Closed joelnitta closed 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).
db_download()
> 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:
N. GBs
(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
Download data:
For
db_download()
, I interactively selected data from three divisions (stopping partway for some of them).N. GBs
is 0 even though the database is actually 27 GB: