tbl_store: Define a store of tables with table-prep formulas: a table...

In pointblank: Data Validation and Organization of Metadata for Local and Remote Tables

Define a store of tables with table-prep formulas: a table store

Description

It can be useful to set up all the data sources you need and just draw from them when necessary. This upfront configuration with tbl_store() lets us define the methods for obtaining tabular data from mixed sources (e.g., database tables, tables generated from flat files, etc.) and provide identifiers for these data preparation procedures.

What results from this work is a convenient way to materialize tables with tbl_get(). We can also get any table-prep formula from the table store with tbl_source(). The content of a table-prep formulas can involve reading a table from a location, or, it can involve data transformation. One can imagine scenarios where we might (1) procure several mutated variations of the same source table, (2) generate a table using disparate data sources, or (3) filter the rows of a database table according to the system time. Another nice aspect of organizing table-prep formulas in a single object is supplying it to the tbl argument of create_agent() or create_informant() via $ notation (e.g, ⁠create_agent(tbl = <tbl_store>$<name>)⁠) or with tbl_source() (e.g., ⁠create_agent(tbl = ~ tbl_source("<name>", <tbl_store>))⁠).

Usage

tbl_store(..., .list = list2(...), .init = NULL)

Arguments

...	Expressions that contain table-prep formulas and table names for data retrieval. Two-sided formulas (e.g, ⁠<LHS> ~ <RHS>⁠) are to be used, where the left-hand side is an identifier and the right-hand contains a statement that obtains a table (i.e., the table-prep formula). If the LHS is omitted then an identifier will be generated for you.
.list	Allows for the use of a list as an input alternative to ....
.init	We can optionally provide an initialization statement (in a one-sided formula) that should be executed whenever any of tables in the table store are obtained. This is useful, for instance, for including a library() call that can be executed before any table-prep formulas in ....

Value

A tbl_store object that contains table-prep formulas.

YAML

A pointblank table store can be written to YAML with yaml_write() and the resulting YAML can be used in several ways. The ideal scenario is to have pointblank agents and informants also in YAML form. This way the agent and informant can refer to the table store YAML (via tbl_source()), and, the processing of both agents and informants can be performed with yaml_agent_interrogate() and yaml_informant_incorporate(). With the following R code, a table store with two table-prep formulas is generated and written to YAML (if no filename is given then the YAML is written to "tbl_store.yml").

R statement for generating the "tbl_store.yml" file:

tbl_store(
  tbl_duckdb ~ db_tbl(small_table, dbname = ":memory:", dbtype = "duckdb"),
  sml_table_high ~ small_table %>% dplyr::filter(f == "high"),
  .init = ~ library(tidyverse)
) %>%
  yaml_write()

YAML representation ("tbl_store.yml"):

type: tbl_store
tbls:
  tbl_duckdb: ~ db_tbl(small_table, dbname = ":memory:", dbtype = "duckdb")
  sml_table_high: ~ small_table %>% dplyr::filter(f == "high")
init: ~library(tidyverse)

This is useful when you want to get fresh pulls of prepared data from a source materialized in an R session (with the tbl_get() function. For example, the sml_table_high table can be obtained by using tbl_get("sml_table_high", "tbl_store.yml"). To get an agent to check this prepared data periodically, then the following example with tbl_source() will be useful:

R code to generate agent that checks sml_table_high and writing the agent to YAML:

create_agent(
  tbl = ~ tbl_source("sml_table_high", "tbl_store.yml"),
  label = "An example that uses a table store.",
  actions = action_levels(warn_at = 0.10)
) %>% 
  col_exists(vars(date, date_time)) %>%
  write_yaml()

The YAML representation ("agent-sml_table_high.yml"):

tbl: ~ tbl_source("sml_table_high", "tbl_store.yml")
tbl_name: sml_table_high
label: An example that uses a table store.
actions:
  warn_fraction: 0.1
locale: en
steps:
  - col_exists:
    columns: vars(date, date_time)

Now, whenever the sml_table_high table needs to be validated, it can be done with yaml_agent_interrogate() (e.g., yaml_agent_interrogate("agent-sml_table_high.yml")).

Examples

Creating an in-memory table store and adding table-prep formulas

The table store provides a way to get the tables we need fairly easily. Think of an identifier for the table you'd like and then provide the code necessary to obtain that table. Then repeat as many times as you like!

Here we'll define two tables that can be materialized later: tbl_duckdb (an in-memory DuckDB database table with pointblank's small_table dataset) and sml_table_high (a filtered version of tbl_duckdb):

store_1 <-
  tbl_store(
    tbl_duckdb ~ 
      db_tbl(
        pointblank::small_table,
        dbname = ":memory:",
        dbtype = "duckdb"
      ),
    sml_table_high ~ 
      db_tbl(
        pointblank::small_table,
        dbname = ":memory:",
        dbtype = "duckdb"
      ) %>%
      dplyr::filter(f == "high")
  )

We can see what's in the table store store_1 by printing it out:

store_1

## -- The `table_store` table-prep formulas
## 1 tbl_duckdb // ~ db_tbl(pointblank::small_table, dbname = ":memory:",
## dbtype = "duckdb")
## 2 sml_table_high // ~ db_tbl(pointblank::small_table, dbname = ":memory:",
## dbtype = "duckdb") %>% dplyr::filter(f == "high")
## ----

It's good to check that the tables can be obtained without error. We can do this with the tbl_get() function. With that function, we need to supply the given name of the table-prep formula (in quotes) and the table store object.

