Reference Manual
#################

Connectivity
------------

Tucuxi can be connected to an external database, or import pending requests from XML files.
For both these features, some translations may be required, to translate identifiers into
the internal Tucuxi format. These translations are handled thanks to config files, allowing
each institution to customize the import depending on their own data.


Drug Ids
--------

A file called 'drugidtranslations.ini' shall be placed in the same folder as Tucuxi.

Its format corresponds to standard .ini files, and allows to link the drug Ids found in
the external data with the drug Ids of the Tucuxi drug models.

On the left side is the external Id, and on the right side the Tucuxi drug Id.

Here is an example:

.. code::

   AMIKP      = amikacin
   GNTP       = gentamicin
   DIGO       = digoxin
   TBR        = tobramycin
   VANCR      = vancomycin
   VANC       = vancomycin
   VANCP      = vancomycin
   CEFER      = cefepime
   vancomycin = vancomycin
   tobramycin = tobramycin

In this example we see that in the external files vancomycin is represented by 3 different Ids.


Formulations and routes
-----------------------

A file called 'formulationandroutetranslations.ini' shall be placed in the same folder as Tucuxi.

It shall contain translations from tuples drug-intake to formulations and routes as defined in the drug model files.

The drug shall be separated from the intake with a dot ".".

Here is an example:

.. code::

   [cefepime.i.v.]
      formulation         = parenteralSolution
      administrationRoute = intravenousDrip
      absorptionModel     = infusion
      administrationName  =

   [tacrolimus.p.o]
      formulation         = parenteralSolution
      administrationRoute = oral
      absorptionModel 	  = extra
      administrationName  =

   [vancomycin.injection iv]
      formulation         = parenteralSolution
      administrationRoute = intravenousDrip
      absorptionModel     = infusion
      administrationName  =

   [vancomycin.i.v.]
      formulation         = parenteralSolution
      administrationRoute = intravenousDrip
      absorptionModel     = infusion
      administrationName  =
      
Covariate Ids
-------------

A file called 'covariateidtranslations.ini' shall be placed in the same folder as Tucuxi.

Its format corresponds to standard .ini files, and allows to link the Covariate Ids found in
the external data with the Covariate Ids used by Tucuxi.

On the left side is the external Id, and on the right side the Tucuxi covariate Id.

Here is an example:

.. code::

   BodyWeight = bodyweight
   BW         = bodyweight
   weight     = bodyweight
   creat      = creatinine
   GestAge    = ga

In this example we see that in the external files bodyweight is represented by 3 different Ids.

Application arguments and flags
-------------------------------

.. table:: Available application arguments
  :align: center
  :widths: 20, 60, 20

  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | **Arguments Name** |                                                                   **Description**                                                                       |         **Default Value**         |
  +====================+=========================================================================================================================================================+===================================+
  | -b or -base-path   |Set the base path of the medical institution's server from which interpretion request can be retrieved.                                                  |            "/services"            |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -f or -listfile    |Set the file containing a list of pending requests. This option allows to try pending requests stored locally instead of by connecting to a REST server. |                ""                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -r or -requestfile |Set the file containing single request. This option allows to start the software with a single request.                                                  |                ""                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -i or -iccafile    |Set the file containing flat request. This option allows to start the software with flat requests.                                                       |                ""                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -p or -port        |Set the port number of the medical institution's server from which interpretion request can be retrieved.                                                |               8889                |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -s or -scheme      |Set the scheme of the medical institution's server from which interpretion request can be retrieved.                                                     |               https               |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -t or -host        |Set the host name of the medical institution's server from which interpretion request can be retrieved.                                                  |              ezecs1               |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -l or -logrest     |Set the path in which the REST logs will be stored.                                                                                                      |        applicationDirPath         |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -certificate       |Set the file containing the SSL certificate.                                                                                                             |                ""                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -d or -drugspath   |Drug files path.                                                                                                                                         | applicationDirPath + "/drugfiles" |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -logtqf            |Sets a folder to log the computing requests files.                                                                                                       |                log                |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  
.. table:: Available application flags
  :align: center
  :widths: 20, 60, 20
  
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | **Arguments Name** |                                                                   **Description**                                                                       |         **Default Value**         |
  +====================+=========================================================================================================================================================+===================================+
  | -a or -standalone  |Run Tucuxi as a standalone software, effectively disabling any feature relying on retrieving medical data from a server.                                 |                \-                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -logfile           |Save application's log messages into a file.                                                                                                             |                \-                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+
  | -nogroupintake     |Do not group intake when imported from flat request file.                                                                                                |                \-                 |
  +--------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------------------+