nodbi - package overview

Functionality

Connect

First, a connection to a database is opened. In the example, no additional parameters are used such as database file or server; see the help page for the respective database.

“Container” is used as term to indicate where conceptually the database holds the data (e.g. a collection in MongoDB, a table in DuckDB). The key parameter of nodbi functions holds the name of the relevant container.

# name of container
key <- "my_container"

# nodbi can connect any of these databases
if (FALSE) {
  src <- src_duckdb()
  src <- src_mongo(collection = key)
  src <- src_sqlite()
  src <- src_postgres()
  src <- src_elastic()
  src <- src_couchdb(
    user = Sys.getenv("COUCHDB_TEST_USER"),
    pwd = Sys.getenv("COUCHDB_TEST_PWD")
  )
}

# this example is run with
src <- src_sqlite()

# note additional parameters can be specified,
# for example for local or remote MongoDb:
help("src_mongo")

docdb_create

Create a container if it does not yet exist and fill with value. The return value is the number of created documents. “Documents” refers to the rows in a data frame such as mtcars, or the number of NDJSON lines, or the number of list items, or the number of objects in an JSON array.

The parameter value in any nodbi function can take a data frame, a list, a JSON string, or a file name or URL pointing to NDJSON.

# check if container already exists
docdb_exists(src = src, key = key)
#> [1] FALSE

# load data from a data frame with row names into
# the container specified in "key" parameter
docdb_create(src = src, key = key, value = mtcars)
#> [1] 32

# load additionally 98 NDJSON records
docdb_create(src, key, "https://httpbin.org/stream/98")
#> Note: container 'my_container' already exists
#> [1] 98

# load additionally mapdata as list
docdb_create(src, key, jsonlite::fromJSON(mapdata, simplifyVector = FALSE))
#> Note: container 'my_container' already exists
#> [1] 2

# show JSON structure of contacts
jsonlite::minify(contacts)
#> [{"_id":"5cd67853f841025e65ce0ce2","isActive":false,"balance":"$3,808.45","age":23,"eyeColor":"green","name":"Lacy Chen","email":"lacychen@conjurica.com","about":"Sunt consequat ad dolore.\nExercitation nisi reprehenderit.","registered":"2014-08-03T12:11:54 -02:00","tags":["nulla","nisi","adipisicing","do","ad","ullamco","irure"],"friends":[{"id":0,"name":"Wooten Goodwin"},{"id":1,"name":"Brandie Woodward"},{"id":2,"name":"Angelique Britt"}]},{"_id":"5cd678531b423d5f04cfb0a1","isActive":false,"balance":"$3,400.50","age":20,"eyeColor":"brown","name":"Rae Colon","email":"raecolon@conjurica.com","about":"Nisi excepteur duis duis aliquip qui id consequat consequat.","registered":"2018-12-19T06:23:35 -01:00","tags":["nostrud","eu","consectetur","adipisicing","labore","ut","voluptate"],"friends":[{"id":0,"name":"Yang Yates"},{"id":1,"name":"Lacy Chen"}]},{"_id":"5cd6785335b63cb19dfa8347","isActive":false,"balance":"$2,579.09","age":30,"eyeColor":"brown","name":"Williamson French","email":"williamsonfrench@conjurica.com","about":"Nulla do sunt consectetur officia. Laboris pariatur incididunt.","registered":"2018-02-14T10:59:57 -01:00","tags":["exercitation","do","magna","ut","consectetur","ex","incididunt"],"friends":[{"id":0,"name":"Coleen Dunn"},{"id":1,"name":"Doris Phillips"},{"id":2,"name":"Concetta Turner"}]},{"_id":"5cd6785325ce3a94dfc54096","isActive":true,"balance":"$1,161.52","age":22,"eyeColor":"brown","name":"Pace Bell","email":"pacebell@conjurica.com","about":"Eiusmod sunt laborum ipsum do cupidatat qui id dolore do.","registered":"2018-08-17T12:23:42 -02:00","tags":["aliqua","consectetur","commodo","velit","cupidatat","duis","dolore"],"friends":[{"id":0,"name":"Baird Keller"},{"id":1,"name":"Francesca Reese"},{"id":2,"name":"Dona Bartlett"}]},{"_id":"5cd678530df22d3625ed8375","isActive":true,"balance":"$2,412.67","age":20,"eyeColor":"blue","name":"Krista Baxter","email":"kristabaxter@conjurica.com","about":"Sint quis nulla ea fugiat. Commodo nisi qui eu sit.","registered":"2017-07-19T05:03:47 -02:00","tags":["sit","cillum","commodo","labore","sint","in","exercitation"],"friends":[{"id":0,"name":"Pace Bell"}]}]

# load additionally contacts JSON data
docdb_create(src, key, contacts)
#> Note: container 'my_container' already exists
#> [1] 5

Check and list any other containers exist in the database:

docdb_list(src = src)
#> [1] "my_container"

Identifiers

The unique document identifier is its _id, corresponding to a primary index with a constraint to be unique in SQL databases.

The _id’s of an input value are either the row names of a data frame (such as mtcars) or top-level elements with the name _id such as in contacts shown just above.

Thus, expect a warning when trying to create documents with _id’s that already exist in the container.

The return value can be 0 when no documents could newly be created, or the number of the subset of documents in value that did not yet exist and could newly be created.

# zero new documents created
docdb_create(src, key, value = mtcars)
#> Note: container 'my_container' already exists
#> Warning: Could not create some documents, reason: UNIQUE constraint failed
#> [1] 0

For updating existing documents, see below function docdb_update().

docdb_get

All documents in a container can now be retrieved with docdb_get().

# load library for more
# readable print output
library(tibble)

# get all documents, irrespective of schema
as_tibble(docdb_get(src, key))
#> # A tibble: 137 × 31
#>    `_id`     isActive balance   age eyeColor name  email about registered tags  
#>    <chr>     <lgl>    <chr>   <int> <chr>    <chr> <chr> <chr> <chr>      <list>
#>  1 5cd67853… TRUE     $2,412…    20 blue     Kris… kris… "Sin… 2017-07-1… <chr> 
#>  2 5cd67853… FALSE    $3,400…    20 brown    Rae … raec… "Nis… 2018-12-1… <chr> 
#>  3 5cd67853… TRUE     $1,161…    22 brown    Pace… pace… "Eiu… 2018-08-1… <chr> 
#>  4 5cd67853… FALSE    $2,579…    30 brown    Will… will… "Nul… 2018-02-1… <chr> 
#>  5 5cd67853… FALSE    $3,808…    23 green    Lacy… lacy… "Sun… 2014-08-0… <chr> 
#>  6 6faccf10… NA       <NA>       NA <NA>     <NA>  <NA>   <NA> <NA>       <NULL>
#>  7 6faccf24… NA       <NA>       NA <NA>     <NA>  <NA>   <NA> <NA>       <NULL>
#>  8 6faccf25… NA       <NA>       NA <NA>     <NA>  <NA>   <NA> <NA>       <NULL>
#>  9 6faccf2e… NA       <NA>       NA <NA>     <NA>  <NA>   <NA> <NA>       <NULL>
#> 10 6faccf2f… NA       <NA>       NA <NA>     <NA>  <NA>   <NA> <NA>       <NULL>
#> # ℹ 127 more rows
#> # ℹ 21 more variables: friends <list>, url <chr>, args <df[,0]>,
#> #   headers <df[,4]>, origin <chr>, id <int>, destination_addresses <list>,
#> #   origin_addresses <list>, rows <list>, status <chr>, mpg <dbl>, cyl <int>,
#> #   disp <dbl>, hp <int>, drat <dbl>, wt <dbl>, qsec <dbl>, vs <int>, am <int>,
#> #   gear <int>, carb <int>

