From ebde4a30120658e0df9bc7db8e6b2e1f15003f56 Mon Sep 17 00:00:00 2001
From: Trent Hauck <trent@trenthauck.com>
Date: Mon, 6 Nov 2023 11:15:03 -0800
Subject: [PATCH] build: update exon (#67)

---
 Cargo.toml              | 6 +++---
 src/bcf_reader.rs       | 2 +-
 src/execution_result.rs | 1 +
 src/exon_reader.rs      | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 0e4a23e..59cabe5 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -8,9 +8,9 @@ crate-type = ["cdylib"]
 name = "biobear"
 
 [dependencies]
-arrow = {version = "46", features = ["pyarrow"]}
-datafusion = "31"
-exon = {version = "0.3.4-beta.3", features = ["all"]}
+arrow = {version = "47", features = ["pyarrow"]}
+datafusion = "32"
+exon = {version = "0.3.8-beta.4", features = ["all"]}
 pyo3 = "0.19"
 thiserror = "1.0"
 tokio = {version = "1", features = ["rt"]}
diff --git a/src/bcf_reader.rs b/src/bcf_reader.rs
index 7565478..77f3569 100644
--- a/src/bcf_reader.rs
+++ b/src/bcf_reader.rs
@@ -64,7 +64,7 @@ impl BCFIndexedReader {
             config = config.with_batch_size(batch_size);
         }
 
-        let ctx = SessionContext::with_config(config);
+        let ctx = SessionContext::new_with_config(config);
 
         let df = self._runtime.block_on(async {
             match ctx.query_bcf_file(self.path.as_str(), region).await {
diff --git a/src/execution_result.rs b/src/execution_result.rs
index f64c9ef..30eac01 100644
--- a/src/execution_result.rs
+++ b/src/execution_result.rs
@@ -56,6 +56,7 @@ impl PyExecutionResult {
         Python::with_gil(|py| {
             // Instantiate pyarrow Table object and use its from_batches method
             let table_class = py.import("pyarrow")?.getattr("Table")?;
+
             let args = PyTuple::new(py, &[batches]);
             let table: PyObject = table_class.call_method1("from_batches", args)?.into();
             Ok(table)
diff --git a/src/exon_reader.rs b/src/exon_reader.rs
index afa7cda..3917c45 100644
--- a/src/exon_reader.rs
+++ b/src/exon_reader.rs
@@ -18,7 +18,7 @@ use std::sync::Arc;
 
 use arrow::ffi_stream::{export_reader_into_raw, ArrowArrayStreamReader, FFI_ArrowArrayStream};
 use arrow::pyarrow::IntoPyArrow;
-use datafusion::common::FileCompressionType;
+use datafusion::datasource::file_format::file_compression_type::FileCompressionType;
 use datafusion::prelude::{SessionConfig, SessionContext};
 use exon::datasources::ExonFileType;
 use exon::ffi::DataFrameRecordBatchStream;