README.md
In cssat/oliveRconnect: Connection Framework for the Oliver API
Getting Data From the Oliver API
Joe Mienko
Overview
oliveRconnect is a package providing a set of functions that help you connect to the Oliver api undergirding the Oliver service management solution www.oliverservices.org.
Authentication Helper Functions
check_for_200() is a wrapper function for httr::status_code() which captures non-200 status codes. extract_poc_token() extracts the "poc.t" cookie from an oliver authentication response.return_subdomain() stores the subdomain.domain combos for for all Oliver environments.post_auth_to_oliver() GETs a "poc.t" cookie and POSTs the cookie back to Oliver to return a session cookie.
Functions to GET oliver data
get_csv_extract() GETs one of four csv files available from the ppm section of the Oliver API. get_org_info() GETs provider information from the organization section of the Oliver API.
Installation
# install.packages("devtools")
devtools::install_github("cssat/oliveRconnect")
Prerequisites
In order to access the Oliver API, you will need to have an active Oliver account. To register for an Oliver account, follow the instructions at the following link: https://www.oliverservices.org/register. At this time, most of the functions have been designed for a user with org_admin, super_admin privileges, or both sets of privileges. Once you have an Oliver username and password, it is best-practice to assign them to environment variables. The examples below assume you have assigned your Oliver username (i.e. email address) and password are assigned to environment variables named OLIVER_ID and OLIVER_PW respectively.
Authentication
The code chunk shows how to pass these parameters to post_auth_to_oliver(). If successful, this function will return the message oliver API authentication established. This tells you that you have connected to Oliver and stored session cookies within your Global R environment.
oliveRconnect::post_auth_to_oliver(oliver_email = Sys.getenv("OLIVER_ID")
,oliver_password = Sys.getenv("OLIVER_PW")
,oliver_env = "production")
Getting Data
The following two functions return data from the Oliver API.
CSV Result from Replica Database
oliveRconnect::get_csv_extract(extract_name = "fss_raw.csv")
Other options for the extract_name parameter within get_csv_extract() include fss_extract.csv, notes_extract.csv, and grassroots_diff.csv.
Parsed JSON Directly from the API
Once a user has been authenticated, you can also parse JSON directly from the API. An example function for doing so is get_org_info(). This function expects an integer vector of organization IDs. If the user has access to all of the organization IDs, the function will return a named vector of those IDs.
get_org_info(c(1, 185))
Partners for Our Children Grassroots Therapy Group. LLC
1 185
If the user does not have access, the function will return as much information as is available.
get_org_info(c(1, 1000))
Partners for Our Children Org Not Available
1 NA
Putting it Together
These individual functions can also be combined with Shiny to produce a visualization of some basic Quality Assurance statistics within the Combined In-Home Services domain.
library(shiny)
library(oliveRconnect)
library(dplyr)
library(quantmod)
library(xts)
library(TTR)
library(highcharter)
library(survminer)
# Define UI for application that draws a barchart
ui <- fluidPage(
# Application title
titlePanel("Family Support Services Timeliness Stats"),
# Sidebar with a select input for provider
sidebarLayout(
sidebarPanel(
selectizeInput(inputId = "provider_select"
,label = "Provider"
,choices = NULL
,multiple = FALSE)
),
# Show a plot of the generated distribution
mainPanel(
highchartOutput('metricplot')
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output, session) {
values <- reactiveValues(authenticated = FALSE)
