gds in GEOmetadb 2023-06-26 version is empty
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malat1_t ▴ 10
@a55f0470
Last seen 12 months ago
Taiwan

Hello,

I hope this is the right place to report the issue. I was testing out GEOmetadb and found that gds in the 2023-06-26 version was empty (see below). In short, I downloaded the full GEOmetadb.sqlite and queried table gds, but found 0 records. I also tried to query gds from GEOmetadb_demo.sqlite and got 3566 records, which seems to worked perfectly well. So it looks like that the 2023-06-26 database was corrupted. Please help to fix the database. Thank you!

> library(GEOmetadb)
> getSQLiteFile()
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz'
Content type 'application/x-gzip' length 779455487 bytes (743.3 MB)
==================================================
downloaded 743.3 MB

Unzipping...
Metadata associate with downloaded file:
                name               value
1     schema version                 1.0
2 creation timestamp 2023-06-26 16:20:46
[1] "/home/username/Work/GEOmetadb/GEOmetadb.sqlite"
> con <- dbConnect(SQLite(),'GEOmetadb.sqlite')
> gds <- dbGetQuery(con, "select * from gds")
> gds
 [1] ID                       gds                      title                   
 [4] description              type                     pubmed_id               
 [7] gpl                      platform_organism        platform_technology_type
[10] feature_count            sample_organism          sample_type             
[13] channel_count            sample_count             value_type              
[16] gse                      order                    update_date             
<0 rows> (or 0-length row.names)
GEOmetadb • 934 views
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Facing same issue, the demo file is working but Unable to download the full version of GEOmetadb.sqlite file from the source "https://gbnci.cancer.gov/geo/" , is it resolved now?

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