GFA: derive block group name from filename on import

fixtures/gfa/connected_mixed_sn.gfa

@@ -0,0 +1,6 @@
+H	VN:Z:1.0
+S	A	AAAA	SN:Z:chr1
+S	B	CCCC	SN:Z:chr1
+S	C	TTTT	SN:Z:chr2
+L	A	+	B	+	*
+L	B	+	C	+	*

fixtures/gfa/disjoint_graphs.gfa

@@ -0,0 +1,7 @@
+H	VN:Z:1.0
+S	1	AAAA
+S	2	CCCC
+S	3	TTTT
+S	4	GGGG
+L	1	+	2	+	*
+L	3	+	4	+	*

fixtures/gfa/paths_no_ref.gfa

@@ -0,0 +1,8 @@
+H	VN:Z:1.0
+S	1	AAAA
+S	2	CCCC
+S	3	TTTT
+L	1	+	2	+	*
+L	2	+	3	+	*
+P	short	1+,2+	*
+P	longer_path	1+,2+,3+	*

fixtures/gfa/ref_tag_multi.gfa

@@ -0,0 +1,7 @@
+H	VN:Z:1.0
+S	1	AAAA	SN:Z:chr1	SO:i:0	SR:i:0
+S	2	CCCC	SN:Z:chr1	SO:i:4	SR:i:0
+S	3	TTTT	SN:Z:chr2	SO:i:0	SR:i:0
+S	4	GGGG	SN:Z:chr2	SO:i:4	SR:i:0
+L	1	+	2	+	*
+L	3	+	4	+	*

fixtures/gfa/ref_tag_single.gfa

@@ -0,0 +1,6 @@
+H	VN:Z:1.0
+S	1	AAAA	SN:Z:chr1	SO:i:0	SR:i:0
+S	2	CCCC	SN:Z:chr1	SO:i:4	SR:i:0
+S	3	TTTT	SN:Z:chr1	SO:i:8	SR:i:0
+L	1	+	2	+	*
+L	2	+	3	+	*

gen-python/src/python_api/repository/imports.rs

@@ -17,7 +17,7 @@ use gen_models::{
 use pyo3::{exceptions::PyRuntimeError, prelude::*};
 
 use super::{PyRepository, run_write};
-use crate::python_api::sequence_part::PySequencePart;
+use crate::python_api::{block_group::PySequenceGraph, sequence_part::PySequencePart};
 
 #[pymethods]
 impl PyRepository {
@@ -80,12 +80,17 @@ impl PyRepository {
         filename: String,
         sample: Option<String>,
         collection: Option<String>,
-    ) -> PyResult<String> {
+    ) -> PyResult<Vec<PySequenceGraph>> {
         let collection = collection.unwrap_or_else(|| self.get_default_collection());
         let sample = sample.unwrap_or_else(|| Sample::DEFAULT_NAME.to_string());
         run_write(&self.context, !self.in_transaction, |ctx| {
             import_gfa(ctx, &PathBuf::from(&filename), &collection, &sample)
-                .map(|_| format!("'{}' imported.", filename))
+                .map(|(_, block_groups)| {
+                    block_groups
+                        .into_iter()
+                        .map(|bg| self.into_py_block_group(bg))
+                        .collect()
+                })
                 .map_err(|e| match e {
                     GFAImportError::OperationError(OperationError::NoChanges) => {
                         PyRuntimeError::new_err(format!("'{}': already exists", filename))

gen-r/src/rust/src/lib.rs

@@ -1073,7 +1073,7 @@ impl Repository {
         filename: String,
         sample: String,
         collection: Nullable<String>,
-    ) -> std::result::Result<String, Error> {
+    ) -> std::result::Result<List, Error> {
         let collection_name = resolve_collection_name(
             self.context.operations().conn(),
             nullable_string_to_option(collection),
@@ -1086,9 +1086,13 @@ impl Repository {
             &collection_name,
             &sample,
         ) {
-            Ok(_) => {
+            Ok((_, block_groups)) => {
                 end_transactions(&self.context).map_err(Error::Other)?;
-                Ok("GFA imported.".to_string())
+                let values = block_groups
+                    .into_iter()
+                    .map(|bg| r!(self.into_sequence_graph(bg)))
+                    .collect::<Vec<_>>();
+                Ok(List::from_values(values))
             }
             Err(r#gen::imports::gfa::GFAImportError::OperationError(OperationError::NoChanges)) => {
                 rollback_transactions(&self.context);

gen-r/tests/testthat/test-basic.R

@@ -76,10 +76,10 @@ test_that("GFA and GenBank import/export work", {
   gfa_out <- tempfile(fileext = ".gfa")
   gb_out  <- tempfile(fileext = ".gb")
 
