regisoc/kibior
A Simple Data Management and Sharing Tool

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kibior: KibioR, an Kibio and Elasticsearch data manipulation package.

kibior: KibioR, an Kibio and Elasticsearch data manipulation package.
In regisoc/kibior: A Simple Data Management and Sharing Tool

Description Format Details Constructor Arguments Public fields Active bindings Methods Author(s) References See Also Examples

Description

KibioR is a lightweight package for data manipulation with Elasticsearch. Its main features allow easy data import, export, download, upload, searching and sharing to any Elasticsearch-based open architecture, scaling to billions of data and TB capability.

Kibior is a Kibio/Elasticsearch client written with R6 class. Instances of Kibior are object that allow to use Elasticsearch power and execute lots of predefined requests such as searching in massive amounts of data, joins between in-memory data and Elasticsearch indices, push and pull data to and from multiples Elasticsearch servers, and more. This little utilitary was built in the context of massive data invading biology and bioinformatics, but is completely versatile and can be applied to other fields. By adding it to R-scripts, it can perform several useful tasks such as: saving intermediary results, sharing them with a collaborator, automating import and upload of lots of files directly, and much more.

Format

R6Class object.

Details

A client to send, retrieve, search, join data in Elasticsearch.

Constructor Arguments

Argument Type Details Default
host character address or name of Elasticsearch server "localhost"
port numeric port of Elasticsearch server 9200
user character if required by the server, the username for authentication NULL
pwd character if required by the server, the password for authentication NULL
verbose logical verbose mode FALSE

created

Public fields

verbose

verbose mode, prints out more informations during execution

quiet_progress

progressbar quiet mode, toggles progress bar

quiet_results

results quiet mode, toggles results printing

Active bindings

host

Access and change the Elasticsearch host

port

Access and change the Elasticsearch port

endpoint

Access the Elasticsearch main endpoint

user

Access the Elasticsearch user.

pwd

Access the Elasticsearch password.

connection

Access the Elasticsearch connection object.

head_search_size

Access and change the head size default value.

cluster_name

Access the cluster name if and only if already connected.

cluster_status

Access the cluster status if and only if already connected.

nb_documents

Access the current cluster total number of documents if and only if already connected.

version

Access the Elasticsearch version if and only if already connected.

elastic_wait

Access and change the Elasticsearch wait time for update commands if and only if already connected.

valid_joins

Access the valid joins available in Kibior.

valid_count_types

Access the valid count types available (mainly observations = rows, variables = columns)

valid_elastic_metadata_types

Access the valid Elasticsearch metadata types available.

valid_push_modes

Access the valid push modes available.

shard_number

Access and modify the number of allocated primary shards when creating an Elasticsearch index.

shard_replicas_number

Access and modify the number of allocated replicas in an Elasticsearch index.

default_id_col

Access and modify the default ID column/field created when pushing data to Elasticsearch.

Methods

Public methods

Method new()

Usage
Kibior$new(
  host = "localhost",
  port = 9200,
  user = NULL,
  pwd = NULL,
  verbose = getOption("verbose")
)
Arguments
host

The target host to connect to Elasticsearch REST API (default: "localhost").

port

The target port (default: 9200).

user

If the server needs authentication, your username (default: NULL).

pwd

If the server needs authentication, your password (default: NULL).

verbose

The verbose mode (default: FALSE).

Details

Initialize a new object, automatically called when calling 'Kibior$new()'

Returns

a new instance/object of Kibior

Examples
\dontrun{
# default initiatlization, connect to "localhost:9200"
kc <- Kibior$new()
# connect to "192.168.2.145:9200"
kc <- Kibior$new("192.168.2.145")
# connect to "es:15005", verbose mode activated
kc <- Kibior$new(host = "elasticsearch", port = 15005, verbose = TRUE)
# connect to "192.168.2.145:9450" with credentials "foo:bar"
kc <- Kibior$new(host = "192.168.2.145", port = 9450, user = "foo", pwd = "bar")
# connect to "elasticsearch:9200"
kc <- Kibior$new("elasticsearch")

# get kibior var from env (".Renviron" file or local env) 
dd <- system.file("doc_env", "kibior_build.R", package = "kibior")
source(dd, local = TRUE)
kc <- .kibior_get_instance_from_env()
kc$quiet_progress <- TRUE

# preparing all examples (do not mind this for this method)
delete_if_exists <- function(index_names){
    tryCatch(
        expr = { kc$delete(index_names) },
        error = function(e){  }
    )
}
delete_if_exists(c(
    "aaa", 
    "bbb", 
    "ccc", 
    "ddd", 
    "sw", 
    "sw_naboo", 
    "sw_tatooine", 
    "sw_alderaan", 
    "sw_from_file", 
    "storms",
    "starwars"
))
}

Method print()

Usage
Kibior$print()
Details

Print simple informations of the current object.

Examples
\dontrun{
print(kc)
}

Method eq()

Usage
Kibior$eq(other = NULL)
Arguments
other

Another instance/object of Kibior (default: NULL).

Details

Tells if another instance of Kibior has the same 'host:port' couple.

Returns

TRUE if hosts and ports are identical, else FALSE

Examples
\dontrun{
kc$eq(kc)
}

Method ne()

Usage
Kibior$ne(other = NULL)
Arguments
other

Another instance/object of Kibior (default: NULL).

Details

Tells if another instance of Kibior has a different 'host:port' couple.

Returns

TRUE if hosts and ports are differents, else FALSE

Examples
\dontrun{
kc$ne(kc)
}

Method create()

Usage
Kibior$create(index_name, force = FALSE)
Arguments
index_name

a vector of index names to create (default: NULL).

force

Erase already existing identical index names? (default: FALSE).

Details

Create one or several indices in Elasticsearch.

Returns

a list containing results of creation per index

Examples
\dontrun{
kc$create("aaa")
kc$create(c("bbb", "ccc"))
}

Method list()

Usage
Kibior$list(get_specials = FALSE)
Arguments
get_specials

a boolean to get special indices (default: FALSE).

Details

List indices in Elasticsearch.

Returns

a list of index names, NULL if no index found

Examples
\dontrun{
kc$list()
kc$list(get_specials = TRUE)
}

Method has()

Usage
Kibior$has(index_name)
Arguments
index_name

a vector of index names to check.

Details

Does Elasticsearch has one or several indices?

Returns

a list with TRUE for found index, else FALSE

Examples
\dontrun{
kc$has("aaa")
kc$has(c("bbb", "ccc"))
}

Method delete()

Usage
Kibior$delete(index_name)
Arguments
index_name

a vector of index names to delete.

Details

Delete one or several indices in Elasticsearch.

Returns

a list containing results of deletion per index, or NULL if no index name match

Examples
\dontrun{
kc$delete("aaa")
kc$delete(c("bbb", "ccc"))
}

Method add_description()

Usage
Kibior$add_description(
  index_name,
  dataset_name,
  source_name,
  index_description,
  version,
  change_log,
  website,
  direct_download,
  version_date,
  license,
  contact,
  references,
  columns = list(),
  force = FALSE
)
Arguments
index_name

the index name to describe

dataset_name

the full length dataset name

source_name

the source/website/entity full length name

index_description

the index description, should be explicit

version

the version of the source dataset

change_log

what have been done from the last version

website

the website to the source dataset website

direct_download

the direct download url of the dataset source

version_date

the version or build date

license

the license attached to this dataset, could be a url

contact

a mailto/contact

references

some paper and other references (e.g. doi, url)

columns

a list of (column_name = column_description) to register (default: list())

force

if FALSE, raise an error if the description already exists, else TRUE to overwrite (default: FALSE)

Details

Add a description of a pushed dataset.

