Skip to content

doc: add book section on NodeDefaults #474

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Feb 2, 2023
Merged

doc: add book section on NodeDefaults #474

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
91 changes: 91 additions & 0 deletions book/src/table_collection_adding_rows.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,94 @@ Again, we can take advantage of being able to pass in any type that is `Into<_>`
```

See the [API docs](https://docs.rs/tskit) for more details and examples.

### Adding nodes using default values

This section is more advanced and may be skipped during a first read.

For some tables it may be common to input the same values over and over for some fields when adding rows.
Let's take a look at how to use default values when adding rows to a node table.

Default instances of `NodeDefaults` contain default values for the `flags`, `individual`, and `population` fields:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults}}
```

Add a node with these values and a given birth time:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:add_node_defaults}}
```

We can use struct update syntax to create a new node marked as a sample while re-using our other defaults:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:add_node_defaults_sample}}
```

See the [`NodeDefaults`](https://docs.rs/tskit/latest/tskit/struct.NodeDefaults.html) section of the API reference for more.

#### Metadata

[Metadata](metadata.md#Metadata) can complicate the picture a bit:

* Metadata types are defined by the client and are thus a generic in the `tskit` API.
* We do not want to impose too many trait bounds on the client-defined types.
* Metadata is optional on a per-row basis for any given table.

[`NodeDefaultsWithMetadata`](https://docs.rs/tskit/latest/tskit/struct.NodeDefaultsWithMetadata.html) handles the case where rows may or may not have metadata.
The metadata type is generic with trait bound [`tskit::NodeMetadata`](https://docs.rs/tskit/latest/tskit/metadata/trait.NodeMetadata.html).
Because metadata are optional per-row, any metadata defaults are stored as an [`Option`](https://doc.rust-lang.org/std/option/).

For the following examples, this will be our metadata type:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_metadata}}
```

##### Case 1: no default metadata

A common use case is that the metadata differs for every row.
For this case, it makes sense for the default value to be the `None` variant of the `Option`.

This case is straightforward:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults_with_metadata}}
```

##### Case 2: default metadata

TL;DR:

* If table row defaults *include* metadata, you can run into use-after-move issues.
Fortunately, the compiler will catch this as an error.
* The solution is for your metadata type to implement `Clone`.

Consider the following case:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults_with_some_metadata_default}}
```

Imagine that the first row we add uses different metadata but all the other default values:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults_with_some_metadata_default_add_first_row}}
```

Nothing interesting has happened.
However, let's take a look at what we need to do if our next row uses a non-default `population` field and the default metadata:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults_with_some_metadata_default_add_second_row}}
```

Note the call to `..defaults.clone()`.
(For that call to compile, `NodeMetadata` must implement `Clone`!.)
Without that, our `defaults` instance would have *moved*, leading to a move-after-use compiler error when we add a third row:

