pnldashboard.Rmd

---
title: "Flexdashboard"
output:
  flexdashboard::flex_dashboard:
      navbar:
      - { title: "PNL Project Dashboard Test", align: right }
      source_code: embed
      orientation: columns
      smart: false
always_allow_html: yes
---


```{r setup, include=FALSE}
library(data.table)
library(DT)
library(magrittr)
library(flexdashboard)
library(knitr)
PATHS <- '*/paths.csv' %>% Sys.glob %>% lapply(fread) %>% rbindlist
EXTRA <- '*/unaccounted_files.csv' %>% Sys.glob %>% lapply(fread,colClasses = c('character', 'character', 'double')) %>% rbindlist
DU <- '*/du.csv' %>% Sys.glob %>% lapply(fread) %>% rbindlist
PARAMS <- '*/params.csv' %>% Sys.glob %>% lapply(fread) %>% rbindlist
```

Overview
=====================================

```{r overview}
#TODO handle empty project paths

PATHS.unique = PATHS[, head(.SD, 1), by=.(projectPath, path)]

PATHS.byProject = PATHS.unique[PATHS.unique[,exists] & ! path %like% '\\.\\./.*', .('project files (G)'=sum(sizeMB)/1024),by=projectPath]

EXTRA.byProject = EXTRA[,.('extra files (G)'=sum(sizeMB)/1024), by=projectPath]

SPACE_TABLE.a = merge(PATHS.byProject, EXTRA.byProject, all.x=T, by="projectPath")

SPACE_TABLE = merge(SPACE_TABLE.a, DU, by="projectPath")[,'total directory size (G)':=diskUsageG][,diskUsageG:=NULL]

DT::datatable(SPACE_TABLE, options = list(bPaginate=F)) %>% DT::formatRound(c('project files (G)', 'extra files (G)', 'total directory size (G)'), 2)
```


```{r projectpages, include=FALSE}
paths.grouped <- PATHS[,.( completed=sum(exists), missing=sum(not(exists)), total=.N, 'size (G)'=sum(sizeMB, na.rm=T)/1024, examplePath=head(path,n=1)), by=.(projectPath, pathKey, pipelineId)]

indentText <- function(text) {
  paste0("    ", gsub("\n", "\n    ", text))
}

summarizePipeline <- function(projectpath, projectSD) {
  pipelinesCol = projectSD[,
          {
          paramid=pipelineId
          paramCombo = PARAMS[projectPath==projectpath & pipelineId==paramid,]
          pipelineDescription = indentText(paramCombo[,pipelineDescription][1])
          setorder(paramCombo, param)
          paramTable = kable(paramCombo[,.(parameter=param, "parameter value"=paramValue)])
          if (nrow(paramCombo) == 0) {
            paramTable = "None given."
          }
          pathsSummary = kable(.SD, digits=1)
          diskUsage = .SD[,sum(.SD$'size (G)')] %>% round(digits=1)
          # TODO will be empty for an empty PATHS table
          caselist = kable(unique(PATHS[projectPath==projectpath & pipelineId==paramid,caseid]))
          knit_expand(text='### PIPELINE #{{pipelineId}} ({{diskUsage}}G)
#### Description
{{pipelineDescription}}

#### Parameters
{{paramTable}}

#### Output Paths
{{pathsSummary}}

#### Caselist
{{caselist}}
')
          }, by=.(pipelineId)][,V1]

  spaceTakenTable = SPACE_TABLE[projectPath==projectpath][,projectPath:=NULL]
  spaceTakenTable.html = kable(spaceTakenTable, align=c("l","l"), digits=1)
  diskUsage = spaceTakenTable[,.SD$'project files (G)'] %>% round(digits=1)
  pageHeader = knit_expand(text='# {{projectpath}} ({{diskUsage}}G) {data-navmenu="Projects"}')
  # Add leading 4 spaces to make description a markdown quotation block, hence preserving its formatting
  projectDescription = indentText(PARAMS[projectPath==projectpath,description][1])
  colSep = "--------------"
  #spaceTakenTable = table[projectPath==projectpath][,projectPath:=NULL] %>% DT::formatRound(c('project files (G)', 'extra files (G)'), 1)
  overviewCol = c("Col1", colSep, knit_expand(text="### {{projectpath}}"), "", "#### Description", projectDescription, "#### Disk space", spaceTakenTable.html)
  c(pageHeader, overviewCol, "  ", "Col2 {.tabset}  ", colSep, pipelinesCol)
}

out = paths.grouped[,
  {
  summarizePipeline(projectPath, .SD)
  }
  , by=.(projectPath)][,V1]

```

`r paste(out, collapse = '\n')`