Returns

the index name if complete, else an error

Examples
\dontrun{
kc$add_description(
    index_name = "sw", 
    dataset_name = "starwars", 
    source_name = "Package dplyr", 
    index_description = "Description of starwars characters, the data comes from the Star 
     Wars API.", 
    version = "dplyr (1.0.0)", 
    link = "http://swapi.dev/", 
    direct_download_link = "http://swapi.dev/", 
    version_date = "2020-05-28", 
    license_link = "MIT", 
    columns = list(
        "name" = "Name of the character",
        "height" = "Height (cm)",
        "mass" = "Weight (kg)",
        "hair_color" = "Hair colors",
        "skin_color" = "Skin colors",
        "eye_color" = "Eye colors",
        "birth_year" = "Year born (BBY = Before Battle of Yavin)",
        "sex" = "The biological sex of the character, namely male, female, 
             hermaphroditic, or none (as in the case for Droids).",
        "gender" = "The gender role or gender identity of the character as determined by 
             their personality or the way they were progammed (as in the case for Droids
             ).",
        "homeworld" = "Name of homeworld",
        "species" = "Name of species",
        "films" = "List of films the character appeared in",
        "vehicles" = "List of vehicles the character has piloted",
        "starships" = "List of starships the character has piloted"
    )
)
}

Method has_description()

Usage
Kibior$has_description(index_name)
Arguments
index_name

the index name to describe

Details

Does the description exists?

Returns

a list splitted by index, with TRUE if the description is found, else FALSE. Removes unknown index names.

Examples
\dontrun{
kc$has_description("s*")
kc$has_description(c("sw", "asdf"))
}

Method missing_descriptions()

Usage
Kibior$missing_descriptions()
Details

List indices that do no have descriptions.

Returns

a vector of indices not present in description.

Examples
\dontrun{
kc$missing_descriptions()
}

Method remove_description()

Usage
Kibior$remove_description(index_name)
Arguments
index_name

the index name to describe

Details

Remove a description.

Returns

a vector of indices not present in description.

Examples
\dontrun{
# remove the description of 'test' index
kc$remove_description("test")
}

Method clean_descriptions()

Usage
Kibior$clean_descriptions()
Details

Remove all descriptions that do not have a index associated.

Returns

a list of index names which have been removed from descriptions.

Examples
\dontrun{
# remove the description of 'test' index
kc$clean_descriptions()
}

Method describe()

Usage
Kibior$describe(index_name, columns = NULL, pretty = FALSE)
Arguments
index_name

the index name to describe

columns

a vector of column names to describe (default: NULL)

pretty

pretty-print the result (default: FALSE)

Details

Get the description of indices and their columns.

Returns

all description, grouped by indices

Examples
\dontrun{
kc$describe("s*")
kc$describe("sw", columns = c("name", "height"))
}

Method describe_index()

Usage
Kibior$describe_index(index_name)
Arguments
index_name

the index name to describe

Details

Get the description text of indices.

Returns

a list of description text, grouped by indices

Examples
\dontrun{
kc$describe_index("s*")
}

Method describe_columns()

Usage
Kibior$describe_columns(index_name, columns)
Arguments
index_name

the index name to describe

columns

a vector of column names to describe

Details

Get the description text of index columns.

Returns

a list of description text, grouped by indices

Examples
\dontrun{
kc$describe_columns("s*", c("name", "height"))
}

Method infos()

Usage
Kibior$infos()
Details

Get informations about Elasticsearch cluster

Returns

a list of statistics about the cluster

Examples
\dontrun{
kc$infos()
}

Method ping()

Usage
Kibior$ping()
Details

Ping cluster connection

Returns

the ping result with some basic infos

Examples
\dontrun{
kc$ping()
}

Method mappings()

Usage
Kibior$mappings(index_name)
Arguments
index_name

a vector of index names to get mappings.

Details

Get mappings of indices

Returns

the list of indices, containing their mapping

Examples
\dontrun{
kc$mappings()
kc$mappings("sw")
kc$mappings(c("sw", "sw_naboo"))
}

Method settings()

Usage
Kibior$settings(index_name)
Arguments
index_name

a vector of index names to get settings.

Details

Get settings of indices

Returns

the list of indices, containing their settings

Examples
\dontrun{
kc$settings()
kc$settings("sw")
kc$settings(c("sw", "sw_tatooine"))
}

Method aliases()

Usage
Kibior$aliases(index_name)
Arguments
index_name

a vector of index names to get aliases.

Details

Get aliases of indices

Returns

the list of indices, containing their aliases

Examples
\dontrun{
kc$aliases()
kc$aliases("sw")
kc$aliases(c("sw", "sw_alderaan"))
}

Method dim()

Usage
Kibior$dim(index_name)
Arguments
index_name

a vector of index names to get aliases.

Details

Shortcut to '$count()' to match the classical 'dim()' function pattern '[line col]'

Returns

the list of indices, containing their number of observations and variables.

Examples
\dontrun{
# Couple [<nb obs> <nb var>] in "sw"
kc$dim("sw")
# Couple [<nb obs> <nb var>] in indices "sw_naboo" and "sw_alderaan"
kc$dim(c("sw_naboo", "sw_alderaan"))
}

Method columns()

Usage
Kibior$columns(index_name)
Arguments
index_name

a vector of index names, can be a pattern.

Details

Get fields/columns of indices.

Returns

a list of indices, each containing their fields/columns.

Examples
\dontrun{
kc$columns("sw")          # direct search
kc$columns("sw_*")        # pattern search
}

Method count()

Usage
Kibior$count(index_name, type = "observations", query = NULL)
Arguments
index_name

a vector of index names to get aliases.

type

a string representing the type to count: "observations" (lines) or "variables" (columns) (default: "observations").

query

a string as a query string syntax (default: NULL).

Details

Count observations or variables in Elasticsearch data

Returns

the list of indices, containing their number of observations or variables. Use '$dim()' for both

Examples
\dontrun{
# Number of observations (nb of records) in "sw"
kc$count("sw")
# Number of observations in indices "sw_naboo" and "sw_tatooine"
kc$count(c("sw_naboo", "sw_tatooine"))
# Number of variables (nb of columns) in index "sw_naboo"
kc$count("sw_naboo", type = "variables")
}

Method avg()

Usage
Kibior$avg(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get the average of numeric columns.

Returns

a tibble with avg, one line by matching index and column.

Examples
\dontrun{
# Avg of "sw" column "height"
kc$avg("sw", "height")
# if pattern
kc$avg("s*", "height")
# multiple indices, multiple columns
kc$avg(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method mean()

Usage
Kibior$mean(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get the mean of numeric columns.

Returns

a tibble with mean, one line by matching index and column.

Examples
\dontrun{
# mean of "sw" column "height"
kc$mean("sw", "height")
# if pattern
kc$mean("s*", "height")
# multiple indices, multiple columns
kc$mean(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method min()

Usage
Kibior$min(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get the minimum of numeric columns.

Returns

a tibble with min, one line by matching index and column.

Examples
\dontrun{
# min of "sw" column "height"
kc$min("sw", "height")
# if pattern
kc$min("s*", "height")
# multiple indices, multiple columns
kc$min(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method max()

Usage
Kibior$max(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get the maximum of numeric columns.

Returns

a tibble with max, one line by matching index and column.

