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Send default collection via push and pull #217

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2 changes: 2 additions & 0 deletions gen-capnp-schemas/gen-models.capnp
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Original file line number Diff line number Diff line change
Expand Up @@ -251,11 +251,13 @@ struct Manifest {
some @3 :List(UInt8);
}
operations @4 :List(ManifestOperation);
defaultCollectionName @5 :Text;
}

struct ManifestDiff {
missingInManifest2 @0 :List(ManifestOperation);
missingInManifest1 @1 :List(ManifestOperation);
defaultCollectionName @2 :Text;
}

struct AnnotationInterval {
Expand Down
33 changes: 32 additions & 1 deletion gen-models/src/manifest.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ use crate::{
manifest, manifest_annotation_file_addition, manifest_diff, manifest_operation,
manifest_operation_file_addition,
},
operations::{FileAddition, Operation, OperationFile, OperationSummary},
operations::{Defaults, FileAddition, Operation, OperationFile, OperationSummary},
traits::Query,
};

Expand Down Expand Up @@ -252,6 +252,7 @@ pub struct Manifest {
pub branch_name: String,
pub end_hash: Option<HashId>,
pub operations: Vec<ManifestOperation>,
pub default_collection_name: String,
}

impl<'a> Capnp<'a> for Manifest {
Expand All @@ -274,6 +275,8 @@ impl<'a> Capnp<'a> for Manifest {
let mut operation_builder = operations_builder.reborrow().get(i as u32);
operation.write_capnp(&mut operation_builder);
}

builder.set_default_collection_name(&self.default_collection_name);
}

fn read_capnp(reader: Self::Reader) -> Self {
Expand All @@ -295,11 +298,18 @@ impl<'a> Capnp<'a> for Manifest {
}
};

let default_collection_name = reader
.get_default_collection_name()
.unwrap()
.to_string()
.unwrap();

Manifest {
manifest_version,
branch_name,
end_hash,
operations,
default_collection_name,
}
}
}
Expand All @@ -308,6 +318,7 @@ impl<'a> Capnp<'a> for Manifest {
pub struct ManifestDiff {
pub missing_in_manifest2: Vec<ManifestOperation>,
pub missing_in_manifest1: Vec<ManifestOperation>,
pub default_collection_name: String,
}

impl<'a> Capnp<'a> for ManifestDiff {
Expand All @@ -330,6 +341,8 @@ impl<'a> Capnp<'a> for ManifestDiff {
let mut operation_builder = missing_in_manifest1_builder.reborrow().get(i as u32);
operation.write_capnp(&mut operation_builder);
}

builder.set_default_collection_name(&self.default_collection_name);
}

fn read_capnp(reader: Self::Reader) -> Self {
Expand All @@ -345,9 +358,16 @@ impl<'a> Capnp<'a> for ManifestDiff {
missing_in_manifest1.push(ManifestOperation::read_capnp(operation_reader));
}

let default_collection_name = reader
.get_default_collection_name()
.unwrap()
.to_string()
.unwrap();

ManifestDiff {
missing_in_manifest2,
missing_in_manifest1,
default_collection_name,
}
}
}
Expand Down Expand Up @@ -415,6 +435,9 @@ impl<'a> ManifestGenerator<'a> {
branch_name: branch_name.to_string(),
end_hash: end_hash.copied(),
operations: manifest_operations,
default_collection_name: Defaults::get(self.conn)
.and_then(|defaults| defaults.collection_name)
.unwrap_or_else(|| "default".to_string()),
})
}
}
Expand Down Expand Up @@ -473,6 +496,7 @@ impl ManifestComparer {
Ok(ManifestDiff {
missing_in_manifest2,
missing_in_manifest1,
default_collection_name: manifest2.default_collection_name.clone(),
})
}
}
Expand Down Expand Up @@ -584,6 +608,7 @@ mod tests {
manifest_version: "1.0".to_string(),
branch_name: "main".to_string(),
end_hash: Some(operation.hash),
default_collection_name: "test collection".to_string(),
operations: vec![ManifestOperation {
operation,
file_additions: vec![],
Expand Down Expand Up @@ -631,6 +656,7 @@ mod tests {
let manifest_diff = ManifestDiff {
missing_in_manifest2: vec![manifest_operation.clone()],
missing_in_manifest1: vec![manifest_operation],
default_collection_name: "test collection".to_string(),
};

