R/showNewProjects.r

In MartinGoros/debi: Dashboard Application for Biostatistics Group

####
# Author: Martin W. Goros
# UT Health San Antonio


showNewProjects <- function(rc_url,rc_token,user=NA,record=NA,start_date=NA,stop_date=NA){

  if(!("RCurl" %in% rownames(installed.packages()))){
install.packages('RCurl')
}
if(!("redcapAPI" %in% rownames(installed.packages()))){
install.packages('redcapAPI')
}
library(RCurl)
library(redcapAPI)

# read redcap data--------------------------------------------------------------
read_redcap <- function(redcap_url,secret_token){
    out <- RCurl::postForm(uri=redcap_url,
                    token=secret_token,
                    content="record",
                    type="flat",
                    format="csv",
                    .opts=curlOptions(ssl.verifypeer=FALSE))

    if(any(out[1]!="\n")){
      tf <- tempfile()
      write(out,file=tf)
      dataout <- read.csv(tf)
      return(dataout)
    }else{
      return(NULL)
    }
}

pull_data <- function(rc_url,rc_token){

  full_data <- read_redcap(redcap_url=rc_url,secret_token=rc_token)
  full_data[full_data==""] <- NA
  rcon <- redcapAPI::redcapConnection(url=rc_url, token=rc_token)
  job_names <- c('job_title','job_alias','job_description','job_start_date','job_end_date','assigned_faculty','assigned_staff','pi_name','pi_department','data_source','funding_type','importance','h_index','modifier_job')
  job_phase_names <- names(redcapAPI::exportRecords(rcon,forms='job_phase'))
  work_names <- names(redcapAPI::exportRecords(rcon,forms='work'))
  research_outcome_names <- names(redcapAPI::exportRecords(rcon,forms='research_outcome'))
  appt_names <- names(redcapAPI::exportRecords(rcon,forms='appointments'))

  job <- subset(full_data,select=c('record_id',job_names))
  job <- job[rowSums(is.na(job[,-1]))!=ncol(job[,-1]), ]

  job_phase <- subset(full_data,select=c('record_id',setdiff(job_phase_names,c('','redcap_survey_identifier'))))
  job_phase <- job_phase[rowSums(is.na(job_phase[,-1]))!=ncol(job_phase[,-1]), ]

  work <- subset(full_data,select=c('record_id',setdiff(work_names,c('work_complete','redcap_survey_identifier'))))
  work <- work[rowSums(is.na(work[,-1]))!=ncol(work[,-1]), ]

  research_outcome <- subset(full_data,select=c('record_id',setdiff(research_outcome_names,c('research_outcome_complete','redcap_survey_identifier'))))
  research_outcome <- research_outcome[rowSums(is.na(research_outcome[,-1]))!=ncol(research_outcome[,-1]), ]

  appointments <- subset(full_data,select=c('record_id',setdiff(appt_names,c('appointments_complete','redcap_survey_identifier'))))
  appointments <- appointments[rowSums(is.na(appointments[,-c(1,length(appt_names))]))!=ncol(appointments[,-c(1,length(appt_names))]), ]

  return(list(job=job,job_phase=job_phase,work=work,research_outcome=research_outcome,appointments=appointments))
}

  rc_url <- rc_url
  rc_token <- rc_token
  
  data <- pull_data(rc_url,rc_token)$job
  data$job_start_date <- as.Date(as.character(data$job_start_date),format='%Y-%m-%d')

  if(!is.na(user)){
    data <- subset(data,(assigned_faculty %in% user) | (assigned_staff %in% user))
  }
  if(!is.na(record)){
    data <- subset(data,record_id %in% record)
  }
  if(!is.na(start_date) | !is.na(stop_date)){
    data$job_start_date <- as.Date(data$job_start_date,format='%Y-%m-%d')

    if(!is.na(start_date) & is.na(stop_date)){
      data <- subset(data,job_start_date >= start_date)
    }
    if(is.na(start_date) & !is.na(stop_date)){
      data <- subset(data,job_start_date <= stop_date)
    }
    if(!is.na(start_date) & !is.na(stop_date)){
      data <- subset(data,job_start_date >= start_date & job_start_date <= stop_date)
    }
  }

  return(data)

}