From 352e6533a883798b8a0f62b6c81e56ae68a9804a Mon Sep 17 00:00:00 2001 From: Dewey Dunnington Date: Wed, 9 Oct 2024 23:27:53 +0000 Subject: [PATCH] feat(r): Add R BigQuery driver wrapper (#2235) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This PR adds a BigQuery driver wrapper for R. It is basically the same as the FlightSQL wrapper with the addition of one helper function to take care of the auth (in R we have the lovely `gargle` package and `bigrquery` which have extensive methods for handling auth in various scenarios). I don't think we have a way to get credentials into CI yet (but at least we have build/package load coverage for when that happens). ``` r library(adbcdrivermanager) # Use the driver manager to connect to a database db <- adbc_database_init( adbcbigquery::adbcbigquery(), token = bigrquery::bq_token(), "adbc.bigquery.sql.project_id" = Sys.getenv("ADBC_BIGQUERY_TEST_PROJECT_ID") ) con <- adbc_connection_init(db) con |> read_adbc( "SELECT zipcode, latitude, longitude FROM `bigquery-public-data.utility_us.zipcode_area` LIMIT 10" ) |> tibble::as_tibble() #> # A tibble: 10 × 3 #> zipcode latitude longitude #> #> 1 96950 15.2 146. #> 2 96952 15.0 146. #> 3 96951 14.2 145. #> 4 96910 13.5 145. #> 5 96929 13.6 145. #> 6 96921 13.5 145. #> 7 96913 13.5 145. #> 8 96932 13.5 145. #> 9 50012 42.0 -93.6 #> 10 52352 42.3 -91.8 ``` Created on 2024-10-09 with [reprex v2.1.1](https://reprex.tidyverse.org) --- .github/workflows/r-extended.yml | 4 +- .github/workflows/r-standard.yml | 2 +- r/adbcbigquery/.Rbuildignore | 17 ++ r/adbcbigquery/.gitignore | 20 ++ r/adbcbigquery/DESCRIPTION | 28 +++ r/adbcbigquery/LICENSE.md | 194 ++++++++++++++++++ r/adbcbigquery/NAMESPACE | 10 + r/adbcbigquery/R/adbcbigquery-package.R | 122 +++++++++++ r/adbcbigquery/README.Rmd | 77 +++++++ r/adbcbigquery/README.md | 79 +++++++ r/adbcbigquery/_pkgdown.yml | 38 ++++ r/adbcbigquery/adbcbigquery.Rproj | 22 ++ r/adbcbigquery/bootstrap.R | 18 ++ r/adbcbigquery/cleanup | 20 ++ r/adbcbigquery/cleanup.win | 18 ++ r/adbcbigquery/configure | 128 ++++++++++++ r/adbcbigquery/configure.win | 23 +++ r/adbcbigquery/cran-comments.md | 9 + r/adbcbigquery/man/adbcbigquery-package.Rd | 33 +++ r/adbcbigquery/man/adbcbigquery.Rd | 39 ++++ r/adbcbigquery/src/.gitignore | 21 ++ r/adbcbigquery/src/Makevars.in | 31 +++ r/adbcbigquery/src/Makevars.win | 34 +++ r/adbcbigquery/src/go/.gitignore | 21 ++ r/adbcbigquery/src/go/symbols.map | 26 +++ r/adbcbigquery/src/init.c | 42 ++++ r/adbcbigquery/tests/testthat.R | 29 +++ .../testthat/test-adbcbigquery-package.R | 57 +++++ r/adbcbigquery/tools/download-go.R | 87 ++++++++ 29 files changed, 1246 insertions(+), 3 deletions(-) create mode 100644 r/adbcbigquery/.Rbuildignore create mode 100644 r/adbcbigquery/.gitignore create mode 100644 r/adbcbigquery/DESCRIPTION create mode 100644 r/adbcbigquery/LICENSE.md create mode 100644 r/adbcbigquery/NAMESPACE create mode 100644 r/adbcbigquery/R/adbcbigquery-package.R create mode 100644 r/adbcbigquery/README.Rmd create mode 100644 r/adbcbigquery/README.md create mode 100644 r/adbcbigquery/_pkgdown.yml create mode 100644 r/adbcbigquery/adbcbigquery.Rproj create mode 100644 r/adbcbigquery/bootstrap.R create mode 100755 r/adbcbigquery/cleanup create mode 100755 r/adbcbigquery/cleanup.win create mode 100755 r/adbcbigquery/configure create mode 100755 r/adbcbigquery/configure.win create mode 100644 r/adbcbigquery/cran-comments.md create mode 100644 r/adbcbigquery/man/adbcbigquery-package.Rd create mode 100644 r/adbcbigquery/man/adbcbigquery.Rd create mode 100644 r/adbcbigquery/src/.gitignore create mode 100644 r/adbcbigquery/src/Makevars.in create mode 100644 r/adbcbigquery/src/Makevars.win create mode 100644 r/adbcbigquery/src/go/.gitignore create mode 100644 r/adbcbigquery/src/go/symbols.map create mode 100644 r/adbcbigquery/src/init.c create mode 100644 r/adbcbigquery/tests/testthat.R create mode 100644 r/adbcbigquery/tests/testthat/test-adbcbigquery-package.R create mode 