Examples
\dontrun{
# max of "sw" column "height"
kc$max("sw", "height")
# if pattern
kc$max("s*", "height")
# multiple indices, multiple columns
kc$max(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method sum()

Usage
Kibior$sum(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get the sum of numeric columns.

Returns

a tibble with sum, one line by matching index and column.

Examples
\dontrun{
# sum of "sw" column "height"
kc$sum("sw", "height")
# if pattern
kc$sum("s*", "height")
# multiple indices, multiple columns
kc$sum(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method stats()

Usage
Kibior$stats(index_name, columns, sigma = NULL, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

sigma

(default: NULL).

query

a string as a query string syntax (default: NULL).

Details

Produces descriptive statistics of a column. Returns a tibble composed of: count, min, max, avg, sum, sum_of_squares, variance, std_deviation (+ upper and lower bounds). Multiple warnings here. One for the count and one for the std_dev. 1/ Counts: they are approximate, see vignette. 2/ Std dev: as stated in ES documentation: "The standard deviation and its bounds are displayed by default, but they are not always applicable to all data-sets. Your data must be normally distributed for the metrics to make sense. The statistics behind standard deviations assumes normally distributed data, so if your data is skewed heavily left or right, the value returned will be misleading."

Returns

a tibble with descriptive stats, one line by matching index.

Examples
\dontrun{
# Stats of "sw" column "height"
kc$stats("sw", "height")
# if pattern
kc$stats("s*", "height")
# multiple indices and sigma definition
kc$stats(c("sw", "sw2"), "height", sigma = 2.5)
# multiple indices, multiple columns
kc$stats(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method percentiles()

Usage
Kibior$percentiles(index_name, columns, percents = NULL, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

percents

a numeric vector of pecents to use (default: NULL).

query

a string as a query string syntax (default: NULL).

Details

Get percentiles of numeric columns.

Returns

a list of tibble, splitted by indices with percentiles inside tibble columns.

Examples
\dontrun{
# percentiles of "sw" column "height", default is with q1, q2 and q3
kc$percentiles("sw", "height")
# if pattern
kc$percentiles("s*", "height")
# defining percents to get
kc$percentiles("s*", "height", percents = c(20, 25))
# multiple indices, multiple columns
kc$percentiles(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method q1()

Usage
Kibior$q1(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get Q1 percentiles from numeric columns.

Returns

a list of tibble, splitted by indices with Q1 inside tibble columns.

Examples
\dontrun{
# Q1 of "sw" column "height"
kc$q1("sw", "height")
# if pattern
kc$q1("s*", "height")
# multiple indices, multiple columns
kc$q1(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method q2()

Usage
Kibior$q2(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get Q2 percentiles from numeric columns.

Returns

a list of tibble, splitted by indices with Q2 inside tibble columns.

Examples
\dontrun{
# Q2 of "sw" column "height"
kc$q2("sw", "height")
# if pattern
kc$q2("s*", "height")
# multiple indices, multiple columns
kc$q2(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method median()

Usage
Kibior$median(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get median from numeric columns. Basically a wrapper around '$q2()'.

Returns

a list of tibble, splitted by indices with median inside tibble columns.

Examples
\dontrun{
# median of "sw" column "height"
kc$median("sw", "height")
# if pattern
kc$median("s*", "height")
# multiple indices, multiple columns
kc$median(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method q3()

Usage
Kibior$q3(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Get Q3 percentiles from numeric columns.

Returns

a list of tibble, splitted by indices with Q3 inside tibble columns.

Examples
\dontrun{
# Q3 of "sw" column "height"
kc$q3("sw", "height")
# if pattern
kc$q3("s*", "height")
# multiple indices, multiple columns
kc$q3(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method summary()

Usage
Kibior$summary(index_name, columns, query = NULL)
Arguments
index_name

a vector of index names.

columns

a vector of column names.

query

a string as a query string syntax (default: NULL).

Details

Summary for numeric columns. Cumulates '$min()', '$max()', '$q1()', '$q2()', '$q3()'.

Returns

a list of tibble, splitted by indices.

Examples
\dontrun{
# summary of "sw" column "height"
kc$summary("sw", "height")
# if pattern
kc$summary("s*", "height")
# multiple indices, multiple columns
kc$summary(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")
}

Method keys()

Usage
Kibior$keys(index_name, column, max_size = 1000)
Arguments
index_name

an index name.

column

a field name of this index (default: NULL).

max_size

the maximum result to return (default: 1000).

Details

Get distinct keys elements of a specific column.

Returns

a vector of keys values from this field/column

Examples
\dontrun{
kc$keys("sw", "name")
kc$keys("sw", "eye_color")
}

Method bam_to_tibble()

Usage
Kibior$bam_to_tibble(bam_data = NULL)
Arguments
bam_data

data from a BAM file (default: NULL).

Details

Transformation function for collapsing the BAM list of lists format into a single list as per the Rsamtools vignette

Returns

a tibble of BAM data

Examples
\dontrun{
dd_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
bam_param <- Rsamtools::ScanBamParam(what = c("pos", "qwidth"))
bam_data <- Rsamtools::scanBam(dd_bai, param = bam_param)
kc$bam_to_tibble(bam_data)
}

Method soft_cast()

Usage
Kibior$soft_cast(
  data,
  caster = getFromNamespace("as_tibble", "tibble"),
  caster_args = list(.name_repair = "unique"),
  warn = TRUE
)
Arguments
data

data to cast.

caster

the caster closure/function (default: tibble::as_tibble)

caster_args

others caster args (default: list(.name_repair = "unique"))

warn

do print warning if error? (default: TRUE)

Details

Casting function that tries to cast a transformation closure. Uses tibble::as_tibble() by default.

Returns

a cast or the unchanged data.

Examples
\dontrun{
kc$soft_cast(datasets::iris)
}

Method get_resource()

Usage
Kibior$get_resource(url_or_filepath, fileext = NULL)
Arguments
url_or_filepath

a filepath or an URL.

fileext

the file extension (default: NULL).

Details

Get a local filepath or an URL data through a tempfile. If the file exists locally, the filepath will be returned, if not, it will tries to download the data and return the temp filepath.

Returns

a filepath.

Examples
\dontrun{
kc$get_resource(system.file("R", "kibior.R", package = "kibior"))
kc$get_resource("https://ftp.ncbi.nlm.nih.gov/entrez/README")
}

Method export()

Usage
Kibior$export(data, filepath, format = "csv", force = FALSE)
Arguments
data

an index name or in-memory data to be extracted to a file.

filepath

the filepath to use as export, must contain the file extention.

format

the file format to use (default: "csv").

force

overwrite the file? (default: FALSE).

Details

Export data to a file. Needs 'rio' package from CRAN. Some data formats are not installed by default. Use 'rio::install_formats()' to be able to parse them.

Returns

the filepath if correctly exported, else an error

Examples
\dontrun{
f <- tempfile(fileext=".csv")
# export and overwrite last file with the same data from Elasticsearch
kc$export(data = "sw", filepath = f)
# export from in-memory data to a file
kc$export(data = dplyr::starwars, filepath = f, force = TRUE)
}

Method import_tabular()

Usage
Kibior$import_tabular(filepath, to_tibble = TRUE, fileext = ".csv")
Arguments
filepath

the filepath to use as import, must contain the file extention.

to_tibble

returns the result as tibble? If FALSE, the raw default rio::import() format will be used (default: TRUE).

fileext

the file extension (default: ".csv").

