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molgenis / data-transform-vkgl

GNU Lesser General Public License v3.0
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Pipeline outputs "" for empty timestamp input #42

Open dennishendriksen opened 3 years ago

dennishendriksen commented 3 years ago

How to Reproduce

Run the pipeline with input based on:

$ head -n 2 vkgl_export_amc_20210614.tsv | cut -f 1-3
timestamp       id      chromosome
                1

Expected

Output is similar to:

$ head -n 2 vkgl_raw_amc_v2.tsv | cut -f 1-3
timestamp       id      chromosome
              1

Observed

All timestamp in the output are empty double quotes.

$ head -n 2 vkgl_raw_amc_v2.tsv | cut -f 1-3
timestamp       id      chromosome
""              1

Importing this file in MOLGENIS results in:

Conversion failure in entity type [vkgl_raw_amc_v2] attribute [timestamp]; Failed to convert from type [java.lang.String] to type [java.time.Instant] for value '"'; nested exception is java.time.format.DateTimeParseException: Text '"' could not be parsed, unparsed text found at index 0