100644 r/adbcbigquery/tools/download-go.R diff --git a/.github/workflows/r-extended.yml b/.github/workflows/r-extended.yml index 3963da25cf..1ca2e821c2 100644 --- a/.github/workflows/r-extended.yml +++ b/.github/workflows/r-extended.yml @@ -44,7 +44,7 @@ jobs: matrix: rversion: [oldrel, release, devel] os: [macOS, windows, ubuntu] - pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake] + pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake, adbcbigquery] fail-fast: false uses: ./.github/workflows/r-check.yml @@ -61,7 +61,7 @@ jobs: matrix: rversion: ["3.6", "4.0", "4.1"] os: [ubuntu] - pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake] + pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake, adbcbigquery] fail-fast: false uses: ./.github/workflows/r-check.yml diff --git a/.github/workflows/r-standard.yml b/.github/workflows/r-standard.yml index 9cc8f7ac94..907d779844 100644 --- a/.github/workflows/r-standard.yml +++ b/.github/workflows/r-standard.yml @@ -50,7 +50,7 @@ jobs: strategy: matrix: os: [ubuntu, macOS, windows] - pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake] + pkg: [adbcdrivermanager, adbcsqlite, adbcpostgresql, adbcflightsql, adbcsnowflake, adbcbigquery] uses: ./.github/workflows/r-check.yml with: diff --git a/r/adbcbigquery/.Rbuildignore b/r/adbcbigquery/.Rbuildignore new file mode 100644 index 0000000000..a622537241 --- /dev/null +++ b/r/adbcbigquery/.Rbuildignore @@ -0,0 +1,17 @@ +^adbcbigquery\.Rproj$ +^\.Rproj\.user$ +^LICENSE\.md$ +^bootstrap\.R$ +^README\.Rmd$ +^src/Makevars$ +^\.vscode$ +^src/go/tmp$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ +^cran-comments\.md$ +^src/\.go-cache$ +^src/\.go-path$ +^configure\.win$ +^\.cache$ +^compile_commands\.json$ diff --git a/r/adbcbigquery/.gitignore b/r/adbcbigquery/.gitignore new file mode 100644 index 0000000000..11519d4042 --- /dev/null +++ b/r/adbcbigquery/.gitignore @@ -0,0 +1,20 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +.Rproj.user +windows/ +docs diff --git a/r/adbcbigquery/DESCRIPTION b/r/adbcbigquery/DESCRIPTION new file mode 100644 index 0000000000..cdfdb71348 --- /dev/null +++ b/r/adbcbigquery/DESCRIPTION @@ -0,0 +1,28 @@ +Package: adbcbigquery +Title: 'Arrow' Database Connectivity ('ADBC') 'BigQuery' Driver +Version: 0.14.0.9000 +Authors@R: c( + person("Dewey", "Dunnington", , "dewey@dunnington.ca", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-9415-4582")), + person("Apache Arrow", email = "dev@arrow.apache.org", role = c("aut", "cph")), + person("Apache Software Foundation", email = "dev@arrow.apache.org", role = c("cph")) + ) +Description: Provides a developer-facing interface to the 'Arrow' Database + Connectivity ('ADBC') 'BigQuery' driver for the purposes of building high-level + database interfaces for users. 'ADBC' is + an API standard for database access libraries that uses 'Arrow' for result + sets and query parameters. +License: Apache License (>= 2) +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 +Suggests: + gargle, + nanoarrow, + testthat (>= 3.0.0) +SystemRequirements: GNU make, Go (>= 1.21) +Config/testthat/edition: 3 +Config/build/bootstrap: TRUE +URL: https://arrow.apache.org/adbc/current/r/adbcbigquery/, https://github.com/apache/arrow-adbc +BugReports: https://github.com/apache/arrow-adbc/issues +Imports: adbcdrivermanager diff --git a/r/adbcbigquery/LICENSE.md b/r/adbcbigquery/LICENSE.md new file mode 100644 index 0000000000..b62a9b5ff7 --- /dev/null +++ b/r/adbcbigquery/LICENSE.md @@ -0,0 +1,194 @@ +Apache License +============== + +_Version 2.0, January 2004_ +_<>_ + +### Terms and Conditions for use, reproduction, and distribution + +#### 1. 