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applications:connect_matlab_mac [2022/05/26 21:17] – gregbalcoapplications:connect_matlab_mac [2022/05/26 22:24] (current) – gregbalco
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 What this does is connect port 3306 (the default MySQL port) on the remote MySQL server, through the SSH tunnel host, to localhost port 12345 on the local machine. Thus, it will appear to a database client (such as MATLAB in this case) that the database is located at localhost:12345. The '&' tells the command to run in the background and return the command line.  What this does is connect port 3306 (the default MySQL port) on the remote MySQL server, through the SSH tunnel host, to localhost port 12345 on the local machine. Thus, it will appear to a database client (such as MATLAB in this case) that the database is located at localhost:12345. The '&' tells the command to run in the background and return the command line. 
 +
 +The port number 12345 is (obviously) arbitrary. You can use anything that is not already in use on your machine. If a port is in use, your computer will behave oddly. Mostly, high-numbered (5 digits) ports are OK. 
  
 Note that this won't work as I have written it here because the SSH host and database IP address don't exist. You'll need to put in the correct values. If you have already been using a different MySQL client, you know what these are. If not, ask Greg or Joe.  Note that this won't work as I have written it here because the SSH host and database IP address don't exist. You'll need to put in the correct values. If you have already been using a different MySQL client, you know what these are. If not, ask Greg or Joe. 
  
-One additional item of importance is that when you are done with this,  you will have to shut down the SSH process that is keeping the tunnel open. If you don't, it will eventually die next time your computer goes to sleep, but it is bad practice to leave zombie processes all over the place. Unfortunately, shutting it off is a bit complicated. First, you have to identify the process that is running SSH. To do this, type in the terminal:+One additional item of importance is that when you are done with this,  you will have to shut down the SSH process that is keeping the tunnel open. If you don't, it will eventually die next time your computer goes to sleep, but it is bad practice to leave zombie processes all over the place. And, in addition, if you have multiple alive and dead processes that are trying to use the same localhost port, that will eventually cause trouble. Shutting it off is very UNIX-y. First, you have to identify the process that is running SSH. To do this, type in the terminal:
  
 ''ps aux | grep 3306'' ''ps aux | grep 3306''
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 This will generate a bunch of information that will look something like this: This will generate a bunch of information that will look something like this:
  
-''balcs             7966   0.0  0.0  4268344    728 s001  S+   11:01PM   0:00.00 grep 3306 +<code> 
-balcs             7652   0.0  0.0  4352368    852   ??  Ss   10:51PM   0:00.01 ssh -f iced@ssh.tunnel.host.org -L 12345:3123.446.789.10:3306 -N -v''+balcs             7966   0.0  0.0  4268344    728 s001  S+   11:01PM   0:00.00 grep 3306 
 +balcs             7652   0.0  0.0  4352368    852   ??  Ss   10:51PM   0:00.01 ssh -f iced@ssh.tunnel.host.org -L 12345:3123.446.789.10:3306 -N -v 
 +</code>
  
 The second line tells you that the SSH process is process 7652 (everything that is running on a *nix system has its own process number). You can shut it down by typing: The second line tells you that the SSH process is process 7652 (everything that is running on a *nix system has its own process number). You can shut it down by typing:
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 == Connecting MATLAB to the database through the SSH tunnel ==  == Connecting MATLAB to the database through the SSH tunnel == 
  
-Now that you have an ssh tunnel open to the database, you need to point MATLAB to it. On current MATLAB, it appears the easiest way to do this is to use the 'JDBC data source configuration' dialog that you have already opened. What this does is create a persistent description of a database connection that you can refer to by name from the command line. So, for example, this:+Now that you have an ssh tunnel open to the database, you need to point MATLAB to it. On current MATLAB, it appears the easiest way to do this is to use the 'JDBC data source configuration' dialog, which can be opened from the 'Database explorer' as indicated in the MATLAB help described above, or can be invoked from the MATLAB command line by typing 'configureJDBCDataSource.' What this does is create a persistent description of a database connection that you can refer to by name from the command line. So, for example, this:
  
 {{:applications:screen_shot_2022-05-26_at_1.57.28_pm.png?400|}} {{:applications:screen_shot_2022-05-26_at_1.57.28_pm.png?400|}}
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 ''dbc = database('new_ICED_reader_through_tunnel','reader','beryllium-10')'' ''dbc = database('new_ICED_reader_through_tunnel','reader','beryllium-10')''
  
-This should return a bunch of information about the database connection. You now have a live connection to the database that can be accessed in a MATLAB script. Try:+This should return a bunch of information about the database connection. You now have a live connection to the database that can be accessed by additional MATLAB commands. Try:
  
-''fetch(dbc,'select name,lat_DD,lon_DD from base_sample where name = "10-MPS-001-COU"')''+''query_result = fetch(dbc,'select name,lat_DD,lon_DD from base_sample where name = "10-MPS-001-COU"')''
  
 This should return: This should return:
  
  
-'''ans =+<code> 
 +query_result =
  
   1×3 table   1×3 table
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     {'10-MPS-001-COU'}    -83.285    -57.975     {'10-MPS-001-COU'}    -83.285    -57.975
-'''+</code>
  
 What you have just done is send an SQL command to the database and obtain a result as a MATLAB variable that you can now work with in MATLAB.  What you have just done is send an SQL command to the database and obtain a result as a MATLAB variable that you can now work with in MATLAB. 
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 ''close(dbc)'' ''close(dbc)''
  
-To learn more about this, look at the MATLAB documentation for the commands 'database' and 'table'. The MATLAB 'table' is kind of a weird construct that has to be deconstructed to be useable as numerical data. +If everything is working as intended, the 'new_ICED_reader_through_tunnel' data source description should be persistent through MATLAB sessions on the same computer. Of course, if you include this in MATLAB code and you are trying to run it on a different computer, you will have to use a data source description that exists on the new computer. Thus, when writing code that uses database connections that you're going to be giving to someone else, put the database connection commands someplace obvious where they can be easily changed.  
 + 
 +To learn more about this, look at the MATLAB documentation for the commands 'database', 'fetch', and 'table'. The MATLAB 'table' is kind of a weird construct that has to be deconstructed to be useable as numerical data.