231 add data retrieval via api vignette

DESCRIPTION

@@ -57,10 +57,11 @@ Suggests:
     kableExtra,
     colorspace,
     magrittr,
-    vdiffr
+    vdiffr,
+    httptest
 License: MIT + file LICENSE
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
 Config/testthat/edition: 3

NAMESPACE

@@ -157,6 +157,7 @@ importFrom(tcplfit2,tcplhit2_core)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,separate_wider_delim)
+importFrom(tidyr,unnest)
 importFrom(tidyr,unnest_longer)
 importFrom(utils,data)
 importFrom(utils,read.csv)

R/sc1_mthds.R

@@ -45,6 +45,8 @@
 #'     \item{bval.apid.tn.med}{Calculate the baseline value (bval) as the plate-wise median,
 #'      by assay plate ID (apid), of the raw values (rval) for test compound wells (wllt = t)
 #'       and neutral control wells (wllt = n).}
+#'     \item{bval.nwlls.med}{Calculate the baseline value (bval) as the median of the raw values 
+#'      (rval) for neutral control wells (wllt = n) by assay endpoint id (aeid).}
 #'   }
 #' } 
 #' 
@@ -131,6 +133,14 @@ sc1_mthds <- function() {
                        by = list(aeid, apid)])
       list(e1)
 
+    },
+    bval.nwlls.med = function(aeids) {
+
+      e1 <- bquote(dat[J(.(aeids)),
+                       bval := median(rval[wllt == "n"], na.rm = TRUE),
+                       by = list(aeid)])
+      list(e1)
+
     },
 
     pval.apid.pwlls.med = function(aeids) {

R/tcplConfDefault.R

@@ -7,8 +7,8 @@
 
 tcplConfDefault <- function () {
 
-  TCPLlite <- file.path(system.file(package = "tcpl"), "csv")
-  tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite")
+  tcpl_key <- "01cbaf22-904f-11ee-954e-325096b39f47"
+  tcplConf(db = NA, user = NA, pass = tcpl_key, host = NULL, drvr = "API")
 
 }
 

R/tcplPlot.R

@@ -68,7 +68,7 @@ tcplPlot <- function(dat = NULL, type = "mc", fld = "m4id", val = NULL, compare.
   list2env(validated_vars, envir = environment())
 
   # check_tcpl_db_schema is a user-defined function found in v3_schema_functions.R file
-  if (check_tcpl_db_schema() | !is.null(dat)) {
+  if (check_tcpl_db_schema() | !is.null(dat) | getOption("TCPL_DRVR") == "API") {
     # check if user supplied data.  If not, load from db connection
     if(is.null(dat)){
       dat <- tcplPlotLoadData(lvl = lvl, fld = fld, val = val, type = type,flags = flags, compare = FALSE) #code defined in tcplPlotUtils.R
@@ -114,7 +114,7 @@ tcplPlot <- function(dat = NULL, type = "mc", fld = "m4id", val = NULL, compare.
       nrow = ncol = 1
     }
     # error message for output="console" and multi=FALSE to avoid multiple plots in console
-    if(nrow(dat) > 1 && output == "console" && multi == FALSE) stop("More than 1 concentration series returned for given field/val combination.  Set output to pdf or reduce the number of curves to 1. Current number of curves: ", nrow(input))
+    if(nrow(dat[compare == FALSE]) != 1 && output == "console" && multi == FALSE) stop("More than 1 concentration series returned for given field/val combination.  Set output to pdf or reduce the number of curves to 1. Current number of curves: ", nrow(dat))
     if(is.null(nrow)){
       nrow <- ifelse(verbose,2,2)
     }
@@ -132,7 +132,7 @@ tcplPlot <- function(dat = NULL, type = "mc", fld = "m4id", val = NULL, compare.
       # tcplPlotlyplot is the user-defined function found in tcplPlot.R file used to connect tcpl and plotly packages
       # tcplggplot is the user-defined function found in tcplPlot.R file used to connect tcpl and ggplot2 packages
         return(tcplPlotlyPlot(dat, lvl)),
-        return(ggsave(filename=paste0(fileprefix,"_",paste0(dat$m4id, collapse = "_"),".",output),
+        return(ggsave(filename=paste0(fileprefix,"_",paste0(ifelse(type=="mc",dat$m4id,dat$s2id), collapse = "_"),".",output),
                       plot= if(is.null(compare.val)) tcplggplot(dat,verbose = verbose, lvl = lvl, flags = flags, yrange = yrange) else tcplggplotCompare(dat[compare == FALSE],dat[compare == TRUE],verbose = verbose, lvl = lvl, flags = flags, yrange = yrange), width = 7, height = 5, dpi=dpi))
       )
     } else {
@@ -399,6 +399,22 @@ tcplPlotlyPlot <- function(dat, lvl = 5){
       }
     }
 