let mut message = TypedBuilder::<manifest_diff::Owned>::new_default();
Expand All @@ -649,6 +675,7 @@ mod tests {

let db_uuid = crate::metadata::get_db_uuid(conn);
crate::files::GenDatabase::create(op_conn, &db_uuid, "test_db", "test_db_path").unwrap();
Defaults::set_default_collection(op_conn, "test collection").unwrap();

let mut session = start_operation(conn);
crate::sequence::Sequence::new()
Expand Down Expand Up @@ -680,6 +707,7 @@ mod tests {
.unwrap();

assert_eq!(manifest.branch_name, "main");
assert_eq!(manifest.default_collection_name, "test collection");
assert_eq!(manifest.operations.len(), 2);
assert_eq!(manifest.operations[0].operation.hash, op1.hash);
assert_eq!(manifest.operations[1].operation.hash, op2.hash);
Expand Down Expand Up @@ -842,6 +870,7 @@ mod tests {
manifest_version: "1.0".to_string(),
branch_name: "main".to_string(),
end_hash: Some(op2.hash),
default_collection_name: "local".to_string(),
operations: vec![
ManifestOperation {
operation: op1.clone(),
Expand All @@ -862,6 +891,7 @@ mod tests {
manifest_version: "1.0".to_string(),
branch_name: "main".to_string(),
end_hash: Some(op3.hash),
default_collection_name: "remote".to_string(),
operations: vec![
ManifestOperation {
operation: op2.clone(),
Expand All @@ -885,6 +915,7 @@ mod tests {

assert_eq!(diff.missing_in_manifest1.len(), 1);
assert_eq!(diff.missing_in_manifest1[0].operation.hash, op3.hash);
assert_eq!(diff.default_collection_name, "remote");
}

#[test]
Expand Down
12 changes: 12 additions & 0 deletions gen-models/src/operations.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1270,6 +1270,18 @@ impl Query for Defaults {
}

impl Defaults {
/// Set the default collection by name.
pub fn set_default_collection(
conn: &OperationsConnection,
collection_name: &str,
) -> SQLResult<()> {
conn.execute(
"UPDATE defaults SET collection_name = ?1 WHERE id = 1",
params![collection_name],
)?;
Ok(())
}

/// Set the default remote by name
pub fn set_default_remote(
conn: &OperationsConnection,
Expand Down
1 change: 1 addition & 0 deletions gen-python/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ looking things up afterward:
import gen

repo = gen.Repository("path/to/.gen")
repo.defaults("my_collection") # default for omitted collection= arguments

sample = repo.import_fasta("path/to.fa") # -> Sample
sg = sample[0] # -> SequenceGraph
Expand Down
31 changes: 31 additions & 0 deletions gen-python/src/python_api/repository/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -192,6 +192,13 @@ impl PyRepository {
path_to_py_path(py, &path)
}

/// Set the collection used when a method's `collection` argument is omitted.
fn defaults(&self, collection: &str) -> PyResult<()> {
Defaults::set_default_collection(self.context.operations().conn(), collection)
.map_err(sqlite_err_to_pyerr)?;
Ok(())
}

// Transaction context manager

/// Returns self so that Python's `with` statement calls `__enter__`/`__exit__`
Expand Down Expand Up @@ -383,6 +390,30 @@ mod python_tests {
});
}

#[test]
fn test_defaults_changes_default_collection() {
pyo3::prepare_freethreaded_python();
Python::with_gil(|py| {
let py_repo = make_repo(py);
let dir = tempdir().unwrap();
let fasta = write_fasta(&dir, "test.fa", "chr1", "ACGTACGT");

py_repo.borrow(py).defaults("configured").unwrap();
let sample = py_repo
.borrow(py)
.import_fasta(
fasta.to_str().unwrap().to_string(),
Some("test".to_string()),
false,
None,
)
.unwrap();

assert_eq!(sample.collection_name, "configured");
assert_eq!(py_repo.borrow(py).get_default_collection(), "configured");
});
}