-  expect_match(
-    repo$import_gfa(fixture_path("simple.gfa"), sample = "sample-a"),
-    "imported", ignore.case = TRUE
-  )
+  result <- repo$import_gfa(fixture_path("simple.gfa"), sample = "sample-a")
+  expect_true(is.list(result))
+  expect_gt(length(result), 0)
+  expect_true(all(sapply(result, inherits, "SequenceGraph")))
   expect_binding_result(try(repo$export_gfa(gfa_out, sample = "sample-a"), silent = TRUE))
 
   expect_binding_result(try(

src/commands/import/gfa.rs

@@ -57,10 +57,15 @@ pub fn execute(cli_context: &CliContext, cmd: Command) -> Result<()> {
         )?;
     }
     match import_gfa(context, &PathBuf::from(cmd.path.clone()), name, sample_name) {
-        Ok(_) => {
-            println!("GFA imported.");
+        Ok((_, block_groups)) => {
             conn.execute("END TRANSACTION;", []).unwrap();
             operation_conn.execute("END TRANSACTION;", []).unwrap();
+            let names: Vec<&str> = block_groups.iter().map(|bg| bg.name.as_str()).collect();
+            println!(
+                "Imported {} sequence graph(s): {}",
+                names.len(),
+                names.join(", ")
+            );
             Ok(())
         }
         Err(GFAImportError::OperationError(OperationError::NoChanges)) => {

src/diffs/gfa.rs

@@ -911,11 +911,15 @@ mod tests {
             Sample::DEFAULT_NAME,
         );
 
-        let new_block_group = Collection::get_block_groups(conn, "test collection 3")
-            .pop()
-            .unwrap();
-        let all_sequences =
-            BlockGroup::get_all_sequences(conn, &new_block_group.id, false).unwrap();
+        let all_sequences: HashSet<String> =
+            Collection::get_block_groups(conn, "test collection 3")
+                .iter()
+                .flat_map(|bg| {
+                    BlockGroup::get_all_sequences(conn, &bg.id, false)
+                        .unwrap()
+                        .into_iter()
+                })
+                .collect();
 
         assert_eq!(
             all_sequences,
@@ -1081,11 +1085,15 @@ mod tests {
             Sample::DEFAULT_NAME,
         );
 
-        let new_block_group = Collection::get_block_groups(conn, "test collection 3")
-            .pop()
-            .unwrap();
-        let all_sequences =
-            BlockGroup::get_all_sequences(conn, &new_block_group.id, false).unwrap();
+        let all_sequences: HashSet<String> =
+            Collection::get_block_groups(conn, "test collection 3")
+                .iter()
+                .flat_map(|bg| {
+                    BlockGroup::get_all_sequences(conn, &bg.id, false)
+                        .unwrap()
+                        .into_iter()
+                })
+                .collect();
 
         assert_eq!(
             all_sequences,

src/exports/gfa.rs

@@ -609,7 +609,8 @@ mod tests {
 
         let _ = import_gfa(&context, &gfa_path, &collection_name, Sample::DEFAULT_NAME);
 
-        let block_group_id = BlockGroup::get_id(&collection_name, Sample::DEFAULT_NAME, "", None);
+        let block_group_id =
+            BlockGroup::get_id(&collection_name, Sample::DEFAULT_NAME, "m123", None);
         let all_sequences = BlockGroup::get_all_sequences(conn, &block_group_id, false).unwrap();
 
         let temp_dir = tempdir().expect("Couldn't get handle to temp directory");
@@ -652,7 +653,12 @@ mod tests {
 
         let _ = import_gfa(&context, &gfa_path, &collection_name, Sample::DEFAULT_NAME);
 
-        let block_group_id = BlockGroup::get_id(&collection_name, Sample::DEFAULT_NAME, "", None);
+        let block_group_id = BlockGroup::get_id(
+            &collection_name,
+            Sample::DEFAULT_NAME,
+            "BBa_J23119#0#BBa_J23119",
+            None,
+        );
         let all_sequences = BlockGroup::get_all_sequences(conn, &block_group_id, false).unwrap();
 
         let temp_dir = tempdir().expect("Couldn't get handle to temp directory");
@@ -695,7 +701,8 @@ mod tests {
 
         let _ = import_gfa(&context, &gfa_path, &collection_name, Sample::DEFAULT_NAME);
 
-        let block_group_id = BlockGroup::get_id(&collection_name, Sample::DEFAULT_NAME, "", None);
+        let block_group_id =
+            BlockGroup::get_id(&collection_name, Sample::DEFAULT_NAME, "123", None);
         let all_sequences = BlockGroup::get_all_sequences(conn, &block_group_id, false).unwrap();
 
         let temp_dir = tempdir().expect("Couldn't get handle to temp directory");