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See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +#' @keywords internal +#' @aliases adbcbigquery-package +"_PACKAGE" + +## usethis namespace: start +#' @useDynLib adbcbigquery, .registration = TRUE +## usethis namespace: end +NULL + +#' ADBC BigQuery Driver +#' +#' @inheritParams adbcdrivermanager::adbc_database_init +#' @inheritParams adbcdrivermanager::adbc_connection_init +#' @inheritParams adbcdrivermanager::adbc_statement_init +#' @param token A token obtained from [bigrquery::bq_token()] or +#' [gargle::token_fetch()]. This is the easiest way to authenticate. +#' @param ... Extra key/value options passed to the driver. +#' +#' @return An [adbcdrivermanager::adbc_driver()] +#' @export +#' +#' @examples +#' adbcbigquery() +#' +adbcbigquery <- function() { + adbcdrivermanager::adbc_driver( + .Call(adbcbigquery_c_bigquery), + subclass = "adbcbigquery_driver_bigquery" + ) +} + +#' @rdname adbcbigquery +#' @importFrom adbcdrivermanager adbc_database_init +#' @export +adbc_database_init.adbcbigquery_driver_bigquery <- function(driver, ..., token = NULL) { + if (!is.null(token)) { + options <- list(options_from_token(token), ...) + } else { + options <- list(...) + } + + adbcdrivermanager::adbc_database_init_default( + driver, + options, + subclass = "adbcbigquery_database" + ) +} + +#' @rdname adbcbigquery +#' @importFrom adbcdrivermanager adbc_connection_init +#' @export +adbc_connection_init.adbcbigquery_database <- function(database, ...) { + options <- list(...) + + adbcdrivermanager::adbc_connection_init_default( + database, + options, + subclass = "adbcbigquery_connection" + ) +} + +#' @rdname adbcbigquery +#' @importFrom adbcdrivermanager adbc_statement_init +#' @export +adbc_statement_init.adbcbigquery_connection <- function(connection, ...) { + options <- list(...) + + adbcdrivermanager::adbc_statement_init_default( + connection, + options, + subclass = "adbcbigquery_statement" + ) +} + +# Converts a bigrquery::bq_token() or garge::token_fetch() into the options +# required by the ADBC driver. +options_from_token <- function(tok) { + if (inherits(tok, "request")) { + tok <- tok$auth_token + } + + if (!inherits(tok, "Token2.0")) { + stop( + sprintf( + "ADBC BigQuery database options from token failed (expected Token2.0, got %s)", + paste(class(tok), sep = " / ") + ) + ) + } + + # Because adbcdrivermanager:::key_value_options() is not exposed, we create the + # options ourselves such that set_options() can automatically expand them. + structure( + c( + "adbc.bigquery.sql.auth_type" = "adbc.bigquery.sql.auth_type.user_authentication", + "adbc.bigquery.sql.auth.client_id" = tok$client$id, + "adbc.bigquery.sql.auth.client_secret" = tok$client$secret, + "adbc.bigquery.sql.auth.refresh_token" = tok$credentials$refresh_token + # Ideally we would also pass on tok$credentials$access_token; however, + # the underlying Go driver does not yet implement the ability to pass this + # information directly (i.e., it will always refresh on connect) + ), + class = "adbc_options" + ) +} diff --git a/r/adbcbigquery/README.Rmd b/r/adbcbigquery/README.Rmd new file mode 100644 index 0000000000..9649eaef2f --- /dev/null +++ b/r/adbcbigquery/README.Rmd @@ -0,0 +1,77 @@ +--- +output: github_document +--- + + + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/README-", + out.width = "100%" +) +``` + +# adbcbigquery + + + + +The goal of adbcbigquery is to provide a low-level developer-facing interface +to the Arrow Database Connectivity (ADBC) BigQuery driver. + +## Installation + +You can install the released version of adbcbigquery from [CRAN](https://cran.r-project.org/) with: + +```r +install.packages("adbcbigquery") +``` + +You can install the development version of adbcbigquery from [GitHub](https://github.com/) with: + +``` r +# install.packages("pak") +pak::pak("apache/arrow-adbc/r/adbcbigquery") +``` + +## Example + +This is a basic example which shows you how to solve a common problem. + +```{r example} +library(adbcdrivermanager) + +# Use the driver manager to connect to a database +db <- adbc_database_init( + adbcbigquery::adbcbigquery(), + token = bigrquery::bq_token(), + "adbc.bigquery.sql.project_id" = Sys.getenv("ADBC_BIGQUERY_TEST_PROJECT_ID") +) +con <- adbc_connection_init(db) + +con |> + read_adbc( + "SELECT zipcode, latitude, longitude + FROM `bigquery-public-data.utility_us.zipcode_area` LIMIT 10" + ) |> + tibble::as_tibble() +``` diff --git a/r/adbcbigquery/README.md b/r/adbcbigquery/README.md new file mode 100644 index 0000000000..86180908ca --- /dev/null +++ b/r/adbcbigquery/README.md @@ -0,0 +1,79 @@ + + + + +# adbcbigquery + + + + +The goal of adbcbigquery is to provide a low-level developer-facing +interface to the Arrow Database Connectivity (ADBC) BigQuery driver. + +## Installation + +You can install the released version of adbcbigquery from +[CRAN](https://cran.r-project.org/) with: + +``` r +install.packages("adbcbigquery") +``` + +You can install the development version of adbcbigquery from +[GitHub](https://github.com/) with: + +``` r +# install.packages("pak") +pak::pak("apache/arrow-adbc/r/adbcbigquery") +``` + +## Example + +This is a basic example which shows you how to solve a common problem. + +``` r +library(adbcdrivermanager) + +# Use the driver manager to connect to a database +db <- adbc_database_init( + adbcbigquery::adbcbigquery(), + token = bigrquery::bq_token(), + "adbc.bigquery.sql.project_id" = Sys.getenv("ADBC_BIGQUERY_TEST_PROJECT_ID") +) +con <- adbc_connection_init(db) + +con |> + read_adbc( + "SELECT zipcode, latitude, longitude + FROM `bigquery-public-data.utility_us.zipcode_area` LIMIT 10" + ) |> + tibble::as_tibble() +#> # A tibble: 10 × 3 +#> zipcode latitude longitude +#> +#> 1 96950 15.2 146. +#> 2 96952 15.0 146. +#> 3 96951 14.2 145. +#> 4 96910 13.5 145. +#> 5 96929 13.6 145. +#> 6 96921 13.5 145. +#> 7 96913 13.5 145. +#> 8 96932 13.5 145. +#> 9 50012 42.0 -93.6 +#> 10 52352 42.3 -91.8 +``` diff --git a/r/adbcbigquery/_pkgdown.yml b/r/adbcbigquery/_pkgdown.yml new file mode 100644 index 0000000000..9d213e123c --- /dev/null +++ b/r/adbcbigquery/_pkgdown.yml @@ -0,0 +1,38 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +url: https://arrow.apache.org/adbc/current/r/adbcbigquery/ +template: + bootstrap: 5 + light-switch: true + # Link back to ADBC R documentation + includes: + before_title: | + + +repo: + url: + home: https://github.com/apache/arrow-adbc/ + source: https://github.com/apache/arrow-adbc/blob/main/r/adbcbigquery/ + issue: https://github.com/apache/arrow-adbc/issues/ + user: https://github.com/ diff --git a/r/adbcbigquery/adbcbigquery.Rproj b/r/adbcbigquery/adbcbigquery.Rproj new file mode 100644 index 0000000000..69fafd4b6d --- /dev/null +++ b/r/adbcbigquery/adbcbigquery.Rproj @@ -0,0 +1,22 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace diff --git a/r/adbcbigquery/bootstrap.R b/r/adbcbigquery/bootstrap.R new file mode 100644 index 0000000000..c3dd879dda --- /dev/null +++ b/r/adbcbigquery/bootstrap.R @@ -0,0 +1,18 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +source("../tools/bootstrap-go.R") diff --git a/r/adbcbigquery/cleanup b/r/adbcbigquery/cleanup new file mode 100755 index 0000000000..2261ddb19a --- /dev/null +++ b/r/adbcbigquery/cleanup @@ -0,0 +1,20 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +rm src/*.o src/go/*.a +rm -rf src/.go-cache +rm -rf src/.go-path diff --git a/r/adbcbigquery/cleanup.win b/r/adbcbigquery/cleanup.win new file mode 100755 index 0000000000..7bee0e8f4d --- /dev/null +++ b/r/adbcbigquery/cleanup.win @@ -0,0 +1,18 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +./cleanup diff --git a/r/adbcbigquery/configure b/r/adbcbigquery/configure new file mode 100755 index 0000000000..84ceb149a8 --- /dev/null +++ b/r/adbcbigquery/configure @@ -0,0 +1,128 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +R_BIN="$R_HOME/bin/R" +RSCRIPT_BIN="$R_HOME/bin/Rscript" + +# Set to non-false for CRAN releases, which require this approach to comply with +# guidance regarding large dependency sources. When non-false, this script +# will fail if the download fails or if checksum verification fails on +# the downloaded file. +DOWNLOAD_DEPENDENCY_ARCHIVE="false" + +# CRAN checks