tbl_get(tbl = "tbl_duckdb", store = store_1)

## # Source:   table<pointblank::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

tbl_get(tbl = "sml_table_high", store = store_1)

## # Source:   lazy query [?? 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 2016-01-05 13:32:00 2016-01-05     6 8-kdg-938     3 2343. TRUE  high 
## 3 2016-01-15 18:46:00 2016-01-15     7 1-knw-093     3  843. TRUE  high 
## 4 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9  838. FALSE high 
## 5 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9  838. FALSE high 
## 6 2016-01-30 11:23:00 2016-01-30     1 3-dka-303    NA 2230. TRUE  high

We can shorten the tbl_store() statement with some syntax that pointblank provides. The sml_table_high table-prep is simply a transformation of tbl_duckdb, so, we can use {{ tbl_duckdb }} in place of the repeated statement. Additionally, we can provide a library() call to the .init argument of tbl_store() so that dplyr is available (thus allowing us to use filter(...) instead of dplyr::filter(...)). Here is the revised tbl_store() call:

store_2 <- 
  tbl_store(
    tbl_duckdb ~ 
      db_tbl(
        pointblank::small_table,
        dbname = ":memory:",
        dbtype = "duckdb"
      ),
    sml_table_high ~ 
      {{ tbl_duckdb }} %>%
      filter(f == "high"),
    .init = ~ library(tidyverse)
  )

Printing the table store store_2 now shows that we used an .init statement:

store_2

## -- The `table_store` table-prep formulas
## 1 tbl_duckdb // ~ db_tbl(pointblank::small_table, dbname = ":memory:",
## dbtype = "duckdb")
## 2 sml_table_high // ~ {{tbl_duckdb}} %>% filter(f == "high") 
## ----
## INIT // ~library(tidyverse)
## ----

Checking again with tbl_get() should provide the same tables as before:

tbl_get(tbl = "tbl_duckdb", store = store_2)

## # Source:   table<pointblank::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

tbl_get(tbl = "sml_table_high", store = store_2)

## # Source:   lazy query [?? 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 2016-01-05 13:32:00 2016-01-05     6 8-kdg-938     3 2343. TRUE  high 
## 3 2016-01-15 18:46:00 2016-01-15     7 1-knw-093     3  843. TRUE  high 
## 4 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9  838. FALSE high 
## 5 2016-01-20 04:30:00 2016-01-20     3 5-bce-642     9  838. FALSE high 
## 6 2016-01-30 11:23:00 2016-01-30     1 3-dka-303    NA 2230. TRUE  high

Using a table store in a data validation workflow

Define a tbl_store object by adding table-prep formulas inside the tbl_store() call.

store_3 <- 
  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")
    ),
    all_revenue ~ db_tbl(
      table = file_tbl(
        file = from_github(
          file = "sj_all_revenue_large.rds",
          repo = "rich-iannone/intendo",
          subdir = "data-large"
        )
      ),
      dbname = ":memory:",
      dbtype = "duckdb"
    ),
    sml_table ~ pointblank::small_table
  )

Let's get a summary of what's in the table store store_3 through printing:

store_3

## -- The `table_store` table-prep formulas
## 1 small_table_duck // ~ db_tbl(table = small_table, dbname = ":memory:",
## dbtype = "duckdb")
## 2 rna // ~db_tbl(table = "rna", dbname = "pfmegrnargs", dbtype =
## "postgres", host = "hh-pgsql-public.ebi.ac.uk", port = 5432, user =
## I("reader"), password = I("NWDMCE5xdipIjRrp"))
## 3 all_revenue // ~ db_tbl(table = file_tbl(file = from_github(file =
## "sj_all_revenue_large.rds", repo = "rich-iannone/intendo", subdir =
## "data-large")), dbname = ":memory:", dbtype = "duckdb")
## 4 sml_table // ~ pointblank::small_table
## ----

Once this object is available, you can check that the table of interest is produced to your specification with the tbl_get() function.

tbl_get(
  tbl = "small_table_duck",
  store = store_3
)

## # 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

Another way to get the same table materialized is by using $ to get the entry of choice for tbl_get().

store_3$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

Creating an agent is easy when all table-prep formulas are encapsulated in a tbl_store object. Use $ notation to pass the appropriate procedure for reading a table to the tbl argument.

agent_1 <-
  create_agent(
    tbl = store_3$small_table_duck
  )

There are other ways to use the table store to assign a target table to an agent, like using the tbl_source() function (which extracts the table-prep formula from the table store).

agent_2 <-
  create_agent(
    tbl = ~ tbl_source(
      tbl = "small_table_duck",
      store = store_3
      )
  )

Writing a table store to a YAML file

The table store can be moved to YAML with yaml_write and the tbl_source() call could then refer to that on-disk table store. Let's do that YAML conversion.

yaml_write(store_3)

The above writes the tbl_store.yml file (by not providing a filename this default filename is chosen).

It can be convenient to read table-prep formulas from a YAML file that's a table store. To achieve this, we can modify the tbl_source() statement in the create_agent() call so that store refers to the on-disk YAML file.

agent_3 <-
  create_agent(
    tbl = ~ tbl_source(
      tbl = "small_table_duck",
      store = "tbl_store.yml"
    )
  )

Function ID

1-8

See Also

Other Planning and Prep: action_levels(), create_agent(), create_informant(), db_tbl(), draft_validation(), file_tbl(), scan_data(), tbl_get(), tbl_source(), validate_rmd()

pointblank documentation built on April 25, 2023, 5:06 p.m.