Details

Import method for tabular data. Needs 'rio' package from CRAN. Works mainly with CSV, TSV, TAB, TXT and ZIPped formats.

Returns

data contained in the file as a tibble, or NULL.

Examples
\dontrun{
f <- tempfile(fileext = ".csv")
rio::export(ggplot2::diamonds, f)
# import to in-memory variable
kc$import_tabular(filepath = f)
# import raw data
kc$import_tabular(filepath = f, to_tibble = FALSE)
}

Method import_features()

Usage
Kibior$import_features(filepath, to_tibble = TRUE, fileext = ".gtf")
Arguments
filepath

the filepath to use as import, must contain the file extention.

to_tibble

returns the result as tibble? If FALSE, the raw default rtracklayer::import() format will be used (default: TRUE).

fileext

the file extension (default: ".gtf").

Details

Import method for features data. Needs 'rtracklayer' package from Bioconductor. Works with BED, GTF, GFFx, and GZIPped formats.

Returns

data contained in the file as a tibble, or NULL.

Examples
\dontrun{
# get sample files
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bed <- system.file("extdata", "cpg.bed", package = "kibior")
# import to in-memory variable
kc$import_features(filepath = f_bed)
kc$import_features(filepath = f_gff)
# import raw data
kc$import_features(filepath = f_bed, to_tibble = FALSE)
kc$import_features(filepath = f_gff, to_tibble = FALSE)
}

Method import_alignments()

Usage
Kibior$import_alignments(filepath, to_tibble = TRUE, fileext = ".bam")
Arguments
filepath

the filepath to use as import, should contain the file extention.

to_tibble

returns the result as tibble? If FALSE, the raw default Rsamtools::scanBam() format will be used (default: TRUE).

fileext

the file extension (default: ".bam").

Details

Import method for alignments data. Needs 'Rsamtools' packages from Bioconductor. Works with BAM format.

Returns

data contained in the file as a tibble, or NULL.

Examples
\dontrun{
# get sample file
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
# import to in-memory variable
kc$import_alignments(filepath = f_bai)
# import raw data
kc$import_alignments(filepath = f_bai, to_tibble = FALSE)
}

Method import_json()

Usage
Kibior$import_json(filepath, to_tibble = TRUE, fileext = ".json")
Arguments
filepath

the filepath to use as import, should contain the file extention.

to_tibble

returns the result as tibble? If FALSE, the raw dataframe format will be used (default: TRUE).

fileext

the file extension (default: ".json").

Details

Import method for JSON format. Needs 'jsonlite' packages from CRAN.

Returns

data contained in the file as a tibble, dataframe or NULL.

Examples
\dontrun{
# get sample file
f_json <- system.file("extdata", "storms100.json", package = "kibior")
# import to in-memory variable
kc$import_json(f_json)
# import raw data
kc$import_json(f_json, to_tibble = FALSE)
}

Method import_sequences()

Usage
Kibior$import_sequences(filepath, to_tibble = TRUE, fasta_type = "auto")
Arguments
filepath

the filepath to use as import, should contain the file extention.

to_tibble

returns the result as tibble? If FALSE, the raw default Rsamtools::scanBam() format will be used (default: TRUE).

fasta_type

type of parsing. It can be "dna", "rna", "aa" ou "auto" (default: "auto")

Details

Import method for sequences data. Needs 'Biostrings' package from Bioconductor. Works with FASTA formats.

Returns

data contained in the file as a tibble, or NULL.

Examples
\dontrun{
# get sample file
f_dna <- system.file("extdata", "dna_human_y.fa.gz", package = "kibior")
f_rna <- system.file("extdata", "ncrna_mus_musculus.fa.gz", package = "kibior")
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
# import to in-memory variable
kc$import_sequences(filepath = f_dna, fasta_type = "dna")
# import raw data
kc$import_sequences(filepath = f_rna, to_tibble = FALSE, fasta_type = "rna")
# import auto
kc$import_sequences(filepath = f_aa)
}

Method guess_import()

Usage
Kibior$guess_import(filepath, to_tibble = TRUE)
Arguments
filepath

the filepath to use as import, must contain the file extention.

to_tibble

returns the result as tibble? (default: TRUE).

Details

Import method that will try to guess importation method. Will also try to read from compressed data if they are. This method will call other import_* methods when trying. Some data formats are not installed by default. Use 'rio::install_formats()' to be able to parse them.

Returns

data contained in the file, or NULL.

Examples
\dontrun{
# get sample file
f_dna <- system.file("extdata", "dna_human_y.fa.gz", package = "kibior")
f_rna <- system.file("extdata", "ncrna_mus_musculus.fa.gz", package = "kibior")
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bed <- system.file("extdata", "cpg.bed", package = "kibior")
# import 
kc$guess_import(f_dna)
kc$guess_import(f_rna)
kc$guess_import(f_aa)
kc$guess_import(f_bai)
kc$guess_import(f_gff)
kc$guess_import(f_bed)
}

Method import()

Usage
Kibior$import(
  filepath,
  import_type = "auto",
  push_index = NULL,
  push_mode = "check",
  id_col = NULL,
  to_tibble = TRUE
)
Arguments
filepath

the filepath to use as import, must contain the file extention.

import_type

can be one of "auto", "tabular", "features", "alignments", "sequences" (default: "auto").

push_index

the name of the index where to push data (default: NULL).

push_mode

the push mode (default: "check").

id_col

the column name of unique IDs (default: NULL).

to_tibble

returns the result as tibble? (default: TRUE).

Details

Generic import method. This method will call other import_* methods when trying. Some data formats are not installed by default.

Returns

data contained in the file, or NULL.

Examples
\dontrun{
# get sample file
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
# import 
kc$import(filepath = f_aa)
# import to Elasticsearch index ("sw_from_file") if not exists
kc$import(filepath = f_bai, push_index = "sw_from_file")
# import to index by recreating it, then pull indexed data
kc$import(filepath = f_gff, push_index = "sw_from_file",
 push_mode = "recreate")
}

Method push()

Usage
Kibior$push(data, index_name, bulk_size = 1000, mode = "check", id_col = NULL)
Arguments
data

the data to push.

index_name

the index name to use in Elasticsearch.

bulk_size

the number of record to send to Elasticsearch in a row (default: 1000).

mode

the push mode, could be "check", "recreate" or "update" (default: "check").

id_col

an column anme to use as ID, must be composed of unique elements (default: NULL).

Details

Push data from in-memory to Elasticsearch. Everything is done by bulk.

Returns

the index_name given if the push ended well, else an error.

