Swap RMySQL for RMariaDB

docs/developers/virtual-environments.md

@@ -1,21 +1,35 @@
-# Virtual Environments
+## Python Virtual Environment
 
-## Add new packages
+### Add new packages
 
-Try to install any new package using `conda`. If a package is not available in one of `conda`'s channels you can install it with `pip` but make sure your virtual environment is active.
+Try to install any new package using `conda install -c CHANNEL PACKAGE_NAME` (you can use `pip` if the package is only available there). Make sure your Python virtual environment is active (`conda activate YOUR_ENV`).
 
-## Update your conda `environment.yaml`
+### Remove packages
+Uninstall packages using the same manager you used to install them `conda remove PACKAGE_NAME` or `pip uninstall PACKAGE_NAME`
 
-After installing a new package you can use the following command in your terminal to update your `environment.yaml` before publishing your pipeline. Note that we ignore the package version for `libfortran` to keep compatibility with Linux:
+### Update your conda `environment.yaml`
 
+After installing or removing a package you can use the following command in your terminal to update your `environment.yaml` before publishing your pipeline. Note that we ignore the package version for `libfortran` to keep compatibility with Linux:
 ```bash
 conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' >  environment.yml
 ```
 
-## Update and prune your conda environment from a `environment.yaml` file
+## R Virtual Environment
 
-Execute the following command in your terminal, see these docs for more [information](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#updating-an-environment)
+### Add new packages
+1. Open your terminal and navigate to RAPIDS' root folder
+2. Run `R` to open an R interactive session
+3. Run `renv::install("PACKAGE_NAME")`
+
+### Remove packages
+1. Open your terminal and navigate to RAPIDS' root folder
+2. Run `R` to open an R interactive session
+3. Run `renv::remove("PACKAGE_NAME")`
+
+### Update your R `renv.lock`
+After installing or removing a package you can use the following command in your terminal to update your `renv.lock` before publishing your pipeline.
+
+1. Open your terminal and navigate to RAPIDS' root folder
+2. Run `R` to open an R interactive session
+3. Run `renv::snapshot()` (renv will ask you to confirm any updates to this file)
 
-```bash
-conda env update --prefix ./env --file environment.yml  --prune
-```

renv.lock

@@ -86,12 +86,12 @@
       "Repository": "CRAN",
       "Hash": "e031418365a7f7a766181ab5a41a5716"
     },
-    "RMySQL": {
+    "RMariaDB": {
-      "Package": "RMySQL",
+      "Package": "RMariaDB",
-      "Version": "0.10.20",
+      "Version": "1.0.10",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "022066398851453f187950137e21daad"
+      "Hash": "d149479ea03e5cbb1e788449ef5e04b4"
     },
     "Rcpp": {
       "Package": "Rcpp",
@@ -156,6 +156,20 @@
       "Repository": "CRAN",
       "Hash": "543776ae6848fde2f48ff3816d0628bc"
     },
+    "bit": {
+      "Package": "bit",
+      "Version": "4.0.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "f36715f14d94678eea9933af927bc15d"
+    },
+    "bit64": {
+      "Package": "bit64",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+    },
     "boot": {
       "Package": "boot",
       "Version": "1.3-24",

src/data/create_participants_files.R

@@ -1,6 +1,6 @@
 source("renv/activate.R")
 
-library(RMySQL)
+library(RMariaDB)
 library(stringr)
 library(purrr)
 library(readr)
@@ -19,7 +19,7 @@ fitbit_ignored = config$FITBIT_SECTION$IGNORED_DEVICE_IDS
 rmysql.settingsfile <- "./.env"
 
 if(config$SOURCE$TYPE == "AWARE_DEVICE_TABLE"){
-  database <- dbConnect(MySQL(), default.file = rmysql.settingsfile, group = group)
+  database <- dbConnect(MariaDB(), default.file = rmysql.settingsfile, group = group)
   if(config$FITBIT_SECTION$ADD == TRUE){
     query <- paste("SELECT",phone_device_id_column, ",",fitbit_device_id_column," as _temp_fitbit_id, brand, label, timestamp FROM aware_device order by timestamp asc")
     fitbit_device_id_column <- "_temp_fitbit_id"

src/data/download_fitbit_data.R

@@ -1,5 +1,5 @@
 source("renv/activate.R")
-library(RMySQL)
+library(RMariaDB)
 library("dplyr", warn.conflicts = F)
 library(readr)
 library(stringr)
@@ -23,7 +23,7 @@ unified_device_id <- tail(device_ids, 1)
 # As opposed to phone data, we dont' filter by date here because data can still be in JSON format, we need to parse it first
 
 if(source$TYPE == "DATABASE"){
-  dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = source$DATABASE_GROUP)
+  dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = source$DATABASE_GROUP)
   query <- paste0("SELECT * FROM ", table, " WHERE ",source$DEVICE_ID_COLUMN," IN ('", paste0(device_ids, collapse = "','"), "')")
   sensor_data <- dbGetQuery(dbEngine, query)
   dbDisconnect(dbEngine)

src/data/download_phone_data.R

@@ -1,6 +1,6 @@
 source("renv/activate.R")
 source("src/data/unify_utils.R")
-library(RMySQL)
+library(RMariaDB)
 library(stringr)
 library("dplyr", warn.conflicts = F)
 library(readr)
@@ -80,7 +80,7 @@ platforms <- participant$PHONE$PLATFORMS
 validate_deviceid_platforms(device_ids, platforms)
 timestamp_filter <- get_timestamp_filter(device_ids, participant, timezone)
 
-dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = group)
+dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = group)
 
 if(is_multiplaform_participant(dbEngine, device_ids, platforms)){
   sensor_data <- unify_raw_data(dbEngine, table, sensor, timestamp_filter, aware_multiplatform_tables, device_ids, platforms)

src/data/workflow_example/download_demographic_data.R

@@ -1,5 +1,5 @@
 source("renv/activate.R")
-library(RMySQL)
+library(RMariaDB)
 library("dplyr", warn.conflicts = F)
 library(readr)
 library(stringr)
@@ -14,7 +14,7 @@ sensor_file <- snakemake@output[[1]]
 participant <- read_yaml(participant_file)
 record_id <- participant$PHONE$LABEL
 
-dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = source$DATABASE_GROUP)
+dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = source$DATABASE_GROUP)
 query <- paste0("SELECT * FROM ", table, " WHERE record_id = '", record_id, "'")
 sensor_data <- dbGetQuery(dbEngine, query)
 dbDisconnect(dbEngine)

src/data/workflow_example/download_target_data.R

@@ -1,5 +1,5 @@
 source("renv/activate.R")
-library(RMySQL)
+library(RMariaDB)
 library("dplyr", warn.conflicts = F)
 library(readr)
 library(stringr)
@@ -15,7 +15,7 @@ sensor_file <- snakemake@output[[1]]
 participant <- read_yaml(participant_file)
 record_id <- participant$PHONE$LABEL
 
-dbEngine <- dbConnect(MySQL(), default.file = "./.env", group = source$DATABASE_GROUP)
+dbEngine <- dbConnect(MariaDB(), default.file = "./.env", group = source$DATABASE_GROUP)
 query <- paste0("SELECT * FROM ", table, " WHERE record_id = '", record_id, "'")
 sensor_data <- dbGetQuery(dbEngine, query)
 dbDisconnect(dbEngine)