feat: better error messages (#203)

* feat: small tweaks * fix: fix clippy
wheretrue · Oct 6, 2023 · ef11a78 · ef11a78
1 parent 7a8bc9f
commit ef11a78
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Showing 5 changed files with 25 additions and 16 deletions.
diff --git a/exon/src/datasources/bam/table_provider.rs b/exon/src/datasources/bam/table_provider.rs
@@ -223,8 +223,8 @@ impl TableProvider for ListingBAMTable {
         }
 
         if regions.is_empty() && self.options.indexed {
-            return Err(DataFusionError::Execution(
-                "INDEXED_BAM table type requires a region filter".to_string(),
+            return Err(DataFusionError::Plan(
+                "INDEXED_BAM table type requires a region filter. See the 'bam_region_filter' function.".to_string(),
             ));
         }
 

diff --git a/exon/src/datasources/vcf/file_opener/indexed_file_opener.rs b/exon/src/datasources/vcf/file_opener/indexed_file_opener.rs
@@ -102,12 +102,6 @@ impl FileOpener for IndexedVCFOpener {
                         async_reader
                     } else {
                         // Otherwise, we read the compressed range from the object store.
-                        tracing::debug!(
-                            "Reading compressed range: {}..{} of {}",
-                            vp_start.compressed(),
-                            vp_end.compressed(),
-                            file_meta.location()
-                        );
 
                         let start = vp_start.compressed() as usize;
                         let end = if vp_start.compressed() == vp_end.compressed() {
@@ -116,6 +110,15 @@ impl FileOpener for IndexedVCFOpener {
                             vp_end.compressed() as usize
                         };
 
+                        tracing::info!(
+                            "Reading compressed range: {}..{} (uncompressed {}..{}) of {}",
+                            vp_start.compressed(),
+                            vp_end.compressed(),
+                            start,
+                            end,
+                            file_meta.location()
+                        );
+
                         let get_options = GetOptions {
                             range: Some(Range { start, end }),
                             ..Default::default()

diff --git a/exon/src/datasources/vcf/table_provider.rs b/exon/src/datasources/vcf/table_provider.rs
@@ -99,7 +99,6 @@ pub struct ListingVCFTableOptions {
 impl ListingVCFTableOptions {
     /// Create a new set of options
     pub fn new(file_compression_type: FileCompressionType, indexed: bool) -> Self {
-        let file_compression_type = file_compression_type;
         let file_extension = ExonFileType::VCF.get_file_extension(file_compression_type);
 
         Self {
@@ -321,8 +320,9 @@ impl TableProvider for ListingVCFTable {
         }
 
         if regions.is_empty() && self.options.indexed {
-            return Err(DataFusionError::NotImplemented(
-                "INDEXED_VCF table reuires a region filter".to_string(),
+            return Err(DataFusionError::Plan(
+                "INDEXED_VCF table requires a region filter. See the UDF 'vcf_region_filter'."
+                    .to_string(),
             ));
         }
 

diff --git a/exon/src/exome/proto/exome.v1.rs b/exon/src/exome/proto/exome.v1.rs
@@ -41,6 +41,15 @@ pub struct Organization {
     #[prost(string, tag = "4")]
     pub updated_at: ::prost::alloc::string::String,
 }
+/// Association between a use and an organization.
+#[allow(clippy::derive_partial_eq_without_eq)]
+#[derive(Clone, PartialEq, ::prost::Message)]
+pub struct UserOrganization {
+    #[prost(message, optional, tag = "1")]
+    pub organization: ::core::option::Option<Organization>,
+    #[prost(string, tag = "2")]
+    pub role: ::prost::alloc::string::String,
+}
 #[allow(clippy::derive_partial_eq_without_eq)]
 #[derive(Clone, PartialEq, ::prost::Message)]
 pub struct GetOrganizationRequest {
@@ -64,7 +73,7 @@ pub struct GetUserOrganizationsRequest {
 #[derive(Clone, PartialEq, ::prost::Message)]
 pub struct GetUserOrganizationsResponse {
     #[prost(message, repeated, tag = "1")]
-    pub organizations: ::prost::alloc::vec::Vec<Organization>,
+    pub organizations: ::prost::alloc::vec::Vec<UserOrganization>,
 }
 /// User
 #[allow(clippy::derive_partial_eq_without_eq)]

diff --git a/exon/src/physical_optimizer/file_repartitioner.rs b/exon/src/physical_optimizer/file_repartitioner.rs
@@ -90,10 +90,7 @@ fn optimize_file_partitions(
             .children()
             .iter()
             .map(|child| {
-                let optimized = optimize_file_partitions(child.clone(), target_partitions)
-                    .map(Transformed::into);
-
-                optimized
+                optimize_file_partitions(child.clone(), target_partitions).map(Transformed::into)
             })
             .collect::<Result<_>>()?;