Examples
\dontrun{
# erase the last push data by recreating the index and re-pushing data
kc$push(dplyr::starwars, index_name = "sw", mode = "recreate")
# characters names are unique, can be used as ID
kc$push(dplyr::starwars, index_name = "sw", mode = "recreate", id_col = "name")
# a bit more complicated: update some data of the dataset "starwars"
# 38 records on 87 filtered
some_new_data <- dplyr::filter(dplyr::starwars, height > 180)
# make them all "gender <- female"
some_new_data["gender"] <- "female"
# update that apply, based on cahracter names to match the right record
kc$push(some_new_data, "sw", mode = "update", id_col = "name")
# view result by querying
kc$pull("sw", query = "height:>180", columns = c("name", "gender"))
}

Method pull()

Usage
Kibior$pull(
  index_name,
  bulk_size = 500,
  max_size = NULL,
  scroll_timer = "3m",
  keep_metadata = FALSE,
  columns = NULL,
  query = NULL
)
Arguments
index_name

the index name to use in Elasticsearch.

bulk_size

the number of record to send to Elasticsearch in a row (default: 500).

max_size

the number of record Elasticsearch will send (default: NULL (all data)).

scroll_timer

the time the scroll API will let the request alive to scroll on the result (default: "3m" (3 minute)).

keep_metadata

does Elasticsearch needs to sent metadata? Data columns will be prefixed by "_source." (default: FALSE).

columns

a vector of columns to select (default: NULL (all columns)).

query

a string formatted to Elasticsearch query syntax, see links for the syntax details (default: NULL)

# Simple syntax details:

Details

Pull data from Elasticsearch. Everything is done by bulk. This method is essentially a wrapper around '$search()' with parameter 'head = FALSE'

Returns

a list of datasets corresponding to the pull request, else an error. Keys of the list are index names matching the request, value are the associated tibbles

Examples
\dontrun{
# push some data sample
kc$push(dplyr::storms, "storms")
# get the whole "sw" index
kc$pull("sw")
# get the whole "sw" index with all metadata
kc$pull("sw", keep_metadata = TRUE)
# get only "name" and "status" columns of indices starting with "s"
# columns not found will be ignored
kc$pull("s*", columns = c("name", "status"))
# limit the size of the result to 10
kc$pull("storms", max_size = 10, bulk_size = 10)
# use Elasticsearch query syntax to select and filter on all indices, for all data
# Here, we want to search for all records taht match the conditions:
# field "height" is strictly more than 180 AND field homeworld is "Tatooine" OR "Naboo"
r <- kc$pull("sw", query = "height:>180 && homeworld:(Tatooine || Naboo)")
# it can be used in conjunction with `columns` to select only columns that matter
r <- kc$pull("sw", query = "height:>180 && homeworld:(Tatooine || Naboo)", columns = 
 c("name", "hair_color", "homeworld"))
}

Method move()

Usage
Kibior$move(
  from_index,
  to_index,
  from_instance = NULL,
  force = FALSE,
  copy = FALSE
)
Arguments
from_index

The source index name (default: NULL).

to_index

The destination index name (default: NULL).

from_instance

If not NULL, the Kibior object of another instance. if NULL (default), this instance will be used. (default: NULL).

force

Does the destination index need to be erase? (default: FALSE)

copy

Does the destination have to be a copy of the source? FALSE (default) will delete source index, TRUE will keep it. (default: FALSE).

Details

Move data from one index to another. It needs to be configured in the 'config/elasticsearch.yml' file to actually work.

Returns

the reindex result

Examples
\dontrun{
kc$push(dplyr::starwars, "sw", mode = "recreate")
# move data from an index to another (change name, same instance)
r <- kc$move(from_index = "sw", to_index = "sw_new")
kc$pull("sw_new")
kc$list()
}

Method copy()

Usage
Kibior$copy(from_index, to_index, from_instance = NULL, force = FALSE)
Arguments
from_index

The source index name (default: NULL).

to_index

The destination index name (default: NULL).

from_instance

If not NULL, the Kibior object of another instance. if NULL (default), this instance will be used. (default: NULL).

force

Does the destination index need to be erase? (default: FALSE)

Details

Copy data from one index to another. It needs to be configured in the 'config/elasticsearch.yml' file to actually work. This method is a wrapper around '$move(copy = TRUE)'.

Returns

the reindex result

Examples
\dontrun{
# copy data from one index to another (same instance)
r <- kc$copy(from_index = "sw_new", to_index = "sw")
kc$pull(c("sw", "sw_new"))
kc$list()
}

Method match()

Usage
Kibior$match(index_name)
Arguments
index_name

the index name to use in Elasticsearch, can be a pattern with '*'.

Details

Match requested index names against Elasticsearch indices list.

Returns

a vector of matching index names, NULL if nothing matches.

Examples
\dontrun{
# search "sw" index name
kc$match("sw")
# search all starting with an "s"
kc$match("s*")
# get all index name, identical to `$list()`
kc$match("*")
# search multiple names 
kc$match(c("sw", "sw_new", "nope"))
# search multiple names with pattern
kc$match(c("s*", "nope"))
}

Method search()

Usage
Kibior$search(
  index_name = "_all",
  keep_metadata = FALSE,
  columns = NULL,
  bulk_size = 500,
  max_size = NULL,
  scroll_timer = "3m",
  head = TRUE,
  query = NULL
)
Arguments
index_name

the index name to use in Elasticsearch (default: NULL).

keep_metadata

does Elasticsearch needs to sent metadata? Data columns will be prefixed by "_source." (default: FALSE).

columns

a vector of columns to select (default: NULL (all columns)).

bulk_size

the number of record to send to Elasticsearch in a row (default: 500).

max_size

the number of record Elasticsearch will send (default: NULL (all data)).

scroll_timer

the time the scroll API will let the request alive to scroll on the result (default: "3m" (3 minutes)).

head

a boolean limiting the search result and time (default: TRUE)

query

a string formatted to Elasticsearch query syntax, see links for the syntax details (default: NULL)

Details

Search data from Elasticsearch. The goal of this method is to discover quickly what data are interesting, thus 'head = TRUE' by default. If you want to get all data, use 'head = FALSE' or '$pull()'. Everything is done by bulk.

Returns

a list of datasets corresponding to the pull request, else an error. Keys of the list are index names matching the request, value are the associated tibbles

Examples
\dontrun{
# search "sw" index, head mode on
kc$search("sw")
# search "sw" index with all metadata, head mode on
kc$search("sw", keep_metadata = TRUE)
# get only "name" field of the head of indices starting with "s"
# if an index does not have the "name" field, it will be empty
kc$search("s*", columns = "name")
# limit the size of the result to 50 to the whole index
kc$search("storms", max_size = 50, bulk_size = 50, head = FALSE)
# use Elasticsearch query syntax to select and filter on all indices, for all data
# Here, we want to search for all records taht match the conditions:
# field "height" is strictly more than 180 AND field homeworld is "Tatooine" OR "Naboo"
kc$search("*", query = "height:>180 && homeworld:(Tatooine || Naboo)")
# it can be used in conjunction with `columns` to select only columns that matter
kc$search("*", query = "height:>180 && homeworld:(Tatooine || Naboo)", columns = 
 c("name", "hair_color", "homeworld"))
}

Method inner_join()

Usage
Kibior$inner_join(...)
Arguments
...

see 'join()' params.

Details

Execute a inner join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# some data for joins examples
kc$push(ggplot2::diamonds, "diamonds")
# prepare join datasets, only big the biggest diamonds are selected (9)
sup_carat <- dplyr::filter(ggplot2::diamonds, carat > 3.5)
r <- kc$push(sup_carat, "diamonds_superior")
# execute a inner_join with one index and one in-memory dataset
kc$inner_join(ggplot2::diamonds, "diamonds_superior")
# execute a inner_join with one index queried, and one in-memory dataset
kc$inner_join(ggplot2::diamonds, "diamonds", right_query 
 = "carat:>3.5")
}

Method full_join()

Usage
Kibior$full_join(...)
Arguments
...

see 'join()' params.

Details

Execute a full join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a full_join with one index and one in-memory dataset
kc$full_join(fair_cut, "diamonds_superior")
# execute a full_join with one index queried, and one in-memory dataset
kc$full_join(sup_carat, "diamonds", right_query = "cut:fair")
}

Method left_join()

Usage
Kibior$left_join(...)
Arguments
...

see 'join()' params.

