R/onLoad.R
In mcneilco/racas: R Package for ACAS
Defines functions
.onLoad
.onLoad <- function(libname, pkgname) {
appConfName <- paste0(applicationSettings$appName,"_CONFIG")
appHomeName <- paste0(applicationSettings$appName,"_HOME")
relativeToAppHome <- file.path(normalizePath(file.path(libname,"..")))
relativeConf <- file.path(normalizePath(relativeToAppHome),"conf","compiled","conf.properties")
appConf <- Sys.getenv(appConfName)
appHome <- Sys.getenv(appHomeName)
if(appHome == "" && appConf == "" && !file.exists(relativeConf)) {
warning(paste0("Config file does not exist relative to package: ",relativeConf,"\n",
appHomeName," not set\n",
appConfName," not set\n\n",
"Not reading configuration file.\n\n",
"Install the racas package in a directory one level below the base ",applicationSettings$appName," install \n",
"OR\n",
"set one of the following environment variables prior to loading this package by adding them to your shell or by running:\n",
"\tSys.setenv(",appHomeName," = \"/path/to/",applicationSettings$appName,"\")\n",
"\tSys.setenv(",appConfName," = \"/path/to/",applicationSettings$appName,"_config_file\")\n\n",
"The priority of these setings are:\n",
"1) ACAS_CONFIG environment variable\n",
"2) ACAS_HOME environment variable\n",
"3) relative path to the config file ",relativeConf),call.=FALSE)
} else {
tryCatch({
#if app configuration location
if(appConf!="") {
configFileLocation <- file.path(appConf)
} else {
#If app home environment variable is set
if(appHome!="") {
configFileLocation <- file.path(appHome,"conf/compiled/conf.properties")
} else {
#if relative path then set home accoridingly
appHome <- relativeToAppHome
configFileLocation <- relativeConf
}
}
packageStartupMessage(paste("Using configuration file:",configFileLocation ))
output <- readConfigFile(configFileLocation, appHome = appHome)
},error = function(ex) {
#error <- capture.output(print(ex))
warning(paste0("Could not load configuration file at:\n\t",
configFileLocation,"\n\n",
"This was the captured error:\n",
"\t",ex),call.=FALSE)
})
}
racasLogger <- createLogger()
assignInNamespace("racasLogger",racasLogger, ns="racas")
racasMessenger <- Messenger$new(envir = environment())
racasMessenger$logger <- racasLogger
assignInNamespace("racasMessenger",racasMessenger, ns="racas")
if(is.null(applicationSettings$server.database.r.driver)) {
dbType <- "Postgres"
} else {
dbType <- tryCatch({
getDBType(applicationSettings$server.database.r.driver)
}, error = function(ex ){
"Postgres"
})
}
definition <- read_json_file(system.file("conf", "definition-ll4.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4 <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ec50"),
categorization_function = categorize.LL4,
get_reported_parameters = get_reported_parameters.LL4,
apply_limits = apply_limits.LL4,
default_fit_settings = get_default_fit_settings("4 parameter D-R"),
simple_to_advanced_fittings_function = updateFitSettings.LL4,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4.txt", package = "racas")),
sortOptions = sortOptions.LL4,
get_curve_attributes = get_curve_attributes.LL4,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4",ll4, ns="racas")
definition <- read_json_file(system.file("conf", "definition-ll4IC50.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4IC50 <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ic50"),
categorization_function = categorize.LL4IC50,
get_reported_parameters = get_reported_parameters.LL4IC50,
apply_limits = apply_limits.LL4IC50,
default_fit_settings = get_default_fit_settings("4 parameter D-R IC50"),
simple_to_advanced_fittings_function = updateFitSettings.LL4IC50,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4IC50.txt", package = "racas")),
sortOptions = sortOptions.LL4IC50,
get_curve_attributes = get_curve_attributes.LL4IC50,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4IC50,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4IC50",ll4IC50, ns="racas")
definition <- read_json_file(system.file("conf", "definition-ll4IC50.json", package = "racas"))
dMax <- structure(list(name = "dmax", ls_kind = "DMax", select = list(
structure(list(name = "dmax", field = "numeric_value"), .Names = c("name",