CPU time to enforce ~2 cores for building. Set GOMAXPROCS to 1 +# when building on CRAN to be safe. +if [ ! "$DOWNLOAD_DEPENDENCY_ARCHIVE" = "false" ] && [ -z "$GOMAXPROCS" ]; then + echo "Using GOMAXPROCS=1 for go build" + echo "Set GOMAXPROCS to a higher value in ~/.Renviron for a faster build" + GOMAXPROCS=1 +elif [ ! -z "$GOMAXPROCS" ]; then + echo "Using GOMAXPROCS=$GOMAXPROCS for go build" +fi + +# Run bootstrap.R. This will have already run if we are installing a source +# package built with pkgbuild::build() with pkgbuild >1.4.0; however, we +# run it again in case this is R CMD INSTALL on a directory or +# devtools::load_all(). This will vendor files from elsewhere in the +# ADBC repo into this package. If the file doesn't exist, we're installing +# from a pre-built tarball. +if [ -f bootstrap.R ]; then + echo "Running bootstrap.R..." + "$RSCRIPT_BIN" bootstrap.R +fi + +# Find the go binary so that we can go build! +# If we've downloaded a specific version of go to src/go/tmp, use that +# one (helpful for testing different version of go locally) +PREVIOUSLY_DOWNLOADED_GO="`pwd`/src/go/tmp/go/bin/go" +if [ -z "$GO_BIN" ] && [ -f "$PREVIOUSLY_DOWNLOADED_GO" ]; then + GO_BIN="$PREVIOUSLY_DOWNLOADED_GO" +fi + +# Check go on PATH +if [ -z "$GO_BIN" ]; then + GO_BIN=`which go` +fi + +# Try some default install locations that might not be on PATH +DEFAULT_GO_WIN="C:/Program Files/Go/bin/go.exe" +if [ -z "$GO_BIN" ] && [ -f "$DEFAULT_GO_WIN" ]; then + GO_BIN="$DEFAULT_GO_WIN" +fi + +DEFAULT_GO_MACOS="/usr/local/go/bin/go" +if [ -z "$GO_BIN" ] && [ -f "$DEFAULT_GO_MACOS" ]; then + GO_BIN="$DEFAULT_GO_MACOS" +fi + +DEFAULT_GO_HOMEBREW_M1="/opt/homebrew/bin/go" +if [ -z "$GO_BIN" ] && [ -f "$DEFAULT_GO_HOMEBREW_M1" ]; then + GO_BIN="$DEFAULT_GO_HOMEBREW_M1" +fi + +if [ -z "$GO_BIN" ]; then + echo "" + echo "The Go compiler is required to install this package. You can install go" + echo "from your faviourite package manager or set the GO_BIN environment variable:" + echo "- apt-get install golang" + echo "- brew install golang" + echo "- dnf install golang" + echo "- apk add go" + echo "- pacman -S go" + echo "...or from the official installers available at https://go.dev/dl/" + exit 1 +fi + +echo "Trying 'go version' with GO_BIN at '$GO_BIN'" +"$GO_BIN" version +if [ $? -ne 0 ]; then + echo "go --version had a non-zero exit code" + exit 1 +fi + +# Get the CC and CXX compilers +CC=`"$R_BIN" CMD config CC` +CXX=`"$R_BIN" CMD config CXX` + +# Attempt to hide symbols where possible +if "$R_BIN" CMD config CC | grep -e "gcc" >/dev/null ; then + SYMBOL_ARGS="-Wl,--version-script=go/symbols.map" +fi + +# On OSX we need -framework Security because of some dependency somewhere +if [ `uname` = "Darwin" ]; then + PKG_LIBS="-framework Security $PKG_LIBS" +fi + +PKG_LIBS="$PKG_LIBS $SYMBOL_ARGS" + +sed \ + -e "s|@gobin@|$GO_BIN|" \ + -e "s|@libs@|$PKG_LIBS|" \ + -e "s|@cc@|$CC|" \ + -e "s|@cxx@|$CXX|" \ + -e "s|@nproc@|$GOMAXPROCS|" \ + src/Makevars.in > src/Makevars + +if [ -f "src/go/adbc/pkg/bigquery/driver.go" ]; then + echo "Found vendored ADBC BigQuery driver" + exit 0 +fi + +echo "Vendored ADBC BigQuery driver was not found." +echo "This source package was probably built incorrectly and it's probably not your fault" +exit 1 diff --git a/r/adbcbigquery/configure.win b/r/adbcbigquery/configure.win new file mode 100755 index 0000000000..caf6740f66 --- /dev/null +++ b/r/adbcbigquery/configure.win @@ -0,0 +1,23 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +# See configure for a description of this process. +# This is only for development: this file and bootstrap.R will be removed +# prior to packaging +if [ -f bootstrap.R ]; then + $R_HOME/bin/Rscript bootstrap.R +fi diff --git a/r/adbcbigquery/cran-comments.md b/r/adbcbigquery/cran-comments.md new file mode 100644 index 0000000000..2d2bbbdc12 --- /dev/null +++ b/r/adbcbigquery/cran-comments.md @@ -0,0 +1,9 @@ + +An update to reflect the updated upstream sources for