+  } else if (lvl == 2) { #single conc
+    # main data
+    if (!is.null(dat$coff) && dat$max_med < 0) {
+      dat$coff <- dat$coff * -1
+    }
+    if (!is.null(dat$coff) && !is.null(dat$hitc) && dat$hitc < 0) {
+      dat$coff <- dat$coff * -1
+    }
+
+    # compare data
+    if (!is.null(compare.dat$coff) && compare.dat$max_med < 0) {
+      compare.dat$coff <- compare.dat$coff * -1
+    }
+    if (!is.null(compare.dat$coff) && !is.null(compare.dat$hitc) && compare.dat$hitc < 0) {
+      compare.dat$coff <- compare.dat$coff * -1
+    }
   }
 
   # function for truncating decimals
@@ -500,7 +516,7 @@ tcplPlotlyPlot <- function(dat, lvl = 5){
       inherit = FALSE,
       hoverinfo = "text",
       text = ~ paste(
-        "</br>", paste0("Cut Off B (", specify_decimal(dat$coff,2), ")")
+        "</br>", paste0("Cut Off B (", specify_decimal(compare.dat$coff,2), ")")
       )
     )
   }
@@ -831,37 +847,47 @@ tcplggplot <- function(dat, lvl = 5, verbose = FALSE, flags = FALSE, yrange = c(
     range()
 
   # check if model_type is 3 or 4, which means an override method was assigned
-  if (lvl == 5 && dat$model_type == 3) { # gain direction
-    # leave coff but bmr should flip if top is negative
-    if (!is.null(dat$top) && !is.na(dat$top) && !is.null(dat$bmr)) {
-      if (dat$top < 0) {
-        dat$bmr <- dat$bmr * -1
+  if (lvl == 5) {
+    if (dat$model_type == 3) { # gain direction
+      # leave coff but bmr should flip if top is negative
+      if (!is.null(dat$top) && !is.na(dat$top) && !is.null(dat$bmr)) {
+        if (dat$top < 0) {
+          dat$bmr <- dat$bmr * -1
+        }
+      }
+    } else if (dat$model_type == 4) { # loss direction
+      # coff and bmr(if top < 0) should be negative
+      if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
+        dat$coff <- dat$coff * -1
+        if (dat$top < 0) {
+          dat$bmr <- dat$bmr * -1
+        }
+      }
+    } else { # bidirectional
+      # check if winning model has negative top.  If so coff,bmr should be negative
+      if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
+        if (dat$top < 0) {
+          dat$coff <- dat$coff * -1
+          dat$bmr <- dat$bmr * -1
+        }
       }
     }
-  } else if (lvl == 5 && dat$model_type == 4) { # loss direction
-    # coff and bmr(if top < 0) should be negative
-    if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
+  } else { #single conc
+    if (!is.null(dat$coff) && dat$max_med < 0) {
       dat$coff <- dat$coff * -1
-      if (dat$top < 0) {
-        dat$bmr <- dat$bmr * -1
-      }
     }
-  } else { # bidirectional
-    # check if winning model has negative top.  If so coff,bmr should be negative
-    if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
-      if (dat$top < 0) {
-        dat$coff <- dat$coff * -1
-        dat$bmr <- dat$bmr * -1
-      }
+    if (!is.null(dat$coff) && !is.null(dat$hitc) && dat$hitc < 0) {
+      dat$coff <- dat$coff * -1
     }
   }
 
+
   # check if ac50 is null and assign NA if it is 
   dat$ac50 <- ifelse(is.null(dat$ac50), NA, dat$ac50)
 
