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SNAP DIY Database

Overview of the system

I put together a little DIY fieldwork database server using nearly entirely open source tools and software. It consists of a Raspberry Pi operating on a local network, which contains a MariaDB server, a SMB file sharing server, an R Shiny server, and automatic scheduled backups, but can be configured or extended to suit whatever situation you're in. This is a more collaborative and distributed setup than a typical Microsoft Access setup (or even worse, a series of scattered spreadsheets :z), since multiple users can simultaneously enter data stored in a unified and central directory, share files across the network, and browse what's going on across an entire project. Microsoft Access, on the other hand, is proprietary, expensive and windows-only software that has poor multi-user support and the learning curve is steeper than its worth (I could go on...).

Moreover, this is a very inexpensive and portable setup. In terms of hardware, you will need a 35$ Raspberry Pi, a 32GB SD card (also ~35$), a small router (this one is 40$ and tiny! https://amzn.to/2HoOM6W), a high ampage external battery (I recommend this one at 43$: https://amzn.to/2Ht8quv) and a couple USB flash drives with storage capacities that suit your needs.

Please refer to the diagram for further details regarding hardware configuration and overall setup.

This documents how I put things together and made things work. Please get in touch if you have any questions!

  • Zack Batist
  • @mtl_zack on twitter
  • zackbatist on github

R code and SQL snippets coming soon!

Installing Raspbian

Insert microSD card into the adapter and insert into a laptop.

Format the microSD card as FAT32 using SD Card Formatter.app.

Etch the Rasbian disk image to the SD card in Etcher.app.

Configure the OS to enable SSH on first boot.

touch /Volumes/boot/ssh

Add network info to enable immediate connection to the network.

touch /Volumes/boot/wpa_supplicant.conf
cd /Volumes/boot
nano wpa_supplicant.conf

Paste this in to wpa_supplicant.conf, changing the country code, network SSID and network password to suit the situation:

country=CA
ctrl_interface=DIR=/var/run/wpa_supplicant GROUP=netdev
update_config=1

network={
    ssid="<network name>"
    psk="<network password>"
}

These last three steps are crucial for working headless!

Eject the microSD card, place it in the Raspberry Pi and boot it up. Wait a couple minutes for it to finish booting up. Then SSH in.

Download updates

Once you SSH into the pi, update all software packages (requires internet connection).

sudo apt-get update -y
sudo apt-get upgrade -y

It is apparently not necessary to update the kernel or firmware. The most up-to-date versions are included in the raspbian disk images, and using sudo rpi-update may install bleeding-edge updates or untested firmware.

More info:

Shutting down (VERY IMPORTANT!)

__NOTE: IT IS EXTREMELY IMPORTANT THAT YOU DON'T YANK THE POWER CHORD TO POWER OFF!!! THAT CAN CORRUPT THE SD CARD AND YOU'LL HAVE TO RE-IMAGE IT OVER AND OVER AGAIN! I KNOW THIS FROM MY OWN PAINFUL AND STUPID EXPERIENCE SO DON'T EVEN DARE! USE THE FOLLOWING SHUTDOWN COMMANDS INSTEAD.

TO SHUTDOWN:

sudo shutdown -h now

More info:

Setting up static IP addresses

It is necessary to set static IP addresses as fallbacks in case wpa_supplicant.conf fails. We need to do this for both wireless and ethernet interfaces.

First we need to get the Raspberry Pi's IP address on each interface:

pi@raspberrypi:~ $ ip -4 addr show | grep global

The output should look something like this:

    inet 169.254.39.157/16 brd 169.254.255.255 scope global eth0
    inet 192.168.0.198/24 brd 192.168.0.255 scope global wlan0

eth0 refers to the ethernet interface, and wlan0 refers to the wireless interface.

Then we need to determine the router's gateway:

pi@raspberrypi:~ $ ip route | grep default | awk '{print $3}'

Should look something like this:

192.168.0.1

Then we need to determine the DNS server or namespace, which is often the same as the router's gateway:

pi@raspberrypi:~ $ nano /etc/resolv.conf

Should look something like this:

# Generated by resolvconf
nameserver 192.168.0.1

Next we have to add this information to /etc/dhcpcd.conf:

sudo nano /etc/dhcpcd.conf

Add the following, substituting the IP address values for the one's that were just determined above.

interface eth0
static ip_address=169.254.39.157/16
static routers=192.168.0.1
static domain_name_servers=192.168.0.1

interface wlan0
static ip_address=192.168.0.198/24
static routers=192.168.0.1
static domain_name_servers=192.168.0.1

Pro-tip: You may need to make a direct connection with your computer to download updates (I tend to tether my cullular connection to my laptop and share the connection over ethernet). In such cases, you will need to edit dhcpcd.conf and comment out the eth0 specifications to enable an alternative ethernet interface with your laptop that is not specific to the router that it is normally connected to. You may not even need an eth0 static IP, but it helps to have that direct ethernet connection in place if you are using the Pi as a network attached storage (NAS) device, i.e. sharing files over the network, as this gives a significant speed boost to file transfers.

