---
title: "Test run for upload system"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Test run for upload system}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval=FALSE
)
```

```{r setup}
library(GwasDataImport)
library(data.table)
library(ieugwasr)
library(dplyr)

# get access
ieugwasr::get_access_token()

# Initialise
fn <- system.file("extdata/pos_0002.txt.gz", package="GwasDataImport")
x <- Dataset$new(filename=fn, igd_id="ieu-b-test2")

# Specify columns
x$determine_columns(list(chr_col=1, snp_col=2, pos_col=3, oa_col=4, ea_col=5, beta_col=7, se_col=8, pval_col=9))

# Process dataset
x$format_dataset()

# Input metadata
x$collect_metadata(list(
	trait="whatever",
	build="HG19/GRCh37",
	category="Continuous",
	subcategory="NA",
	group_name="public",
	population="European",
	sex="Males and Females"
))

# Upload metadata
x$api_metadata_upload()

# Upload summary data
x$api_gwasdata_upload()

# Check status
x$api_qc_status()

# Check existing files
x$api_gwasdata_check() %>% httr::content()

# Delete everything
x$api_gwasdata_delete()
```