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:

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:

[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:

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¶

Available application arguments¶
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

Available application flags¶
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.	-