SSH

SSH enables you to control the raspberry pi over the local network via the command line.

In Terminal.app run the following command:

ssh pi@<ip address>

This terminal window should now be considered a remote client to the raspberry pi. Everything you do here occurs on the raspberry pi.

If you get the following warning, just go and edit ~/.ssh/known_hosts and delete the key for the corresponding SSH connection. This might happen when trying to connect to a fresh install of the Raspbian OS.

Default password is raspberry.

The pi's IP address can be found in the router control panel, which can be accessed by entering the router's IP address into the browser's address bar, and entering the default username and password when prompted.

The pi's IP address, along with IP addresses for all devices connected to the network, will be listed under a page titled simething like 'DHCP client list'.

Pro tip: In your router settings, under the DHCP menu, you should be able to reserve an IP address for the Raspberry Pi. Find the Pi's MAC address by running ifconfig (it's after ether under the wlan0 heading), and assign it an IP towards the upper end of the range allocated to the local network. This helps keep things consistent and makes for a more efficient headless setup.

More info:

Router's IP address: 192.168.0.254
Username: admin
Password: admin

SSH via direct ethernet connection (MacOS)

Raspbian is configured by default to receive an IP address from a DHCP server, a role that is typically fulfilled by a wireless router. This can be done without a router by configuring the sharing options in MacOS.

From System Preferences, go to the Sharing window.

From the box on the left, enable 'Internet Sharing'. You may have to select a 'Thunderbolt Ethernet' under the Wi-Fi dropdown before checking off the 'Internet Sharing' box.

In Terminal, use ifconfig. Under bridge100, note the IP address in the inet field, most likely 192.168.2.1. Add one to the final digit to determine the likely IP address of the Raspberry Pi (192.168.2.2 in this case).

Note: This will not work if the wireless network is secured by a 802.1x firewall, which are commonly implemented by most university, hospital and government networks.

More info:

Mounting a USB drive

While Raspberry Pi does support auto USB mounting when starting the machine, it can be a bit flaky. Therefore we will use the device ID to ensure that there is more certainty of a proper mount. So we need to determine the UUID of the USB device by running this command:

ls -al /dev/disk/by-uuid

and cross checking it with the devices listed after entering:

lsblk

Infer the correct UUID based on the drive's capacity and through elimination of other possibilities, and note it down somewhere.

Now create the directory where we want to mount the drive:

sudo mkdir /media/backup

Give the directory adequate permissions:

sudo chmod -R 777 /media/TrenchData

Note: This command gives unrestricted read, write and execute permissions to all users! Configure your permissions to suit your needs!

Open the fstab file:

sudo nano /etc/fstab

At the end of that file, add the following command, replacing the UUID with the one pertaining to the specific device and the directory with the intended mount point:

UUID=783A-120B /media/backup auto noatime,nofail,umask=000 0 0

Note: This is the correct code for FAT32 formatted drives only. FAT32 handles permissions is a slightly different way than NTFS and linux-based filesystems (i.e. ext4) and you will need to configure them accordingly. However, I recommend the use of FAT32 in general, since it is interoperable between virtually all operating systems, whereas others are not.

Now the USB drive will be auto mounted and ready to use. Don’t forget to restart your Raspberry Pi to test it out.

sudo shutdown -h now

File sharing on a local network

Install Samba:

sudo apt-get install samba samba-common-bin

Create your shared directory: If your intent is to share the files from an external USB storage drive, follow the instructions above to mount it.

Edit the Samba configuration file:

sudo nano /etc/samba/smb.conf

and add the following:

[TrenchData]
Comment = Pi shared folder
Path = /media/TrenchData
Browseable = yes
Writeable = Yes
only guest = no
create mask = 0777
directory mask = 0777
Public = yes
Guest ok = yes

Ensure that Path = the directory you want to share, such as the mount point of an external drive.

This configuration allows anyone to read, write, and execute files in a volume named share, either by logging in as a Samba user or as a guest. If you don’t want to allow guest users, omit the guest ok = yes line.

To set up users and passwords:

sudo s smbpasswd -a pi

I'm not certain if it is necessary for the samba user to be a user on the Raspberry Pi's filesystem.

Then, restart Samba:

sudo /etc/init.d/samba restart

From now on, Samba will start automatically whenever you power on your Pi.

Find your Pi on the network

You’ll now be able to find your Raspberry Pi file server (named RASPBERRYPI by default) from any device on your local network.

