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Fails to load TSV #33

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mccalluc opened this issue Jun 13, 2018 · 0 comments
Open

Fails to load TSV #33

mccalluc opened this issue Jun 13, 2018 · 0 comments

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@mccalluc
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When I upload this:

id	url	species
bed.gz	https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz	Homo sapiens
bed.gz.tbi	https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz.tbi	Homo sapiens
bam	https://data.broadinstitute.org/igvdata/BodyMap/hg19/IlluminaHiSeq2000_BodySites/brain_merged/accepted_hits.bam	Homo sapiens
vcf.gz	https://s3.amazonaws.com/1000genomes/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz	Homo sapiens
vcf.gz.tbi	https://s3.amazonaws.com/1000genomes/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi	Homo sapiens
seg.gz	https://data.broadinstitute.org/igvdata/test/igv-web/segmented_data_080520.seg.gz	Homo sapiens
bigwig	https://s3.amazonaws.com/igv.broadinstitute.org/data/hg19/encode/wgEncodeBroadHistoneGm12878H3k4me3StdSig.bigWig	Homo sapiens
txt	http://s3.amazonaws.com/igv.broadinstitute.org/annotations/ca21/ca21_refFlat.txt	Homo sapiens

in the django_docker_engine demo, and try to run lineup, I get this error in the docker logs:

INFO:root:Reading from envar
Traceback (most recent call last):
  File "../csv2js.py", line 67, in <module>
    print(tab.make_outside_data_js())
  File "/var/tabular.py", line 199, in make_outside_data_js
    column_defs = self._make_column_defs()
  File "/var/tabular.py", line 239, in _make_column_defs
    values = get_typed_column(col, self.rows)
  File "/var/tabular.py", line 51, in get_typed_column
    return [typed(s) for s in get_raw_column(column, list_of_dicts)]
  File "/var/tabular.py", line 51, in <listcomp>
    return [typed(s) for s in get_raw_column(column, list_of_dicts)]
  File "/var/tabular.py", line 76, in typed
    assert type(s) == str
AssertionError

This in turn means that outside_data.js is empty, and (because we don't have robust error handling) the screen is just empty.

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