Added initial Vagrantfile and bootstrap.sh
Now installs VEP and runs to generate VCFs OK
Basic app skeleton
Initial thoughts and outline of the API
Added basic service implementation, likely more or less complete. We switched to port 3001, mainly because we don't want to conflict during testing.
Substantial work whipping this module into shape. Better initialization to not leave stuff in /tmp, and a lot of work on initializing the process
Fixes moving data to /var/local for better persistence after bootstrap
Again getting stuff out of /tmp
Added basic parameters to the annotate wrapper. It’s about ready to test
Added a mock command we can use for testing
Added a simple front endpoint we can use, mostly as a test ping to check we are connected to the right application
Added some initial test code
Tested file uploading
Added test to make sure we get the input file back unchanged
Added handling of input and output files to the mock command, so we can test it’s behaviour on IO.
Marked the commands as executable
Updated the commands themselves
Fixed the parameter handling in the service, and the process spawning
Testing reading files. Still broken, mostly due to res.sendfile’s inability to handle hidden files
Integrated the command system, so that now .pid files can be read. This involved delegating res.sendfile to the separate send module, as res.sendfile doesn’t allow hidden files to be sent.