   # check if dtxsid is NA, pull wllt in from lvl 3
-  if (is.na(dat$dsstox_substance_id) | is.na(dat$chnm)) {
-    wllt <- unique(tcplLoadData(lvl = 0, fld = list("spid","acid"), 
+  if (getOption("TCPL_DRVR") != "API" && (is.na(dat$dsstox_substance_id) | is.na(dat$chnm))) {
+    wllt <- unique(tcplLoadData(type = ifelse(lvl == 2, "sc", "mc"), lvl = 0, fld = list("spid","acid"), 
                                 list(dat$spid, tcplLoadAcid(fld = "aeid", val = dat$aeid)$acid))$wllt)
     if (length(wllt) == 1) {
       if (wllt == 'c' | wllt == 'p') {
@@ -885,13 +911,18 @@ tcplggplot <- function(dat, lvl = 5, verbose = FALSE, flags = FALSE, yrange = c(
         dat$chnm <- ""
       }
       else {
-        data$dsstox_substance_id <- paste0("Well type: ", wllt)
-        data$chnm <- ""
+        dat$dsstox_substance_id <- paste0("Well type: ", wllt)
+        dat$chnm <- ""
       }
     } 
     else {
-      warning(paste0("wllt for SPID: ", dat$spid, " is missing or length > 1. 
+      if (length(wllt) > 1) {
+        dat$dsstox_substance_id <- paste0("Well type: ", paste(wllt, collapse = ", "))
+        dat$chnm <- ""
+      } else {
+        warning(paste0("wllt for SPID: ", dat$spid, " is missing. 
                      Leaving dsstox_substance_id and chnm as NA."))
+      }
     }
   }
 
@@ -915,7 +946,7 @@ tcplggplot <- function(dat, lvl = 5, verbose = FALSE, flags = FALSE, yrange = c(
   if (lvl == 2) {
     gg <- ggplot(l3_dat, aes(x = conc)) +
       geom_hline(aes(yintercept = dat$max_med, linetype = "Max Median"), color="red") +
-      geom_hline(aes(yintercept = ifelse(dat$max_med >= 0, dat$coff, dat$coff * -1), linetype="Cutoff"), color="blue") +
+      geom_hline(aes(yintercept = dat$coff, linetype="Cutoff"), color="blue") +
       geom_point(aes(y = resp)) +
       scale_x_continuous(limits = l3_range, trans = ifelse(0 %in% l3_dat$conc,"identity","log10")) +
       scale_y_continuous(limits = yrange) +
@@ -1093,62 +1124,77 @@ tcplggplotCompare <- function(dat, compare.dat, lvl = 5, verbose = FALSE, flags
 
   if (dat$conc_unit != compare.dat$conc_unit || dat$normalized_data_type != compare.dat$normalized_data_type) stop("Units do not match.")
 
-  # main data
   # check if model_type is 3 or 4, which means an override method was assigned
-  if (lvl == 5 && dat$model_type == 3) { # gain direction
-    # leave coff but bmr should flip if top is negative
-    if (!is.null(dat$top) && !is.na(dat$top) && !is.null(dat$bmr)) {
-      if (dat$top < 0) {
-        dat$bmr <- dat$bmr * -1
-      }
-    }
-  } else if (lvl == 5 && dat$model_type == 4) { # loss direction
-    # coff and bmr(if top < 0) should be negative
-    if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
-      dat$coff <- dat$coff * -1
-      if (dat$top < 0) {
-        dat$bmr <- dat$bmr * -1
+  if (lvl == 5) {
+    # main data
+    if (dat$model_type == 3) { # gain direction
+      # leave coff but bmr should flip if top is negative
+      if (!is.null(dat$top) && !is.na(dat$top) && !is.null(dat$bmr)) {
+        if (dat$top < 0) {
+          dat$bmr <- dat$bmr * -1
+        }
       }
-    }
-  } else { # bidirectional
-    # check if winning model has negative top.  If so coff,bmr should be negative
-    if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
-      if (dat$top < 0) {
+    } else if (dat$model_type == 4) { # loss direction
+      # coff and bmr(if top < 0) should be negative
+      if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
         dat$coff <- dat$coff * -1
-        dat$bmr <- dat$bmr * -1
+        if (dat$top < 0) {
+          dat$bmr <- dat$bmr * -1
+        }
       }
-    }
-  }
-
-  # compare data
-  # check if model_type is 3 or 4, which means an override method was assigned
-  if (lvl == 5 && compare.dat$model_type == 3) { # gain direction
-    # leave coff but bmr should flip if top is negative
-    if (!is.null(compare.dat$top) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
-      if (compare.dat$top < 0) {
-        compare.dat$bmr <- compare.dat$bmr * -1
+    } else { # bidirectional
+      # check if winning model has negative top.  If so coff,bmr should be negative
+      if (!is.null(dat$top) && !is.null(dat$coff) && !is.na(dat$top) && !is.null(dat$bmr)) {
+        if (dat$top < 0) {
+          dat$coff <- dat$coff * -1
+          dat$bmr <- dat$bmr * -1
+        }
       }
     }
-  } else if (lvl == 5 && compare.dat$model_type == 4) { # loss direction
-    # coff and bmr(if top < 0) should be negative
-    if (!is.null(compare.dat$top) && !is.null(compare.dat$coff) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
-      compare.dat$coff <- compare.dat$coff * -1
-      if (compare.dat$top < 0) {
-        compare.dat$bmr <- compare.dat$bmr * -1
+
+    # compare data
+    if (compare.dat$model_type == 3) { # gain direction
+      # leave coff but bmr should flip if top is negative
+      if (!is.null(compare.dat$top) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
+        if (compare.dat$top < 0) {
+          compare.dat$bmr <- compare.dat$bmr * -1
+        }
       }
-    }
-  } else { # bidirectional
-    # check if winning model has negative top.  If so coff,bmr should be negative
-    if (!is.null(compare.dat$top) && !is.null(compare.dat$coff) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
-      if (compare.dat$top < 0) {
+    } else if (compare.dat$model_type == 4) { # loss direction
+      # coff and bmr(if top < 0) should be negative
+      if (!is.null(compare.dat$top) && !is.null(compare.dat$coff) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
         compare.dat$coff <- compare.dat$coff * -1
-        compare.dat$bmr <- compare.dat$bmr * -1
+        if (compare.dat$top < 0) {
+          compare.dat$bmr <- compare.dat$bmr * -1
+        }
       }
+    } else { # bidirectional
+      # check if winning model has negative top.  If so coff,bmr should be negative
+      if (!is.null(compare.dat$top) && !is.null(compare.dat$coff) && !is.na(compare.dat$top) && !is.null(compare.dat$bmr)) {
+        if (compare.dat$top < 0) {
+          compare.dat$coff <- compare.dat$coff * -1
+          compare.dat$bmr <- compare.dat$bmr * -1
+        }
+      }
+    }
+  } else { #single conc
+    # main data
+    if (!is.null(dat$coff) && dat$max_med < 0) {
+      dat$coff <- dat$coff * -1
+    }
+    if (!is.null(dat$coff) && !is.null(dat$hitc) && dat$hitc < 0) {
+      dat$coff <- dat$coff * -1
+    }
+
+    # compare data
+    if (!is.null(compare.dat$coff) && compare.dat$max_med < 0) {
+      compare.dat$coff <- compare.dat$coff * -1
+    }
+    if (!is.null(compare.dat$coff) && !is.null(compare.dat$hitc) && compare.dat$hitc < 0) {
+      compare.dat$coff <- compare.dat$coff * -1
     }
   }
 
