From 65d6aca73534c6f65ef7a22ad68d26cb097ebe3c Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Wed, 10 Jan 2024 17:05:29 -0500
Subject: [PATCH 1/2] Set input file encoding to latin1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Without this, the encoding of strings for the output will be invalid
UTF-8. This gives errors when the file is read by various tools such as

with DuckDB:

```shell
$ duckdb -c "$(cat <<'EOF'
> SELECT DISTINCT chnm FROM 'brick/invitrodb.parquet/part-*.parquet';
> EOF
> )"
Error: Invalid Input Error: Invalid string encoding found in Parquet file: value "(\xB1)-cis-3-Methyl fentanyl hydrochloride" is not valid UTF8!
```

or with `pyarrow` when converting to `pandas`:

```
pyarrow.lib.ArrowException: Unknown error: Wrapping (�)-Bornyl acetate failed
```
---
 stages/download.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/stages/download.R b/stages/download.R
index ecdcd5e..fca14d7 100644
--- a/stages/download.R
+++ b/stages/download.R
@@ -8,7 +8,9 @@ invitrodb = "https://clowder.edap-cluster.com/files/63642290e4b04f6bb140a10d/blo
 options(timeout = 600)
 download.file(invitrodb, destfile = stage, mode = "wb")
 
-df = readr::read_csv(stage)
+# Need encoding due to the ± character:
+#   $ perl -F, -nE 'next unless /[^\x00-\x7F]/; say $F[3]' staging/invitrodb.csv  | sort | uniq -c
+df = readr::read_csv( file = stage, locale = readr::locale(encoding = "latin1") )
 out = fs::dir_create("brick/invitrodb.parquet")
 
 # See

From 79147a935db3d14abb5aa590ef73676f07b5a776 Mon Sep 17 00:00:00 2001
From: Zakariyya Mughal <zaki.mughal@gmail.com>
Date: Wed, 10 Jan 2024 19:51:16 -0500
Subject: [PATCH 2/2] Update dvc.lock

---
 dvc.lock | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/dvc.lock b/dvc.lock
index 0b029e0..2acdb68 100644
--- a/dvc.lock
+++ b/dvc.lock
@@ -19,11 +19,11 @@ stages:
       size: 33866
     - path: stages/download.R
       hash: md5
-      md5: fde14a12dfe43458e11081702c2d3625
-      size: 831
+      md5: ec800973d471bab40b8abda8e60f39cc
+      size: 1025
     outs:
     - path: brick/invitrodb.parquet
       hash: md5
-      md5: 79a0001b906d40f06a0efa2fea6a4bc1.dir
-      size: 718228047
+      md5: 110a6e966af64a8ad0c686b7bf8c908e.dir
+      size: 718228060
       nfiles: 4