"field")), structure(list(name = "dmax", field = "string_value"), .Names = c("name",
"field")),
structure(list(name = "dmaxUncertainty", field = "uncertainty"), .Names = c("name",
"field")), structure(list(name = "dmaxUncertaintyType", field = "uncertainty_type"), .Names = c("name",
"field")), structure(list(name = "dmaxOperatorKind", field = "operator_kind"), .Names = c("name",
"field")))), .Names = c("name", "ls_kind", "select"))
addLocation <- length(definition$analysis_group[[1]]$analysis_group_state[[1]]$analysis_group_value)+1
definition$analysis_group[[1]]$analysis_group_state[[1]]$analysis_group_value[[addLocation]] <- dMax
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4IC50DMax <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ic50"),
categorization_function = categorize.LL4IC50,
get_reported_parameters = get_reported_parameters.LL4IC50DMax,
apply_limits = apply_limits.LL4IC50,
default_fit_settings = get_default_fit_settings("4 parameter D-R IC50"),
simple_to_advanced_fittings_function = updateFitSettings.LL4IC50,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4IC50.txt", package = "racas")),
sortOptions = sortOptions.LL4IC50DMax,
get_curve_attributes = get_curve_attributes.LL4IC50DMax,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4IC50,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4IC50DMax",ll4IC50DMax, ns="racas")
definition <- read_json_file(system.file("conf", "definition-kifit.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
kifit <- ModelFit$new(drc_function = ki_fct.5,
paramNames = c("min", "max", "ki", "ligandConc", "kd"),
categorization_function = categorize.ki,
get_reported_parameters = get_reported_parameters.ki,
apply_limits = apply_limits.ki,
default_fit_settings = get_default_fit_settings("Ki Fit"),
simple_to_advanced_fittings_function = updateFitSettings.Ki,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ki.txt", package = "racas")),
sortOptions = sortOptions.ki,
get_curve_attributes = get_curve_attributes.ki,
get_saved_fitted_parameters = get_saved_fitted_parameters.ki,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("kifit",kifit, ns="racas")
definition <- read_json_file(system.file("conf", "definition-mm2.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
mm2 <- ModelFit$new(drc_function = drc::MM.2,
paramNames = c("vmax", "km"),
categorization_function = categorize.MM2,
get_reported_parameters = get_reported_parameters.MM2,
apply_limits = apply_limits.MM2,
default_fit_settings = get_default_fit_settings("Michaelis-Menten"),
simple_to_advanced_fittings_function = updateFitSettings.MM2,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "mm2.txt", package = "racas")),
sortOptions = sortOptions.MM2,
get_curve_attributes = get_curve_attributes.MM2,
get_saved_fitted_parameters = get_saved_fitted_parameters.MM2,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("mm2",mm2, ns="racas")
definition <- read_json_file(system.file("conf", "definition-scatter.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
scatter <- ModelFit$new(curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("scatter",scatter, ns="racas")
definition <- read_json_file(system.file("conf", "definition-substrateInhibition.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
substrateInhibition <- ModelFit$new(drc_function = substrateInhibition.3,
paramNames = c("vmax", "km", "ki"),
categorization_function = categorize.substrateInhibition,
get_reported_parameters = get_reported_parameters.substrateInhibition,
apply_limits = apply_limits.substrateInhibition,
default_fit_settings = get_default_fit_settings("Substrate Inhibition"),
simple_to_advanced_fittings_function = updateFitSettings.substrateInhibition,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "substrateInhibition.txt", package = "racas")),
sortOptions = sortOptions.substrateInhibition,
get_curve_attributes = get_curve_attributes.substrateInhibition,
get_saved_fitted_parameters = get_saved_fitted_parameters.substrateInhibition,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("substrateInhibition",substrateInhibition, ns="racas")
}
mcneilco/racas documentation built on Feb. 22, 2024, 10:07 p.m.