the latest +Apache Arrow ADBC libraries version. + +## R CMD check results + +0 errors | 0 warnings | 1 note + +* This is a new release. diff --git a/r/adbcbigquery/man/adbcbigquery-package.Rd b/r/adbcbigquery/man/adbcbigquery-package.Rd new file mode 100644 index 0000000000..3f4bda2196 --- /dev/null +++ b/r/adbcbigquery/man/adbcbigquery-package.Rd @@ -0,0 +1,33 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/adbcbigquery-package.R +\docType{package} +\name{adbcbigquery-package} +\alias{adbcbigquery-package} +\title{adbcbigquery: 'Arrow' Database Connectivity ('ADBC') 'BigQuery' Driver} +\description{ +Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'BigQuery' driver for the purposes of building high-level database interfaces for users. 'ADBC' \url{https://arrow.apache.org/adbc/} is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://arrow.apache.org/adbc/current/r/adbcbigquery/} + \item \url{https://github.com/apache/arrow-adbc} + \item Report bugs at \url{https://github.com/apache/arrow-adbc/issues} +} + +} +\author{ +\strong{Maintainer}: Dewey Dunnington \email{dewey@dunnington.ca} (\href{https://orcid.org/0000-0002-9415-4582}{ORCID}) + +Authors: +\itemize{ + \item Apache Arrow \email{dev@arrow.apache.org} [copyright holder] +} + +Other contributors: +\itemize{ + \item Apache Software Foundation \email{dev@arrow.apache.org} [copyright holder] +} + +} +\keyword{internal} diff --git a/r/adbcbigquery/man/adbcbigquery.Rd b/r/adbcbigquery/man/adbcbigquery.Rd new file mode 100644 index 0000000000..c01048467f --- /dev/null +++ b/r/adbcbigquery/man/adbcbigquery.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/adbcbigquery-package.R +\name{adbcbigquery} +\alias{adbcbigquery} +\alias{adbc_database_init.adbcbigquery_driver_bigquery} +\alias{adbc_connection_init.adbcbigquery_database} +\alias{adbc_statement_init.adbcbigquery_connection} +\title{ADBC BigQuery Driver} +\usage{ +adbcbigquery() + +\method{adbc_database_init}{adbcbigquery_driver_bigquery}(driver, ..., token = NULL) + +\method{adbc_connection_init}{adbcbigquery_database}(database, ...) + +\method{adbc_statement_init}{adbcbigquery_connection}(connection, ...) +} +\arguments{ +\item{driver}{An \code{\link[adbcdrivermanager:adbc_driver]{adbc_driver()}}.} + +\item{...}{Extra key/value options passed to the driver.} + +\item{token}{A token obtained from \code{\link[bigrquery:bq_token]{bigrquery::bq_token()}} or +\code{\link[gargle:token_fetch]{gargle::token_fetch()}}. This is the easiest way to authenticate.} + +\item{database}{An \link[adbcdrivermanager:adbc_database_init]{adbc_database}.} + +\item{connection}{An \link[adbcdrivermanager:adbc_connection_init]{adbc_connection}} +} +\value{ +An \code{\link[adbcdrivermanager:adbc_driver_void]{adbcdrivermanager::adbc_driver()}} +} +\description{ +ADBC BigQuery Driver +} +\examples{ +adbcbigquery() + +} diff --git a/r/adbcbigquery/src/.gitignore b/r/adbcbigquery/src/.gitignore new file mode 100644 index 0000000000..e040acd74e --- /dev/null +++ b/r/adbcbigquery/src/.gitignore @@ -0,0 +1,21 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +adbc.h +Makevars +.go-cache +.go-path diff --git a/r/adbcbigquery/src/Makevars.in b/r/adbcbigquery/src/Makevars.in new file mode 100644 index 0000000000..5a43d7fddb --- /dev/null +++ b/r/adbcbigquery/src/Makevars.in @@ -0,0 +1,31 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +PKG_CPPFLAGS=-I$(CURDIR)/src -DADBC_EXPORT="" +PKG_LIBS=-L$(CURDIR)/go -ladbc_driver_bigquery -lresolv @libs@ + +CGO_CC = @cc@ +CGO_CXX = @cxx@ +CGO_CFLAGS = $(ALL_CPPFLAGS) +GOMAXPROCS = @nproc@ + +.PHONY: all gostatic +all: $(SHLIB) +$(SHLIB): gostatic + +gostatic: + (cd "$(CURDIR)/go/adbc"; GOMAXPROCS=$(GOMAXPROCS) GOPATH="$(CURDIR)/.go-path" GOCACHE="$(CURDIR)/.go-cache" GOFLAGS=-modcacherw CC="$(CGO_CC)" CXX="$(CGO_CXX)" CGO_CFLAGS="$(CGO_CFLAGS)" CGO_LDFLAGS="$(PKG_LIBS)" "@gobin@" build -v -tags driverlib -o $(CURDIR)/go/libadbc_driver_bigquery.a -buildmode=c-archive "./pkg/bigquery") diff --git a/r/adbcbigquery/src/Makevars.win b/r/adbcbigquery/src/Makevars.win new file mode 100644 index 0000000000..df9fb94b96 --- /dev/null +++ b/r/adbcbigquery/src/Makevars.win @@ -0,0 +1,34 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +PKG_CPPFLAGS=-I$(CURDIR) -DADBC_EXPORT="" +PKG_LIBS=-L$(CURDIR)/go -ladbc_driver_bigquery + +CGO_CC = `"${R_HOME}/bin${R_ARCH_BIN}/R.exe" CMD config CC` +CGO_CXX = `"${R_HOME}/bin${R_ARCH_BIN}/R.exe" CMD config CXX` +CGO_CFLAGS = $(ALL_CPPFLAGS) +GO_BIN = $(CURDIR)/go/tmp/go/bin/go.exe + +.PHONY: all gostatic gobin +all: $(SHLIB) +$(SHLIB): gostatic + +gostatic: gobin + (cd "$(CURDIR)/go/adbc"; CC="$(CGO_CC)" CXX="$(CGO_CXX)" CGO_CFLAGS="$(CGO_CFLAGS)" "$(GO_BIN)" build -v -tags driverlib -o $(CURDIR)/go/libadbc_driver_bigquery.a -buildmode=c-archive "./pkg/bigquery") + +gobin: + (cd ..; "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "tools/download-go.R") diff --git a/r/adbcbigquery/src/go/.gitignore b/r/adbcbigquery/src/go/.gitignore new file mode 100644 index 0000000000..7a1a0b2c70 --- /dev/null +++ b/r/adbcbigquery/src/go/.gitignore @@ -0,0 +1,21 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +adbc/ +tmp/ +libadbc_driver_bigquery.a +libadbc_driver_bigquery.h diff --git a/r/adbcbigquery/src/go/symbols.map b/r/adbcbigquery/src/go/symbols.map new file mode 100644 index 0000000000..18a0eb29c3 --- /dev/null +++ b/r/adbcbigquery/src/go/symbols.map @@ -0,0 +1,26 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +{ + global: + # Only expose symbols needed for R + R_init_adbcbigquery; + adbcbigquery_c_bigquery; + + local: + *; +}; diff --git a/r/adbcbigquery/src/init.c b/r/adbcbigquery/src/init.c new file mode 100644 index 0000000000..168205de66 --- /dev/null +++ b/r/adbcbigquery/src/init.c @@ -0,0 +1,42 @@ +// Licensed to the Apache Software Foundation (ASF) under one +// or more contributor license agreements. See the NOTICE file +// distributed with this work for additional information +// regarding copyright ownership. The ASF licenses this file +// to you under the Apache License, Version 2.0 (the +// "License"); you may not use this file except in compliance +// with the License. You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, +// software distributed under the License is distributed on an +// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +// KIND, either express or implied. See the License for the +// specific language governing permissions and limitations +// under the License. + +#define R_NO_REMAP +#include +#include + +typedef int AdbcStatusCode; +struct AdbcError; +AdbcStatusCode AdbcDriverInit(int version, void* raw_driver, struct AdbcError* error); + +static SEXP init_func_xptr = 0; + +SEXP adbcbigquery_c_bigquery(void) { return init_func_xptr; } + +static const R_CallMethodDef CallEntries[] = { + {"adbcbigquery_c_bigquery", (DL_FUNC)&adbcbigquery_c_bigquery, 0}, {NULL, NULL, 0}}; + +void R_init_adbcbigquery(DllInfo* dll) { + R_registerRoutines(dll, NULL, CallEntries, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); + + init_func_xptr = + PROTECT(R_MakeExternalPtrFn((DL_FUNC)AdbcDriverInit, R_NilValue, R_NilValue)); + Rf_setAttrib(init_func_xptr, R_ClassSymbol, Rf_mkString("adbc_driver_init_func")); + R_PreserveObject(init_func_xptr); + UNPROTECT(1); +} diff --git a/r/adbcbigquery/tests/testthat.R b/r/adbcbigquery/tests/testthat.R new file mode 100644 index 0000000000..d91df554ab --- /dev/null +++ b/r/adbcbigquery/tests/testthat.R @@ -0,0 +1,29 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/tests.html +# * https://testthat.r-lib.org/reference/test_package.html#special-files + +library(testthat) +library(adbcbigquery) + +test_check("adbcbigquery") diff --git a/r/adbcbigquery/tests/testthat/test-adbcbigquery-package.R b/r/adbcbigquery/tests/testthat/test-adbcbigquery-package.R new file mode 100644 index 0000000000..1f0037a955 --- /dev/null +++ b/r/adbcbigquery/tests/testthat/test-adbcbigquery-package.R @@ -0,0 +1,57 