Details

Execute a left join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a left_join with one index and one in-memory dataset
kc$left_join(fair_cut, "diamonds_superior")
# execute a left_join with one index queried, and one in-memory dataset
kc$left_join(sup_carat, "diamonds", right_query 
 = "cut:fair")
}

Method right_join()

Usage
Kibior$right_join(...)
Arguments
...

see 'join()' params.

Details

Execute a right join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a right_join with one index and one in-memory dataset
kc$right_join(fair_cut, "diamonds_superior")
# execute a right_join with one index queried, and one in-memory dataset
kc$right_join(sup_carat, "diamonds", right_query 
 = "cut:fair")
}

Method semi_join()

Usage
Kibior$semi_join(...)
Arguments
...

see 'join()' params.

Details

Execute a semi join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a semi_join with one index and one in-memory dataset
kc$semi_join(fair_cut, "diamonds_superior")
# execute a semi_join with one index queried, and one in-memory dataset
kc$semi_join(sup_carat, "diamonds", right_query 
 = "cut:fair")
}

Method anti_join()

Usage
Kibior$anti_join(...)
Arguments
...

see 'join()' params.

Details

Execute a anti join between two datasets using 'dplyr' joins. The datasets can be in-memory (variable name) or the name of an currently stored Elasticsearch index. Joins cannot be done on column of type "list" ("by" argument).

Returns

a tibble

Examples
\dontrun{
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a anti_join with one index and one in-memory dataset
kc$anti_join(fair_cut, "diamonds_superior")
# execute a anti_join with one index queried, and one in-memory dataset
kc$anti_join(sup_carat, "diamonds", right_query 
 = "cut:fair")
# 
# Do not mind this, removing example indices
elastic::index_delete(kc$connection, "*")
kc <- NULL
}

Method clone()

The objects of this class are cloneable with this method.

Usage
Kibior$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Régis Ongaro-Carcy, regis.ongaro-carcy2@crchudequebec.ulaval.ca

References

Kibio.science: http://kibio.science,
Elasticsearch documentation: https://www.elastic.co/guide/en/elasticsearch/reference/current/index.html

See Also

kibior

you should use count for more accurate count.

https://www.elastic.co/guide/en/elasticsearch/reference/current/common-options.html#time-units for time-units and https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-query-string-query.html#query-string-syntax for the Elasticsearch query string syntax.

: https://www.elastic.co/guide/en/elasticsearch/reference/current/docs-reindex.html Elasticsearch reindex feature for more information.

: https://www.elastic.co/guide/en/elasticsearch/reference/current/docs-reindex.html Elasticsearch reindex feature for more information.

https://www.elastic.co/guide/en/elasticsearch/reference/current/common-options.html#time-units for time-units and https://www.elastic.co/guide/en/elasticsearch/reference/current/query-dsl-query-string-query.html#query-string-syntax for the Elasticsearch query string syntax.

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## ------------------------------------------------
## Method `Kibior$new`
## ------------------------------------------------

## Not run: 
# default initiatlization, connect to "localhost:9200"
kc <- Kibior$new()
# connect to "192.168.2.145:9200"
kc <- Kibior$new("192.168.2.145")
# connect to "es:15005", verbose mode activated
kc <- Kibior$new(host = "elasticsearch", port = 15005, verbose = TRUE)
# connect to "192.168.2.145:9450" with credentials "foo:bar"
kc <- Kibior$new(host = "192.168.2.145", port = 9450, user = "foo", pwd = "bar")
# connect to "elasticsearch:9200"
kc <- Kibior$new("elasticsearch")

# get kibior var from env (".Renviron" file or local env) 
dd <- system.file("doc_env", "kibior_build.R", package = "kibior")
source(dd, local = TRUE)
kc <- .kibior_get_instance_from_env()
kc$quiet_progress <- TRUE

# preparing all examples (do not mind this for this method)
delete_if_exists <- function(index_names){
    tryCatch(
        expr = { kc$delete(index_names) },
        error = function(e){  }
    )
}
delete_if_exists(c(
    "aaa", 
    "bbb", 
    "ccc", 
    "ddd", 
    "sw", 
    "sw_naboo", 
    "sw_tatooine", 
    "sw_alderaan", 
    "sw_from_file", 
    "storms",
    "starwars"
))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$print`
## ------------------------------------------------

## Not run: 
print(kc)

## End(Not run)



## ------------------------------------------------
## Method `Kibior$eq`
## ------------------------------------------------

## Not run: 
kc$eq(kc)

## End(Not run)



## ------------------------------------------------
## Method `Kibior$ne`
## ------------------------------------------------

## Not run: 
kc$ne(kc)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$create`
## ------------------------------------------------

## Not run: 
kc$create("aaa")
kc$create(c("bbb", "ccc"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$list`
## ------------------------------------------------

## Not run: 
kc$list()
kc$list(get_specials = TRUE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$has`
## ------------------------------------------------

## Not run: 
kc$has("aaa")
kc$has(c("bbb", "ccc"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$delete`
## ------------------------------------------------

## Not run: 
kc$delete("aaa")
kc$delete(c("bbb", "ccc"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$add_description`
## ------------------------------------------------

## Not run: 
kc$add_description(
    index_name = "sw", 
    dataset_name = "starwars", 
    source_name = "Package dplyr", 
    index_description = "Description of starwars characters, the data comes from the Star 
     Wars API.", 
    version = "dplyr (1.0.0)", 
    link = "http://swapi.dev/", 
    direct_download_link = "http://swapi.dev/", 
    version_date = "2020-05-28", 
    license_link = "MIT", 
    columns = list(
        "name" = "Name of the character",
        "height" = "Height (cm)",
        "mass" = "Weight (kg)",
        "hair_color" = "Hair colors",
        "skin_color" = "Skin colors",
        "eye_color" = "Eye colors",
        "birth_year" = "Year born (BBY = Before Battle of Yavin)",
        "sex" = "The biological sex of the character, namely male, female, 
             hermaphroditic, or none (as in the case for Droids).",
        "gender" = "The gender role or gender identity of the character as determined by 
             their personality or the way they were progammed (as in the case for Droids
             ).",
        "homeworld" = "Name of homeworld",
        "species" = "Name of species",
        "films" = "List of films the character appeared in",
        "vehicles" = "List of vehicles the character has piloted",
        "starships" = "List of starships the character has piloted"
    )
)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$has_description`
## ------------------------------------------------

## Not run: 
kc$has_description("s*")
kc$has_description(c("sw", "asdf"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$missing_descriptions`
## ------------------------------------------------

## Not run: 
kc$missing_descriptions()

## End(Not run)


## ------------------------------------------------
## Method `Kibior$remove_description`
## ------------------------------------------------

## Not run: 
# remove the description of 'test' index
kc$remove_description("test")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$clean_descriptions`
## ------------------------------------------------

## Not run: 
# remove the description of 'test' index
kc$clean_descriptions()

## End(Not run)


## ------------------------------------------------
## Method `Kibior$describe`
## ------------------------------------------------

## Not run: 
kc$describe("s*")
kc$describe("sw", columns = c("name", "height"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$describe_index`
## ------------------------------------------------

## Not run: 
kc$describe_index("s*")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$describe_columns`
## ------------------------------------------------

## Not run: 
kc$describe_columns("s*", c("name", "height"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$infos`
## ------------------------------------------------

## Not run: 
kc$infos()

## End(Not run)


## ------------------------------------------------
## Method `Kibior$ping`
## ------------------------------------------------