More info:

https://www.raspberrypi.org/magpi/samba-file-server/

Remote desktop

Install TightVNC

sudo apt-get install tightvncserver

Set up a TightVNC server

tightvncserver :1

When prompted for a password, just use the default (raspberry). It will be truncated to raspberr (8 characters) but that's fine.

When prompted if you want to set a view-only password, input 'n' for no.

Connect to the TightVNC server remotely

MacOS has a remote desktop client built in called 'Screen Sharing.app'. Search for it using spotlight (Command + Space) or by opening a finder window and then hitting Command + K. On Windows, you must install RealVNC (it is also available on MacOS, but I prefer the built-in app). In either 'Screen Sharing.app' or RealVNC, paste the TightVNC server info in the address bar, formatted like this:

vnc://<raspberry pi IP address>:5901

The Raspberry Pi's IP address can be determined by SSH-ing into it and running the command ifconfig, or by checking the DHCP client list on the router's control panel. It should appear as 192.168.0.10x, x being a replacable digit. The '1' in '5901' refers to the port to be connected to, which corresponds with the :1 when setting up the vnc server.

More info:

Automated backups of MariaDB databases

Scripting the backup

Here is a script that exports the complete data of our database and saves it as a compressed gzip file. The script also automatically affixes the archive file with the date and time of the backup (UTC time zone).

The script will be created in the home directory for simplicity’s sake:

cd ~
sudo nano dbbackup.sh

Here is the content of dbbackup.sh:

#!/bin/bash
$OUTPUT_FILE = /media/backup/mysqldump/SNAP_$(date +"%Y%m%d_%H%M%S").gzip
$USERNAME = <MySQL username>
$PASSWORD = <MySQL password>
$DATABASE_NAME = <Database name>

sudo mysqldump -u$USERNAME -p$PASSWORD $DATABASE_NAME | gzip > $OUTPUT_FILE

Replace the username, password, database name and file path according to your situation. Ensure that the permissions are properly set to allow you to write to the specified directory.

Finally, we need to set the script to be executable:

sudo chmod 755 dbbackup.sh

Making it automatic

cron is a time-based scheduling utility in Unix/Linux operating systems such as Raspbian. It reads a configure file, commonly referred to as crontab where jobs are scheduled using a special syntax. To access the crontab simply enter crontab -e and add a line at the end of the file to schedule a job.

To run dbbackup.sh every 30 minutes, add the following line at the end of the crontab:

*/30 * * * * /home/pi/dbbackup.sh

More info:

MariaDB

MariaDB is essentially the same thing as MySQL. MariaDB was forked from MySQL after Oracle bought Sun Microsystems, who maintains MySQL, and there was some worry about licensing issues due to Oracle's poor reputation with regards to the maintenance and development of open source software (LibreOffice is a similar fork of OpenOffice, which was also bought by Oracle around the same time). All tutorials and online resources for MySQL are also applicable for MariaDB.

Installing and configuring MariaDB

sudo apt-get install mariadb-server

The MariaDB configuration file needs to be modified to enable remote access to the database across the network. Access the config file:

sudo nano /etc/mysql/mariadb.conf.d/50-server.cnf

Replace the bind-address from 127.0.0.1 to 0.0.0.0.

This changes the local address(es) that MySQL/MariaDB will listen to for connections on. The Raspberry Pi default is 127.0.0.1 for localhost only.

Save the file and restart the MySQL service:

sudo service mysql restart

Installing and running MariaDB locally on a MacOS

MariaDB can be installed via homebrew using the following command:

brew install mariadb

Then update homebrew, refresh the index of retrievable packages, and upgrade any installed packages:

brew update
brew upgrade

Starting and stopping the MariaDB server on MacOS

To start the MariaDB server:

mysql.server start

To stop the MariaDB server:

mysql.server stop

To install homebrew:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Creating a database:

CREATE DATABASE MY_DATABASE_NAME;

Adding and configuring users

Gotta do this as the root user:

sudo mysql

Create the new user:

CREATE USER 'MY_USERNAME'@'localhost' IDENTIFIED BY 'MY_PASSWORD';

Grant the user remote access from any IP address:

GRANT ALL PRIVILEGES ON MY_DATABASE_NAME.* TO 'MY_USERNAME'@'%' IDENTIFIED BY 'MY_PASSWORD';
FLUSH PRIVILEGES;

To allow access from a fixed IP address:

GRANT ALL PRIVILEGES ON MY_DATABASE_NAME.* TO 'MY_USERNAME'@'12.34.56.78' IDENTIFIED BY 'MY_PASSWORD';
FLUSH PRIVILEGES;

To login as a specific user:

mysql -u MY_USERNAME -p

Input your password as prompted.

