Obtain a materialized table via a table store
The tbl_get() function gives us the means to materialize a table that has an entry in a table store (i.e., has a table-prep formula with a unique name). The table store that is used for this can be in the form of a tbl_store object (created with the tbl_store() function) or an on-disk YAML representation of a table store (created by using yaml_write() with a tbl_store object).
Should you want a table-prep formula from a table store to use as a value for tbl (in create_agent(), create_informant(), or set_tbl()), then have a look at the tbl_source() function.
tbl_get(tbl, store = NULL)
tbl: The table to retrieve from a table store. This table could be identified by its name (e.g., tbl = "large_table") or by supplying a reference using a subset (with $) of the tbl_store object (e.g., tbl = store$large_table). If using the latter method then nothing needs to be supplied to store.
store: Either a table store object created by the tbl_store()
function or a path to a table store YAML file created by yaml_write().
A table object.
Define a tbl_store object by adding several table-prep formulas in tbl_store().
store <-
tbl_store(
small_table_duck ~ db_tbl(
table = small_table,
dbname = ":memory:",
dbtype = "duckdb"
),
~ db_tbl(
table = "rna",
dbname = "pfmegrnargs",
dbtype = "postgres",
host = "hh-pgsql-public.ebi.ac.uk",
port = 5432,
user = I("reader"),
password = I("NWDMCE5xdipIjRrp")
),
sml_table ~ pointblank::small_table
)
Once this object is available, we can access the tables named: "small_table_duck", "rna", and "sml_table". Let's check that the "rna" table is accessible through tbl_get():
tbl_get(
tbl = "rna",
store = store
)
## # Source: table<rna> [?? x 9]
## # Database: postgres [reader@hh-pgsql-public.ebi.ac.uk:5432/pfmegrnargs]
## id upi timestamp userstamp crc64 len seq_short
## <int64> <chr> <dttm> <chr> <chr> <int> <chr>
## 1 24583872 URS000177… 2019-12-02 13:26:08 rnacen C380… 511 ATTGAACG…
## 2 24583873 URS000177… 2019-12-02 13:26:08 rnacen BC42… 390 ATGGGCGA…
## 3 24583874 URS000177… 2019-12-02 13:26:08 rnacen 19A5… 422 CTACGGGA…
## 4 24583875 URS000177… 2019-12-02 13:26:08 rnacen 66E1… 534 AGGGTTCG…
## 5 24583876 URS000177… 2019-12-02 13:26:08 rnacen CC8F… 252 TACGTAGG…
## 6 24583877 URS000177… 2019-12-02 13:26:08 rnacen 19E4… 413 ATGGGCGA…
## 7 24583878 URS000177… 2019-12-02 13:26:08 rnacen AE91… 253 TACGAAGG…
## 8 24583879 URS000177… 2019-12-02 13:26:08 rnacen E21A… 304 CAGCAGTA…
## 9 24583880 URS000177… 2019-12-02 13:26:08 rnacen 1AA7… 460 CCTACGGG…
## 10 24583881 URS000177… 2019-12-02 13:26:08 rnacen 2046… 440 CCTACGGG…
## # … with more rows, and 2 more variables: seq_long <chr>, md5 <chr>
An alternative method for getting the same table materialized is by using $
to get the formula of choice from tbls and passing that to tbl_get(). The
benefit of this is that we can use autocompletion to show us what's available
in the table store (i.e., appears after typing the $).
store$small_table_duck %>% tbl_get()
## # Source: table<small_table> [?? x 8]
## # Database: duckdb_connection
## date_time date a b c d e f
## <dttm> <date> <int> <chr> <dbl> <dbl> <lgl> <chr>
## 1 2016-01-04 11:00:00 2016-01-04 2 1-bcd-345 3 3423. TRUE high
## 2 2016-01-04 00:32:00 2016-01-04 3 5-egh-163 8 10000. TRUE low
## 3 2016-01-05 13:32:00 2016-01-05 6 8-kdg-938 3 2343. TRUE high
## 4 2016-01-06 17:23:00 2016-01-06 2 5-jdo-903 NA 3892. FALSE mid
## 5 2016-01-09 12:36:00 2016-01-09 8 3-ldm-038 7 284. TRUE low
## 6 2016-01-11 06:15:00 2016-01-11 4 2-dhe-923 4 3291. TRUE mid
## 7 2016-01-15 18:46:00 2016-01-15 7 1-knw-093 3 843. TRUE high
## 8 2016-01-17 11:27:00 2016-01-17 4 5-boe-639 2 1036. FALSE low
## 9 2016-01-20 04:30:00 2016-01-20 3 5-bce-642 9 838. FALSE high
## 10 2016-01-20 04:30:00 2016-01-20 3 5-bce-642 9 838. FALSE high
## # … with more rows
1-10
Other Planning and Prep: action_levels(), create_agent(), create_informant(), db_tbl(), draft_validation(), file_tbl(), scan_data(), tbl_source(), tbl_store(), validate_rmd()
Useful links