Add support for table metadata schema

Cargo.toml

@@ -58,3 +58,7 @@ name = "tree_traversals"
 
 [[example]]
 name = "forward_simulation"
+
+[[example]]
+name = "metadata_schema"
+required-features = ["derive"]

examples/metadata_schema.rs

@@ -0,0 +1,29 @@
+use tskit::prelude::*;
+use tskit::TableCollection;
+
+#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::PopulationMetadata)]
+#[serializer("serde_json")]
+struct PopulationMetadata {
+    name: String,
+}
+
+fn main() {
+    let from_fp11 = r#"
+    {
+        "codec": "json",
+        "type": "object",
+        "name": "Population metadata",
+        "properties": {"name": {"type": "string"}}
+    }"#;
+
+    let mut tables = TableCollection::new(10.0).unwrap();
+    tables
+        .add_population_with_metadata(&PopulationMetadata {
+            name: "YRB".to_string(),
+        })
+        .unwrap();
+    tables
+        .set_json_metadata_schema_from_str(tskit::MetadataSchema::Populations, from_fp11)
+        .unwrap();
+    tables.dump("testit.trees", 0).unwrap();
+}

python_scripts/read_tablesfile.py

@@ -0,0 +1,7 @@
+import tskit
+import sys
+
+for f in sys.argv[1:]:
+    tables = tskit.TableCollection.load(f)
+    for pop in tables.populations:
+        print(pop)

python_scripts/requirements.txt

@@ -0,0 +1 @@
+tskit = "0.5.1"

src/lib.rs

@@ -435,7 +435,7 @@ pub use mutation_table::{MutationTable, MutationTableRow, OwnedMutationTable};
 pub use node_table::{NodeTable, NodeTableRow, OwnedNodeTable};
 pub use population_table::{OwnedPopulationTable, PopulationTable, PopulationTableRow};
 pub use site_table::{OwnedSiteTable, SiteTable, SiteTableRow};
-pub use table_collection::TableCollection;
+pub use table_collection::{MetadataSchema, TableCollection};
 pub use traits::IndividualLocation;
 pub use traits::IndividualParents;
 pub use traits::NodeListGenerator;

src/table_collection.rs

@@ -24,9 +24,23 @@ use crate::TskReturnValue;
 use crate::TskitTypeAccess;
 use crate::{tsk_id_t, tsk_size_t};
 use crate::{EdgeId, NodeId};
+use libc::{c_char, strlen};
 use ll_bindings::tsk_table_collection_free;
 use mbox::MBox;
 
+pub enum MetadataSchema {
+    Toplevel,
+    Edges,
+    Nodes,
+    Sites,
+    Mutations,
+    Individuals,
+    Populations,
+    Migrations,
+    #[cfg(feature = "provenance")]
+    Provenance,
+}
+
 /// A table collection.
 ///
 /// This is a thin wrapper around the C type
@@ -1202,6 +1216,35 @@ impl TableCollection {
         };
         handle_tsk_return_value!(rv)
     }
+
+    /// Set a metadata schema
+    ///
+    /// # Examples
+    ///
+    pub fn set_json_metadata_schema_from_str(
+        &mut self,
+        level: MetadataSchema,
+        schema: impl AsRef<str>,
+    ) -> TskReturnValue {
+        println!("{} {}", schema.as_ref(), schema.as_ref().len());
+        let cstr = std::ffi::CString::new(schema.as_ref()).unwrap();
+        println!("{:?}", cstr);
+        let len = unsafe { strlen(cstr.as_bytes_with_nul().as_ptr() as *const c_char) };
+        println!("{:?}", cstr);
+        println!("{}", len);
+        let rv = match level {
+            MetadataSchema::Populations => unsafe {
+                ll_bindings::tsk_population_table_set_metadata_schema(
+                    &mut (*self.inner).populations,
+                    cstr.as_bytes_with_nul().as_ptr() as *const c_char,
+                    len.try_into().unwrap(),
+                )
+            },
+            _ => unimplemented!("haven't done it yet"),
+        };
+        println!("rv = {}", rv);
+        handle_tsk_return_value!(rv)
+    }
 }
 
 impl TableAccess for TableCollection {
@@ -2296,3 +2339,43 @@ mod test_adding_migrations {
         }
     }
 }
+
+#[cfg(test)]
+mod test_metadata_schema {
+    use super::*;
+
+    #[test]
+    fn population_metadata_schema() {
+        let json_schema3 = r#"{"codec":"json","type":"object","name":"Population metadata","properties:"{"name":{"type":"string"}}}"#;
+        let json_schema3 = r#"{"codec":"json","type":"object","name":"Population metadata","properties":{"name":{"type":"string"}}}"#;
+        let json_schema2 = r#"{"codec":"json","name":"Population metadata","properties":{"name":{"type":"string"}},"type":"object"}"#;
+        let json_schema = r#"{"codec":"json","name":"Population metadata","properties":{"name":{"type":"string"}},"type":"object"}"#;
+
+        // YOU CANNOT HAVE A TRAILING COMMA AT THE END!!!!!!
+        let from_fp11 = r#"
+    {
+        "codec": "json",
+        "type": "object",
+        "name": "Population metadata",
+        "properties": {"name": {"type": "string"}}
+    }"#;
+
+        assert_eq!(json_schema, json_schema2);
+        let mut tables = TableCollection::new(10.).unwrap();
+        assert!(tables
+            .set_json_metadata_schema_from_str(MetadataSchema::Populations, from_fp11)
+            .is_ok());
+        assert!(!unsafe { (*tables.as_ptr()).populations.metadata_schema.is_null() });
+        let len = unsafe { (*tables.as_ptr()).populations.metadata_schema_length };
+        assert!(len > 0, "{}", len);
+        let schema =
+            unsafe { std::ffi::CStr::from_ptr((*tables.as_ptr()).populations.metadata_schema) };
+        assert_eq!(schema.to_str().unwrap(), from_fp11);
+        tables.dump("foo.trees", 0).unwrap();
+
+        //let tables = TableCollection::new_from_file("bananas.tables").unwrap();
+        //let schema =
+        //    unsafe { std::ffi::CStr::from_ptr((*tables.as_ptr()).populations.metadata_schema) };
+        //println!("from tskit = {}", schema.to_str().unwrap());
+    }
+}