ropensci / restez

:sleeping: :open_file_folder: Create and Query a Local Copy of GenBank in R
https://docs.ropensci.org/restez
Other
25 stars 5 forks source link

restez_status() shows zero GB in database even though it has data #32

Closed joelnitta closed 2 years ago

joelnitta commented 2 years ago

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