Migration guides¶

Migrating from RAPIDS 0.4.x or older¶

There are four actions that you need to take if you were using RAPIDS 0.4.3 or older (before Feb 9^th, 2021):

Check the new Overview page

Check the new Overview page. Hopefully, it is a better overview of RAPIDS and provides answers to Frequently Asked Questions.

Deploy RAPIDS in a new folder

Clone RAPIDS 1.x in a new folder (do not pull the updates in your current folder)
Activate your conda environment
Install renv again snakemake -j1 renv_install (for Ubuntu take advantage of the platform specific R renv instructions)
Restore renv packages snakemake -j1 renv_restore (for Ubuntu take advantage of the platform specific R renv instructions)
Move your participant files pxx.yaml to the new folder
Move your time segment files to the new folder
Move your .env file to the new folder

Migrate your .env file to the new credentials.yaml format

The .env file is not used anymore, the same credential groups are stored in credentials.yaml, migrate your .env file by running:

python tools/update_format_env.py

Reconfigure your config.yaml

Reconfigure your config.yaml file by hand (don’t copy and paste the old one). Some keys and values changed but the defaults should be compatible with the things you know from RAPIDS 0.x (see below).

The most relevant changes to RAPIDS that you need to know about are:

We introduced the concept of data streams

RAPIDS abstracts sensor data logged by different devices, platforms and stored in different data containers as data streams.

The default data stream for PHONE is aware_mysql, and the default for FITBIT is fitbitjson_mysql. This is compatible with the old functionality (AWARE and JSON Fitbit data stored in MySQL). These values are set in [PHONE_DATA_STREAMS][USE] and [FITBIT_DATA_STREAMS][USE].

You can add new data stream formats (sensing apps) and containers (database engines, file types, etc.).

If you were processing your Fitbit data either in JSON or plain text (parsed) format, and it was stored in MySQL or CSV files, the changes that you made to your raw data will be compatible. Just choose fitbitjson_mysql, fitbitparsed_mysql, fitbitjson_csv, fitbitparsed_csv accordingly and set it in [FITBIT_DATA_STREAMS][USE].

In the future, you will not have to change your raw data; you will be able to just change column mappings/values in the data stream’s format.yaml file.

We introduced multiple time zones

You can now process data from participants that visited multiple time zones. The default is still a single time zone (America/New_York). See how to handle multiple time zones

The keyword multiple is now infer

When processing data from smartphones, RAPIDS allows you to infer the OS of a smartphone by using the keyword multiple in the [PLATFORM] key of participant files. Now RAPIDS uses infer instead of multiple Nonetheless, multiple still works for backward compatibility.

A global DATABASE_GROUP does not exist anymore

There is no global DATABASE_GROUP anymore. Each data stream that needs credentials to connect to a database has its own DATABASE_GROUP config key. The groups are defined in credentials.yaml instead of the .env.

[DEVICE_SENSOR][TABLE] is now [DEVICE_SENSOR][CONTAINER]

We renamed the keys [DEVICE_SENSOR][TABLE] to [DEVICE_SENSOR][CONTAINER] to reflect that, with the introduction of data streams, they can point to a database table, file, or any other data container.

Creating participant files from the AWARE_DEVICE_TABLE is deprecated

In previous versions of RAPIDS, you could create participant files automatically using the aware_device table. We deprecated this option but you can still achieve the same results if you export the output of the following SQL query as a CSV file and follow the instructions to create participant files from CSV files:

SELECT device_id, device_id as fitbit_id, CONCAT("p", _id) as empatica_id, CONCAT("p", _id) as pid, if(brand = "iPhone", "ios", "android") as platform, CONCAT("p", _id)  as label, DATE_FORMAT(FROM_UNIXTIME((timestamp/1000)- 86400), "%Y-%m-%d") as start_date, CURRENT_DATE as end_date from aware_device order by _id;

SCR_SCRIPT and SRC_LANGUAGE are replaced by SRC_SCRIPT

The attributes SCR_SCRIPT and SRC_LANGUAGE of every sensor PROVIDER are replaced by SRC_SCRIPT. SRC_SCRIPT is a relative path from the RAPIDS root folder to that provider’s feature script. We did this to simplify and clarify where the features scripts are stored.

There are no actions to take unless you created your own feature provider; update it with your feature script path.

Migrating from RAPIDS beta¶

If you were relying on the old docs and the most recent version of RAPIDS you are working with is from or before Oct 13, 2020 you are using the beta version of RAPIDS.

You can start using the RAPIDS 0.1.0 right away, just take into account the following:

Deploy RAPIDS in a new folder

Install a new copy of RAPIDS (the R and Python virtual environments didn’t change so the cached versions will be reused)
Make sure you don’t skip a new Installation step to give execution permissions to the RAPIDS script: chmod +x rapids
Move your old .env file
Move your participant files

Migrate your participant files

You can migrate your old participant files to the new YAML format:

python tools/update_format_participant_files.py

Follow the new Configuration guide

Learn more about the new way to run RAPIDS

Get familiar with the new way of Executing RAPIDS