# get just 2 documents using limit and note that
# only fields for these documents are returned
as_tibble(docdb_get(src, key, limit = 2L))
#> # A tibble: 2 × 11
#>   `_id`       isActive balance   age eyeColor name  email about registered tags 
#>   <chr>       <lgl>    <chr>   <int> <chr>    <chr> <chr> <chr> <chr>      <lis>
#> 1 5cd678530d… TRUE     $2,412…    20 blue     Kris… kris… Sint… 2017-07-1… <chr>
#> 2 5cd678531b… FALSE    $3,400…    20 brown    Rae … raec… Nisi… 2018-12-1… <chr>
#> # ℹ 1 more variable: friends <list>

docdb_query

One of the most powerful functions of nodbi is docdb_query() because it permits to combine a query to select documents and to filter for fields of interest.

# query for some documents
docdb_query(src = src, key = key, query = '{"mpg": {"$gte": 30}}')
#>              _id  mpg cyl disp  hp drat    wt  qsec vs am gear carb
#> 1       Fiat 128 32.4   4 78.7  66 4.08 2.200 19.47  1  1    4    1
#> 2    Honda Civic 30.4   4 75.7  52 4.93 1.615 18.52  1  1    4    2
#> 3 Toyota Corolla 33.9   4 71.1  65 4.22 1.835 19.90  1  1    4    1
#> 4   Lotus Europa 30.4   4 95.1 113 3.77 1.513 16.90  1  1    5    2

Both parameters query (obligatory) and fields (optional) use, across all databases, MongoDB syntax such as documented for queries and fields.

# query some fields from some documents; 'query' is a mandatory
# parameter and is used here in its position in the signature
docdb_query(src, key, '{"mpg": {"$gte": 30}}', fields = '{"wt": 1, "mpg": 1}')
#>              _id    wt  mpg
#> 1       Fiat 128 2.200 32.4
#> 2    Honda Civic 1.615 30.4
#> 3 Toyota Corolla 1.835 33.9
#> 4   Lotus Europa 1.513 30.4

Unless fields specifies "_id": 0, the _id field is always included in the output of docdb_query().

# query some fields from some documents, limit return to one document
docdb_query(src, key, '{"mpg": {"$gte": 30}}', fields = '{"_id": 0, "mpg": 1}', limit = 1L)
#>    mpg
#> 1 32.4

Queries can be more complex such as in this example, showing a dot notation of a sub-field and an example operator (regular expression).

# query some subitem fields from some documents
str(docdb_query(
  src, key,
  query = '{"$or": [{"age": {"$gt": 21}},
           {"friends.name": {"$regex": "^B[a-z]{3,9}.*"}}]}',
  fields = '{"age": 1, "friends.name": 1}'
))
#> 'data.frame':    3 obs. of  3 variables:
#>  $ _id         : chr  "5cd67853f841025e65ce0ce2" "5cd6785335b63cb19dfa8347" "5cd6785325ce3a94dfc54096"
#>  $ age         : int  23 30 22
#>  $ friends.name:List of 3
#>   ..$ : chr  "Wooten Goodwin" "Brandie Woodward" "Angelique Britt"
#>   ..$ : chr  "Coleen Dunn" "Doris Phillips" "Concetta Turner"
#>   ..$ : chr  "Baird Keller" "Francesca Reese" "Dona Bartlett"

Queries work across documents of different structure such as here.

# query with results across documents
docdb_query(
  src, key,
  query = '{"$or": [{"age": {"$gt": 21}}, {"mpg": {"$gte": 30}}]}',
  fields = '{"name": 1, "disp": 1}'
)
#>                        _id              name disp
#> 1                 Fiat 128              <NA> 78.7
#> 2              Honda Civic              <NA> 75.7
#> 3           Toyota Corolla              <NA> 71.1
#> 4             Lotus Europa              <NA> 95.1
#> 5 5cd67853f841025e65ce0ce2         Lacy Chen   NA
#> 6 5cd6785335b63cb19dfa8347 Williamson French   NA
#> 7 5cd6785325ce3a94dfc54096         Pace Bell   NA