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +test_that("adbcbigquery() works", { + expect_s3_class(adbcbigquery(), "adbc_driver") +}) + +test_that("default options can open a database and execute a query", { + test_credentials_file <- Sys.getenv("ADBC_BIGQUERY_TEST_CREDENTIALS_FILE", "") + skip_if(identical(test_credentials_file, "")) + + client <- gargle::gargle_oauth_client_from_json(test_credentials_file) + token <- gargle::token_fetch( + scopes = c( + "https://www.googleapis.com/auth/bigquery" + ), + client = client + ) + + db <- adbcdrivermanager::adbc_database_init( + adbcbigquery(), + "adbc.bigquery.sql.project_id" = Sys.getenv("ADBC_BIGQUERY_TEST_PROJECT_ID"), + token = token + ) + expect_s3_class(db, "adbcbigquery_database") + + con <- adbcdrivermanager::adbc_connection_init(db) + expect_s3_class(con, "adbcbigquery_connection") + + stmt <- adbcdrivermanager::adbc_statement_init(con) + expect_s3_class(stmt, "adbcbigquery_statement") + adbcdrivermanager::adbc_statement_release(stmt) + + result <- as.data.frame( + adbcdrivermanager::read_adbc( + con, + "SELECT zipcode, latitude, longitude + FROM `bigquery-public-data.utility_us.zipcode_area` LIMIT 10" + ) + ) + expect_identical(names(result), c("zipcode", "latitude", "longitude")) + expect_identical(nrow(result), 10L) +}) diff --git a/r/adbcbigquery/tools/download-go.R b/r/adbcbigquery/tools/download-go.R new file mode 100644 index 0000000000..5f178f4c80 --- /dev/null +++ b/r/adbcbigquery/tools/download-go.R @@ -0,0 +1,87 @@ +# Licensed to the Apache Software Foundation (ASF) under one +# or more contributor license agreements. See the NOTICE file +# distributed with this work for additional information +# regarding copyright ownership. The ASF licenses this file +# to you under the Apache License, Version 2.0 (the +# "License"); you may not use this file except in compliance +# with the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, +# software distributed under the License is distributed on an +# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +# KIND, either express or implied. See the License for the +# specific language governing permissions and limitations +# under the License. + +tmp_dir <- "src/go/tmp" + +go_version <- Sys.getenv("R_ADBC_GO_VERSION_DOWNLOAD", "1.21.8") + +go_platform <- tolower(Sys.info()[["sysname"]]) +if (!(go_platform %in% c("darwin", "linux", "windows"))) { + stop(sprintf("Go binary not available for os '%s'", go_platform)) +} + +r_arch <- R.version$arch +if (identical(r_arch, "aarch64")) { + go_arch <- "arm64" +} else if (identical(r_arch, "x86_64")) { + go_arch <- "amd64" +} else if (identical(r_arch, "i386")) { + go_arch <- "386" +} else { + stop(sprintf("Go binary not available for arch '%s'", r_arch)) +} + +if (identical(go_platform, "windows")) { + go_ext <- "zip" + go_bin <- paste0(tmp_dir, "/go/bin/go.exe") +} else { + go_ext <- "tar.gz" + go_bin <- paste0(tmp_dir, "/go/bin/go") +} + +archive_filename <- sprintf("go%s.%s-%s.%s", + go_version, + go_platform, + go_arch, + go_ext +) + +archive_url <- sprintf("https://go.dev/dl/%s", archive_filename) +archive_dest <- file.path(tmp_dir, archive_filename) + +if (!dir.exists(tmp_dir)) { + dir.create(tmp_dir) +} + +if (!file.exists(archive_dest)) { + download.file(archive_url, archive_dest, mode = "wb") +} + +# This step takes a while and there is no good way to communicate progress. +# We need to make sure that if the user cancels that we delete the partially +# extracted files (or else `go version`` passes but some parts of the standard +# library may be missing) +do_extract <- function() { + extract_completed <- FALSE + on.exit({ + if (!extract_completed) { + unlink(file.path(tmp_dir, "go"), recursive = TRUE) + } + }) + + if (identical(go_ext, "zip")) { + unzip(archive_dest, exdir = tmp_dir) + } else { + stopifnot(untar(archive_dest, exdir = tmp_dir, verbose = TRUE) == 0L) + } + + extract_completed <- TRUE +} + +if (!file.exists(go_bin)) { + do_extract() +}