## Not run: 
kc$ping()

## End(Not run)


## ------------------------------------------------
## Method `Kibior$mappings`
## ------------------------------------------------

## Not run: 
kc$mappings()
kc$mappings("sw")
kc$mappings(c("sw", "sw_naboo"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$settings`
## ------------------------------------------------

## Not run: 
kc$settings()
kc$settings("sw")
kc$settings(c("sw", "sw_tatooine"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$aliases`
## ------------------------------------------------

## Not run: 
kc$aliases()
kc$aliases("sw")
kc$aliases(c("sw", "sw_alderaan"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$dim`
## ------------------------------------------------

## Not run: 
# Couple [<nb obs> <nb var>] in "sw"
kc$dim("sw")
# Couple [<nb obs> <nb var>] in indices "sw_naboo" and "sw_alderaan"
kc$dim(c("sw_naboo", "sw_alderaan"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$columns`
## ------------------------------------------------

## Not run: 
kc$columns("sw")          # direct search
kc$columns("sw_*")        # pattern search

## End(Not run)


## ------------------------------------------------
## Method `Kibior$count`
## ------------------------------------------------

## Not run: 
# Number of observations (nb of records) in "sw"
kc$count("sw")
# Number of observations in indices "sw_naboo" and "sw_tatooine"
kc$count(c("sw_naboo", "sw_tatooine"))
# Number of variables (nb of columns) in index "sw_naboo"
kc$count("sw_naboo", type = "variables")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$avg`
## ------------------------------------------------

## Not run: 
# Avg of "sw" column "height"
kc$avg("sw", "height")
# if pattern
kc$avg("s*", "height")
# multiple indices, multiple columns
kc$avg(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$mean`
## ------------------------------------------------

## Not run: 
# mean of "sw" column "height"
kc$mean("sw", "height")
# if pattern
kc$mean("s*", "height")
# multiple indices, multiple columns
kc$mean(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$min`
## ------------------------------------------------

## Not run: 
# min of "sw" column "height"
kc$min("sw", "height")
# if pattern
kc$min("s*", "height")
# multiple indices, multiple columns
kc$min(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$max`
## ------------------------------------------------

## Not run: 
# max of "sw" column "height"
kc$max("sw", "height")
# if pattern
kc$max("s*", "height")
# multiple indices, multiple columns
kc$max(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$sum`
## ------------------------------------------------

## Not run: 
# sum of "sw" column "height"
kc$sum("sw", "height")
# if pattern
kc$sum("s*", "height")
# multiple indices, multiple columns
kc$sum(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$stats`
## ------------------------------------------------

## Not run: 
# Stats of "sw" column "height"
kc$stats("sw", "height")
# if pattern
kc$stats("s*", "height")
# multiple indices and sigma definition
kc$stats(c("sw", "sw2"), "height", sigma = 2.5)
# multiple indices, multiple columns
kc$stats(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$percentiles`
## ------------------------------------------------

## Not run: 
# percentiles of "sw" column "height", default is with q1, q2 and q3
kc$percentiles("sw", "height")
# if pattern
kc$percentiles("s*", "height")
# defining percents to get
kc$percentiles("s*", "height", percents = c(20, 25))
# multiple indices, multiple columns
kc$percentiles(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$q1`
## ------------------------------------------------

## Not run: 
# Q1 of "sw" column "height"
kc$q1("sw", "height")
# if pattern
kc$q1("s*", "height")
# multiple indices, multiple columns
kc$q1(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$q2`
## ------------------------------------------------

## Not run: 
# Q2 of "sw" column "height"
kc$q2("sw", "height")
# if pattern
kc$q2("s*", "height")
# multiple indices, multiple columns
kc$q2(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$median`
## ------------------------------------------------

## Not run: 
# median of "sw" column "height"
kc$median("sw", "height")
# if pattern
kc$median("s*", "height")
# multiple indices, multiple columns
kc$median(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$q3`
## ------------------------------------------------

## Not run: 
# Q3 of "sw" column "height"
kc$q3("sw", "height")
# if pattern
kc$q3("s*", "height")
# multiple indices, multiple columns
kc$q3(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$summary`
## ------------------------------------------------

## Not run: 
# summary of "sw" column "height"
kc$summary("sw", "height")
# if pattern
kc$summary("s*", "height")
# multiple indices, multiple columns
kc$summary(c("sw", "sw2"), c("height", "mass"), query = "homeworld:naboo")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$keys`
## ------------------------------------------------

## Not run: 
kc$keys("sw", "name")
kc$keys("sw", "eye_color")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$bam_to_tibble`
## ------------------------------------------------

## Not run: 
dd_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
bam_param <- Rsamtools::ScanBamParam(what = c("pos", "qwidth"))
bam_data <- Rsamtools::scanBam(dd_bai, param = bam_param)
kc$bam_to_tibble(bam_data)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$soft_cast`
## ------------------------------------------------

## Not run: 
kc$soft_cast(datasets::iris)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$get_resource`
## ------------------------------------------------

## Not run: 
kc$get_resource(system.file("R", "kibior.R", package = "kibior"))
kc$get_resource("https://ftp.ncbi.nlm.nih.gov/entrez/README")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$export`
## ------------------------------------------------

## Not run: 
f <- tempfile(fileext=".csv")
# export and overwrite last file with the same data from Elasticsearch
kc$export(data = "sw", filepath = f)
# export from in-memory data to a file
kc$export(data = dplyr::starwars, filepath = f, force = TRUE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import_tabular`
## ------------------------------------------------

## Not run: 
f <- tempfile(fileext = ".csv")
rio::export(ggplot2::diamonds, f)
# import to in-memory variable
kc$import_tabular(filepath = f)
# import raw data
kc$import_tabular(filepath = f, to_tibble = FALSE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import_features`
## ------------------------------------------------

## Not run: 
# get sample files
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bed <- system.file("extdata", "cpg.bed", package = "kibior")
# import to in-memory variable
kc$import_features(filepath = f_bed)
kc$import_features(filepath = f_gff)
# import raw data
kc$import_features(filepath = f_bed, to_tibble = FALSE)
kc$import_features(filepath = f_gff, to_tibble = FALSE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import_alignments`
## ------------------------------------------------

## Not run: 
# get sample file
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
# import to in-memory variable
kc$import_alignments(filepath = f_bai)
# import raw data
kc$import_alignments(filepath = f_bai, to_tibble = FALSE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import_json`
## ------------------------------------------------

## Not run: 
# get sample file
f_json <- system.file("extdata", "storms100.json", package = "kibior")
# import to in-memory variable
kc$import_json(f_json)
# import raw data
kc$import_json(f_json, to_tibble = FALSE)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import_sequences`
## ------------------------------------------------

## Not run: 
# get sample file
f_dna <- system.file("extdata", "dna_human_y.fa.gz", package = "kibior")
f_rna <- system.file("extdata", "ncrna_mus_musculus.fa.gz", package = "kibior")
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
# import to in-memory variable
kc$import_sequences(filepath = f_dna, fasta_type = "dna")
# import raw data
kc$import_sequences(filepath = f_rna, to_tibble = FALSE, fasta_type = "rna")
# import auto
kc$import_sequences(filepath = f_aa)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$guess_import`
## ------------------------------------------------