Field names

The JSON data handled by package nodbi may have a large number of field included nested fields in objects (see for example name within array friends above). Thus, an argument is provided for docdb_query() so that the function returns only the comprehensive list of all field names in documents selected with a query (or in all documents in the container if query = "{}" is specified).

docdb_query(src, key, query = '{"_id": {"$regex": "^[0-9]"}}', listfields = TRUE)
#>  [1] "about"                            "age"                             
#>  [3] "args"                             "balance"                         
#>  [5] "destination_addresses"            "email"                           
#>  [7] "eyeColor"                         "friends"                         
#>  [9] "friends.id"                       "friends.name"                    
#> [11] "headers"                          "headers.Accept"                  
#> [13] "headers.Host"                     "headers.User-Agent"              
#> [15] "headers.X-Amzn-Trace-Id"          "id"                              
#> [17] "isActive"                         "name"                            
#> [19] "origin"                           "origin_addresses"                
#> [21] "registered"                       "rows"                            
#> [23] "rows.elements"                    "rows.elements.distance"          
#> [25] "rows.elements.distance.somevalue" "rows.elements.distance.text"     
#> [27] "rows.elements.duration"           "rows.elements.duration.somevalue"
#> [29] "rows.elements.duration.text"      "rows.elements.status"            
#> [31] "status"                           "tags"                            
#> [33] "url"

The dot notation is a path from a root field to the nested field, and this notation can be used in query and fields parameters of docdb_query().

docdb_update

Queries can also be used for updating (patching) selected documents with a new value. The return value of docdb_update() corresponds to the number of documents that were updated.

This is another powerful function because value can come from a data frame, a list, a JSON string, or a file name or URL pointing to NDJSON, and if value includes row names or _id’s, these are used to identify the documents to be updated.

# number of documents corresponding to query
nrow(docdb_query(src, key, query = '{"carb": 3}'))
#> [1] 3

# update all documents using JSON, replacing the previously existing values
docdb_update(src, key, value = '{"vs": 9, "xy": [1, 2]}', query = '{"carb": 3}')
#> [1] 3

# update with value that includes _id's
docdb_update(src, key, value = '{"_id": "Merc 450SLC", "xy": 33}', query = "{}")
#> [1] 1

# show updated values
docdb_query(src, key, query = '{"carb": 3}', fields = '{"xy": 1}')
#>           _id   xy
#> 1  Merc 450SE 1, 2
#> 2  Merc 450SL 1, 2
#> 3 Merc 450SLC   33

docdb_delete

Documents and containers can be deleted with docdb_delete(). Its return value corresponds to the success of the delete operation.

# number of documents corresponding to query
nrow(docdb_query(src, key, query = '{"age": {"$lte": 23}}'))
#> [1] 4

# to delete selected documents, specify a query parameter
docdb_delete(src, key, query = '{"age": {"$lte": 23}}')
#> [1] TRUE

# this deletes the complete container from database
docdb_delete(src, key)
#> [1] TRUE

# check if still exists
docdb_exists(src, key)
#> [1] FALSE

Disconnect and shutdown

Package nodbi includes an automatic mechanism for shutting down, at the time of quit() or session restart, those databases that require it (SQLite, DuckDB, PostgreSQL).

Nevertheless, it is good practice to manually disconnect and shut down connections as specific to the database, for example for SQLite:

src
#> src: sqlite
#> SQLite library version: 3.46.0
#>  size: NA MB
#>  dbname: :memory:
#> Warning: Database is only in memory, will not persist after R ends! Consider to copy it with 
#> RSQLite::sqliteCopyDatabase(
#>   from = <your nodbi::src_sqlite() object>$con, 
#>   to = <e.g. RSQLite::dbConnect(RSQLite::SQLite(), 'local_file.db')>
#>   )

# shutdown
DBI::dbDisconnect(src$con, shutdown = TRUE)
rm(src)