Load BQ dataset from config file, drop explicit py billing project

[calbach]

fixes #2 fixes #12

[deflaux]

The R setup snippet is sadly long now.

Since this change isn't merged get, can you please move the constants to the bottom so that people are more likely to see and change them? I think this looks a bit more compact, thanks!

## Only install missing libraries, per https://stackoverflow.com/a/23286257/4138705.
install_if_missing <- function(packages) {
  if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
    install.packages(setdiff(packages, rownames(installed.packages())))
  }
}
install_if_missing(c('viridis', 'ggthemes', 'scales', 'skimr', 'lubridate', 'bigrquery', 'tidyverse'))

library(viridis)    # A nice color scheme for plots.
library(ggthemes)   # Common themes to change the look and feel of plots.
library(scales)     # Graphical scales map data to aesthetics in plots.
library(skimr)      # Better summaries of data.
library(lubridate)  # Date library from the tidyverse.
library(bigrquery)  # BigQuery R client.
library(tidyverse)  # Data wrangling packages.

## Get the BigQuery curated dataset for the current workspace context.
DATASET <- system(paste("echo ",
    "$(jq -r '.CDR_VERSION_CLOUD_PROJECT' .all_of_us_config.json).",
    "$(jq -r '.CDR_VERSION_BIGQUERY_DATASET' .all_of_us_config.json)"),
    intern = TRUE)
BILLING_PROJECT_ID <- Sys.getenv('GOOGLE_PROJECT')
bigrquery::set_service_token(Ronaldo::getServiceAccountKey())

## Plot setup.
theme_set(theme_minimal()) # Default theme for plots.
#' Returns a data frame with a y position and a label, for use annotating ggplot boxplots.
#'
#' @param d A data frame.
#' @return A data frame with column y as max and column label as length.
get_boxplot_fun_data <- function(df) {
  return(data.frame(y = max(df), label = stringr::str_c('N = ', length(df))))
}

## ---------------[ CHANGE THESE AS NEEDED] ---------------------------------------
# Set default parameter values so that all snippets run successfully with no edits needed.
MEASUREMENT_OF_INTEREST <- 'hemoglobin'
# Tip: the next four parameters could be set programmatically using one row from
# the result of measurements_of_interest_summary.sql
MEASUREMENT_CONCEPT_ID <- 3000963        # Hemoglobin
UNIT_CONCEPT_ID <- 8713                  # gram per deciliter
MEASUREMENT_NAME <- '<this should be the measurement name>'
UNIT_NAME <- '<this should be the unit name>'

[calbach]

Done.