Copy database to / from a remote server

Insecure method

If you have direct access to the remote server and aren't worried about security:

mysqldump -h [server] -u [user] -p[password] [databasename] | mysql -h [server] -u [user] -p[password] [databasename]

Secure method (SSH)

If you can SSH into the remote server you can use this:

mysqldump -h [server] -u [user] -p[password] [databasename] | ssh [ssh_username]@remote_domain.com mysql -u [user] -p[password] [databasename]

You will then be promoted for the ssh password of the remote server.

Copying a single table

If you want to copy only a single table, specify the tablename after the 'from' database name. If the table already exists it is overwritten.

mysqldump -h [server] -u [user] -p[password] [databasename] [tablename] | mysql -h [server] -u [user] -p[password] [databasename]

NOTE: The left side is the 'from', the right side is the 'to'. [server] can be localhost on either side.

NOTE: There is NO space between -p and [password].

Setting up MS Access as a front-end for a MariaDB backend

Download and install the Visual C++ Redistributable for Visual Studio 2015 from https://www.microsoft.com/en-ca/download/details.aspx?id=48145.

Download and install the MySQL ODBC Connector from https://dev.mysql.com/downloads/connector/odbc/.

Open the ODBC Data Source Administrator, and add a new data source under the 'User DSN' tab.

Select the MySQL ODBC Unicode Driver from the list of available drivers and include the information needed to connect to the remote database. You may need to set up a SSH tunnel using PuTTY (see below).

Give the connection a name and close both the MySQL ODBC Connector window and the ODBC Data Source Administrator.

Open a blank MS Access database. Under the 'Import & Link' subsection of the 'External Data' ribbon section, select 'ODBC Database' and choose to 'link to the data source by creating a linked table', then hit next.

In the Select Data Source window, go to the Machine Data Source tab and select the connection that was just made. Then select all the tables that you want to link with.

Linked tables have a globe icon next to their names, and all modifications to these tables are implemented on the remote server.

Setting up a SSH tunnel using PuTTY

Migrating from MS Access to MariaDB using MySQL Workbench

NOTE: THIS SECTION IS STILL INCOMPLETE AND HAS EFFECTIVELY BEEN ABANDONED. ALTHOUGH FRAGMETARY, IT MAY INCLUDE SOME USEFUL INFORMATION. USE AT YOUR OWN RISK.

Setting up the source database

Open the database in Access. Under Database Tools, select Visual Basic. In the Immediate window type the following and then hit enter to verify whether you are Admin:

? CurrentUser

Then on the next line include the following:

CurrentProject.Connection.Execute "GRANT SELECT ON MSysRelationships TO Admin"

Close the database.

Setting up the ODBC connection

Ensure that the MS Access drivers are installed from https://www.microsoft.com/en-us/download/details.aspx?id=54920. Ensure that the architecture is consistent with your setup.

Start the MySQL Workbench Migration Wizard, then press Open ODBC Administrator.

Navigate to the 'Drivers' tab and ensure that Microsoft Access Driver (*.mdb, *.accdb) is available and installed.

Navigate to the 'User DSN' tab to create a DSN for the database file to be migrated. Press 'Add', select Microsoft Access Driver (*.mdb, *.accdb), hit 'Select' and then find the database in the directory (you may need to collapse the c:/ directory by double clicking it and going into /Users/ in order to find it). Give the DSN a name and then press OK to close the ODBC Data Source Administrator.

Setting up source parameters

Select 'Start Migration' in the Migration Wizard.

The Source Selection page is where you provide the information about the Access database you are migrating from, the ODBC driver to use, and the parameters for the MS Access connection

For Database System select 'Microsoft Access'.

Connection Method should be 'ODBC Data Source'.

For DSN select the ODBC Data Source that we just created in the ODBC Data Source Administrator.

Keep the default character set.

Test the connection, and then hit 'Next'.

Setting up target parameters

The Source Selection page is where you provide the information about the MySQL/MariaDB target database.

Under the Stored Connection dropdown select Manage Stored Collections, which should open a new window to create a new database connection.

Select 'New' and give the connection a name.

Under 'Connection Method' select Standard TCP/IP over SSH.

The SSH Hostname, SSH Username and SSH Password should be the same IP address that you use to connect to the Raspberry Pi remotely. Append :22 to the end of the hostname to specify the port to be used for this connection.

Keep the default MySQL Hostname and MySQL Server Port. Username and Password pertain to the specific database users doing the migration (access as root in most cases).

Then hit Test Connection.

SSH Hostname: <IP address>:22
SSH Username: pi
SSH Password: raspberry
MySQL Hostname: 127.0.0.1
MySQL Server Port: 3306
Username: root
Password: <root password>

More info:

Splitting MS Access databases for shared use

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