From 682da1dd903b351dbcab8e133f9e8040adc1ffbf Mon Sep 17 00:00:00 2001
From: Carl Kadie <carlk@msn.com>
Date: Thu, 18 Jan 2024 14:23:38 -0800
Subject: [PATCH] udpate http_two on the rust side

---
 Cargo.lock               |  7 +++++++
 Cargo.toml               |  1 +
 src/lib.rs               |  2 +-
 tests/tests_api_cloud.rs | 21 ++++++++++++---------
 4 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 8ea6715..9847920 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -173,6 +173,7 @@ dependencies = [
  "statrs",
  "temp_testdir",
  "thiserror",
+ "thousands",
  "tokio",
  "url",
 ]
@@ -2070,6 +2071,12 @@ dependencies = [
  "syn 2.0.13",
 ]
 
+[[package]]
+name = "thousands"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3bf63baf9f5039dadc247375c29eb13706706cfde997d0330d05aa63a77d8820"
+
 [[package]]
 name = "tinyvec"
 version = "1.6.0"
diff --git a/Cargo.toml b/Cargo.toml
index 03d6b3b..e7bad73 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -79,6 +79,7 @@ pyo3-asyncio = { version = "0.20.0", features = [
 ] }
 temp_testdir = "0.2.3"
 object_store = { version = "0.9.0", features = ["aws","http"]}
+thousands = "0.2.0"
 
 
 [build-dependencies]
diff --git a/src/lib.rs b/src/lib.rs
index 067a396..edb7128 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -7162,7 +7162,7 @@ fn matrix_subset_no_alloc<
 #[fetch_data::ctor]
 static STATIC_FETCH_DATA: FetchData = FetchData::new(
     include_str!("../bed_reader/tests/registry.txt"),
-    "https://raw.githubusercontent.com/fastlmm/bed-reader/rustybed/bed_reader/tests/data/",
+    "https://raw.githubusercontent.com/fastlmm/bed-sample-files/main/",
     "BED_READER_DATA_DIR",
     "github.io",
     "fastlmm",
diff --git a/tests/tests_api_cloud.rs b/tests/tests_api_cloud.rs
index 80a441d..33530e3 100644
--- a/tests/tests_api_cloud.rs
+++ b/tests/tests_api_cloud.rs
@@ -11,6 +11,7 @@ use bed_reader::path_to_url_string;
 use bed_reader::sample_bed_file;
 use bed_reader::sample_bed_object_path;
 use bed_reader::sample_bed_url;
+use bed_reader::sample_file;
 use bed_reader::sample_object_path;
 use bed_reader::sample_object_paths;
 use bed_reader::BedCloud;
@@ -29,6 +30,7 @@ use object_store::aws::AmazonS3Builder;
 use object_store::local::LocalFileSystem;
 use object_store::path::Path as StorePath;
 use object_store::ObjectStore;
+use thousands::Separable;
 use tokio::runtime;
 use url::Url;
 
@@ -2422,29 +2424,30 @@ async fn http_one() -> Result<(), Box<BedErrorPlus>> {
 
 #[tokio::test]
 async fn http_two() -> Result<(), Box<BedErrorPlus>> {
+    let local_fam_file = sample_file("synthetic_v1_chr-10.fam")?;
+    let local_bim_file = sample_file("synthetic_v1_chr-10.bim")?;
     // cmk make this a const
     let empty_skip_set = HashSet::<MetadataFields>::new();
     let metadata = Metadata::new()
-        .read_fam(
-            r"C:\Users\carlk\Downloads\S-BSST936\example\synthetic_small_v1_chr-10.fam",
-            &empty_skip_set,
-        )?
+        .read_fam(local_fam_file, &empty_skip_set)?
         .0
-        .read_bim(
-            r"C:\Users\carlk\Downloads\S-BSST936\example\synthetic_small_v1_chr-10.bim",
-            &empty_skip_set,
-        )?
+        .read_bim(local_bim_file, &empty_skip_set)?
         .0;
 
     // Open the bed file with a URL and any needed cloud options, then use as before.
     let mut bed_cloud = BedCloud::builder(
-        "https://www.ebi.ac.uk/biostudies/files/S-BSST936/example/synthetic_small_v1_chr-10.bed",
+        "https://www.ebi.ac.uk/biostudies/files/S-BSST936/genotypes/synthetic_v1_chr-10.bed",
         [("timeout", "100")], // cmk must figure this out
     )?
     .metadata(&metadata)
     .skip_early_check()
     .build()
     .await?;
+    println!(
+        "iid_count={}, sid_count={}",
+        bed_cloud.iid_count().await?.separate_with_underscores(),
+        bed_cloud.sid_count().await?.separate_with_underscores()
+    );
     println!("{:?}", bed_cloud.iid().await?.slice(s![..5]));
     println!("{:?}", bed_cloud.sid().await?.slice(s![..5]));
     println!(