```rust, noplaygound, ignore
{{#include ../../tests/book_table_collection.rs:node_defaults_with_some_metadata_default_add_third_row}}
```
92 changes: 80 additions & 12 deletions tests/book_table_collection.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -169,9 +169,15 @@ fn get_data_from_edge_table() {
#[test]
fn test_adding_node_table_row_with_defaults() {
let mut tables = tskit::TableCollection::new(10.).unwrap();
// ANCHOR: node_defaults
let defaults = tskit::NodeDefaults::default();
// ANCHOR_END: node_defaults
// ANCHOR: add_node_defaults
let node = tables.add_node_with_defaults(0.0, &defaults).unwrap();
// ANCHOR_END: add_node_defaults
assert_eq!(node, 0);

// ANCHOR: add_node_defaults_sample
let node = tables
.add_node_with_defaults(
0.0,
Expand All @@ -184,6 +190,7 @@ fn test_adding_node_table_row_with_defaults() {
},
)
.unwrap();
// ANCHOR_END: add_node_defaults_sample
assert!(tables.nodes().flags(node).unwrap().is_sample());
}

Expand Down Expand Up @@ -215,15 +222,17 @@ macro_rules! impl_node_metadata_traits {
}

mod node_metadata {
#[derive(serde::Serialize, serde::Deserialize)]
#[derive(Debug, serde::Serialize, serde::Deserialize, Eq, PartialEq)]
// ANCHOR: node_metadata
pub struct NodeMetadata {
pub value: i32,
}
// ANCHOR_END: node_metadata
impl_node_metadata_traits!();
}

mod node_metadata_clone {
#[derive(Clone, serde::Serialize, serde::Deserialize)]
#[derive(Debug, Eq, PartialEq, Clone, serde::Serialize, serde::Deserialize)]
pub struct NodeMetadata {
pub value: i32,
}
Expand All @@ -234,10 +243,18 @@ mod node_metadata_clone {
fn test_adding_node_table_row_with_defaults_and_metadata() {
use node_metadata::NodeMetadata;
let mut tables = tskit::TableCollection::new(10.0).unwrap();
// ANCHOR: node_defaults_with_metadata

// Create a type alias for brevity
type DefaultsWithMetadata = tskit::NodeDefaultsWithMetadata<NodeMetadata>;
// Default metadata is None
let defaults = DefaultsWithMetadata::default();
let _ = tables.add_node_with_defaults(0.0, &defaults).unwrap();
let _ = tables

// A row with no metadata
let n0 = tables.add_node_with_defaults(0.0, &defaults).unwrap();

// A row with metadata
let n1 = tables
.add_node_with_defaults(
0.0,
&DefaultsWithMetadata {
Expand All @@ -247,32 +264,54 @@ fn test_adding_node_table_row_with_defaults_and_metadata() {
},
)
.unwrap();
let _ = tables

// Another row with metadata, different from the last.
let n2 = tables
.add_node_with_defaults(
0.0,
&DefaultsWithMetadata {
population: 3.into(),
metadata: Some(NodeMetadata { value: 42 }),
population: 1.into(),
metadata: Some(NodeMetadata { value: 1234 }),
..defaults
},
)
.unwrap();
// ANCHOR_END: node_defaults_with_metadata
assert!(tables.nodes().metadata::<NodeMetadata>(n0).is_none());
assert_eq!(
tables
.nodes()
.metadata::<NodeMetadata>(n1)
.unwrap()
.unwrap(),
NodeMetadata { value: 42 }
);
assert_eq!(
tables
.nodes()
.metadata::<NodeMetadata>(n2)
.unwrap()
.unwrap(),
NodeMetadata { value: 1234 }
);
}

#[test]
fn test_adding_node_table_row_with_defaults_and_metadata_requiring_clone() {
use node_metadata_clone::NodeMetadata;
let mut tables = tskit::TableCollection::new(10.0).unwrap();
type DefaultsWithMetadata = tskit::NodeDefaultsWithMetadata<NodeMetadata>;

// ANCHOR: node_defaults_with_some_metadata_default
// What if there is default metadata for all rows?
let defaults = DefaultsWithMetadata {
metadata: Some(NodeMetadata { value: 42 }),
..Default::default()
};
// ANCHOR_END: node_defaults_with_some_metadata_default

// We can scoop all non-metadata fields even though
// type is not Copy/Clone
let _ = tables
// ANCHOR: node_defaults_with_some_metadata_default_add_first_row
let n0 = tables
.add_node_with_defaults(
0.0,
&DefaultsWithMetadata {
Expand All @@ -281,11 +320,21 @@ fn test_adding_node_table_row_with_defaults_and_metadata_requiring_clone() {
},
)
.unwrap();
// ANCHOR_END: node_defaults_with_some_metadata_default_add_first_row
assert_eq!(
tables
.nodes()
.metadata::<NodeMetadata>(n0)
.unwrap()
.unwrap(),
NodeMetadata { value: 2 * 42 }
);

// But now, we start to cause a problem:
// If we don't clone here, our metadata type moves,
// so our defaults are moved.
let _ = tables
// ANCHOR: node_defaults_with_some_metadata_default_add_second_row
let n1 = tables
.add_node_with_defaults(
0.0,
&DefaultsWithMetadata {
Expand All @@ -294,10 +343,20 @@ fn test_adding_node_table_row_with_defaults_and_metadata_requiring_clone() {
},
)
.unwrap();
// ANCHOR_END: node_defaults_with_some_metadata_default_add_second_row
assert_eq!(
tables
.nodes()
.metadata::<NodeMetadata>(n1)
.unwrap()
.unwrap(),
NodeMetadata { value: 42 }
);

// Now, we have a use-after-move error
// if we hadn't cloned in the last step.
let _ = tables
// ANCHOR: node_defaults_with_some_metadata_default_add_third_row
let n2 = tables
.add_node_with_defaults(
0.0,
&DefaultsWithMetadata {
Expand All @@ -306,4 +365,13 @@ fn test_adding_node_table_row_with_defaults_and_metadata_requiring_clone() {
},
)
.unwrap();
// ANCHOR_END: node_defaults_with_some_metadata_default_add_third_row
assert_eq!(
tables
.nodes()
.metadata::<NodeMetadata>(n2)
.unwrap()
.unwrap(),
NodeMetadata { value: 42 }
);
}