# Return the UI for a modal dialog with data selection input. If 'failed'
# is TRUE, then display a message that the previous value was invalid.
loginModal <- function(failed = FALSE) {
modalDialog(title = "Enter Oliver Credentials",
textInput("username", "Username:"),
passwordInput("password", "Password:"),
selectInput("environment", "Environment:"
,choices = c("staging", "production")
,selected = "production"),
footer = tagList(
actionButton("ok", "OK")
)
)
}
# Show modal when app is loaded
# This `observe` is suspended only with right user credentials
obs1 <- observe({
showModal(loginModal())
})
# When OK button is pressed, attempt to authenticate. If Oliver
# returns 200, remove the modal
obs2 <- observe({
req(input$ok)
isolate({
Username <- input$username
Password <- input$password
Environment <- input$environment
})
post_auth_to_oliver(oliver_email = Username
,oliver_password = Password
,oliver_env = Environment)
if (authentication_objects$session$status_code == 200) {
#Logged <<- TRUE
values$authenticated <- TRUE
obs1$suspend()
removeModal()
} else {
values$authenticated <- FALSE
}
})
fss_raw <- reactive({
if (values$authenticated) {
get_csv_extract("fss_raw.csv") %>%
dplyr::filter(!is.na(service_confirmation)) %>%
dplyr::mutate(initial_contact_observed = ifelse(is.na(initial_contact), 0, 1)
,first_ftf_observed = ifelse(is.na(first_face_to_face), 0, 1)
,initial_contact = dplyr::coalesce(initial_contact
,first_face_to_face
,end_of_service
,lubridate::now())
,first_face_to_face = dplyr::coalesce(first_face_to_face
,end_of_service
,lubridate::now())
,hours_to_fc = difftime(lubridate::as_datetime(initial_contact)
,lubridate::as_datetime(service_confirmation)
,units = "hours")
,hours_to_fftf = difftime(lubridate::as_datetime(first_face_to_face)
,lubridate::as_datetime(initial_contact)
,units = "hours")
,hours_to_fftf = lubridate::as.duration(hours_to_fftf)
,hours_to_fc = lubridate::as.duration(hours_to_fc)
) %>%
dplyr::select(oliver_referral_id, hours_to_fc, hours_to_fftf
,initial_contact_observed, first_ftf_observed
,org_id)
}
})
org_list <- reactive({
if (values$authenticated) {
provider_vector <- fss_raw() %>%
select(org_id) %>%
distinct() %>%
.$org_id
oliveRconnect::get_org_info(provider_vector)
} else {
c(`No Organization Returned` = 1)
}
})
observeEvent(org_list(), {
updateSelectizeInput(session = session
,inputId = "provider_select"
,choices = org_list())
})
km_medians <- reactive({
if (values$authenticated) {
fit_fc <- survival::survfit(survival::Surv(time = hours_to_fc
,event = initial_contact_observed) ~ org_id,
data = fss_raw())
fit_fftf <- survival::survfit(survival::Surv(time = hours_to_fftf
,event = first_ftf_observed) ~ org_id,
data = fss_raw())
fit_list <- list(fc = fit_fc
,fftf = fit_fftf)
survminer::surv_median(fit = fit_list
,combine = TRUE) %>%
dplyr::mutate(median = lubridate::duration(num = median
,units = "second")/lubridate::dhours(1)
,strata = readr::parse_number(strata))
} else {
dplyr::data_frame(strata = 1, median = 0, id = c("fc", "fftf"))
}
})
output$metricplot <- renderHighchart({
highchart() %>%
hc_chart(type = 'column') %>%
hc_legend(enabled = FALSE) %>%
hc_xAxis(categories = c('First Contact', 'First Face-to-Face Contact')
,title = list(text = 'Measurement')) %>%
hc_yAxis(title = list(text = 'Median Hours to Event')) %>%
hc_plotOptions(series = list(dataLabels = list(enabled = TRUE))) %>%
hc_add_series(data = c(round(filter(km_medians()
,strata == input$provider_select, id == "fc")
%>% .$median, 2),
round(filter(km_medians()
,strata == input$provider_select, id == "fftf")
%>% .$median, 2))) %>%
hc_add_theme(hc_theme_gridlight()) %>%
hc_colors(c('#d01010', '#d01010')) %>%
hc_tooltip(enabled = FALSE)
})
}
# Run the application
shinyApp(ui = ui, server = server)
cssat/oliveRconnect documentation built on May 9, 2019, 8:42 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Getting Data From the Oliver API
Joe Mienko
Overview
oliveRconnect is a package providing a set of functions that help you connect to the Oliver api undergirding the Oliver service management solution www.oliverservices.org.