## Not run: 
# get sample file
f_dna <- system.file("extdata", "dna_human_y.fa.gz", package = "kibior")
f_rna <- system.file("extdata", "ncrna_mus_musculus.fa.gz", package = "kibior")
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bed <- system.file("extdata", "cpg.bed", package = "kibior")
# import 
kc$guess_import(f_dna)
kc$guess_import(f_rna)
kc$guess_import(f_aa)
kc$guess_import(f_bai)
kc$guess_import(f_gff)
kc$guess_import(f_bed)

## End(Not run)


## ------------------------------------------------
## Method `Kibior$import`
## ------------------------------------------------

## Not run: 
# get sample file
f_aa <- system.file("extdata", "pep_mus_spretus.fa.gz", package = "kibior")
f_gff <- system.file("extdata", "chr_y.gff3.gz", package = "kibior")
f_bai <- system.file("extdata", "test.bam.bai", package = "kibior")
# import 
kc$import(filepath = f_aa)
# import to Elasticsearch index ("sw_from_file") if not exists
kc$import(filepath = f_bai, push_index = "sw_from_file")
# import to index by recreating it, then pull indexed data
kc$import(filepath = f_gff, push_index = "sw_from_file",
 push_mode = "recreate")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$push`
## ------------------------------------------------

## Not run: 
# erase the last push data by recreating the index and re-pushing data
kc$push(dplyr::starwars, index_name = "sw", mode = "recreate")
# characters names are unique, can be used as ID
kc$push(dplyr::starwars, index_name = "sw", mode = "recreate", id_col = "name")
# a bit more complicated: update some data of the dataset "starwars"
# 38 records on 87 filtered
some_new_data <- dplyr::filter(dplyr::starwars, height > 180)
# make them all "gender <- female"
some_new_data["gender"] <- "female"
# update that apply, based on cahracter names to match the right record
kc$push(some_new_data, "sw", mode = "update", id_col = "name")
# view result by querying
kc$pull("sw", query = "height:>180", columns = c("name", "gender"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$pull`
## ------------------------------------------------

## Not run: 
# push some data sample
kc$push(dplyr::storms, "storms")
# get the whole "sw" index
kc$pull("sw")
# get the whole "sw" index with all metadata
kc$pull("sw", keep_metadata = TRUE)
# get only "name" and "status" columns of indices starting with "s"
# columns not found will be ignored
kc$pull("s*", columns = c("name", "status"))
# limit the size of the result to 10
kc$pull("storms", max_size = 10, bulk_size = 10)
# use Elasticsearch query syntax to select and filter on all indices, for all data
# Here, we want to search for all records taht match the conditions:
# field "height" is strictly more than 180 AND field homeworld is "Tatooine" OR "Naboo"
r <- kc$pull("sw", query = "height:>180 && homeworld:(Tatooine || Naboo)")
# it can be used in conjunction with `columns` to select only columns that matter
r <- kc$pull("sw", query = "height:>180 && homeworld:(Tatooine || Naboo)", columns = 
 c("name", "hair_color", "homeworld"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$move`
## ------------------------------------------------

## Not run: 
kc$push(dplyr::starwars, "sw", mode = "recreate")
# move data from an index to another (change name, same instance)
r <- kc$move(from_index = "sw", to_index = "sw_new")
kc$pull("sw_new")
kc$list()

## End(Not run) 


## ------------------------------------------------
## Method `Kibior$copy`
## ------------------------------------------------

## Not run: 
# copy data from one index to another (same instance)
r <- kc$copy(from_index = "sw_new", to_index = "sw")
kc$pull(c("sw", "sw_new"))
kc$list()

## End(Not run) 


## ------------------------------------------------
## Method `Kibior$match`
## ------------------------------------------------

## Not run: 
# search "sw" index name
kc$match("sw")
# search all starting with an "s"
kc$match("s*")
# get all index name, identical to `$list()`
kc$match("*")
# search multiple names 
kc$match(c("sw", "sw_new", "nope"))
# search multiple names with pattern
kc$match(c("s*", "nope"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$search`
## ------------------------------------------------

## Not run: 
# search "sw" index, head mode on
kc$search("sw")
# search "sw" index with all metadata, head mode on
kc$search("sw", keep_metadata = TRUE)
# get only "name" field of the head of indices starting with "s"
# if an index does not have the "name" field, it will be empty
kc$search("s*", columns = "name")
# limit the size of the result to 50 to the whole index
kc$search("storms", max_size = 50, bulk_size = 50, head = FALSE)
# use Elasticsearch query syntax to select and filter on all indices, for all data
# Here, we want to search for all records taht match the conditions:
# field "height" is strictly more than 180 AND field homeworld is "Tatooine" OR "Naboo"
kc$search("*", query = "height:>180 && homeworld:(Tatooine || Naboo)")
# it can be used in conjunction with `columns` to select only columns that matter
kc$search("*", query = "height:>180 && homeworld:(Tatooine || Naboo)", columns = 
 c("name", "hair_color", "homeworld"))

## End(Not run)


## ------------------------------------------------
## Method `Kibior$inner_join`
## ------------------------------------------------

## Not run: 
# some data for joins examples
kc$push(ggplot2::diamonds, "diamonds")
# prepare join datasets, only big the biggest diamonds are selected (9)
sup_carat <- dplyr::filter(ggplot2::diamonds, carat > 3.5)
r <- kc$push(sup_carat, "diamonds_superior")
# execute a inner_join with one index and one in-memory dataset
kc$inner_join(ggplot2::diamonds, "diamonds_superior")
# execute a inner_join with one index queried, and one in-memory dataset
kc$inner_join(ggplot2::diamonds, "diamonds", right_query 
 = "carat:>3.5")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$full_join`
## ------------------------------------------------

## Not run: 
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a full_join with one index and one in-memory dataset
kc$full_join(fair_cut, "diamonds_superior")
# execute a full_join with one index queried, and one in-memory dataset
kc$full_join(sup_carat, "diamonds", right_query = "cut:fair")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$left_join`
## ------------------------------------------------

## Not run: 
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a left_join with one index and one in-memory dataset
kc$left_join(fair_cut, "diamonds_superior")
# execute a left_join with one index queried, and one in-memory dataset
kc$left_join(sup_carat, "diamonds", right_query 
 = "cut:fair")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$right_join`
## ------------------------------------------------

## Not run: 
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a right_join with one index and one in-memory dataset
kc$right_join(fair_cut, "diamonds_superior")
# execute a right_join with one index queried, and one in-memory dataset
kc$right_join(sup_carat, "diamonds", right_query 
 = "cut:fair")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$semi_join`
## ------------------------------------------------

## Not run: 
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a semi_join with one index and one in-memory dataset
kc$semi_join(fair_cut, "diamonds_superior")
# execute a semi_join with one index queried, and one in-memory dataset
kc$semi_join(sup_carat, "diamonds", right_query 
 = "cut:fair")

## End(Not run)


## ------------------------------------------------
## Method `Kibior$anti_join`
## ------------------------------------------------

## Not run: 
# prepare join datasets, fair cuts 
fair_cut <- dplyr::filter(ggplot2::diamonds, cut == "Fair")  # 1605 lines
sup_carat <- kc$pull("diamonds_superior")$diamonds_superior
# execute a anti_join with one index and one in-memory dataset
kc$anti_join(fair_cut, "diamonds_superior")
# execute a anti_join with one index queried, and one in-memory dataset
kc$anti_join(sup_carat, "diamonds", right_query 
 = "cut:fair")
# 
# Do not mind this, removing example indices
elastic::index_delete(kc$connection, "*")
kc <- NULL

## End(Not run)

regisoc/kibior documentation built on Aug. 15, 2021, 9:51 p.m.

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