R Package Documentation
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Defines functions .onLoad
.onLoad <- function(libname, pkgname) {
appConfName <- paste0(applicationSettings$appName,"_CONFIG")
appHomeName <- paste0(applicationSettings$appName,"_HOME")
relativeToAppHome <- file.path(normalizePath(file.path(libname,"..")))
relativeConf <- file.path(normalizePath(relativeToAppHome),"conf","compiled","conf.properties")
appConf <- Sys.getenv(appConfName)
appHome <- Sys.getenv(appHomeName)
if(appHome == "" && appConf == "" && !file.exists(relativeConf)) {
warning(paste0("Config file does not exist relative to package: ",relativeConf,"\n",
appHomeName," not set\n",
appConfName," not set\n\n",
"Not reading configuration file.\n\n",
"Install the racas package in a directory one level below the base ",applicationSettings$appName," install \n",
"OR\n",
"set one of the following environment variables prior to loading this package by adding them to your shell or by running:\n",
"\tSys.setenv(",appHomeName," = \"/path/to/",applicationSettings$appName,"\")\n",
"\tSys.setenv(",appConfName," = \"/path/to/",applicationSettings$appName,"_config_file\")\n\n",
"The priority of these setings are:\n",
"1) ACAS_CONFIG environment variable\n",
"2) ACAS_HOME environment variable\n",
"3) relative path to the config file ",relativeConf),call.=FALSE)
} else {
tryCatch({
#if app configuration location
if(appConf!="") {
configFileLocation <- file.path(appConf)
} else {
#If app home environment variable is set
if(appHome!="") {
configFileLocation <- file.path(appHome,"conf/compiled/conf.properties")
} else {
#if relative path then set home accoridingly
appHome <- relativeToAppHome
configFileLocation <- relativeConf
}
}
packageStartupMessage(paste("Using configuration file:",configFileLocation ))
output <- readConfigFile(configFileLocation, appHome = appHome)
},error = function(ex) {
#error <- capture.output(print(ex))
warning(paste0("Could not load configuration file at:\n\t",
configFileLocation,"\n\n",
"This was the captured error:\n",
"\t",ex),call.=FALSE)
})
}
racasLogger <- createLogger()
assignInNamespace("racasLogger",racasLogger, ns="racas")
racasMessenger <- Messenger$new(envir = environment())
racasMessenger$logger <- racasLogger
assignInNamespace("racasMessenger",racasMessenger, ns="racas")
if(is.null(applicationSettings$server.database.r.driver)) {
dbType <- "Postgres"
} else {
dbType <- tryCatch({
getDBType(applicationSettings$server.database.r.driver)
}, error = function(ex ){
"Postgres"
})
}
definition <- read_json_file(system.file("conf", "definition-ll4.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4 <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ec50"),
categorization_function = categorize.LL4,
get_reported_parameters = get_reported_parameters.LL4,
apply_limits = apply_limits.LL4,
default_fit_settings = get_default_fit_settings("4 parameter D-R"),
simple_to_advanced_fittings_function = updateFitSettings.LL4,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4.txt", package = "racas")),
sortOptions = sortOptions.LL4,
get_curve_attributes = get_curve_attributes.LL4,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4",ll4, ns="racas")
definition <- read_json_file(system.file("conf", "definition-ll4IC50.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4IC50 <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ic50"),
categorization_function = categorize.LL4IC50,
get_reported_parameters = get_reported_parameters.LL4IC50,
apply_limits = apply_limits.LL4IC50,
default_fit_settings = get_default_fit_settings("4 parameter D-R IC50"),
simple_to_advanced_fittings_function = updateFitSettings.LL4IC50,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4IC50.txt", package = "racas")),
sortOptions = sortOptions.LL4IC50,
get_curve_attributes = get_curve_attributes.LL4IC50,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4IC50,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4IC50",ll4IC50, ns="racas")
definition <- read_json_file(system.file("conf", "definition-ll4IC50.json", package = "racas"))
dMax <- structure(list(name = "dmax", ls_kind = "DMax", select = list(
structure(list(name = "dmax", field = "numeric_value"), .Names = c("name",
"field")), structure(list(name = "dmax", field = "string_value"), .Names = c("name",
"field")),
