Leaf API fails to start

[artgoldberg]

Hi Folks

I'm following the Leaf installation directions. In step 8a systemctl start leaf_api.service fails to start the Leaf API. This is the error reported by systemctl status:

● leaf_api.service - Leaf API Service
   Loaded: loaded (/var/opt/leafapi/services/leaf_api.service; linked; vendor preset: disabled)
   Active: failed (Result: signal) since Sat 2021-05-08 12:11:33 EDT; 1min 0s ago
  Process: 90214 ExecStart=/usr/bin/dotnet API.dll (code=killed, signal=ABRT)
 Main PID: 90214 (code=killed, signal=ABRT)

May 08 12:11:33 omop-leaf systemd[1]: Started Leaf API Service.
May 08 12:11:33 omop-leaf dotnet[90214]: Unhandled exception. System.ArgumentNullException: Value cannot be null. (Parameter 'path1')
May 08 12:11:33 omop-leaf dotnet[90214]: at System.IO.Path.Combine(String path1, String path2)
May 08 12:11:33 omop-leaf dotnet[90214]: at API.Program.Main(String[] args) in /var/opt/leafapi/leaf_download/leaf/src/server/API/Program.cs:line 28
May 08 12:11:33 omop-leaf systemd[1]: leaf_api.service: main process exited, code=killed, status=6/ABRT
May 08 12:11:33 omop-leaf systemd[1]: Unit leaf_api.service entered failed state.
May 08 12:11:33 omop-leaf systemd[1]: leaf_api.service failed.

It appears that creation of the log fails because Environment.GetEnvironmentVariable(Config.Logging.Directory) is null. For more details see the attached debugging data, which contains slightly annotated copies of terminal interactions.

My hypothesis is that leaf_api.service.conf should not be empty, but I see no instructions on what it should contain.

Regards
Arthur

2021-05-08_debug.txt

[artgoldberg]

I resolved the problem. When running in a bash shell, the environment variables need to be exported so that they're available in the dotnet process that gets launched. E.g., to make SERILOG_DIR available in Environment.GetEnvironmentVariable(Config.Logging.Directory) it needs to be defined with:

export SERILOG_DIR=/var/log/leaf/                 

[ndobb]

Thanks for letting us know, @artgoldberg. I reviewed your attached code and didn't see any issues but that makes sense. @mh2727, maybe we can incorporate some of Arthur's code into https://leafdocs.rit.uw.edu/installation/installation_steps/7_env/? We mention using a .conf file but aren't too explicit for Linux setup (our rationale for that if I recall correctly was that there are many ways to configure env variables and we didn't want to be overly prescriptive, though perhaps we can provide examples and be more clear about ensuring the variables are visible to the API at runtime).

[artgoldberg]

Thanks @ndobb , but it's more complicated than I thought and not fully resolved. When launching the API with dotnet run, the env vars are available to the C# code. That is, this code:

	Console.WriteLine($"Config.Logging.Directory: {Config.Logging.Directory}");
	Console.WriteLine($"Config.Logging.FileTemplate: {Config.Logging.FileTemplate}");
	Console.WriteLine($"Environment.GetEnvironmentVariable(Config.Logging.Directory): {Environment.GetEnvironmentVariable(Config.Logging.Directory)}");

generates this output:

Config.Logging.Directory: SERILOG_DIR
Config.Logging.FileTemplate: leaf-api-{Date}.log
Environment.GetEnvironmentVariable(Config.Logging.Directory): /var/log/leaf/

But when launching the API with:

# Make the systemd aware of the service
systemctl daemon-reload

# Start the service
systemctl start leaf_api.service

the env vars are not available to the API. E. g., the same code generates this:

[root@omop-leaf leafapi]# systemctl status -l leaf_api.service
● leaf_api.service - Leaf API Service
   Loaded: loaded (/var/opt/leafapi/services/leaf_api.service; linked; vendor preset: disabled)
   Active: failed (Result: signal) since Mon 2021-05-10 18:32:20 EDT; 10s ago
  Process: 99400 ExecStart=/usr/bin/dotnet API.dll (code=killed, signal=ABRT)
 Main PID: 99400 (code=killed, signal=ABRT)

May 10 18:32:20 omop-leaf systemd[1]: Started Leaf API Service.
May 10 18:32:20 omop-leaf dotnet[99400]: Config.Logging.Directory: SERILOG_DIR
May 10 18:32:20 omop-leaf dotnet[99400]: Config.Logging.FileTemplate: leaf-api-{Date}.log
May 10 18:32:20 omop-leaf dotnet[99400]: Environment.GetEnvironmentVariable(Config.Logging.Directory):
May 10 18:32:20 omop-leaf dotnet[99400]: Unhandled exception. System.ArgumentNullException: Value cannot be null. (Parameter 'path1')
May 10 18:32:20 omop-leaf dotnet[99400]: at System.IO.Path.Combine(String path1, String path2)
May 10 18:32:20 omop-leaf dotnet[99400]: at API.Program.Main(String[] args) in /var/opt/leafapi/leaf_download/leaf/src/server/API/Program.cs:line 32

[artgoldberg]

Hi again @ndobb and @mh2727 . My initial tests indicate that to use environment variables in systemd on Linux we need to employ either the Environment command in the leaf_api.service file or the EnvironmentFile command in the .service file and create a leaf_api.service.conf file. I'll take the latter approach, so that the env vars are defined separately.

[mh2727]

Hi @artgoldberg.

The latter approach would be a cleaner way of setting up Leaf.

If it's helpful, your Environment variables should be in leaf_api.service.conf like so: https://leafdocs.rit.uw.edu/installation/installation_steps/7_env/#7-set-environment-variables.

And in your .service file, you would define the EnvironmentFile line like so:
EnvironmentFile=/path/to/leaf_api.service.conf.

[artgoldberg]

@ndobb and @mh2727
Yes, that makes sense Mehadi.
Good news, the Leaf API is running.