Authentication Helper Functions
check_for_200()is a wrapper function forhttr::status_code()which captures non-200 status codes.extract_poc_token()extracts the "poc.t" cookie from an oliver authentication response.return_subdomain()stores the subdomain.domain combos for for all Oliver environments.post_auth_to_oliver()GETs a "poc.t" cookie and POSTs the cookie back to Oliver to return a session cookie.
Functions to GET oliver data
get_csv_extract()GETs one of four csv files available from the ppm section of the Oliver API.get_org_info()GETs provider information from the organization section of the Oliver API.
Installation
# install.packages("devtools")
devtools::install_github("cssat/oliveRconnect")
Prerequisites
In order to access the Oliver API, you will need to have an active Oliver account. To register for an Oliver account, follow the instructions at the following link: https://www.oliverservices.org/register. At this time, most of the functions have been designed for a user with org_admin, super_admin privileges, or both sets of privileges. Once you have an Oliver username and password, it is best-practice to assign them to environment variables. The examples below assume you have assigned your Oliver username (i.e. email address) and password are assigned to environment variables named OLIVER_ID and OLIVER_PW respectively.
Authentication
The code chunk shows how to pass these parameters to post_auth_to_oliver(). If successful, this function will return the message oliver API authentication established. This tells you that you have connected to Oliver and stored session cookies within your Global R environment.
oliveRconnect::post_auth_to_oliver(oliver_email = Sys.getenv("OLIVER_ID")
,oliver_password = Sys.getenv("OLIVER_PW")
,oliver_env = "production")
Getting Data
The following two functions return data from the Oliver API.
CSV Result from Replica Database
oliveRconnect::get_csv_extract(extract_name = "fss_raw.csv")
Other options for the extract_name parameter within get_csv_extract() include fss_extract.csv, notes_extract.csv, and grassroots_diff.csv.
Parsed JSON Directly from the API
Once a user has been authenticated, you can also parse JSON directly from the API. An example function for doing so is get_org_info(). This function expects an integer vector of organization IDs. If the user has access to all of the organization IDs, the function will return a named vector of those IDs.
get_org_info(c(1, 185))
Partners for Our Children Grassroots Therapy Group. LLC
1 185
If the user does not have access, the function will return as much information as is available.
get_org_info(c(1, 1000))
Partners for Our Children Org Not Available
1 NA
Putting it Together
These individual functions can also be combined with Shiny to produce a visualization of some basic Quality Assurance statistics within the Combined In-Home Services domain.
library(shiny)
library(oliveRconnect)
library(dplyr)
library(quantmod)
library(xts)
library(TTR)
library(highcharter)
library(survminer)
# Define UI for application that draws a barchart
ui <- fluidPage(
# Application title
titlePanel("Family Support Services Timeliness Stats"),
# Sidebar with a select input for provider
sidebarLayout(
sidebarPanel(
selectizeInput(inputId = "provider_select"
,label = "Provider"
,choices = NULL
,multiple = FALSE)
),
# Show a plot of the generated distribution
mainPanel(
highchartOutput('metricplot')
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output, session) {
values <- reactiveValues(authenticated = FALSE)
