junos
/
rapids
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

Update installation.rst

pull/95/head
JulioV 2020-05-18 12:21:21 -04:00 committed by GitHub
parent 549db08d85
commit ba1d6a2beb
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 17 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
docs/usage/installation.rst
View File

@ -3,7 +3,7 @@
Installation
===============
This instructions have been tested on macOS (Catalina and Mojave) and Ubuntu 16.04. If you find a problem, please report it on our GitHub page.
These instructions have been tested on macOS (Catalina and Mojave) and Ubuntu 16.04. If you find a problem, please create a GitHub issue or contact us.
macOS (tested on Catalina 10.15)
--------------------------------
@ -17,11 +17,10 @@ macOS (tested on Catalina 10.15)
- ``brew install mysql``
- ``brew services start mysql``
#. Install R, pandoc and rmarkdown:
#. Install R and pandoc:
- ``brew install r``
- ``brew install pandoc``
- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
#. Install miniconda:
@ -44,7 +43,7 @@ macOS (tested on Catalina 10.15)
- ``snakemake renv_install``
- ``snakemake renv_init``
- ``snakemake renv_restore``
- This step will take several minutes to complete. Please be patient and let it run until completion.
- This step could take several minutes to complete. Please be patient and let it run until completion.
#. See Usage section below.
@ -68,7 +67,6 @@ Linux (tested on Ubuntu 16.04)
- ``brew install r``
- ``brew install gcc@6`` (needed due to this bug_)
- ``HOMEBREW_CC=gcc-6 brew install pandoc``
- ``R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'``
#. Install miniconda using these instructions_
@ -87,47 +85,47 @@ Linux (tested on Ubuntu 16.04)
- ``snakemake renv_install``
- ``snakemake renv_init``
- ``snakemake renv_restore``
- This step will take several minutes to complete. Please be patient and let it run until completion.
- This step could take several minutes to complete. Please be patient and let it run until completion.
#. See Usage section below.
Usage
======
Once you have the installation for your specific operating system complete, you can follow these steps to start using RAPIDS.
Once RAPIDS is installed, follow these steps to start processing mobile data.
.. _db-configuration:
#. Configure the database connection:
- Create an empty file called `.env` in the root directory (``rapids/``)
- Add the following lines and replace your database specific credentials (user, password, and host):
- Add the following lines and replace your database specific credentials (user, password, host, and database):
.. code-block:: bash
[MY_GROUP]
user=MyUSER
password=MyPassword
host=MyIP
user=MY_USER
password=MY_PASSWORD
host=MY_HOST
port=3306
database=MyDB
database=MY_DATABASE
.. note::
``MY_GROUP`` is a custom label you assign when setting up the database configuration. It has to match ``DATABASE_GROUP`` in the ``config.yaml`` file_. It does not have to relate to your database credentials.
``MY_GROUP`` is a custom label for your credentials. It has to match ``DATABASE_GROUP`` in the ``config.yaml`` file_. It is not related to your database configuration.
#. Configure the participants you want to analyze:
#. Setup the participants' devices whose data you want to analyze:
- **Automatically**. You can automatically include all devices that are stored in the ``aware_device`` table, if you have especial requirements see the Manual configuration::
- **Automatically**. You can automatically include all devices that are stored in the ``aware_device`` table. If you have especial requirements see the Manual configuration::
snakemake download_participants
snakemake -j1 download_participants
- **Manually**. Create one file per participant in the ``rapids/data/external/`` directory. The file should NOT have an extension (i.e. no .txt). The name of the file will become the label for that participant in the pipeline.
- The first line of the file should be the Aware ``device_id`` for that participant. If one participant has multiple device_ids (i.e. Aware had to be re-installed), add all device_ids separated by commas.
- The second line should list the device's operating system (``android`` or ``ios``)
- The third line is a human friendly label that will appear in any plots for that participant.
- The forth line contains a start and end date separated by a comma (e.g. ``20201301,20202505``). Only data wihtin these dates will be included in the pipeline.
- The third line is an optional human friendly label that will appear in any plots for that participant.
- The forth line is optional and contains a start and end date separated by a comma ``YYYYMMDD,YYYYMMDD`` (e.g. ``20201301,20202505``). Only data wihtin these dates will be included in the pipeline, if no dates are specified all data from that device will be included.
For example, let's say participant `p01` had two AWARE device_ids and they were running Android between Feb 1st 2020 and March 3rd 2020. Their participant file would be named ``p01`` and contain:
@ -140,7 +138,7 @@ Once you have the installation for your specific operating system complete, you
#. Configure the sensors to process:
- The variable ``SENSORS`` in the ``config.yaml`` file_ should match existent sensor tables in your Aware database (See :ref:`rapids-structure` for more information). Each item in this list will be processed in RAPIDS.
- The variable ``SENSORS`` in the ``config.yaml`` file_ should match existent sensor tables in your Aware database (See :ref:`rapids-structure` for more information). Each sensor in this list will be processed in RAPIDS.
.. note::