structure(list(name = "dmaxUncertainty", field = "uncertainty"), .Names = c("name",
"field")), structure(list(name = "dmaxUncertaintyType", field = "uncertainty_type"), .Names = c("name",
"field")), structure(list(name = "dmaxOperatorKind", field = "operator_kind"), .Names = c("name",
"field")))), .Names = c("name", "ls_kind", "select"))
addLocation <- length(definition$analysis_group[[1]]$analysis_group_state[[1]]$analysis_group_value)+1
definition$analysis_group[[1]]$analysis_group_state[[1]]$analysis_group_value[[addLocation]] <- dMax
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
ll4IC50DMax <- ModelFit$new(drc_function = drc::LL.4,
paramNames = c("slope", "min", "max", "ic50"),
categorization_function = categorize.LL4IC50,
get_reported_parameters = get_reported_parameters.LL4IC50DMax,
apply_limits = apply_limits.LL4IC50,
default_fit_settings = get_default_fit_settings("4 parameter D-R IC50"),
simple_to_advanced_fittings_function = updateFitSettings.LL4IC50,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ll4IC50.txt", package = "racas")),
sortOptions = sortOptions.LL4IC50DMax,
get_curve_attributes = get_curve_attributes.LL4IC50DMax,
get_saved_fitted_parameters = get_saved_fitted_parameters.LL4IC50,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("ll4IC50DMax",ll4IC50DMax, ns="racas")
definition <- read_json_file(system.file("conf", "definition-kifit.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
kifit <- ModelFit$new(drc_function = ki_fct.5,
paramNames = c("min", "max", "ki", "ligandConc", "kd"),
categorization_function = categorize.ki,
get_reported_parameters = get_reported_parameters.ki,
apply_limits = apply_limits.ki,
default_fit_settings = get_default_fit_settings("Ki Fit"),
simple_to_advanced_fittings_function = updateFitSettings.Ki,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "ki.txt", package = "racas")),
sortOptions = sortOptions.ki,
get_curve_attributes = get_curve_attributes.ki,
get_saved_fitted_parameters = get_saved_fitted_parameters.ki,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("kifit",kifit, ns="racas")
definition <- read_json_file(system.file("conf", "definition-mm2.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
mm2 <- ModelFit$new(drc_function = drc::MM.2,
paramNames = c("vmax", "km"),
categorization_function = categorize.MM2,
get_reported_parameters = get_reported_parameters.MM2,
apply_limits = apply_limits.MM2,
default_fit_settings = get_default_fit_settings("Michaelis-Menten"),
simple_to_advanced_fittings_function = updateFitSettings.MM2,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "mm2.txt", package = "racas")),
sortOptions = sortOptions.MM2,
get_curve_attributes = get_curve_attributes.MM2,
get_saved_fitted_parameters = get_saved_fitted_parameters.MM2,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("mm2",mm2, ns="racas")
definition <- read_json_file(system.file("conf", "definition-scatter.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
scatter <- ModelFit$new(curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("scatter",scatter, ns="racas")
definition <- read_json_file(system.file("conf", "definition-substrateInhibition.json", package = "racas"))
queriesAndTypeMap <- entityDefinitionToQueriesAndTypeMap(definition, dbType)
substrateInhibition <- ModelFit$new(drc_function = substrateInhibition.3,
paramNames = c("vmax", "km", "ki"),
categorization_function = categorize.substrateInhibition,
get_reported_parameters = get_reported_parameters.substrateInhibition,
apply_limits = apply_limits.substrateInhibition,
default_fit_settings = get_default_fit_settings("Substrate Inhibition"),
simple_to_advanced_fittings_function = updateFitSettings.substrateInhibition,
model_equation_img = get_text_file_contents(system.file(file.path("rmd","equations"), "substrateInhibition.txt", package = "racas")),
sortOptions = sortOptions.substrateInhibition,
get_curve_attributes = get_curve_attributes.substrateInhibition,
get_saved_fitted_parameters = get_saved_fitted_parameters.substrateInhibition,
curveid_query = queriesAndTypeMap$curveSQL,
experiment_query = queriesAndTypeMap$experimentSQL,
raw_results_persistence_path = 'curvefit/rawdata',
typeMap = queriesAndTypeMap$typeMap
)
assignInNamespace("substrateInhibition",substrateInhibition, ns="racas")
}
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