-
-
   # check if data is outside bounds of yrange. If so, expand yrange bounds
   if (!identical(yrange, c(NA,NA))) {
     yrange[1] <- min(dat$resp_min, dat$coff, yrange[1], unlist(dat$resp), 
@@ -1160,7 +1206,7 @@ tcplggplotCompare <- function(dat, compare.dat, lvl = 5, verbose = FALSE, flags
   check_wllt <- function(data) {
     # check if dtxsid is NA, pull wllt in from lvl 3
     if (is.na(data$dsstox_substance_id) | is.na(data$chnm)) {
-      wllt <- unique(tcplLoadData(lvl = 0, fld = list("spid","acid"), 
+      wllt <- unique(tcplLoadData(type = ifelse(lvl == 2, "sc", "mc"), lvl = 0, fld = list("spid","acid"), 
                                   list(data$spid, tcplLoadAcid(fld = "aeid", val = data$aeid)$acid))$wllt)
       if (length(wllt) == 1) {
         if (wllt == 'c' | wllt == 'p') {
@@ -1189,14 +1235,21 @@ tcplggplotCompare <- function(dat, compare.dat, lvl = 5, verbose = FALSE, flags
         }
       } 
       else {
-        warning(paste0("wllt for SPID: ", data$spid, " is missing or length > 1. 
+        if (length(wllt) > 1) {
+          data$dsstox_substance_id <- paste0("Well type: ", paste(wllt, collapse = ", "))
+          data$chnm <- ""
+        } else {
+          warning(paste0("wllt for SPID: ", data$spid, " is missing. 
                      Leaving dsstox_substance_id and chnm as NA."))
+        }
       }
     }
     return(data)
   }
-  dat <- check_wllt(dat)
-  compare.dat <- check_wllt(compare.dat)
+  if (getOption("TCPL_DRVR") != "API") {
+    dat <- check_wllt(dat)
+    compare.dat <- check_wllt(compare.dat)
+  }
 
   dat$winning_model_string <- paste0("Model A(", dat$modl, ")")
   compare.dat$winning_model_string <- paste0("Model B(", compare.dat$modl, ")")