validation_report.Rmd

---
title: 'Validation report'
output:
  html_document:
     toc: true
     df_print: kable
  pdf_document: default
  word_document: default
params:
  inputFile: config/model_inputs.xlsx
  outputDir: log
  optional_sheets: !r NULL
---
```{css, echo=FALSE}
div.error { background-color: IndianRed; }
div.warning { background-color: lightyellow; }
div.info { background-color: lightblue; }
.table caption { font-weight:bold; color:black; }
```
# Validation Results
<br><br>

## Input Data Check:
<br><br>
```{r, echo=FALSE, results='hide',  message=FALSE, warning=FALSE}
source("ValidateInput.R")
source("ValidateInput_plot.R")
Validate(inputFile = params$inputFile, outputDir = params$outputDir, optional_sheets=params$optional_sheets)
```

```{r echo=FALSE, results='asis'}
result <- read.csv(paste(params$outputDir, "input_validation_results.csv", sep="/"))
outfile <- paste(params$outputDir, "input_validation_results.png", sep="/")
plot_result(result, outfile)
knitr::include_graphics(normalizePath(outfile))

# set caption color
set_caption_color <- function(state){
    if (state == "error") {
      cat('<div class="error">')
    }
    else if (state == "warning") {
      cat('<div class="warning">')
    }
    else if (state == "info"){
     cat('<div class="info">')
    }
    else{
      cat("</div>")
    }
  }
```

-   Please check below csv files in `r params$outputDir` folder for any row based validation issue:


```{r echo=FALSE, comment='', results='asis', warning=FALSE, message=TRUE, paged.print=TRUE}
files <- list.files(path=params$outputDir, pattern = "(info|warning|error).*.csv")

metadata <- read.csv(paste(params$outputDir, "input_validation_results.csv", sep="/"))
for (f in files){
  filename <- normalizePath(paste(params$outputDir, f, sep="/"))
  message(paste0(filename,"\n\n"))
  rule_name <- gsub('^.+?_violation_(.+?).csv', '\\1', f)
  sheet_name <- stringr::str_replace(f, gsub('^.+?(_(error|info|warning))', '\\1', f), "")
  info <- metadata %>%
    filter(name == rule_name)
  tbl_description <- info %>%
    mutate(text_value=paste0(severity, ": ", description)) %>%
    select(text_value) %>%
    unique() %>% 
   .$text_value
  vars <- all.vars(as.formula(
    info %>% 
    mutate(expression = paste("~ ", expression, sep="")) %>%
    select(expression) %>%
    .$expression))
  key <- key_cols[sheet_name][[1]]
  extra_cols <- rule_cols[rule_name][[1]]
  data <- read.csv(paste(params$outputDir, f, sep="/"))
  data <- data %>% select(unique(c(all_of(key), all_of(extra_cols), all_of(vars))))
  set_caption_color(str_split(tbl_description, ":", simplify = TRUE)[1])
  print(knitr::kable(data, caption=tbl_description, format='pipe', align = "l"))
  set_caption_color("none")
}
```
## Model Requirement Check:
<br><br>
```{r echo=FALSE, comment='', warning=FALSE}
cat(readLines(paste(params$outputDir, "model_input_check.log", sep = "/")), sep = '\n')
```
## Custom Data Check:
<br><br>
```{r echo=FALSE, comment='', results = 'asis', warning=FALSE}
  for (f in sort(list.files(file.path(params$outputDir, "custom"), "*.png"))){
    filename <- normalizePath(file.path(params$outputDir, "custom", f))
    cat("\n\n\n")
    cat("![](",filename,")")
    cat("\n\n\n")
  }
  custom_metadata <- read.csv(normalizePath(file.path(params$outputDir, "custom", "custom_validation_results.csv")))
  for (i in 1:nrow(custom_metadata)){
    f <- as.character(custom_metadata[i, "name"])
    baddata <- read.csv(normalizePath(f))
    tbl_description <- paste(as.character(custom_metadata[i, "severity"]), ": ", as.character(custom_metadata[i, "description"]))
    set_caption_color(custom_metadata[i, "severity"])
    print(knitr::kable(baddata, caption=tbl_description, format='pipe', align = "l"))
    set_caption_color("none")
  }
  
```
## Additional Logs:
<br><br>
```{r echo=FALSE, comment='', warning=FALSE}
logfiles <- list.files(path=params$outputDir,
                        recursive=T,
                        pattern=.errorLogfile
                        ,full.names=T)
cat(readLines(logfiles[[1]]), sep = '\n')
```