Question

outdated GEOmetadb.sqlite

1

Entering edit mode

Robert Castelo ★ 3.3k

@rcastelo

Last seen 2 days ago

Barcelona/Universitat Pompeu Fabra

Dear GEOmetadb maintainers,

Thanks for this great package, I use it to quickly (programmatically) find certain types of RNAseq data that I'm interested in. I've downloaded the GEOmetadb SQLite database using the current release version of the GEOmetadb Bioconductor package, but the timestamp reported by the getSQLiteFile() function says that the version of the database is from Nov 3rd, 2021:

> getSQLiteFile(destdir="/Users/robert")
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz'
Content type 'application/x-gzip' length 791740945 bytes (755.1 MB)
==================================================
downloaded 755.1 MB

Unzipping...
Metadata associate with downloaded file:
                name               value
1     schema version                 1.0
2 creation timestamp 2021-11-03 01:18:38
[1] "/Users/robert/GEOmetadb.sqlite"

Would it be possible to have a more up to date version of the database, which is hosted at the URL https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz ?

GEOmetadb • 676 views

ADD COMMENT • link 14 months ago • updated 3 months ago Robert Castelo ★ 3.3k

2

Entering edit mode

Actually https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz return an empty file. Is the project still maintained?

ADD REPLY • link 3 months ago Ivan ▴ 20

2

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I can reproduce the error with the current release of GEOmetadb:

library(GEOmetadb)
getSQLiteFile(destdir="/home/rcastelo")
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz'
downloaded 0 bytes

Unzipping...
Error: no such table: metaInfo

Maybe Sean Davis can tell something about this.

ADD REPLY • link 3 months ago Robert Castelo ★ 3.3k