Indeed appropriately shouty
| LoadVCF.warnDuplicates(sampleIDs) | ||
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| new MatrixVCFReader(params, fileListEntries, referenceGenome, header1) | ||
| new MatrixVCFReader(params.copy(files = fileListEntries.map(_.getPath)), fileListEntries, referenceGenome, header1) |
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This feels inconsistent across the readers.
StringTableReader is special-cased in SemanticHash to use the fileStatuses but its params.files is still the original glob-pattern-containing params.
pathsUsed as introduced a long time ago to protect against silly pipelines like:
hl.read_matrix_table('foo.mt').write('foo.mt')This works fine for non-globbed data sources like matrix tables and tables. However, even in the original PR #8327, it seems we would always fail to notice:
hl.export_vcf(hl.import_vcf('chr*.vcf'), 'chr1.vcf')It seems to me that the durable & reliable fix to this is for pathsUsed to always be the list of post-globbed files/blobs. I have a mild preference to treat params as an immutable record of what the user requested.
Taking this one step further: pathsUsed could be a list of FileStatus (which is a super type of FileListEntry) and FileStatus could have an eTag. This avoids O(N_FILES) calls to google to get the etag of all the files. Any reader that uses glob will already have a FileListEntry for every file. I suspect readers that don't use glob do still check the existence of the files ahead of time. They should just keep a FileStatus (which is proof of existence anyway) around so that we can later get its etag.
We don't catch this in |
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Ahh! Drat. OK, I'm glad we know why. |
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I'll follow this change up wth adding support for that, as well as addressing your comment. |
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Semhash support: #13922 |
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Fixes #13915
MatrixVCFReaderaccepts glob patterns (wildcards in glob names). This bamboozledSemanticHashwhich had assumed all files had been resolved. This change fixes this by adding explicitFileNotFoundExceptionhandling toSemanticHashand replacing theparams.filesobject ofMatrixVCFReaderwith the resolved paths.