# Return the UI for a modal dialog with data selection input. If 'failed'
# is TRUE, then display a message that the previous value was invalid.
loginModal <- function(failed = FALSE) {
modalDialog(title = "Enter Oliver Credentials",
textInput("username", "Username:"),
passwordInput("password", "Password:"),
selectInput("environment", "Environment:"
,choices = c("staging", "production")
,selected = "production"),
footer = tagList(
actionButton("ok", "OK")
)
)
}
# Show modal when app is loaded
# This `observe` is suspended only with right user credentials
obs1 <- observe({
showModal(loginModal())
})
# When OK button is pressed, attempt to authenticate. If Oliver
# returns 200, remove the modal
obs2 <- observe({
req(input$ok)
isolate({
Username <- input$username
Password <- input$password
Environment <- input$environment
})
post_auth_to_oliver(oliver_email = Username
,oliver_password = Password
,oliver_env = Environment)
if (authentication_objects$session$status_code == 200) {
#Logged <<- TRUE
values$authenticated <- TRUE
obs1$suspend()
removeModal()
} else {
values$authenticated <- FALSE
}
})
fss_raw <- reactive({
if (values$authenticated) {
get_csv_extract("fss_raw.csv") %>%
dplyr::filter(!is.na(service_confirmation)) %>%
dplyr::mutate(initial_contact_observed = ifelse(is.na(initial_contact), 0, 1)
,first_ftf_observed = ifelse(is.na(first_face_to_face), 0, 1)
,initial_contact = dplyr::coalesce(initial_contact
,first_face_to_face
,end_of_service
,lubridate::now())
,first_face_to_face = dplyr::coalesce(first_face_to_face
,end_of_service
,lubridate::now())
,hours_to_fc = difftime(lubridate::as_datetime(initial_contact)
,lubridate::as_datetime(service_confirmation)
,units = "hours")
,hours_to_fftf = difftime(lubridate::as_datetime(first_face_to_face)
,lubridate::as_datetime(initial_contact)
,units = "hours")
,hours_to_fftf = lubridate::as.duration(hours_to_fftf)
,hours_to_fc = lubridate::as.duration(hours_to_fc)
) %>%
dplyr::select(oliver_referral_id, hours_to_fc, hours_to_fftf
,initial_contact_observed, first_ftf_observed
,org_id)
}
})
org_list <- reactive({
if (values$authenticated) {
provider_vector <- fss_raw() %>%
select(org_id) %>%
distinct() %>%
.$org_id
oliveRconnect::get_org_info(provider_vector)
} else {
c(`No Organization Returned` = 1)
}
})
observeEvent(org_list(), {
updateSelectizeInput(session = session
,inputId = "provider_select"
,choices = org_list())
})
km_medians <- reactive({
if (values$authenticated) {
fit_fc <- survival::survfit(survival::Surv(time = hours_to_fc
,event = initial_contact_observed) ~ org_id,
data = fss_raw())
fit_fftf <- survival::survfit(survival::Surv(time = hours_to_fftf
,event = first_ftf_observed) ~ org_id,
data = fss_raw())
fit_list <- list(fc = fit_fc
,fftf = fit_fftf)
survminer::surv_median(fit = fit_list
,combine = TRUE) %>%
dplyr::mutate(median = lubridate::duration(num = median
,units = "second")/lubridate::dhours(1)
,strata = readr::parse_number(strata))
} else {
dplyr::data_frame(strata = 1, median = 0, id = c("fc", "fftf"))
}
})
output$metricplot <- renderHighchart({
highchart() %>%
hc_chart(type = 'column') %>%
hc_legend(enabled = FALSE) %>%
hc_xAxis(categories = c('First Contact', 'First Face-to-Face Contact')
,title = list(text = 'Measurement')) %>%
hc_yAxis(title = list(text = 'Median Hours to Event')) %>%
hc_plotOptions(series = list(dataLabels = list(enabled = TRUE))) %>%
hc_add_series(data = c(round(filter(km_medians()
,strata == input$provider_select, id == "fc")
%>% .$median, 2),
round(filter(km_medians()
,strata == input$provider_select, id == "fftf")
%>% .$median, 2))) %>%
hc_add_theme(hc_theme_gridlight()) %>%
hc_colors(c('#d01010', '#d01010')) %>%
hc_tooltip(enabled = FALSE)
})
}
# Run the application
shinyApp(ui = ui, server = server)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.