restez_status() shows zero GB in database even though it has data
joelnitta opened this issue · 0 comments
joelnitta commented
Download data:
library(restez)
rstz_pth <- file.path(tempdir(), 'database')
if (!dir.exists(rstz_pth)) {
dir.create(rstz_pth)
}
restez_path_set(filepath = rstz_pth)
db_download()
restez_connect()
db_create()
For db_download()
, I interactively selected data from three divisions (stopping partway for some of them).
> restez_status()
Checking setup status at ...
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Restez path ...
... Path '/var/folders/gp/h66562zx3ps986y5z2jzrc0h0000gn/T//RtmphjFjmR/database/restez'
... Does path exist? 'Yes'
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Download ...
... Path '/var/folders/gp/h66562zx3ps986y5z2jzrc0h0000gn/T//RtmphjFjmR/database/restez/downloads'
... Does path exist? 'Yes'
... N. files 25
... N. GBs 2.12
... GenBank division selections 'Invertebrate, Phage, Primate'
... GenBank Release 250
... Last updated '2022-07-07 16:23:45'
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Database ...
... Path '/var/folders/gp/h66562zx3ps986y5z2jzrc0h0000gn/T//RtmphjFjmR/database/restez/sql_db'
... Does path exist? 'Yes'
... N. GBs 0
... Is database connected? 'Yes'
... Does the database have data? 'Yes'
... Number of sequences 1371729
... Min. sequence length 0
... Max. sequence length Inf
... Last_updated '2022-07-07 16:57:48'
N. GBs
is 0 even though the database is actually 27 GB:
(base) Joels-iMac:restez joelnitta$ cd /var/folders/gp/h66562zx3ps986y5z2jzrc0h0000gn/T//RtmphjFjmR/database/restez/
(base) Joels-iMac:restez joelnitta$ ls
README.txt download_log.tsv gb_release.txt seqlengths.tsv sql_db
add_log.tsv downloads selection_log.tsv session_info.txt sql_db.wal
(base) Joels-iMac:restez joelnitta$ ls -lah
total 56885328
drwxr-xr-x 12 joelnitta staff 384B Jul 7 17:01 .
drwxr-xr-x 3 joelnitta staff 96B Jul 7 16:12 ..
-rw-r--r-- 1 joelnitta staff 446B Jul 7 16:12 README.txt
-rw-r--r-- 1 joelnitta staff 962B Jul 7 16:57 add_log.tsv
-rw-r--r-- 1 joelnitta staff 890B Jul 7 16:23 download_log.tsv
drwxr-xr-x 27 joelnitta staff 864B Jul 7 16:23 downloads
-rw-r--r-- 1 joelnitta staff 4B Jul 7 16:20 gb_release.txt
-rw-r--r-- 1 joelnitta staff 119B Jul 7 16:20 selection_log.tsv
-rw-r--r-- 1 joelnitta staff 24B Jul 7 16:26 seqlengths.tsv
-rw-r--r-- 1 joelnitta staff 750B Jul 7 16:12 session_info.txt
-rw-r--r-- 1 joelnitta staff 27G Jul 7 16:57 sql_db
-rw-r--r-- 1 joelnitta staff 0B Jul 7 17:01 sql_db.wal