#[test]
fn test_import_fasta_creates_block_group() {
pyo3::prepare_freethreaded_python();
Expand Down
34 changes: 29 additions & 5 deletions src/operation_management.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -777,20 +777,26 @@ fn push_to_file_remote(
None
};

let diff = if let Some(remote_manifest) = remote_manifest {
ManifestComparer::diff_manifests(&local_manifest, &remote_manifest)?
let diff = if let Some(remote_manifest) = &remote_manifest {
ManifestComparer::diff_manifests(&local_manifest, remote_manifest)?
} else {
// Empty remote - all local operations are missing
ManifestDiff {
missing_in_manifest2: local_manifest.operations.clone(),
missing_in_manifest1: vec![],
default_collection_name: remote_manifest.as_ref().map_or_else(
|| "default".to_string(),
|manifest| manifest.default_collection_name.clone(),
),
}
};

if !diff.missing_in_manifest1.is_empty() {
return Err(RemoteOperationError::RemoteBranchAhead);
}

Defaults::set_default_collection(remote_op_conn, &local_manifest.default_collection_name)?;

if !diff.missing_in_manifest2.is_empty() {
apply_operations_to_remote(
local_context,
Expand Down Expand Up @@ -1023,18 +1029,23 @@ fn pull_from_file_remote(
))
})?;

let diff = if let Some(remote_hash) = remote_branch.current_operation_hash {
let remote_manifest = ManifestGenerator::new(remote_op_conn)
.generate_manifest(&current_branch.name, Some(&remote_hash))?;
let remote_manifest = ManifestGenerator::new(remote_op_conn).generate_manifest(
&current_branch.name,
remote_branch.current_operation_hash.as_ref(),
)?;
let diff = if remote_branch.current_operation_hash.is_some() {
ManifestComparer::diff_manifests(&local_manifest, &remote_manifest)?
} else {
// There's nothing in the remote, so just make it empty since we have nothing to pull.
ManifestDiff {
missing_in_manifest2: vec![],
missing_in_manifest1: vec![],
default_collection_name: remote_manifest.default_collection_name.clone(),
}
};

Defaults::set_default_collection(operation_conn, &remote_manifest.default_collection_name)?;

if diff.missing_in_manifest1.is_empty() {
return Ok(());
}
Expand Down Expand Up @@ -1069,6 +1080,8 @@ fn pull_from_remote_server(
)?;
let diff = send_manifest_to_remote(remote_name, remote_url, &manifest)?;

Defaults::set_default_collection(operation_conn, &diff.default_collection_name)?;

if diff.missing_in_manifest1.is_empty() {
return Ok(());
}
Expand Down Expand Up @@ -2773,6 +2786,7 @@ mod tests {
"remote operation",
HashId::random_str(),
);
Defaults::set_default_collection(remote_op_conn, "remote collection").unwrap();

let remote_url = format!(
"file://{}",
Expand All @@ -2794,6 +2808,10 @@ mod tests {
let local_ops = Operation::all(op_conn);
let remote_ops = Operation::all(remote_op_conn);
assert_eq!(local_ops, remote_ops);
assert_eq!(
Defaults::get(op_conn).and_then(|defaults| defaults.collection_name),
Some("remote collection".to_string())
);
}

#[test]
Expand Down Expand Up @@ -2932,6 +2950,7 @@ mod tests {
description: "second operation".to_string(),
};
let op2 = end_operation(&context, &mut session, &op_info, "test2", None).unwrap();
Defaults::set_default_collection(op_conn, "local collection").unwrap();

let remote_context = setup_gen_on_disk();
let remote_url = format!(
Expand All @@ -2952,6 +2971,11 @@ mod tests {
.join(op2.hash.to_string());
assert!(remote_op1_dir.exists());
assert!(remote_op2_dir.exists());
assert_eq!(
Defaults::get(remote_context.operations().conn())
.and_then(|defaults| defaults.collection_name),
Some("local collection".to_string())
);
}

#[test]
Expand Down
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